The document discusses a study analyzing whole genome sequencing data of 11 carbapenem-resistant Acinetobacter baumannii isolates from Vietnam. It finds that 10 of the 11 Vietnamese strains were multidrug-resistant and susceptible only to colistin. All strains harbored genes conferring resistance to aminoglycosides, beta-lactams, and other classes of antibiotics. A comparison of these Vietnamese strains to 108 published genomes from Southeast Asia identified 19 different sequence types, with ST/2 being the most common. The study reveals high genetic diversity of A. baumannii in Vietnam and the region.
This study investigated drug resistance patterns among Mycobacterium tuberculosis isolates from 239 re-treatment tuberculosis patients in Sudan. 143 bacterial isolates were recovered, with 98.6% identified as M. tuberculosis complex and 1.4% as non-tuberculous mycobacteria. Drug susceptibility testing found that 38.3% of isolates were multidrug-resistant and a further 17% were resistant to a single first-line drug. Multidrug resistance was highest among patients who had previously failed treatment (75% of isolates), while over half of patients who had defaulted on previous treatment were susceptible to all first-line drugs. The findings suggest a considerable level of drug resistance in re-treatment TB patients in Sudan.
Bacterial Profile and Antimicrobial Resistance Pattern of Pus Isolates in Ben...Ahmed Elberry
This study analyzed bacterial culture data from pus samples collected from 2008-2014 at Beni-Suef University Hospital in Egypt to identify the prevalent bacteria and their antibiotic resistance patterns. Pseudomonas spp. was the most commonly isolated bacteria (20.9%), followed by MSSA (14.3%). Gram-negative bacteria like Pseudomonas spp., E. coli, and Klebsiella spp. showed high resistance to many antibiotics but lower resistance to imipenem, amikacin, and meropenem. MSSA was resistant to penicillin and erythromycin but sensitive to vancomycin. The results provide guidance for empiric antibiotic treatment of wound infections in the
Challenges in the management of HAP-VAP include multidrug-resistant pathogens becoming more common. Combination antibiotic therapy is recommended for patients with risk factors for multidrug-resistant infections or septic shock. Newer beta-lactam/beta-lactamase inhibitor combinations such as ceftolozane-tazobactam and ceftazidime-avibactam show promise in treating resistant gram-negative bacteria including ESBL, AmpC, KPC, and OXA-48 producers.
Multidrug Resistance Pattern of Staphylococcus Aureus Isolates in Maiduguri ...Scientific Review SR
This study investigated the multidrug resistance patterns of Staphylococcus aureus isolates in Maiduguri, Nigeria. Samples were collected from hospitals and tested for S. aureus, which was isolated from 38.8% of samples, primarily from wound swabs. Antibiotic sensitivity testing found high resistance to ciprofloxacin (64.3%), ampicillin (59.5%), and chloramphenicol (54.8%). Multiple antibiotic resistance was observed in over 92% of isolates. The multiple antibiotic resistance index was highest at 0.6 (23.8%) and 0.5 (19.0%), indicating resistance to multiple drugs. The results demonstrate high multidrug resistance in S. aureus isolates from the
Multidrug Resistance Pattern of Staphylococcus Aureus Isolates in Maiduguri M...Scientific Review
Multi drug-resistant (MDR) isolates of Staphylococcus aureus are on rise and are becoming a challenge for timely and appropriate treatment. The present study was carried out with an objective to isolate Staphylococcus aureus from clinical samples and determine their sensitivity. Out of 110 samples collected, 44 were shown to contained S. aureus. The isolates were subjected to antibiotic sensitivity tests using 10 different and commonly used antibiotics by modified Kirby- Bauer disc diffusion technique. Out of the total isolates (42) tested, only 7.1% were susceptible to all the antibiotics. Multiple resistance was eminent in over 92% with highest occurrence in 4.8% where the entire antibiotics were resisted. Multiple antibiotic resistance indixes (MAR index) indicated that 0.6 index occurred most (23.8%) followed by 0.5 (19.0%). On the other hand, 0.1 and 0.8 indexes were the lowest with 0.0% and 1.0% occurrence respectively. Ciprofloxacin was resisted by most of the organisms (64.3%) while amoxicillin (64.3%) and streptomycin (61.9%) were most efficacious. With over 90% isolate having MAR index ≥ 0.2, the multiple drug resistance by the S. aureus is quite alarming and might suggest inappropriate antibiotic usage by the sampled population. Therefore, the need to strategize the nature of antibiotic treatment against S. aureus and massive campaign on indiscriminate antibiotic use is urgent.
Journal Presentation on Antibiotic Susceptibility Pattern in Cancer Patientsnayanadiv
This retrospective study analyzed 1178 blood samples from cancer patients with suspected bloodstream infections at a tertiary cancer hospital in India from 2016. The study found a blood culture positivity rate of 27.35% and Gram-negative bacteria accounted for over half of infections. Escherichia coli was the most common organism isolated. Antibiotic resistance was high, especially for cephalosporins. Sensitivity to amikacin was the highest for most Gram-negative bacteria. The study provides important local data on infectious organisms and antibiotic susceptibility to help guide effective treatment of bloodstream infections in cancer patients.
Prevalence and Characterisation of Beta Lactamases in Multi Drug Resistant Gr...iosrjce
This document discusses a study on the prevalence and characterization of beta-lactamases in multidrug resistant gram-negative bacteria isolated from intensive care units (ICUs) in a tertiary care hospital in central India. The study aims to identify gram-negative pathogens from ICU specimens, determine antimicrobial resistance patterns and prevalence of ESBLs, AmpC, and carbapenemases through phenotypic and genotypic methods. A literature review found increasing antimicrobial resistance in ICUs due to selective pressure from antibiotic overuse. ICUs have high rates of multidrug resistant infections. The study aims to detect resistance genes and their co-existence to guide optimal treatment and infection control in ICUs.
This document summarizes a study on multi-drug resistant Mycobacterium tuberculosis conducted in South Gujarat, India. A total of 90 samples were collected and analyzed using staining, culture and drug susceptibility testing. Of the 33 culture positive samples, 96.96% were M. tuberculosis and 3.04% were atypical mycobacteria. Drug susceptibility testing found that 39.39% of strains were multi-drug resistant, 6.06% were sensitive to all drugs tested, and 54.55% were resistant to one or more drugs other than the combination defining multi-drug resistance. The results indicate a prevalence of multi-drug resistant tuberculosis in the study region.
This study investigated drug resistance patterns among Mycobacterium tuberculosis isolates from 239 re-treatment tuberculosis patients in Sudan. 143 bacterial isolates were recovered, with 98.6% identified as M. tuberculosis complex and 1.4% as non-tuberculous mycobacteria. Drug susceptibility testing found that 38.3% of isolates were multidrug-resistant and a further 17% were resistant to a single first-line drug. Multidrug resistance was highest among patients who had previously failed treatment (75% of isolates), while over half of patients who had defaulted on previous treatment were susceptible to all first-line drugs. The findings suggest a considerable level of drug resistance in re-treatment TB patients in Sudan.
Bacterial Profile and Antimicrobial Resistance Pattern of Pus Isolates in Ben...Ahmed Elberry
This study analyzed bacterial culture data from pus samples collected from 2008-2014 at Beni-Suef University Hospital in Egypt to identify the prevalent bacteria and their antibiotic resistance patterns. Pseudomonas spp. was the most commonly isolated bacteria (20.9%), followed by MSSA (14.3%). Gram-negative bacteria like Pseudomonas spp., E. coli, and Klebsiella spp. showed high resistance to many antibiotics but lower resistance to imipenem, amikacin, and meropenem. MSSA was resistant to penicillin and erythromycin but sensitive to vancomycin. The results provide guidance for empiric antibiotic treatment of wound infections in the
Challenges in the management of HAP-VAP include multidrug-resistant pathogens becoming more common. Combination antibiotic therapy is recommended for patients with risk factors for multidrug-resistant infections or septic shock. Newer beta-lactam/beta-lactamase inhibitor combinations such as ceftolozane-tazobactam and ceftazidime-avibactam show promise in treating resistant gram-negative bacteria including ESBL, AmpC, KPC, and OXA-48 producers.
Multidrug Resistance Pattern of Staphylococcus Aureus Isolates in Maiduguri ...Scientific Review SR
This study investigated the multidrug resistance patterns of Staphylococcus aureus isolates in Maiduguri, Nigeria. Samples were collected from hospitals and tested for S. aureus, which was isolated from 38.8% of samples, primarily from wound swabs. Antibiotic sensitivity testing found high resistance to ciprofloxacin (64.3%), ampicillin (59.5%), and chloramphenicol (54.8%). Multiple antibiotic resistance was observed in over 92% of isolates. The multiple antibiotic resistance index was highest at 0.6 (23.8%) and 0.5 (19.0%), indicating resistance to multiple drugs. The results demonstrate high multidrug resistance in S. aureus isolates from the
Multidrug Resistance Pattern of Staphylococcus Aureus Isolates in Maiduguri M...Scientific Review
Multi drug-resistant (MDR) isolates of Staphylococcus aureus are on rise and are becoming a challenge for timely and appropriate treatment. The present study was carried out with an objective to isolate Staphylococcus aureus from clinical samples and determine their sensitivity. Out of 110 samples collected, 44 were shown to contained S. aureus. The isolates were subjected to antibiotic sensitivity tests using 10 different and commonly used antibiotics by modified Kirby- Bauer disc diffusion technique. Out of the total isolates (42) tested, only 7.1% were susceptible to all the antibiotics. Multiple resistance was eminent in over 92% with highest occurrence in 4.8% where the entire antibiotics were resisted. Multiple antibiotic resistance indixes (MAR index) indicated that 0.6 index occurred most (23.8%) followed by 0.5 (19.0%). On the other hand, 0.1 and 0.8 indexes were the lowest with 0.0% and 1.0% occurrence respectively. Ciprofloxacin was resisted by most of the organisms (64.3%) while amoxicillin (64.3%) and streptomycin (61.9%) were most efficacious. With over 90% isolate having MAR index ≥ 0.2, the multiple drug resistance by the S. aureus is quite alarming and might suggest inappropriate antibiotic usage by the sampled population. Therefore, the need to strategize the nature of antibiotic treatment against S. aureus and massive campaign on indiscriminate antibiotic use is urgent.
Journal Presentation on Antibiotic Susceptibility Pattern in Cancer Patientsnayanadiv
This retrospective study analyzed 1178 blood samples from cancer patients with suspected bloodstream infections at a tertiary cancer hospital in India from 2016. The study found a blood culture positivity rate of 27.35% and Gram-negative bacteria accounted for over half of infections. Escherichia coli was the most common organism isolated. Antibiotic resistance was high, especially for cephalosporins. Sensitivity to amikacin was the highest for most Gram-negative bacteria. The study provides important local data on infectious organisms and antibiotic susceptibility to help guide effective treatment of bloodstream infections in cancer patients.
Prevalence and Characterisation of Beta Lactamases in Multi Drug Resistant Gr...iosrjce
This document discusses a study on the prevalence and characterization of beta-lactamases in multidrug resistant gram-negative bacteria isolated from intensive care units (ICUs) in a tertiary care hospital in central India. The study aims to identify gram-negative pathogens from ICU specimens, determine antimicrobial resistance patterns and prevalence of ESBLs, AmpC, and carbapenemases through phenotypic and genotypic methods. A literature review found increasing antimicrobial resistance in ICUs due to selective pressure from antibiotic overuse. ICUs have high rates of multidrug resistant infections. The study aims to detect resistance genes and their co-existence to guide optimal treatment and infection control in ICUs.
This document summarizes a study on multi-drug resistant Mycobacterium tuberculosis conducted in South Gujarat, India. A total of 90 samples were collected and analyzed using staining, culture and drug susceptibility testing. Of the 33 culture positive samples, 96.96% were M. tuberculosis and 3.04% were atypical mycobacteria. Drug susceptibility testing found that 39.39% of strains were multi-drug resistant, 6.06% were sensitive to all drugs tested, and 54.55% were resistant to one or more drugs other than the combination defining multi-drug resistance. The results indicate a prevalence of multi-drug resistant tuberculosis in the study region.
The study analyzed 100 multidrug-resistant Acinetobacter baumannii isolates from intensive care unit patients in Tehran, Iran between 2006 and 2011 to evaluate changes in genotypic diversity and antimicrobial susceptibility patterns. Resistance to antimicrobials tested increased between 0-30% within 5 years. By 2011, 6-100% of isolates were resistant to each agent tested. Genotypic changes among isolates were also drastic, with novel international clone variants comprising 36% of isolates in 2011. Resistance is growing for last-resort antimicrobials such as colistin and tigecycline.
ANTIMICROBIAL RESISTANCE PATTERNS AMONG ACINETOBACTER BAUMANNII ISOLATED FROM...inventionjournals
Acinetobacter baumannii (Ab) is a troublesome and increasingly problematic healthcareassociated pathogen, especially in critical care unit (ICU) and cardiovascular internal medicine (CIM). This organism has a capacity for long-term survival in the hospital environment. This study aimed to investigate the drug resistance patterns of Ab strains isolated from Thongnhat Dongnai General Hospital and the relationships between Ab isolations with clinical wards and year of patients. The antibiotic susceptibility of 279 Ab isolates for aminoglycosides, fluro-quinolons, cephalosporins, carbapenems, colistin and bactrim was determined using Kirby-Bauer disk diffusion method. The minimum inhibitor concentration (MIC) of 146 Ab isolates for Meropenem was determined using E-test method according to CLSI guide-line. A total 279 A. baumannii strains out of 1,976 positive isolates were collected from various specimens during study period. Among Ab-positive specimens, the most isolated specimen was sputum (26.6%, χ 2 =161.705 p<0.000),><0.000)><0.000),><0.000). Among 279 Ab isolated, resistance from 53.16% – 63.52% to aminoglycosides, 23.6% – 68.58% to fluroquinolons, 59.61% to 97.93% to cephalosporins, 60.27% to 80.7% to carbapenem, 10.53% to 66.48% to antibiotic combinations, 0.75% to colistin and 61.71% to bactrim. Among 146 multidrug-resistant Ab, 53.42% MICmeropenem ≥ 32 μg/ml and only 18.49% strains were susceptible to Meropenem. Due to the high antimicrobial resistance to two clinical wards (ICU and CIM) and carbapenems by disk agar diffusion test and E-test; we must focus on both a wiser use of antimicrobials and the prevention of infection. Continuous monitoring of antimicrobial susceptibility and strict adherence to infection prevention guidelines are essential to eliminate major outbreaks in the future.
ANTIMICROBIAL RESISTANCE PATTERNS AMONG ACINETOBACTER BAUMANNII ISOLATED FROM...inventionjournals
Acinetobacter baumannii (Ab) is a troublesome and increasingly problematic healthcareassociated pathogen, especially in critical care unit (ICU) and cardiovascular internal medicine (CIM). This organism has a capacity for long-term survival in the hospital environment. This study aimed to investigate the drug resistance patterns of Ab strains isolated from Thongnhat Dongnai General Hospital and the relationships between Ab isolations with clinical wards and year of patients. The antibiotic susceptibility of 279 Ab isolates for aminoglycosides, fluro-quinolons, cephalosporins, carbapenems, colistin and bactrim was determined using Kirby-Bauer disk diffusion method. The minimum inhibitor concentration (MIC) of 146 Ab isolates for Meropenem was determined using E-test method according to CLSI guide-line. A total 279 A. baumannii strains out of 1,976 positive isolates were collected from various specimens during study period. Among Ab-positive specimens, the most isolated specimen was sputum (26.6%, χ 2 =161.705 p<0.000),><0.000)><0.000),><0.000). Among 279 Ab isolated, resistance from 53.16% – 63.52% to aminoglycosides, 23.6% – 68.58% to fluroquinolons, 59.61% to 97.93% to cephalosporins, 60.27% to 80.7% to carbapenem, 10.53% to 66.48% to antibiotic combinations, 0.75% to colistin and 61.71% to bactrim. Among 146 multidrug-resistant Ab, 53.42% MICmeropenem ≥ 32 μg/ml and only 18.49% strains were susceptible to Meropenem. Due to the high antimicrobial resistance to two clinical wards (ICU and CIM) and carbapenems by disk agar diffusion test and E-test; we must focus on both a wiser use of antimicrobials and the prevention of infection. Continuous monitoring of antimicrobial susceptibility and strict adherence to infection prevention guidelines are essential to eliminate major outbreaks in the future
m-Complete genome sequencing and evolutionary analysis of dengueBriseiri Heine
This document describes a study that analyzed dengue virus serotype 1 (DENV1) isolates from a 2009 outbreak in Kerala, South India. Whole genome sequencing was performed on two isolates, and phylogenetic analysis showed they grouped with isolates from Thailand, Comoros, Singapore, and Brunei. The isolates shared four unique mutations and a deletion in the 30 -non-translated region. This study provides the first complete genome characterization of DENV1 strains from India, revealing a genetically distinct viral strain was the cause of this localized outbreak.
This study analyzed the antibiotic susceptibility patterns of gram-negative bacteria isolated from clinical samples at a large specialty hospital in India from 2014. It found that 81% of bacterial isolates were gram-negative bacilli, led by Enterobacteriaceae species, Acinetobacter spp., and Pseudomonas aeruginosa. Antibiotic resistance rates were high and increasing among these pathogens, particularly to beta-lactams, cephalosporins, fluoroquinolones, and carbapenems. The results demonstrate the growing threat of multidrug-resistant gram-negative infections and emphasize the need for prudent antibiotic use.
Abstract— Methicillin-resistant Staphylococcus aureus (MRSA) poses a great risk to burn patients with potential to cause significant morbidity and mortality. This study aimed to find out the prevalence of MRSA and its susceptibility, in burn wound infection/colonization in a Tertiary Care Hospital in North India. A retrospective study was conducted among patients admitted in burn ward of our hospital, between January to December 2012. All the patients irrespective of age, sex, duration of hospital stay, percentage and degree of burn were included in our study. Wound swabs from 1294 patients hospitalized in burn ward were analysed for bacteriological examination. Swabs were inoculated on Blood agar, MacConkey agar and Brain heart infusion broth. Isolates were examined for colony characteristics, Gram staining and biochemical tests. Antimicrobial susceptibility testing was done by modified Stokes disc diffusion method. Detection of MRSA was done by cefoxitin (30g) disc diffusion method. Among the Staphylococcus aureus (S.aureus) isolates, 56.7% (80/141) were found to be MRSA while 43.3% (61/141) were Methicillin Susceptible S.aureus (MSSA). All the MRSA isolates were resistant to penicillin, cephalexin and cefazolin. Resistance to erythromycin, clindamycin, ofloxacin, ciprofloxacin, gentamicin, amikacin, rifampicin, chloramphenicol was found to be 74%, 97.4%, 96%, 100%, 97.4%, 84.6%, 11.5%, 10.3%. All MRSA isolates were found to be sensitive to vancomycin and teicoplanin while 1.3% were resistant to linezolid. Although survival rates for burn patients have improved substantially over the years, nosocomial infections still remain a major challenge in burn care. This concludes that there is high prevalence of nosocomial infections specially the presence of multidrug resistant bacteria like Methicillin Resistant Staphylococcus aureus among burn patients suggest continuous surveillance of burn wound infections and development and stringent implementation of antibiotic policy.
1. This study investigated the prevalence of integrons and antimicrobial resistance genes in 110 clinical isolates of Enterobacter species collected from hospitals in Tehran, Iran between 2012-2013.
2. The study found that 45 isolates (41%) contained integrons, with class 1 integrons being most common. Integron-positive isolates showed higher resistance to antibiotics like augmentin, trimethoprim-sulfamethoxazole, and cefoxitin.
3. Ten integron-positive isolates were found to be ESBL producers. Common resistance genes identified included blaTEM (20%), blaCTX-M-1 (15.6%), and genes encoding aminoglycoside
GENETIC CHARACTERIZATION OF SEROTYPE AND GENETIC RELATEDNESS OF FOOT-AND-MOUT...EuFMD
This study analyzed 95 foot-and-mouth disease virus (FMDV) samples collected between 2018-2019 from Vietnam, Laos, and Cambodia to determine their genetic relatedness. 40 samples tested positive for FMDV through 3D qRT-PCR analysis. Genome sequencing of the VP1 region showed that FMDVs in Vietnam and Laos belonged to serotypes O/ME-SA/Panasia and O/SEA/Mya-98, while viruses in Cambodia belonged to serotypes O/ME-SA/Panasia and A/ASIA/SEA-97. Phylogenetic analysis revealed that Cambodia's A/ASIA/SEA-97 and Vietnam's O/SEA/My
This study characterized carbapenem-resistant Acinetobacter baumannii (CNSAb) isolates collected from burn patients at a hospital in Tehran, Iran. Of the 92 A. baumannii isolates tested, 69 were confirmed to be CNSAb based on imipenem resistance. Antibiotic susceptibility testing found high resistance rates to multiple classes of antibiotics. Molecular analysis identified several beta-lactamase genes conferring resistance. Most isolates belonged to international clones and sequence types previously seen worldwide. Genetic analysis using multiple methods found diversity but also the presence of dominant strains. The study provides information on the antibiotic resistance and genetic characteristics of CNSAb in Iranian burn patients.
Characterization of Mycobacterium Tuberculosis Complex Strains: A Multicenter...CrimsonpublishersCJMI
Characterization of Mycobacterium Tuberculosis Complex Strains: A Multicenter Retrospective Greek Study by Lamprini Gkaravela in Cohesive Journal of Microbiology & Infectious Disease
Role of Nonfermenting Gram-Negative Bacilli Responsible for Respiratory Tract...Premier Publishers
The majority of nonfermenting gram-negative bacilli are responsible for respiratory tract infections. The aims of this study are to identify the nonfermenting gram-negative bacilli species in respiratory tract infections, to describe their antibiotic resistance and to describe the factors associated with these bacteria. It is a prospective study of 54 respiratory samples for a period of six months from October 2019 to March 2020 in the laboratory of the University Hospital of Befelatanana Antananarivo. Among the 54 respiratory samples, the microbiological results showed 12 (22.2%) cases of nonfermenting gram-negative bacilli. These bacilli were represented by 7 (58.3%) cases of Acinetobacter baumannii, 4 (33.3%) cases of Pseudomonas aeruginosa and 1 (8.3%) case of Stenotrophomonas maltophilia. Concerning the associated factors, subjects under 40 years (24%) (p=0.77; NS), men (30.8%) (p=0.03) and subjects hospitalized in intensive care units (40.7%) (p=0.003) were the most affected by the nonfermenting gram-negative bacilli. Regarding antibiotic resistance, it varies from 71.4% to 100% for Acinetobacter baumannii and 0% to 100% for Pseudomonas aeruginosa. The Stenotrophomonas maltophilia isolate had a broad spectrum ß-lactamase but was sensitive to the other antibiotics. Nonfermenting gram-negative bacilli are responsible for severe nosocomial pneumonia and the majorities are multi-resistant bacteria.
Prevalence of non-fermenter as uro pathogen in tertiary care hospital in Chid...pharmaindexing
This study aimed to determine the prevalence of non-fermenting gram-negative bacilli (non-fermenters) as causes of urinary tract infections (UTIs) at a hospital in India over an 18-month period. The study found that of the 317 urine culture samples that showed significant bacteriuria, 131 (9.7%) were caused by non-fermenters. Pseudomonas species was the most common non-fermenter isolated, accounting for 80.6% of cases, while Acinetobacter species accounted for 19.3% of cases. Antibiotic sensitivity testing showed varying resistance patterns between the two bacteria.
This study analyzed 8,749 clinical samples collected from July 2010 to December 2012 at a tertiary hospital in Odisha, India. Of these, 137 samples (3%) yielded Acinetobacter species. Most isolates were from pus/swabs (56.9%), blood (13.1%), and urine (12.4%). Risk factors for Acinetobacter infection included older age, hospitalization, longer hospital stays, comorbidities, and invasive procedures. Many isolates were multidrug-resistant (54.7% resistant to >3 antibiotic classes) or pan-drug resistant (5.8% resistant to all antibiotics tested). Isolates were most sensitive to imipenem, meropenem, and pip
ENHANCED DIAGNOSIS EFFICACY OF A NEWLY DEVELOPLED ELISA KIT FOR FMDV IN POOL ...EuFMD
This document summarizes a study that compares the diagnostic efficacy of a newly developed ELISA kit from the Animal and Plant Quarantine Agency (APQA) in South Korea to the OIE reference Pirbright ELISA kit for detecting foot-and-mouth disease virus (FMDV) in samples from Southeast Asian countries. Clinical samples collected from 2015-2019 from Vietnam, Laos, Cambodia, and Myanmar were tested using both kits. The results showed that the APQA kit had better sensitivity for detecting FMDV serotype O compared to the Pirbright kit. For FMDV serotype A, the APQA kit performed better on some samples while the Pirbright kit was more sensitive on others. Overall, the APQA
This document discusses the global threat of antimicrobial resistance (AMR) and the role that drug and therapeutics committees (DTCs) can play in containing AMR. It outlines the global spread of drug-resistant pathogens and infections. The overuse and misuse of antibiotics in both human and animal settings is a major cause of growing AMR. DTCs can help address this by developing antibiotic policies and formularies, educating on appropriate use, and monitoring antibiotic consumption and resistance patterns. Examples from Kenya and Thailand demonstrate how DTCs have successfully implemented strategies like antibiotic order forms to improve antibiotic use.
This study analyzed ticks collected from four vegetation sites in South Korea over two years to understand tick populations and the prevalence of severe fever with thrombocytopenia syndrome virus (SFTSV). The dominant tick species was Haemaphysalis longicornis, which made up over 95% of collected nymphs and adults. H. longicornis nymph numbers peaked in June 2020 while adult numbers peaked in July 2019 and June 2020. Testing found the virus in H. longicornis pools in August-October 2020, with the highest minimum infection rate in August. Most ticks and virus-positive pools were found in grassland and grave sites. The results provide insights into controlling SFTSV risk through tick management
This document analyzes genetic markers associated with artemisinin resistance in Plasmodium falciparum parasites collected in western Kenya before and after the introduction of artemisinin combination therapies (ACTs). Twenty-five single nucleotide polymorphisms (SNPs) on chromosomes 13 and 14 and pfmdr1 gene copy number were analyzed. Fifteen SNPs were present in pre-ACT isolates, but only six were present in post-ACT isolates. Post-ACT isolates had significantly higher pfmdr1 copy numbers than pre-ACT isolates. No SNPs were associated with parasite clearance half-life. The results suggest the genetic signature of artemisinin resistance in African parasites may differ from that in Southeast Asian parasites.
Escherichia coli was the predominant pathogen isolated (70.52%) from the urine cultures of 538 patients with urinary tract infections in Surat, India. Antibiotics like ampicillin showed high resistance rates of over 90% among isolated gram-negative pathogens. However, gram-negative pathogens demonstrated the highest sensitivity to amikacin, netromycin, piperacillin/tazobactum and cefoperazone/sulbactum with resistance rates below 5%. The study highlights the increasing antimicrobial resistance seen with commonly used antibiotics and identifies alternative antibiotic options for empirical therapy of urinary tract infections in the region.
The study analyzed 100 multidrug-resistant Acinetobacter baumannii isolates from intensive care unit patients in Tehran, Iran between 2006 and 2011 to evaluate changes in genotypic diversity and antimicrobial susceptibility patterns. Resistance to antimicrobials tested increased between 0-30% within 5 years. By 2011, 6-100% of isolates were resistant to each agent tested. Genotypic changes among isolates were also drastic, with novel international clone variants comprising 36% of isolates in 2011. Resistance is growing for last-resort antimicrobials such as colistin and tigecycline.
ANTIMICROBIAL RESISTANCE PATTERNS AMONG ACINETOBACTER BAUMANNII ISOLATED FROM...inventionjournals
Acinetobacter baumannii (Ab) is a troublesome and increasingly problematic healthcareassociated pathogen, especially in critical care unit (ICU) and cardiovascular internal medicine (CIM). This organism has a capacity for long-term survival in the hospital environment. This study aimed to investigate the drug resistance patterns of Ab strains isolated from Thongnhat Dongnai General Hospital and the relationships between Ab isolations with clinical wards and year of patients. The antibiotic susceptibility of 279 Ab isolates for aminoglycosides, fluro-quinolons, cephalosporins, carbapenems, colistin and bactrim was determined using Kirby-Bauer disk diffusion method. The minimum inhibitor concentration (MIC) of 146 Ab isolates for Meropenem was determined using E-test method according to CLSI guide-line. A total 279 A. baumannii strains out of 1,976 positive isolates were collected from various specimens during study period. Among Ab-positive specimens, the most isolated specimen was sputum (26.6%, χ 2 =161.705 p<0.000),><0.000)><0.000),><0.000). Among 279 Ab isolated, resistance from 53.16% – 63.52% to aminoglycosides, 23.6% – 68.58% to fluroquinolons, 59.61% to 97.93% to cephalosporins, 60.27% to 80.7% to carbapenem, 10.53% to 66.48% to antibiotic combinations, 0.75% to colistin and 61.71% to bactrim. Among 146 multidrug-resistant Ab, 53.42% MICmeropenem ≥ 32 μg/ml and only 18.49% strains were susceptible to Meropenem. Due to the high antimicrobial resistance to two clinical wards (ICU and CIM) and carbapenems by disk agar diffusion test and E-test; we must focus on both a wiser use of antimicrobials and the prevention of infection. Continuous monitoring of antimicrobial susceptibility and strict adherence to infection prevention guidelines are essential to eliminate major outbreaks in the future.
ANTIMICROBIAL RESISTANCE PATTERNS AMONG ACINETOBACTER BAUMANNII ISOLATED FROM...inventionjournals
Acinetobacter baumannii (Ab) is a troublesome and increasingly problematic healthcareassociated pathogen, especially in critical care unit (ICU) and cardiovascular internal medicine (CIM). This organism has a capacity for long-term survival in the hospital environment. This study aimed to investigate the drug resistance patterns of Ab strains isolated from Thongnhat Dongnai General Hospital and the relationships between Ab isolations with clinical wards and year of patients. The antibiotic susceptibility of 279 Ab isolates for aminoglycosides, fluro-quinolons, cephalosporins, carbapenems, colistin and bactrim was determined using Kirby-Bauer disk diffusion method. The minimum inhibitor concentration (MIC) of 146 Ab isolates for Meropenem was determined using E-test method according to CLSI guide-line. A total 279 A. baumannii strains out of 1,976 positive isolates were collected from various specimens during study period. Among Ab-positive specimens, the most isolated specimen was sputum (26.6%, χ 2 =161.705 p<0.000),><0.000)><0.000),><0.000). Among 279 Ab isolated, resistance from 53.16% – 63.52% to aminoglycosides, 23.6% – 68.58% to fluroquinolons, 59.61% to 97.93% to cephalosporins, 60.27% to 80.7% to carbapenem, 10.53% to 66.48% to antibiotic combinations, 0.75% to colistin and 61.71% to bactrim. Among 146 multidrug-resistant Ab, 53.42% MICmeropenem ≥ 32 μg/ml and only 18.49% strains were susceptible to Meropenem. Due to the high antimicrobial resistance to two clinical wards (ICU and CIM) and carbapenems by disk agar diffusion test and E-test; we must focus on both a wiser use of antimicrobials and the prevention of infection. Continuous monitoring of antimicrobial susceptibility and strict adherence to infection prevention guidelines are essential to eliminate major outbreaks in the future
m-Complete genome sequencing and evolutionary analysis of dengueBriseiri Heine
This document describes a study that analyzed dengue virus serotype 1 (DENV1) isolates from a 2009 outbreak in Kerala, South India. Whole genome sequencing was performed on two isolates, and phylogenetic analysis showed they grouped with isolates from Thailand, Comoros, Singapore, and Brunei. The isolates shared four unique mutations and a deletion in the 30 -non-translated region. This study provides the first complete genome characterization of DENV1 strains from India, revealing a genetically distinct viral strain was the cause of this localized outbreak.
This study analyzed the antibiotic susceptibility patterns of gram-negative bacteria isolated from clinical samples at a large specialty hospital in India from 2014. It found that 81% of bacterial isolates were gram-negative bacilli, led by Enterobacteriaceae species, Acinetobacter spp., and Pseudomonas aeruginosa. Antibiotic resistance rates were high and increasing among these pathogens, particularly to beta-lactams, cephalosporins, fluoroquinolones, and carbapenems. The results demonstrate the growing threat of multidrug-resistant gram-negative infections and emphasize the need for prudent antibiotic use.
Abstract— Methicillin-resistant Staphylococcus aureus (MRSA) poses a great risk to burn patients with potential to cause significant morbidity and mortality. This study aimed to find out the prevalence of MRSA and its susceptibility, in burn wound infection/colonization in a Tertiary Care Hospital in North India. A retrospective study was conducted among patients admitted in burn ward of our hospital, between January to December 2012. All the patients irrespective of age, sex, duration of hospital stay, percentage and degree of burn were included in our study. Wound swabs from 1294 patients hospitalized in burn ward were analysed for bacteriological examination. Swabs were inoculated on Blood agar, MacConkey agar and Brain heart infusion broth. Isolates were examined for colony characteristics, Gram staining and biochemical tests. Antimicrobial susceptibility testing was done by modified Stokes disc diffusion method. Detection of MRSA was done by cefoxitin (30g) disc diffusion method. Among the Staphylococcus aureus (S.aureus) isolates, 56.7% (80/141) were found to be MRSA while 43.3% (61/141) were Methicillin Susceptible S.aureus (MSSA). All the MRSA isolates were resistant to penicillin, cephalexin and cefazolin. Resistance to erythromycin, clindamycin, ofloxacin, ciprofloxacin, gentamicin, amikacin, rifampicin, chloramphenicol was found to be 74%, 97.4%, 96%, 100%, 97.4%, 84.6%, 11.5%, 10.3%. All MRSA isolates were found to be sensitive to vancomycin and teicoplanin while 1.3% were resistant to linezolid. Although survival rates for burn patients have improved substantially over the years, nosocomial infections still remain a major challenge in burn care. This concludes that there is high prevalence of nosocomial infections specially the presence of multidrug resistant bacteria like Methicillin Resistant Staphylococcus aureus among burn patients suggest continuous surveillance of burn wound infections and development and stringent implementation of antibiotic policy.
1. This study investigated the prevalence of integrons and antimicrobial resistance genes in 110 clinical isolates of Enterobacter species collected from hospitals in Tehran, Iran between 2012-2013.
2. The study found that 45 isolates (41%) contained integrons, with class 1 integrons being most common. Integron-positive isolates showed higher resistance to antibiotics like augmentin, trimethoprim-sulfamethoxazole, and cefoxitin.
3. Ten integron-positive isolates were found to be ESBL producers. Common resistance genes identified included blaTEM (20%), blaCTX-M-1 (15.6%), and genes encoding aminoglycoside
GENETIC CHARACTERIZATION OF SEROTYPE AND GENETIC RELATEDNESS OF FOOT-AND-MOUT...EuFMD
This study analyzed 95 foot-and-mouth disease virus (FMDV) samples collected between 2018-2019 from Vietnam, Laos, and Cambodia to determine their genetic relatedness. 40 samples tested positive for FMDV through 3D qRT-PCR analysis. Genome sequencing of the VP1 region showed that FMDVs in Vietnam and Laos belonged to serotypes O/ME-SA/Panasia and O/SEA/Mya-98, while viruses in Cambodia belonged to serotypes O/ME-SA/Panasia and A/ASIA/SEA-97. Phylogenetic analysis revealed that Cambodia's A/ASIA/SEA-97 and Vietnam's O/SEA/My
This study characterized carbapenem-resistant Acinetobacter baumannii (CNSAb) isolates collected from burn patients at a hospital in Tehran, Iran. Of the 92 A. baumannii isolates tested, 69 were confirmed to be CNSAb based on imipenem resistance. Antibiotic susceptibility testing found high resistance rates to multiple classes of antibiotics. Molecular analysis identified several beta-lactamase genes conferring resistance. Most isolates belonged to international clones and sequence types previously seen worldwide. Genetic analysis using multiple methods found diversity but also the presence of dominant strains. The study provides information on the antibiotic resistance and genetic characteristics of CNSAb in Iranian burn patients.
Characterization of Mycobacterium Tuberculosis Complex Strains: A Multicenter...CrimsonpublishersCJMI
Characterization of Mycobacterium Tuberculosis Complex Strains: A Multicenter Retrospective Greek Study by Lamprini Gkaravela in Cohesive Journal of Microbiology & Infectious Disease
Role of Nonfermenting Gram-Negative Bacilli Responsible for Respiratory Tract...Premier Publishers
The majority of nonfermenting gram-negative bacilli are responsible for respiratory tract infections. The aims of this study are to identify the nonfermenting gram-negative bacilli species in respiratory tract infections, to describe their antibiotic resistance and to describe the factors associated with these bacteria. It is a prospective study of 54 respiratory samples for a period of six months from October 2019 to March 2020 in the laboratory of the University Hospital of Befelatanana Antananarivo. Among the 54 respiratory samples, the microbiological results showed 12 (22.2%) cases of nonfermenting gram-negative bacilli. These bacilli were represented by 7 (58.3%) cases of Acinetobacter baumannii, 4 (33.3%) cases of Pseudomonas aeruginosa and 1 (8.3%) case of Stenotrophomonas maltophilia. Concerning the associated factors, subjects under 40 years (24%) (p=0.77; NS), men (30.8%) (p=0.03) and subjects hospitalized in intensive care units (40.7%) (p=0.003) were the most affected by the nonfermenting gram-negative bacilli. Regarding antibiotic resistance, it varies from 71.4% to 100% for Acinetobacter baumannii and 0% to 100% for Pseudomonas aeruginosa. The Stenotrophomonas maltophilia isolate had a broad spectrum ß-lactamase but was sensitive to the other antibiotics. Nonfermenting gram-negative bacilli are responsible for severe nosocomial pneumonia and the majorities are multi-resistant bacteria.
Prevalence of non-fermenter as uro pathogen in tertiary care hospital in Chid...pharmaindexing
This study aimed to determine the prevalence of non-fermenting gram-negative bacilli (non-fermenters) as causes of urinary tract infections (UTIs) at a hospital in India over an 18-month period. The study found that of the 317 urine culture samples that showed significant bacteriuria, 131 (9.7%) were caused by non-fermenters. Pseudomonas species was the most common non-fermenter isolated, accounting for 80.6% of cases, while Acinetobacter species accounted for 19.3% of cases. Antibiotic sensitivity testing showed varying resistance patterns between the two bacteria.
This study analyzed 8,749 clinical samples collected from July 2010 to December 2012 at a tertiary hospital in Odisha, India. Of these, 137 samples (3%) yielded Acinetobacter species. Most isolates were from pus/swabs (56.9%), blood (13.1%), and urine (12.4%). Risk factors for Acinetobacter infection included older age, hospitalization, longer hospital stays, comorbidities, and invasive procedures. Many isolates were multidrug-resistant (54.7% resistant to >3 antibiotic classes) or pan-drug resistant (5.8% resistant to all antibiotics tested). Isolates were most sensitive to imipenem, meropenem, and pip
ENHANCED DIAGNOSIS EFFICACY OF A NEWLY DEVELOPLED ELISA KIT FOR FMDV IN POOL ...EuFMD
This document summarizes a study that compares the diagnostic efficacy of a newly developed ELISA kit from the Animal and Plant Quarantine Agency (APQA) in South Korea to the OIE reference Pirbright ELISA kit for detecting foot-and-mouth disease virus (FMDV) in samples from Southeast Asian countries. Clinical samples collected from 2015-2019 from Vietnam, Laos, Cambodia, and Myanmar were tested using both kits. The results showed that the APQA kit had better sensitivity for detecting FMDV serotype O compared to the Pirbright kit. For FMDV serotype A, the APQA kit performed better on some samples while the Pirbright kit was more sensitive on others. Overall, the APQA
This document discusses the global threat of antimicrobial resistance (AMR) and the role that drug and therapeutics committees (DTCs) can play in containing AMR. It outlines the global spread of drug-resistant pathogens and infections. The overuse and misuse of antibiotics in both human and animal settings is a major cause of growing AMR. DTCs can help address this by developing antibiotic policies and formularies, educating on appropriate use, and monitoring antibiotic consumption and resistance patterns. Examples from Kenya and Thailand demonstrate how DTCs have successfully implemented strategies like antibiotic order forms to improve antibiotic use.
This study analyzed ticks collected from four vegetation sites in South Korea over two years to understand tick populations and the prevalence of severe fever with thrombocytopenia syndrome virus (SFTSV). The dominant tick species was Haemaphysalis longicornis, which made up over 95% of collected nymphs and adults. H. longicornis nymph numbers peaked in June 2020 while adult numbers peaked in July 2019 and June 2020. Testing found the virus in H. longicornis pools in August-October 2020, with the highest minimum infection rate in August. Most ticks and virus-positive pools were found in grassland and grave sites. The results provide insights into controlling SFTSV risk through tick management
This document analyzes genetic markers associated with artemisinin resistance in Plasmodium falciparum parasites collected in western Kenya before and after the introduction of artemisinin combination therapies (ACTs). Twenty-five single nucleotide polymorphisms (SNPs) on chromosomes 13 and 14 and pfmdr1 gene copy number were analyzed. Fifteen SNPs were present in pre-ACT isolates, but only six were present in post-ACT isolates. Post-ACT isolates had significantly higher pfmdr1 copy numbers than pre-ACT isolates. No SNPs were associated with parasite clearance half-life. The results suggest the genetic signature of artemisinin resistance in African parasites may differ from that in Southeast Asian parasites.
Escherichia coli was the predominant pathogen isolated (70.52%) from the urine cultures of 538 patients with urinary tract infections in Surat, India. Antibiotics like ampicillin showed high resistance rates of over 90% among isolated gram-negative pathogens. However, gram-negative pathogens demonstrated the highest sensitivity to amikacin, netromycin, piperacillin/tazobactum and cefoperazone/sulbactum with resistance rates below 5%. The study highlights the increasing antimicrobial resistance seen with commonly used antibiotics and identifies alternative antibiotic options for empirical therapy of urinary tract infections in the region.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
2. Antibiotics 2021, 10, 563 2 of 15
resistant to many antibiotics and may acquire resistance via mutational changes in chromo-
somal structure and through horizontal gene transfer [4]. The spread and dissemination of
multidrug-resistant (MDR) and extremely drug-resistant (XDR) A. baumannii have become
a public health concern in both developing and developed countries. The prevalence of
resistance towards last-resort antibiotics such as carbapenems and colistin is increasing
globally [4,5]. The treatment of carbapenem-resistant A. baumannii (CRAb) is becoming a
global challenge. CRAb is emerging worldwide, and the majority of these isolates often
show MDR or XDR patterns [6,7]. They are also associated with an increased length of
stay at hospital ICUs [8]. CRAb is associated with increased mortalities in patients with
bloodstream infections in low- and middle-income countries [9]. It is considered one of the
most common pathogens of nosocomial infections in Southeast Asia [10].
Vietnam is one of the Southeast Asian countries with the highest resistance prevalences
amongst Gram-negative pathogens in the Asia-Pacific region [11]. It is considered the
“hottest” spot of MDR A. baumannii in Asia. A. baumannii was considered one of the
most frequent causes of ventilator-associated respiratory infection [12–14] and secondary
meningitis [15] in Vietnamese ICUs. From 2008 to 2011, 101 clinical A. baumannii strains
were isolated from ICU patients in two medical settings in Vietnam [16]. Between 2012
and 2014, 252 Acinetobacter spp. were isolated from patients admitted to three hospitals
in southern Vietnam. Among them, 160 were confirmed as A. baumannii [17]. Between
2014 and 2015, A. baumannii posed serious therapeutic problems in ICU patients at a major
tertiary hospital in Ho Chi Minh City [18]. Several separate studies have been carried
out on A. baumannii in Southeast Asian countries and showed increases in the general
distribution of A. baumannii in hospitals in Vietnam [12,17–20], Malaysia [21], Thailand [22],
the Philippines [23] and Indonesia [24]. However, no comparison of the circulating strains
and no multinational transboundary studies have been carried out to investigate the
resistance profiles, MLST and the lineage of A. baumannii in the Southeast Asia region.
Thus, the current study aimed to analyze the whole-genome sequencing (WGS) data
of carbapenem-resistant A. baumannii isolates obtained from Vietnamese patients and
compare their AMR genes, MLST types and genetic diversity with published genomes of
strains from Southeast Asia.
2. Results and Discussion
2.1. Whole-Genome Sequencing Data, MLST and cgMLST Analysis
Genome sequencing of 11 Vietnamese A. baumannii isolates yielded an average read
length of 262,090 per isolate (range 1,137,862–2,537,360). The isolates’ mean coverage was
105.9-fold (range from 72-fold to 149-fold) (Table S1). To check for possible contamina-
tion and accurate species identification, the software Kraken2 was used, which classifies
each read (or contig) [25]. At the genus level, the first match for all isolates was always
“Acinetobacter”, on average, 97.61% of the reads (maximum 99.18%, minimum 89.61%). At
the species level, the first match for all 11 isolates was always “Acinetobacter baumannii”,
on average, 78.24% of the reads. Genome assembly yielded an average genome size of
4,070,357 bp with a minimum of 3,792,190 bp. The GC content was, on average, 38.97%.
The mean N50 of the 11 assembled genomes was 88.347 bp (range 41,904–184,445 bp)
(Table S2). MLST analyses of eleven Vietnamese A. baumannii strains based on the Pasteur
scheme allocated nine strains into a distinct ST. Six strains were assigned to ST/2, two were
assigned to ST/571 and one was assigned to ST/164. Two isolates were allocated into two
new STs (ST/1411-1412) (Table 1).
MLST analysis confirmed the considerable genetic diversity of A. baumannii in the
investigated strains from Southeast Asia. Six strains were removed as they did not fit our
quality criteria. MLST analyses based on the Pasteur scheme identified 19 sequence types
(ST) for 107 strains, and a strain from Thailand could not be assigned to a distinct sequence
type due to new alleles. ST/2 was the most prevalent sequence type circulating in the
Southeast Asian countries. It was found in 62 strains isolated from humans from Vietnam,
Myanmar, Thailand, Singapore and Malaysia, followed by ST/164 and ST/16, which were
3. Antibiotics 2021, 10, 563 3 of 15
found in nine and six strains, respectively. A strain obtained from the soil in Malaysia was
assigned to ST/46.
Table 1. Strain types (ST) of 108 A. baumannii strains isolated in Southeast Asia according to the
Pasteur scheme.
MLST Frequency Country
ST/2 62
Vietnam (6), Myanmar (19), Thailand (33),
Singapore (3), Malaysia (1)
ST/164 9 Vietnam (1), Myanmar (5), Thailand (3)
ST/16 6 Myanmar (2), Thailand (4)
ST/23 4 Myanmar (3), Thailand (1)
ST/25 4 Myanmar (3), Thailand (1)
ST/1 3 Myanmar (3)
ST/215 3 Thailand (3)
ST/571 3 Vietnam (2), Thailand (1)
ST/374 2 Malaysia (2)
ST/575 2 Myanmar (2)
ST/46 1 Malaysia, soil (1)
ST/52 1 Thailand (1)
ST/109 1 Myanmar (1)
ST/129 1 Taiwan (1) *
ST/220 1 Malaysia (1)
ST/360 1 Malaysia (1)
ST/739 1 Malaysia (1)
ST/1411 1 Vietnam (1), new ST
ST/1412 1 Vietnam (1), new ST
ND 1 Thailand (1)
20 108 Total
* Taiwan is part of the area of Greater China and is used as an example of a trading country with Southeast
Asian countries.
The MLST analyses showed that more than half of the human strains (62 out of 107)
in the current study were assigned to ST/2 (Pasteur). ST/2 belongs to the international
clone II and is the most dominant type globally [26]. In previous studies, most of the CRAb
isolates were found belong to the ST2 lineage in strains isolated from Thailand [22] and
Myanmar [27] and among strains isolated from all five countries that contributed to this
study. From 2008 to 2011, 101 clinical A. baumannii strains were isolated from patients in
two medical settings in Vietnam. Most of the A. baumannii isolates obtained from a hospital
in Hanoi were ST/91 and ST/231, whereas almost all strains from a hospital in Ho Chi
Minh City were ST/136, ST/195 and ST/254 [16]. ST/1, ST/575 and ST/109 were found
only in Myanmar, while ST/46, 220, 360, 374 and ST/739 were found only in Malaysia.
ST/52 and ST/215 were found only in Thailand, while ST/129 was found only in Taiwan
(Table 1). The published knowledge on the general distribution of STs of A. baumannii in
the population of Southeast Asia is scarce. These findings are, moreover, in agreement with
those of Gaiarsa et al., who demonstrated that the Pasteur scheme is more appropriate for
epidemiological studies of A. baumannii [28] and proposed it to be the scheme of choice in
parallel with cgMLST.
In the current study, we applied the cgMLST scheme included in the SeqSphere+
Ridom software tools, using a gene-by-gene approach to compare and describe the ge-
4. Antibiotics 2021, 10, 563 4 of 15
ographical relationship and the lineage among A. baumannii strains from Vietnam and
Southeast Asia. The Vietnamese strains showed high diversity. Five strains appeared in
three different clusters, and six strains were unique singletons. WGS showed a higher
discriminatory power than conventional typing methods [6]. It allows a more precise track-
back analysis of the strains, particularly when analyzing carbapenem-resistant A. baumannii
isolates, which threaten the global healthcare system. We observed 14 different clusters
(1 to 14) using cgMLST SeqSphere+ analysis. Clusters 1 and 5 contained isolates from
Thailand and Myanmar. However, isolates were obtained from different countries and
clustered in two distinctive clusters but shared the same Pasteur sequence type (ST/2).
Cluster 11 contained one strain from Thailand and one from Vietnam and shared the same
Pasteur sequence type (ST/164). Our analyses demonstrate that the strains are highly
diverse. However, there was a good correlation between MLST and cgMLST clusters. All
strains in the same cluster were assigned to the same ST. The predominant type ST/2 based
on the Pasteur scheme could be sub-divided into eleven different clusters and distinct
lineages when cgMLST was employed. These results show a superior discriminatory ability
of cgMLST compared to the conventional MLST [29].
2.2. Antibiotic Susceptibility Testing (AST) and AMR Determinants of Vietnamese Strains
Antibiotic resistance is a serious problem in the Asia-Pacific region, and A. baumannii
strains are among the most accounted for Gram-negative bacteria (GNB) causing uri-
nary tract infections in this region [30]. Ten out of eleven A. baumannii strains originat-
ing from Vietnam were MDR, displayed resistance to fluoroquinolones (ciprofloxacin
and levofloxacin), carbapenems (imipenem, meropenem and ertapenem), third-generation
cephalosporins (cefotaxime, ceftazidime, ceftazidime/avibactam and ceftolozane/tazobactam),
fourth-generation cephalosporins (cefepime), piperacillin, piperacillin/tazobactam, chlo-
ramphenicol and fosfomycin and were susceptible only to colistin. Resistance to the
tetracycline derivative tigecycline (MIC = 1 µg/mL) and trimethoprim/sulfamethoxazole
(MIC 4/76 µg/mL) was seen in nine strains (Table S3). All MDR strains (n = 10) were
carbapenem-resistant with MIC values of 8 µg/mL to imipenem (IMP) and 0.5 µg/mL
to ertapenem (ERT). The MIC values to meropenem (MER) ranged from 32 to 128 µg/mL,
higher than the MIC value (16 µg/mL) reported for the A. baumannii DMS06669 strain
isolated in a Vietnam hospital [31]. From 2012 to 2014, resistance to cephalosporins, fluo-
roquinolones and carbapenems was 90% among 904 A. baumannii isolates from patients
with hospital-acquired or ventilator-associated pneumonia in Vietnam [13], while colistin
(MIC90, ≤0.25 mg/L) and tigecycline (MIC90, 4 mg/L) showed appreciable activity against
A. baumannii. MIC90 for meropenem and imipenem was 32 mg/L in more than 80% of
74 strains isolated from tracheal aspirate specimens taken from patients with suspected
ventilator-associated pneumonia from January 2011 to June 2012 [32]. All MIC values of
tested antibiotics in the current study are shown in Table 2. One strain showed susceptibil-
ity to almost all tested antibiotics. It may has been isolated from a patient from rural areas
where the use of antibiotics is seldom because they always depend on medicinal plants in
treatment, in contrast to other patients.
The genome of all strains (100%) harbored ant(3”)-IIa, which confers resistance to
aminoglycosides, while the armA gene was found in eight (72.7%) isolates, and aph(6)-Id
and aph(3”)-Ib were found in seven (63.6%) isolates. All isolates harbored at least one of the
blaOXA-51 variants and blaADC-25, which confer resistance to ß-lactams, while blaOXA-23 and
blaTEM-1 were found in nine (81.8%) and six (54.5%) isolates, respectively. More than half of
the Vietnamese strains harbored genes that confer resistance to tetracyclines, sulfonamides
and macrolides (Table S4).
5. Antibiotics 2021, 10, 563 5 of 15
Table 2. The MIC (µg/mL) for the 11 sequenced Vietnamese A. baumannii strains as evaluated with MICRONAUT software.
ID CIP LEV AMK COL CMP FOS TGC T/S PIP PIT CTX CAZ CAA CTA CEP IMP MER ERT
18Y0059 2 2 32 ≤1 16 64 =1 4/76 16 64/4 2 128 16/4 8/4 =128 8 =64 0.5
18Y0060 2 2 32 ≤1 16 64 =1 4/76 16 64/4 2 128 16/4 8/4 =128 8 =64 0.5
18Y0061 2 2 32 ≤1 16 64 =1 4/76 16 64/4 2 128 16/4 8/4 =64 8 =64 0.5
18Y0064 2 2 32 ≤1 16 64 =1 4/76 16 64/4 2 128 16/4 8/4 =64 8 =128 0.5
18Y0065 2 2 32 ≤1 16 64 =1 =2/38 16 64/4 2 128 16/4 8/4 =128 8 =64 0.5
18Y0066 2 2 32 ≤1 16 64 0.5 4/76 16 64/4 2 =64 =16/4 8/4 =64 8 =128 0.5
18Y0067 2 2 32 ≤1 16 64 =1 4/76 16 64/4 2 =64 =16/4 8/4 =64 8 =64 0.5
18Y0068 ≤0.25 ≥0.5 ≤4 ≤1 16 64 ≤0.25 =4/76 ≤8 ≤4/4 =2 ≤1 ≤1/4 ≤1/4 ≤1 ≤1 ≤0.125 =0.25
18Y0072 2 2 ≤4 ≤1 16 64 ≤0.25 ≤1/19 16 64/4 2 128 =16/4 8/4 =128 8 =32 0.5
18Y0074 2 2 32 ≤1 16 64 0.5 4/76 16 64/4 2 128 =16/4 8/4 =32 8 =64 0.5
18Y0075 2 2 32 ≤1 16 64 =1 =4/76 16 64/4 2 128 16/4 8/4 =128 8 =64 0.5
The minimum inhibitory concentration (MIC), ciprofloxacin (CIP), levofloxacin (LEV), amikacin (AMK), colistin (COL), chloramphenicol
(CMP), fosfomycin (FOS), tigecycline (TGC), trimethoprim/sulfamethoxazole (T/S), piperacillin (PIP), piperacillin/tazobactam (PIT),
cefotaxime (CTX), ceftazidime (CAZ), ceftazidime/avibactam (CAA), ceftolozane/tazobactam (CTA), cefepime (CEP), imipenem (IMP),
meropenem (MER) and ertapenem (ERT).
The prevalence of MDR/CRAb was very high. The results are in agreement with
previous reports: most CRAb strains display resistance to at least one compound in three
or more antimicrobial categories and are designated as MDR [6,7]. Resistance against
imipenem was seen in 91.6% of XDR A. baumannii strains isolated from patients in three
hospitals in southern Vietnam between 2012 and 2014 [17]. A strain resistant to all tested
classes of antibiotics except ciprofloxacin and colistin was isolated from the sputum of a
patient with hospital-acquired pneumonia at the general hospital of Dong Nai [19]. Ex-
amination of 79 strains recovered from patients with pneumonia in Thong Nhat Dong
Nai General Hospital showed carbapenem resistance and MDR in 80% and 90% of iso-
lates, respectively [33]. This study highlights the very high prevalence of MDR/CRAb in
the General Hospital of Phutho, Hanoi. Clinically, A. baumannii has become a notorious
nosocomial pathogen worldwide [26], and the emergence of MDR/CRAb has serious
consequences in the healthcare system in Southeast Asia [10]. The general distribution
of A. baumannii is increasing in hospitals in Vietnam [19], Thailand [22,34], the Philip-
pines [23], Malaysia [21], Indonesia [24] and Taiwan [35]. Our results support previous
data from Southeast Asian hospitals, where a substantial increase in the MDR/CRAb
isolation rate was demonstrated [10]. Identification of the genetic determinants associated
with carbapenem resistance in A. baumannii is helping to explain the continuous selection
and ongoing transmission within the healthcare system of Vietnam and other Southeast
Asian countries.
2.3. Predicted Phenotype and AMR Determinants of A. baumannii from Southeast Asia
To compare the findings of AMR determinants in Vietnam to neighboring countries,
we downloaded and analyzed A. baumannii sequence data from Southeast Asia. The fre-
quency and percentage of resistance genes conferring specific antibiotic resistance were
identified in 108 A. baumannii whole genomes. Our WGS approach identified different
AMR genes, among which at least 47 genes confer resistance to ß-lactams, 18 to amino-
glycosides, 8 to phenicoles, 4 to tetracyclines, 3 to sulfonamides and 3 to macrolides and
lincosamide (Table S4).
2.3.1. Resistance to β-Lactams
In total, forty-seven AMR genes mediating resistance to ß-lactams, including
cephalosporins and carbapenems, were identified. The Ambler class D β-lactamases
were present in almost all strains. The variants of the intrinsic blaOXA-51-like carbapenemase
gene were found in 103 (95.5%) strains; blaOXA-66 was the most frequent and was found in
68 (61%) isolates, followed by blaOXA-91, blaOXA-402 and blaOXA-64. Five isolates (4.5%) were
devoid of blaOXA-51-like. The blaOXA-23 variant was found in 90 (83%) isolates, and blaOXA-58
was found in 13 (12%) isolates. In terms of Ambler class A β-lactamases, blaTEM-1 was
6. Antibiotics 2021, 10, 563 6 of 15
found in 55 (51%) isolates, followed by bla-PER- in 8 (7.5%) isolates, bla-CARB-16 in 5 isolates,
bla-VEB-21 in 4 isolates and bla-SHV-5 in 1 strain. Regarding Ambler class B β-lactamases,
blaNDM-1 was found in nine (8%) isolates, and blaIMP-14 was found in two strains. Sixteen
Acinetobacter-derived cephalosporinase blaADC variants of the Ambler class C β-lactamases
were identified. The blaADC-25 variant was the most frequent variant and was detected in all
isolates (100%), followed by blaADC-73 in 50 (46%) isolates, blaADC-52 in 8 isolates, blaADC-30
and blaADC-26 in 7 isolates and blaADC-76, blaADC-169 and blaADC-199 in 6 isolates (Table S4).
Four Ambler classes of β-lactamases (i.e., classes A, B, C and D) were identified in
the current study. Various resistance genes conferring resistance to carbapenems and
cephalosporins were found in A. baumannii isolated from Southeast Asia. The blaOXA-23
and blaOXA-51-like variants were among the most frequent AMR genes identified. Both are
currently spreading on plasmids and associated with resistance to all β-lactam compounds,
including carbapenems [21,36]. The ADC beta-lactamases are cephalosporinases with
extended-spectrum resistance to cephalosporins. All strains harbored blaADC-25, and ap-
proximately half of the strains (46%) harbored blaADC-73, which are considered significant
determinants responsible for cephalosporins resistance in A. baumannii [37]. More than
half of the strains (51%) harbored blaTEM-1. It encodes a class A β-lactamase and has been
found in CRAb strains from different regions worldwide [38–40].
2.3.2. Resistance to Aminoglycosides
In the 108 analyzed strains, 18 AMR genes conferring resistance to aminoglycosides
were identified. Aminoglycoside-modifying enzymes (AMEs), including acetyltransferases
(AACs), methyltransferase (armA), phosphotransferases (APHs) and nucleotidyltrans-
ferases (ANTs), were identified. The new subclass of intrinsic aminoglycoside nucleotidyl-
transferase, ANT(3”)-IIa, was widely distributed and was found in almost all strains (99%),
followed by the intrinsic aminoglycoside O-phosphotransferase aph(6)-Id and aph(3”)-Ib
found in 83 (77%) strains. To date, over a hundred AMEs have been described, and AACs
represent the largest group of AMEs [41]. In the current study, AAC genes were detected
in 12% of the isolates, while ANT and APH genes were distributed in almost all isolates
(Table 3). Moreover, the intrinsic aminoglycoside methyltransferase (MET) armA was found
in 73 (76.5%) isolates. ArmA is the most important class of plasmid-mediated MET enzymes
that confer resistance to gentamicin in Enterobacteriaceae [42]. Aminoglycosides are broad-
spectrum antibiotics used against a wide range of infections caused by Gram-negative
bacteria in clinical settings. However, their efficacy has been reduced by resistance develop-
ment [7,43]. This finding highlights the diversity of aminoglycoside-resistant A. baumannii
strains mediated by ANTs, APHs, armA and AACs of AMEs in Southeast Asian countries.
2.3.3. Resistance to Phenicoles, Tetracyclines, Macrolides, Sulfonamides and Rifamycin
At least eight genes encoding resistance to phenicoles (cmlA, catB8, cmlA1, floR, cmlA5,
catB3, catA1 and cmlA6) were identified. CatB8 was the most frequent and found in 14 (13%)
isolates, followed by cmlA in 6 isolates and floR in 4 isolates. Most A. baumannii isolates
are intrinsically resistant to chloramphenicol [44]. However, genes encoding resistance
to phenicoles were found only in 13% of the isolates. Four genes encoding resistance
to tetracycline (tet.B, tet.39, tet.A, tet.M) were identified. Tet.B was identified in 79 (73%)
isolates, and tet.39 was identified in 15 (14%) isolates. Tet.B is a tetracycline efflux protein
that confers resistance to tetracycline but not to tigecycline [45]. In the current survey,
it was found in the majority of strains. Two genes encoding macrolide resistance were
identified. Mph.E and msr.E were identified in 77% and 79% of the isolates, respectively.
Three genes encoding resistance to sulfonamides (sul1, sul2 and sul3) were identified. Sul2
and sul1 variants were found in 66% and 29% of the strains, respectively, while sul3 was
found in one isolate. Both sul2 and sul1 are mediated by transposons and plasmids [46].
The presence of one or both genes in A. baumannii isolates might confer resistance to
trimethoprim/sulfamethoxazole. The arr-2 gene confers resistance to rifampicin was
found in 14 (13%) strains (Table 3). Several resistance mechanisms for different antibiotic
7. Antibiotics 2021, 10, 563 7 of 15
classes exist in A. baumannii [47] and were found in the current study. Genes encoding
resistance to macrolides, tetracyclines, sulfonamides and phenicoles were seen in 77%,
73%, 66% and 13% of the isolates, respectively. The circulation of genes at such high
frequency in Southeast Asia is alarming and highlights the urgent need to take effective
control measures.
Table 3. AMR genes detected in 108 whole-genome sequences of A. baumannii originating from Southeast Asia.
Antibiotic Class
AMR Resistance Genes
Mechanism Predicted
Phenotype
Origin of Strains
Gene Family Frequency (%)
Aminoglycosides
ant(3“)-IIa 107 (99%)
NUT:
Nucleotidyltransferase
Streptomycin,
spectinomycin
Viet, Myan, Thai, Sing,
Mala, Tiaw
aph(3“)-Ib 83 (77%) PHT: Phosphotransferase Streptomycin
Viet, Myan, Thai, Sing,
Mala, Tiaw
aph(6)-Id 83 (77%) PHT: Phosphotransferase Streptomycin
Viet, Myan, Thai, Sing,
Mala, Tiaw
armA_1 73 (63.5%) MET: Methyltransferase Gentamicin
Viet, Myan, Thai, Sing,
Mala, Tiaw
aph(3’)-Ia 53 (49%) PHT: Phosphotransferase Kanamycin
Viet, Myan, Thai, Sing,
Mala, Tiaw
aadA1 22 (20%)
NUT:
Nucleotidyltransferase Streptomycin Viet, Myan, Thai,
Sing, Tiaw
aph(3’)-Via 15 (14%) PHT: Phosphotransferase Amikacin,
kanamycin Viet, Myan, Thai,
ant(2“)-Ia 14 (13%)
NUT:
Nucleotidyltransferase
Gentamicin,
kanamycin Viet, Myan, Thai
aac(6’)-Ib 12 (11%) ACT: Acetyltransferase Gentamicin Viet, Myan, Thai, Tiaw
aac(3)-IId 11 (10%) ACT: Acetyltransferase Gentamicin Myan, Thai
β-lactams
blaOXA-51-like 103 (95.5%) Ambler class D
β-lactamases
β-lactam
(carbapenem)
Viet, Myan, Thai, Sing,
Mala, Tiaw
blaOXA-66 68 (61%) blaOXA-51 variant β-lactam
(carbapenem)
Viet, Myan, Thai, Sing,
Mala, Tiaw
blaOXA-91 10 (9%) blaOXA-51 variant β-lactam
(carbapenem) Viet, Myan, Thai
blaOXA-23 90 (83%) Ambler class D
β-lactamases
β-lactam
(carbapenem)
Viet, Myan, Thai, Sing,
Mala, Tiaw
blaOXA-58 13 (12%) Ambler class D
β-lactamases
β-lactam
(carbapenem) Viet, Myan, Thai, Mala
blaTEM-1 55 (51%) Ambler class A
β-lactamases β-lactam
Viet, Myan, Thai,
Sing, Mala
blaADC-25 108 (100%) Ambler class C
β-lactamases
β-lactam
(cephalosporin)
Viet, Myan, Thai, Sing,
Mala, Tiaw
blaADC-73 50 (46%) Ambler class C
β-lactamases
β-lactam
(cephalosporin) Viet, Myan, Thai
blaNDM-1 9 (8.5%) Ambler class B
β-lactamases
β-lactam
(carbapenem) Viet, Myan, Thai
Phenicoles catB8 14 (13%) Enzymes inactivation Chloramphenicol Viet, Myan, Thai, Tiaw
Macrolide
mph.E. 83 (77%) Enzymes inactivation Macrolide
Viet, Myan, Thai, Sing,
Mala, Tiaw
msr.E. 85 (79%) Antibiotic efflux Macrolide
Viet, Myan, Thai, Sing,
Mala, Tiaw
Sulfonamides
sul1 31 (29%)
Antibiotic target
replacement
Sulfonamide
Viet, Myan, Thai, Sing,
Mala, Tiaw
sul2 71 (66%)
Antibiotic target
replacement
Sulfonamide
Viet, Myan, Thai, Sing,
Mala, Tiaw
Tetracyclines
tet.39. 15 (14%) Antibiotic efflux Tetracycline Viet, Myan, Thai
tet.B. 79 (73%) Antibiotic efflux Tetracycline
Viet, Myan, Thai, Sing,
Mala, Tiaw
Rifamycin arr-2 14 (13%) Rifamycin Myan, Thai,
Viet (Vietnam), Myan (Myanmar), Thai (Thailand), Sing (Singapore), Mala (Malaysia), Tiaw (Taiwan).
8. Antibiotics 2021, 10, 563 8 of 15
2.3.4. Antibiotic Efflux Pumps
Four categories of efflux pumps were found in A. baumannii isolates of Southeast
Asian origin, including the resistance-nodulation-division (RND) superfamily, the major
facilitator superfamily (MFS), the multidrug and toxic compound extrusion (MATE) family
and the small multidrug resistance (SMR) family transporters. Among these different
pumps, the MFS transporter (amvA), RND (adeFGH, adeIJK and adeL), SMR (abeS) and
MATE (abeM) were most frequent and found in almost all isolates (99–100%). RND ef-
flux pump-coding genes (adeN, adeR, adeS and adeAB) were found in 92.2%–94.5% of the
strains (Table S4). Resistance mediated by antibiotic efflux pump-encoding genes is well
documented in A. baumannii [7,20]. Efflux pumps play significant roles in developing
AMR in A. baumannii [48]. The chromosomally encoded tripartite efflux pump adeABC is a
worldwide-distributed RND superfamily efflux pump in A. baumannii and was found in
approximately 80% of the clinical strains. The overexpression of adeABC efflux pumps is
mainly associated with reduced susceptibility to tigecycline [49], fluoroquinolones, tetracy-
cline, chloramphenicol and erythromycin, confers resistance to aminoglycosides [50,51]
and may contribute resistance to carbapenems [39]. The circulation of numerous efflux
pumps with high frequency suggests a significant rise in A. baumannii antibiotic resistance
in Southeast Asia. Acinetobacter baumannii AbaF was found in 104 (96%) strains isolated
from all contributing countries. AbaF is a major facilitator superfamily (MFS) antibiotic
efflux pump interfering with protein synthesis. Its expression in E. coli increases resistance
to fosfomycin. The high frequency of resistance to fosfomycin was seen in the tested strains
and in a previous study on A. baumannii [7]. It has been reported that the abaF gene is
involved in fosfomycin resistance in A. baumannii and plays a role in biofilm formation and
virulence mechanisms [52].
2.4. Acquired Resistance in A. baumannii of Southeast Asian Origin
Examination of all strains in the current study, either sequenced strains from Viet-
nam or downloaded genomes from PlasmidFinder [53] and Platon [54] as two different
tools to investigate the potential presence of plasmids, failed to detect plasmids or plas-
mid replicons in all strains, except for one strain from Myanmar which harbored only
two replicons (Col.MG828._1 and Col8282_1). This information is included in Table S5.
Moreover, the comprehensive ResFinder server [55] was used to investigate the potential
acquired AMR genes in the A. baumannii strains. ResFinder can identify acquired genes
and chromosomal mutations mediating AMR in a total or partial DNA sequence. Several
genes encoding resistance to aminoglycosides, β-lactams, tetracycline, sulfonamides and
macrolides were found. The Acinetobacter-derived cephalosporinase blaADC.25 conferring re-
sistance to cephalosporin was identified in all isolates (100%), and the two genes conferring
resistance to carbapenems, blaOXA-23 and blaOXA-51-like (blaOXA-66 variant), were detected in
83% and 61% of the strains, respectively. Moreover, different variants of blaTEM, blaCARB,
blaIMP, blaVEB, blaPER, aph.6.Id, aph.3.Ia, aph.3.Ib, tet, sul and armA were identified using
the ResFinder database. The presence of various plasmids in the genome of A. bauman-
nii [56] and its ability to acquire foreign DNA [57,58] enhance the acquisition of AMR
genes. Several reports suggested that mobile genetic elements play significant roles in the
horizontal transfer of AMR genes in A. baumannii, particularly genes that confer resistance
to aminoglycosides, chloramphenicol and tetracycline [59–61]. Identification of a wide
variety of AMR genes by ResFinder in the current study highlights the role of horizontal
gene transfer in the development of resistance in A. baumannii in Southeast Asia.
3. Materials and Methods
3.1. Identification of Bacterial Isolates and Antibiotics Susceptibility Testing (AST)
In total, eleven non-repetitive A. baumannii strains isolated from Vietnamese patients
at the General Hospital of Phutho, Hanoi, were received by the Institute of Bacterial
Infections and Zoonoses (IBIZ, Jena) for species confirmation and typing. The strains
were isolated from blood, sputum, CSF and abscess samples of patients admitted to
9. Antibiotics 2021, 10, 563 9 of 15
the hospital in 2017. The agreement for receiving the genetic samples according to the
Nagoya Protocol was obtained from the Natural Resources and Environment Minister.
No additional ethical approval was required. All strains were identified at species level
using a combination of matrix-assisted laser desorption/ionization mass spectrometry
(MALDI-TOF MS) with a log value of 2.300 and the intrinsic blaOXA-51-like-PCR [62]. The
minimum inhibitory concentration (MIC) was determined by the broth microdilution
method using an automated MICRONAUT-S system (Micronaut, MERLIN Diagnostics
GmbH, Bornheim-Hersel Germany) according to the manufacturer’s instructions. The
results were evaluated as susceptible, intermediate and resistant automatically with the
built-in MICRONAUTS software. The MIC values for a panel of the 18 antibiotics were
interpreted according to the Clinical and Laboratory Standards Institute (CLSI) breakpoint
guidelines available for A. baumannii as previously described [7].
3.2. Whole-Genome Sequencing and Collection of Sequence Data from Southeast Asia
DNA extraction was performed using the High-Pure template preparation kit (Roche
Applied Sciences, Mannheim, Germany) according to the manufacturer’s instructions.
The library preparation and paired-end sequencing on an Illumina MiSeq sequencer were
performed for the 11 Vietnamese A. baumannii strains as previously described [7]. Briefly,
the Nextera XT DNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) was utilized to
prepare the sequencing library, followed by paired-end sequencing on an Illumina MiSeq
sequencer (Illumina, San Diego, CA, USA).
Raw sequencing data were downloaded from NCBIs’ Sequence Read Archive (https:
//www.ncbi.nlm.nih.gov/sra/?term, accessed on 1 November 2020) according to the following
criteria: Search for species [Acinetobacter baumannii] with the geo_loc_name_country_continent
[Asia] provided 1025 genomes. The results were filtered, and the search items following the
Library Layout [paired], Library Source [genomic] and Platform [Illumina] were eligible
for inclusion. Raw sequence data of all A. baumannii strains belonging to the search criteria
from Southeast Asian countries were included in the study. Data of 103 A. baumannii
strains were extracted. Of these, 49 A. baumannii genomes were from Thailand (BioProjects:
PRJNA623108, PRJNA627433, PRJNA647677 and PRJNA389557], 38 were from Myan-
mar (BioProject: PRJDB8528), 11 were from Malaysian BioProjects (PRJNA565663 and
PRJNA185400), four were from a Singapori BioProject (PRJNA627433), and one was from a
Taiwanese BioProject (PRJNA627433). No genomes were found for Vietnam, Indonesia, the
Philippines, Cambodia, Laos, Brunei and Timor-Leste (Table 4).
Table 4. Numbers, geographical origin and source of A. baumannii genomes investigated in the current study from
Southeast Asia.
No. Country Geographical Location No. of Strains No. of Strains Analyzed Source of Sequence
1 Thailand Southeast Asia 49 49 NCBI
2 Myanmar Southeast Asia 38 37 NCBI
3 Malaysia Southeast Asia 11 7 NCBI
4 Vietnam Southeast Asia 11 11 IBIZ/FLI
5 Singapore Southeast Asia 4 3 NCBI
6 Indonesia Southeast Asia 0 0 -
7 Philippines Southeast Asia 0 0 -
8 Cambodia Southeast Asia 0 0 -
9 Laos Southeast Asia 0 0 -
10 Brunei Southeast Asia 0 0 -
11 Timor-Leste Southeast Asia 0 0 -
12 Taiwan East Asia/Trade country 1 1 NCBI
Total 114 108
10. Antibiotics 2021, 10, 563 10 of 15
3.3. Bioinformatic Data Analysis
Data analysis of sequences from eleven samples sequenced within this study and
downloaded sequences was performed with the pipeline WGSBAC (v2.0.0) [7,63,64]. In
short, raw sequencing data quality was controlled by WGSBAC with FastQC (v. 0.11.5) [65],
and coverage was determined. Shovill (v. 1.0.4), based on SPAdes (v3.14.0) [25], was used
for assembly. Assembly quality was checked with QUAST (v. 5.0.2) [66]. Kraken 2 (v.
2.0.7 beta) [67], in combination with the database MiniKraken (v2), was used to classify
reads and assemblies and to check for contamination. In silico determination of classical
multilocus sequence typing (MLST) was performed based on the assembled genomes using
mlst software (v. 2.16.1) according to the Acinetobacter baumannii#2 scheme published by
Diancourt and coworkers and referred to as the Pasteur scheme [68]. For antimicrobial
resistance profiling and determination of AMR genes, the databases from NCBI AMR
Finder Plus [69], ResFinder [55] and CARD [70] were used. Core-Genome MLST (cgMLST)
was performed by employing the software Ridom SeqSphere+, version 5.1.0 (Ridom GmbH,
Münster, Germany) [71]. PlasmidFinder [53] and Platon [54] were used to investigate the
potential presence of plasmids and plasmid replicons.
4. Conclusions and the Way Forward
Southeast Asia encompasses eleven countries with a wide diversity in history, cul-
ture and religion: Brunei, Myanmar (Burma), Cambodia, Timor-Leste, Indonesia, Laos,
Malaysia, the Philippines, Singapore, Thailand and Vietnam. According to the Southeast
Asia Infectious Disease Clinical Research Network, a previous multinational, multicen-
ter cross-sectional study showed that A. baumannii was among the causative pathogens
of sepsis in South Asian countries [72] and that CRAb was the most common nosoco-
mial pathogen associated with infection in ICUs in this region [10]. In silico analysis
of 108 whole genomes of A. baumannii strains isolated from Southeast Asia successfully
assigned 107 strains into distinct STs using the Pasteur scheme. MLST analysis confirmed
the considerable diversity of A. baumannii, and ST/2 was the most prevalent sequence
type. The strains harbored a wide variety of AMR genes mediating resistance mostly
to β-lactams (including cephalosporins and carbapenems), aminoglycosides, phenicoles,
tetracyclines, sulfonamides and macrolides. However, the strain resistance phenotype is
unknown except for Vietnamese strains. Several antibiotic resistance mechanisms for vari-
ous antibiotic classes were observed, including β-lactamases, aminoglycoside-modifying
enzymes, permeability defects, alteration and replacement of antibiotic target sites, enzy-
matic inactivation, multidrug efflux pumps and acquisition of AMR genes. A. baumannii
combines clonal spread with high genetic flexibility. The clonal spread of ST/2 is obvious,
but there is a lot of evolutionary dynamic outside ST/2 and, most concerning, also within
ST2. Aminoglycosides mediating resistance genes ant(3”)-IIa, aph(6)-Id, armA and aph(3”)-
Ib, and blaOXA-64, blaOXA-23, blaTEM-1 and blaADC-73 genes mediating resistance to β-lactams,
as well as tet.B mediating resistance to tetracyclines, are the highest variable genes within
ST/2. These might be genes playing a role in improving the adaptation to the environment.
Therefore, both decreased antibiotic consumption and infection prevention and control
(IPC) (mainly tackling the clinical component of the spread) are required to counteract this
pathogen’s spread.
In general, the prevalence of MDR increases due to limited infection control measures
and the lack of antimicrobial stewardship teams in healthcare settings. Moreover, antibi-
otics are sold without a prescription in rural and urban pharmacies in many developing
countries, including Southeast Asian countries [73]. Notably, awareness of antibiotic re-
sistance is missing, particularly in rural areas [73]. Uncontrolled travel throughout this
region and transboundary trade of animals and foodstuffs have contributed to increasing
AMR prevalence. Resistance to carbapenems is increasingly being reported in Southeast
Asia health facilities where the antibiotic is not routinely used and is emerging despite
its restricted uses due to high costs. A way forward for this region is to design multina-
tional collaborative efforts geared towards investigating the molecular epidemiology of
11. Antibiotics 2021, 10, 563 11 of 15
CRAb and its burden on healthcare systems and understanding the underlying genetic
mechanisms associated with resistance to carbapenems. In 2013, the Vietnamese Ministry
of Health was the first ministry in the WHO Western Pacific region to develop a national
action plan on AMR. The antimicrobial resistance reference laboratory and surveillance
program were initiated in Vietnam in 2017 [74]. However, within a region characterized
by open borders, an environment with high prevalences of AMR organisms and patient
self-treatment, a multinational transboundary surveillance program is urgently needed [75].
Multinational unified antimicrobial stewardship and broad-scale collaboration would ul-
timately enable the persons in charge to identify existing hotspots, possible reservoirs
and possible practices, cultures and attitudes that may predispose different communities
to CRAb infections. Control of selling antibiotics without prescription and increasing
awareness are required. Implementing the Vietnamese way, i.e., developing a national
action plan on AMR and establishing an antimicrobial resistance reference laboratory, is a
supreme priority. Such efforts would be critical in creating targeted policies on carbapenem
compounds’ rational use and controlling AMR’s dissemination and emergence in general.
This will be significant because carbapenems are expected to become cheaper and readily
available in the future in most countries.
Supplementary Materials: The following are available online at https://www.mdpi.com/article/10
.3390/antibiotics10050563/s1. Table S1: The average read length and the coverage of 108 A. baumannii
isolates from Southeast Asia. Table S2: The data of genome assembly of 11 A. baumannii isolates from
Vietnam. Table S3: The results of antibiotic susceptibility testing of Vietnamese A. baumannii isolates.
Table S4: Metadata, MLST, AMR genes and the predicted antibiotic classes of 108 A. baumannii isolates
from Southeast Asia. Table S5: The results of PlasmidFinder for all A. baumannii strains provide some
information about the presence of replicons.
Author Contributions: G.W., H.N., L.D.S. and M.W.P. conceptualization, designed research, analyzed
data and wrote the paper; J.L. downloaded sequences and performed the bioinformatic analysis;
N.H.N. and T.N.M.N. collected the samples and made a preliminary identification of the Vietnamese
strains; G.W. performed the work and wrote the first draft. All authors read and approved the
final manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: All study data are included in the article and supporting information.
The data have also been submitted to the European Nucleotide Archive (ENA). The project accession
number is PRJEB43552.
Acknowledgments: We thank Gernot Schmoock, Johannes Solle, Claudia Grosser and Birgit Schikowski
for excellent technical assistance.
Conflicts of Interest: The authors declare that the research was conducted in the absence of any
commercial or financial relationships that could be construed as a potential conflict of interest.
References
1. Kurihara, M.N.L.; Sales, R.O.; Silva, K.E.D.; Maciel, W.G.; Simionatto, S. Multidrug-resistant Acinetobacter baumannii outbreaks: A
global problem in healthcare settings. Rev. Soc. Bras. Med. Trop. 2020, 53, e20200248. [CrossRef]
2. Tian, H.; Chen, L.; Wu, X.; Li, F.; Ma, Y.; Cai, Y.; Song, S. Infectious complications in severe acute pancreatitis: Pathogens, drug
resistance, and status of nosocomial infection in a university-affiliated teaching hospital. Dig. Dis. Sci. 2019. [CrossRef] [PubMed]
3. Metan, G.; Zarakolu, P.; Otlu, B.; Tekin, I.; Aytac, H.; Bolek, E.C.; Metin, B.C.; Arsava, E.M.; Unal, S. Emergence of colistin and
carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (CCR-Acb) complex in a neurological intensive care unit
followed by successful control of the outbreak. J. Infect. Public Health 2019. [CrossRef]
4. Pormohammad, A.; Mehdinejadiani, K.; Gholizadeh, P.; Mohtavinejad, N.; Dadashi, M.; Karimaei, S.; Safari, H.; Azimi, T. Global
prevalence of colistin resistance in clinical isolates of Acinetobacter baumannii: A systematic review and meta-analysis. Microb.
Pathog. 2019. [CrossRef] [PubMed]
12. Antibiotics 2021, 10, 563 12 of 15
5. Theriault, N.; Tillotson, G.; Sandrock, C.E. Global travel and Gram-negative bacterial resistance; implications on clinical
management. Expert Rev. Anti-Infect. Ther. 2020. [CrossRef]
6. Nodari, C.S.; Cayô, R.; Streling, A.P.; Lei, F.; Wille, J.; Almeida, M.S.; de Paula, A.I.; Pignatari, A.C.C.; Seifert, H.; Higgins, P.G.;
et al. Genomic analysis of carbapenem-resistant Acinetobacter baumannii isolates belonging to major endemic clones in South
America. Front. Microbiol. 2020, 11, 584603. [CrossRef]
7. Wareth, G.; Linde, J.; Hammer, P.; Nguyen, N.H.; Nguyen, T.N.M.; Splettstoesser, W.D.; Makarewicz, O.; Neubauer, H.; Sprague,
L.D.; Pletz, M.W. Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii
isolates from Germany and Vietnam. Int. J. Antimicrob. Agents 2020, 56, 106127. [CrossRef] [PubMed]
8. Niu, T.; Xiao, T.; Guo, L.; Yu, W.; Chen, Y.; Zheng, B.; Huang, C.; Yu, X.; Xiao, Y. Retrospective comparative analysis of risk factors
and outcomes in patients with carbapenem-resistant Acinetobacter baumannii bloodstream infections: Cefoperazone-sulbactam
associated with resistance and tigecycline increased the mortality. Infect. Drug Resist. 2018, 11, 2021–2030. [CrossRef]
9. Stewardson, A.J.; Marimuthu, K.; Sengupta, S.; Allignol, A.; El-Bouseary, M.; Carvalho, M.J.; Hassan, B.; Delgado-Ramirez, M.A.;
Arora, A.; Bagga, R.; et al. Effect of carbapenem resistance on outcomes of bloodstream infection caused by Enterobacteriaceae in
low-income and middle-income countries (PANORAMA): A multinational prospective cohort study. Lancet. Infect. Dis. 2019, 19,
601–610. [CrossRef]
10. Suwantarat, N.; Carroll, K.C. Epidemiology and molecular characterization of multidrug-resistant Gram-negative bacteria in
Southeast Asia. Antimicrob. Resist. Infect. Control 2016, 5, 15. [CrossRef] [PubMed]
11. Kiratisin, P.; Chongthaleong, A.; Tan, T.Y.; Lagamayo, E.; Roberts, S.; Garcia, J.; Davies, T. Comparative in vitro activity of
carbapenems against major Gram-negative pathogens: Results of Asia-Pacific surveillance from the COMPACT II study. Int. J.
Antimicrob. Agents 2012, 39, 311–316. [CrossRef]
12. Phu, V.D.; Nadjm, B.; Duy, N.H.A.; Co, D.X.; Mai, N.T.H.; Trinh, D.T.; Campbell, J.; Khiem, D.P.; Quang, T.N.; Loan, H.T.;
et al. Ventilator-associated respiratory infection in a resource-restricted setting: Impact and etiology. J. Intensive Care 2017, 5,
69. [CrossRef]
13. Biedenbach, D.J.; Giao, P.T.; Hung Van, P.; Su Minh Tuyet, N.; Thi Thanh Nga, T.; Phuong, D.M.; Vu Trung, N.; Badal, R.E.
Antimicrobial-resistant Pseudomonas aeruginosa and Acinetobacter baumannii From patients with hospital-acquired or ventilator-
associated pneumonia in Vietnam. Clin. Ther. 2016, 38, 2098–2105. [CrossRef]
14. Nhu, N.T.K.; Lan, N.P.H.; Campbell, J.I.; Parry, C.M.; Thompson, C.; Tuyen, H.T.; Hoang, N.V.M.; Tam, P.T.T.; Le, V.M.; Nga,
T.V.T.; et al. Emergence of carbapenem-resistant Acinetobacter baumannii as the major cause of ventilator-associated pneumonia
in intensive care unit patients at an infectious disease hospital in southern Vietnam. J. Med. Microbiol. 2014, 63, 1386–1394.
[CrossRef] [PubMed]
15. Trung, N.T.; Van Son, T.; Quyen, D.T.; Anh, D.T.; Sang, V.V.; Lam, N.X.; Manh, N.D.; Duong, V.P.; Cuong, B.T.; Tuyen, Q.D.; et al.
Significance of nucleic acid testing in diagnosis and treatment of post-neurosurgical meningitis caused by multidrug-resistant
Acinetobacter baumannii: A case report. J. Med. Case Rep. 2016, 10, 313. [CrossRef]
16. Tada, T.; Miyoshi-Akiyama, T.; Kato, Y.; Ohmagari, N.; Takeshita, N.; Hung, N.V.; Phuong, D.M.; Thu, T.A.; Binh, N.G.; Anh, N.Q.;
et al. Emergence of 16S rRNA methylase-producing Acinetobacter baumannii and Pseudomonas aeruginosa isolates in hospitals in
Vietnam. BMC Infect. Dis. 2013, 13, 251. [CrossRef] [PubMed]
17. Tuan Anh, N.; Nga, T.V.T.; Tuan, H.M.; Tuan, N.S.; Y, D.M.; Vinh Chau, N.V.; Baker, S.; Duong, H.H.T. Molecular epidemiology
and antimicrobial resistance phenotypes of Acinetobacter baumannii isolated from patients in three hospitals in southern Vietnam.
J. Med. Microbiol. 2017, 66, 46–53. [CrossRef]
18. Tran, G.M.; Ho-Le, T.P.; Ha, D.T.; Tran-Nguyen, C.H.; Nguyen, T.S.M.; Pham, T.T.N.; Nguyen, T.A.; Nguyen, D.A.; Hoang, H.Q.;
Tran, N.V.; et al. Patterns of antimicrobial resistance in intensive care unit patients: A study in Vietnam. BMC Infect. Dis. 2017, 17,
429. [CrossRef]
19. Si-Tuan, N.; Ngoc, H.M.; Nhat, L.D.; Nguyen, C.; Pham, H.Q.; Huong, N.T. Genomic features, whole-genome phylogenetic and
comparative genomic analysis of extreme-drug-resistant ventilator-associated pneumonia Acinetobacter baumannii strain in a
Vietnam hospital. Infect. Genet. Evol. 2020, 80, 104178. [CrossRef]
20. Leus, I.V.; Weeks, J.W.; Bonifay, V.; Smith, L.; Richardson, S.; Zgurskaya, H.I. Substrate specificities and efflux efficiencies of RND
efflux pumps of Acinetobacter baumannii. J. Bacteriol. 2018, 200. [CrossRef]
21. Rao, M.; Rashid, F.A.; Shukor, S.; Hashim, R.; Ahmad, N. Detection of antimicrobial resistance genes associated with carbapenem
resistance from the whole-genome sequence of Acinetobacter baumannii isolates from Malaysia. Can. J. Infect. Dis. Med. Microbiol.
2020, 2020, 5021064. [CrossRef]
22. Thirapanmethee, K.; Srisiri, A.N.T.; Houngsaitong, J.; Montakantikul, P.; Khuntayaporn, P.; Chomnawang, M.T. Prevalence of
OXA-Type β-Lactamase genes among carbapenem-resistant Acinetobacter baumannii clinical isolates in Thailand. Antibiotics 2020,
9, 864. [CrossRef] [PubMed]
23. Velasco, J.M.; Valderama, M.T.; Margulieux, K.; Diones, P.C.; Peacock, T.; Navarro, F.C.; Liao, C.; Chua, D.; Macareo, L.; Crawford,
J.; et al. Comparison of carbapenem-resistant microbial pathogens in combat and non-combat wounds of military and civilian
patients seen at a tertiary military hospital, Philippines (2013–2017). Mil. Med. 2020, 185, e197–e202. [CrossRef]
24. Karuniawati, A.; Saharman, Y.R.; Lestari, D.C. Detection of carbapenemase encoding genes in Enterobacteriaceae, Pseudomonas
aeruginosa, and Acinetobacter baumanii isolated from patients at Intensive Care Unit Cipto Mangunkusumo Hospital in 2011. Acta
Med. Indones. 2013, 45, 101–106.
13. Antibiotics 2021, 10, 563 13 of 15
25. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski,
A.D.; et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. J. Comput.
Mol. Cell Biol. 2012, 19, 455–477. [CrossRef]
26. Hamidian, M.; Nigro, S.J. Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii.
Microb. Genom. 2019, 5. [CrossRef]
27. Tada, T.; Uchida, H.; Hishinuma, T.; Watanabe, S.; Tohya, M.; Kuwahara-Arai, K.; Mya, S.; Zan, K.N.; Kirikae, T.; Tin, H.H.
Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates from hospitals in Myanmar. J. Glob. Antimicrob.
Resist. 2020, 22, 122–125. [CrossRef] [PubMed]
28. Gaiarsa, S.; Batisti Biffignandi, G.; Esposito, E.P.; Castelli, M.; Jolley, K.A.; Brisse, S.; Sassera, D.; Zarrilli, R. Comparative analysis of
the two Acinetobacter baumannii multilocus sequence typing (MLST) schemes. Front. Microbiol. 2019, 10, 930. [CrossRef] [PubMed]
29. Hua, X.; Zhang, L.; He, J.; Leptihn, S.; Yu, Y. Population biology and epidemiological studies of Acinetobacter baumannii in the era
of whole-genome sequencing: Is the oxford scheme still appropriate? Front. Microbiol. 2020, 11, 775. [CrossRef] [PubMed]
30. Jean, S.S.; Coombs, G.; Ling, T.; Balaji, V.; Rodrigues, C.; Mikamo, H.; Kim, M.J.; Rajasekaram, D.G.; Mendoza, M.; Tan, T.Y.; et al.
Epidemiology and antimicrobial susceptibility profiles of pathogens causing urinary tract infections in the Asia-Pacific region:
Results from the Study for Monitoring Antimicrobial Resistance Trends (SMART), 2010–2013. Int. J. Antimicrob. Agents 2016, 47,
328–334. [CrossRef]
31. Si-Tuan, N.; Ngoc, H.M.; Hang, P.T.T.; Nguyen, C.; Van, P.H.; Huong, N.T. New eight genes identified at the clinical multidrug-
resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital. Ann. Clin. Microbiol. Antimicrob. 2017, 16, 74. [CrossRef]
32. Le Minh, V.; Nhu, N.T.K.; Phat, V.V.; Thompson, C.; Lan, N.P.H.; Nga, T.V.T.; Tam, P.T.T.; Tuyen, H.T.; Nhu, T.D.H.; Van Hao, N.;
et al. In vitro activity of colistin in antimicrobial combination against carbapenem-resistant Acinetobacter baumannii isolated from
patients with ventilator-associated pneumonia in Vietnam. J. Med. Microbiol. 2015, 64, 1162–1169. [CrossRef] [PubMed]
33. Hoang Quoc, C.; Nguyen Thi Phuong, T.; Nguyen Duc, H.; Tran Le, T.; Tran Thi Thu, H.; Nguyen Tuan, S.; Phan Trong, L.
Carbapenemase genes and multidrug resistance of Acinetobacter baumannii: A cross-sectional study of patients with pneumonia in
Southern Vietnam. Antibiotics 2019, 8, 148. [CrossRef] [PubMed]
34. Leungtongkam, U.; Thummeepak, R.; Wongprachan, S.; Thongsuk, P.; Kitti, T.; Ketwong, K.; Runcharoen, C.; Chantratita, N.;
Sitthisak, S. Dissemination of bla(OXA-23), bla(OXA-24), bla(OXA-58), and bla(NDM-1) Genes of Acinetobacter baumannii isolates
from four tertiary hospitals in Thailand. Microb. Drug Resist. 2018, 24, 55–62. [CrossRef] [PubMed]
35. Chen, T.L.; Lee, Y.T.; Kuo, S.C.; Hsueh, P.R.; Chang, F.Y.; Siu, L.K.; Ko, W.C.; Fung, C.P. Emergence and distribution of plasmids
bearing the blaOXA-51-like gene with an upstream ISAba1 in carbapenem-resistant Acinetobacter baumannii isolates in Taiwan.
Antimicrob. Agents Chemother. 2010, 54, 4575–4581. [CrossRef]
36. Khurshid, M.; Rasool, M.H.; Ashfaq, U.A.; Aslam, B.; Waseem, M.; Xu, Q.; Zhang, X.; Guo, Q.; Wang, M. Dissemination of
bla(OXA-23)-harbouring carbapenem-resistant Acinetobacter baumannii clones in Pakistan. J. Glob. Antimicrob. Resist. 2020, 21,
357–362. [CrossRef]
37. Lee, S.Y.; Oh, M.H.; Yun, S.H.; Choi, C.W.; Park, E.C.; Song, H.S.; Lee, H.; Yi, Y.S.; Shin, J.; Chung, C.; et al. Genomic
characterization of extensively drug-resistant Acinetobacter baumannii strain, KAB03 belonging to ST451 from Korea. Infect. Genet.
Evol. 2018, 65, 150–158. [CrossRef]
38. Vranić-Ladavac, M.; Bedenić, B.; Minandri, F.; Ištok, M.; Bošnjak, Z.; Frančula-Zaninović, S.; Ladavac, R.; Visca, P. Carbapenem
resistance and acquired class D beta-lactamases in Acinetobacter baumannii from Croatia 2009–2010. Eur. J. Clin. Microbiol. Infect.
Dis. Off. Publ. Eur. Soc. Clin. Microbiol. 2014, 33, 471–478. [CrossRef]
39. Zhu, L.J.; Pan, Y.; Gao, C.Y.; Hou, P.F. Distribution of carbapenemases and efflux pump in carbapenem-resistance
Acinetobacter Baumannii. Ann. Clin. Lab. Sci. 2020, 50, 241–246.
40. Krizova, L.; Poirel, L.; Nordmann, P.; Nemec, A. TEM-1 β-lactamase as a source of resistance to sulbactam in clinical strains of
Acinetobacter baumannii. J. Antimicrob. Chemother. 2013, 68, 2786–2791. [CrossRef] [PubMed]
41. Kim, S.Y.; Park, Y.J.; Yu, J.K.; Kim, Y.S. Aminoglycoside susceptibility profiles of Enterobacter cloacae isolates harboring the
aac(6’)-Ib gene. Korean J. Lab. Med. 2011, 31, 279–281. [CrossRef] [PubMed]
42. Fritsche, T.R.; Castanheira, M.; Miller, G.H.; Jones, R.N.; Armstrong, E.S. Detection of methyltransferases conferring high-level
resistance to aminoglycosides in Enterobacteriaceae from Europe, North America, and Latin America. Antimicrob. Agents Chemother.
2008, 52, 1843–1845. [CrossRef]
43. Mortazavi, S.M.; Farshadzadeh, Z.; Janabadi, S.; Musavi, M.; Shahi, F.; Moradi, M.; Khoshnood, S. Evaluating the frequency of
carbapenem and aminoglycoside resistance genes among clinical isolates of Acinetobacter baumannii from Ahvaz, south-west Iran.
New Microbes New Infect. 2020, 38, 100779. [CrossRef] [PubMed]
44. Roca, I.; Marti, S.; Espinal, P.; Martínez, P.; Gibert, I.; Vila, J. CraA, a major facilitator superfamily efflux pump associated with
chloramphenicol resistance in Acinetobacter baumannii. Antimicrob. Agents Chemother. 2009, 53, 4013–4014. [CrossRef] [PubMed]
45. Roberts, M.C. Update on acquired tetracycline resistance genes. FEMS Microbiol. Lett. 2005, 245, 195–203. [CrossRef] [PubMed]
46. Sköld, O. Resistance to trimethoprim and sulfonamides. Vet. Res. 2001, 32, 261–273. [CrossRef]
47. Gordon, N.C.; Wareham, D.W. Multidrug-resistant Acinetobacter baumannii: Mechanisms of virulence and resistance. Int. J.
Antimicrob. Agents 2010, 35, 219–226. [CrossRef]
48. Coyne, S.; Courvalin, P.; Perichon, B. Efflux-mediated antibiotic resistance in Acinetobacter spp. Antimicrob. Agents Chemother.
2011, 55, 947–953. [CrossRef]
14. Antibiotics 2021, 10, 563 14 of 15
49. Lee, Y.T.; Chen, H.Y.; Yang, Y.S.; Chou, Y.C.; Chang, T.Y.; Hsu, W.J.; Lin, I.C.; Sun, J.R. AdeABC Efflux pump controlled by adeRS
two-component system conferring resistance to tigecycline, omadacycline and eravacycline in clinical carbapenem-resistant
Acinetobacter nosocomialis. Front. Microbiol. 2020, 11, 584789. [CrossRef]
50. Abbott, I.; Cerqueira, G.M.; Bhuiyan, S.; Peleg, A.Y. Carbapenem resistance in Acinetobacter baumannii: Laboratory challenges,
mechanistic insights and therapeutic strategies. Expert Rev. Anti-Infect. Ther. 2013, 11, 395–409. [CrossRef]
51. Ranjbar, R.; Zayeri, S.; Afshar, D. High frequency of adeA, adeB and adeC genes among Acinetobacter baumannii isolates. Iran. J.
Public Health 2020, 49, 1539–1545. [CrossRef]
52. Sharma, A.; Sharma, R.; Bhattacharyya, T.; Bhando, T.; Pathania, R. Fosfomycin resistance in Acinetobacter baumannii is mediated
by efflux through a major facilitator superfamily (MFS) transporter-AbaF. J. Antimicrob. Chemother. 2017, 72, 68–74. [CrossRef]
53. Carattoli, A.; Zankari, E.; García-Fernández, A.; Voldby Larsen, M.; Lund, O.; Villa, L.; Møller Aarestrup, F.; Hasman, H. In silico
detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother.
2014, 58, 3895–3903. [CrossRef]
54. Schwengers, O.; Barth, P.; Falgenhauer, L.; Hain, T.; Chakraborty, T.; Goesmann, A. Platon: Identification and characterization of
bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microb.
Genom. 2020, 6. [CrossRef]
55. Zankari, E.; Hasman, H.; Cosentino, S.; Vestergaard, M.; Rasmussen, S.; Lund, O.; Aarestrup, F.M.; Larsen, M.V. Identification of
acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 2012, 67, 2640–2644. [CrossRef] [PubMed]
56. Salgado-Camargo, A.D.; Castro-Jaimes, S.; Gutierrez-Rios, R.M.; Lozano, L.F.; Altamirano-Pacheco, L.; Silva-Sanchez, J.; Pérez-
Oseguera, Á.; Volkow, P.; Castillo-Ramírez, S.; Cevallos, M.A. Structure and evolution of Acinetobacter baumannii plasmids. Front.
Microbiol. 2020, 11, 1283. [CrossRef]
57. Krizova, L.; Dijkshoorn, L.; Nemec, A. Diversity and evolution of AbaR genomic resistance islands in Acinetobacter baumannii
strains of European clone I. Antimicrob. Agents Chemother. 2011, 55, 3201–3206. [CrossRef] [PubMed]
58. Lin, M.F.; Lan, C.Y. Antimicrobial resistance in Acinetobacter baumannii: From bench to bedside. World J. Clin. Cases 2014, 2,
787–814. [CrossRef] [PubMed]
59. Lin, M.F.; Chang, K.C.; Yang, C.Y.; Yang, C.M.; Xiao, C.C.; Kuo, H.Y.; Liou, M.L. Role of integrons in antimicrobial susceptibility
patterns of Acinetobacter baumannii. Jpn. J. Infect. Dis. 2010, 63, 440–443. [PubMed]
60. Huang, L.Y.; Chen, T.L.; Lu, P.L.; Tsai, C.A.; Cho, W.L.; Chang, F.Y.; Fung, C.P.; Siu, L.K. Dissemination of multidrug-resistant,
class 1 integron-carrying Acinetobacter baumannii isolates in Taiwan. Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol.
Infect. Dis. 2008, 14, 1010–1019. [CrossRef]
61. Rabea, R.A.; Zaki, M.E.S.; Fahmy, E.M.; Fathelbab, A. Molecular study of nodulation division genes and integron genes in
Acinetobacter baumannii. Clin. Lab. 2020, 66. [CrossRef]
62. Turton, J.F.; Woodford, N.; Glover, J.; Yarde, S.; Kaufmann, M.E.; Pitt, T.L. Identification of Acinetobacter baumannii by detection of
the blaOXA-51-like carbapenemase gene intrinsic to this species. J. Clin. Microbiol. 2006, 44, 2974–2976. [CrossRef] [PubMed]
63. Linde, J.; Homeier-Bachmann, T.; Dangel, A.; Riehm, J.M.; Sundell, D.; Öhrman, C.; Forsman, M.; Tomaso, H. Genotyping of
Francisella tularensis subsp. holarctica from hares in Germany. Microorganisms 2020, 8, 1932. [CrossRef]
64. García-Soto, S.; Abdel-Glil, M.Y.; Tomaso, H.; Linde, J.; Methner, U. Emergence of multidrug-resistant Salmonella enterica
Subspecies enterica serovar infantis of multilocus sequence type 2283 in German broiler farms. Front. Microbiol. 2020, 11, 1741.
[CrossRef] [PubMed]
65. Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data. v. 0.11.5. Available online: https://www.
bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 1 August 2020).
66. Gurevich, A.; Saveliev, V.; Vyahhi, N.; Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 2013, 29,
1072–1075. [CrossRef] [PubMed]
67. Wood, D.E.; Lu, J.; Langmead, B. Improved metagenomic analysis with Kraken 2. Genome. Biol. 2019, 20, 257. [CrossRef]
68. Diancourt, L.; Passet, V.; Nemec, A.; Dijkshoorn, L.; Brisse, S. The population structure of Acinetobacter baumannii: Expanding
multiresistant clones from an ancestral susceptible genetic pool. PLoS ONE 2010, 5, e10034. [CrossRef] [PubMed]
69. Feldgarden, M.; Brover, V.; Haft, D.H.; Prasad, A.B.; Slotta, D.J.; Tolstoy, I.; Tyson, G.H.; Zhao, S.; Hsu, C.H.; McDermott, P.F.; et al.
Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations
in a collection of isolates. Antimicrob. Agents Chemother. 2019, 63. [CrossRef]
70. Jia, B.; Raphenya, A.R.; Alcock, B.; Waglechner, N.; Guo, P.; Tsang, K.K.; Lago, B.A.; Dave, B.M.; Pereira, S.; Sharma, A.N.; et al.
CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017,
45, D566–D573. [CrossRef]
71. Higgins, P.G.; Prior, K.; Harmsen, D.; Seifert, H. Development and evaluation of a core genome multilocus typing scheme for
whole-genome sequence-based typing of Acinetobacter baumannii. PLoS ONE 2017, 12, e0179228. [CrossRef]
72. Network, S.A.I.D.C.R. Causes and outcomes of sepsis in Southeast Asia: A multinational, multicentre cross-sectional study.
Lancet. Glob. Health 2017, 5, e157–e167. [CrossRef]
73. Nga do, T.T.; Chuc, N.T.; Hoa, N.P.; Hoa, N.Q.; Nguyen, N.T.; Loan, H.T.; Toan, T.K.; Phuc, H.D.; Horby, P.; Van Yen, N.; et al.
Antibiotic sales in rural and urban pharmacies in northern Vietnam: An observational study. BMC Pharmacol. Toxicol. 2014, 15, 6.
[CrossRef] [PubMed]
15. Antibiotics 2021, 10, 563 15 of 15
74. Kinh, N.V.; Wertheim, H.F.L.; Thwaites, G.E.; Khue, L.N.; Thai, C.H.; Khoa, N.T.; Thi Bich Ha, N.; Trung, N.V.; Crook, D.; van
Doorn, H.R. Developing an antimicrobial resistance reference laboratory and surveillance programme in Vietnam. Lancet Glob.
Health 2017, 5, e1186–e1187. [CrossRef]
75. Li, R.; van Doorn, H.R.; Wertheim, H.F.L.; Khue, L.N.; Ha, N.T.B.; Dat, V.Q.; Hanh, C.T.; Nga, D.T.T.; Trang, N.N.M.; Nadjm, B.;
et al. Combating antimicrobial resistance: Quality standards for prescribing for respiratory infections in Vietnam. Lancet Glob.
Health 2016, 4, e789. [CrossRef]