This study investigates the uroculturome and antimicrobial susceptibility of microbial communities in urine from 128 healthy individuals and 161 patients with urinary tract infections (UTIs). Results show that Escherichia coli is the most common pathogen in UTIs, while a diverse range of microbes, including various fungi and gram-positive and gram-negative bacteria, were identified in both groups. The research emphasizes the need for targeted studies to understand the urinary microbiome's role and suggests antibiotic stewardship based on antimicrobial susceptibility testing.

1. A comparative study on uroculturome
antimicrobial susceptibility in apparently
healthy and urinary tract infected humans
Bhoj R Singh1, Himani Agri2*
Presented at 6th Edition of World Congress on Infectious Diseases (Infection 2024) Dates: June 24-26, 2024 at Paris, France
1Principal Scientist (Microbiology) & Head of the Division of Epidemiology
2*Ph.D. Scholar, Vet. Public Health and Epidemiology
ICAR-Indian Veterinary Research Institute, Izatnagar-243 122, India
Email: br.singh@icar.gov.in/ brs18762@gmail.com
Epidemiology, ICAR-IVRI, Izatnagar

2. Abstract
The uroculturome indicates the profile of culturable microbes inhabiting the urinary tract, and it is often required to do a urine
culture to find an effective antimicrobial to treat UTIs. This study targeted to understand the profile of culturable pathogens in the urine of
apparently healthy (128) and humans with clinical UTIs (161). All the urine samples were analyzed to quantify microbial load and
determine the diversity and antimicrobial susceptibility of microbes following standard microbiological methods. In urine samples from
UTI cases, microbial counts were 1.2×104 ± 6.02×103 colony-forming units (cfu)/ mL, while in urine samples from apparently healthy
humans, the average count was 3.33± 1.34×103 cfu/ mL. In eight samples (six from UTI cases and two from apparently healthy people) of
urine, Candida (C. albicans 3, C. catenulata 1, C. krusei 1, C. tropicalis 1, C. parapsiplosis 1, C. gulliermondii 1) and Rhizopus species (1) were
detected. Candida krusei was detected only in a single urine sample from a healthy person and C. albicans was detected both in urine of
healthy and clinical UTI cases. Fungal strains were always detected with one or more types of bacteria. Gram-positive bacteria were more
commonly (OR, 1.98; CI99, 1.01-3.87) detected in urine samples of apparently healthy humans, and Gram -ve bacteria (OR, 2.74; CI99, 1.44-
5.23) in urines of UTI cases. From urine samples of 161 UTI cases, a total of 90 different types of microbes were detected and, 73 samples
had only a single type of bacteria. In contrast, 49, 29, 3, 4, 1, and 2 samples had 2, 3, 4, 5, 6 and 7 types of bacteria, respectively. The most
common bacteria detected in urine of UTI cases was Escherichia coli detected in 52 samples, in 20 cases as the single type of bacteria, other
34 types of bacteria were detected in pure form in 53 cases. From 128 urine samples of apparently healthy people, 88 types of microbes
were detected either singly or in association with others, from 64 urine samples only a single type of bacteria was detected while 34, 13, 3,
11, 2 and 1 samples yielded 2, 3, 4, 5, 6 and seven types of microbes, respectively. In the urine of apparently healthy humans too, E. coli was
the most common bacteria, detected in pure culture from 10 samples followed by Staphylococcus haemolyticus (9), S. intermedius (5), and S.
aureus (5), and similar types of bacteria also dominated in cases of mixed occurrence, E. coli was detected in 26, S. aureus in 22 and S.
haemolyticus in 19 urine samples, respectively. Gram +ve bacteria isolated from urine samples' irrespective of health status were more
often (p, <0.01) resistant than Gram -ve bacteria to ajowan oil, holy basil oil, cinnamaldehyde, and cinnamon oil, but more susceptible to
sandalwood oil (p, <0.01). However, for antibiotics, Gram +ve were more often susceptible than Gram -ve bacteria to cephalosporins,
doxycycline, and nitrofurantoin. The study concludes that to understand the role of good and bad bacteria in the urinary tract microbiome
more targeted studies are needed to discern the isolates at the pathotype level. Further, the study suggests the use of antibiotics by
observing good antibiotic stewardship following antibiotic susceptibility testing (AST) only.
Keywords: Uro-microbiome, UTI, Antimicrobial susceptibility testing (AST), Herbal antimicrobials, ESBL, Carbapenem resistance,
MDR, Multiple herbal drug resistance
Epidemiology, ICAR-IVRI, Izatnagar

3. Uroculturome
• Culturable microbiota of urine.
• Life within life.
• Bacteria modulate our lives through changing physiological functions, changes
may either be induced or affected by the use of antimicrobials (Singh et al., 2024,
Singh, 2012; Schluter and Foster, 2012)
• Urine incontinence and urinary tract microbiome (Price et al., 2020)
• Urinary tract problems are associated with dysbiosis and can be corrected by
inducing eubiosis (Colella et al., 2023; Kawalec and Zwoli´nska, 2022).
• Bounderies in eubiotic and dysbiotic microflora are often blurred, most of the
urinary tract infections (UTI) are associated with opportunistic pathogens also
present as normal inhabitants there (Chesca et al., 2022; Mironov et al., 2021)
Epidemiology, ICAR-IVRI, Izatnagar

4. Common causes of UTI reported (Singh, 2019)
• In Humans: Ten most commonly bacteria from UTI cases: Escherichia,
Staphylococcus, Streptococcus, Enterococcus, Enterobacter, Proteus, Aerococcus,
Erwinia, Klebsiella and Pseudomonas genus Rare causes: Actinobacillus,
Bacillus, Budvicia, Candida, Citrobacter, Edwardsiella, Moraxella, Morganella,
Serratia and Vibrio spp.
• In animals, the most common causes of UTIs: Escherichia, Staphylococcus,
Streptococcus, Proteus, Bacillus, Enterobacter, Enterococcus, Micrococcus,
Moraxella and Acinetobacter.
• In carnivore animals: The major causes of UTIs: E. coli, Staphylococcus,
Streptococcus, Proteus, Enterobacter, Micrococcus, Moraxella, Enterococcus,
Acinetobacter and Aeromonas species.
• In herbivore animals: E. coli, the leading cause of UTI, causing almost one-third
of total infections followed by Streptococcus, Staphylococcus species and B.
sphaericus.
Epidemiology, ICAR-IVRI, Izatnagar

5. Objectives
• Understanding diversity of culturable urine microflora of healthy
and sick (UTI) humans
• To understand the difference in antimicrobial susceptibility of
aerobically growing bacteria present in healthy and sick (UTI)
humans.
Epidemiology, ICAR-IVRI, Izatnagar

6. Samples and their processing
• Study period: January 2020 to February 2024 in Bareilly, India.
• Urine samples: Collected from128 apparently healthy adult humans and from 161 cases of
UTI with written informed consent.
• Samples were inoculated (2 µL) within 30 min of receipt of samples (brought to lab within
30 min of collection) on blood agar and MacConkey agar medium for bacteria and on
Sabouraud’s dextrose medium for fungi, incubated aerobically for bacteria at 37oC for 24 h
and 5-7 days at 30oC for fungi.
• All colonies growing on inoculated plates were counted if countable (≤200).
• Bacterial and fungal isolates were identified based on their growth, morphological,
staining, and biochemical characteristics and further confirmed using their MALDITOF-MS
profiles (Brenner et al., 2005; Carter, 1975; Singh 2009).
• All isolates were tested for antimicrobial susceptibility to conventional antibiotics (CLSI,
2017) and herbal antimicrobials (Singh et al., 2020).
Epidemiology, ICAR-IVRI, Izatnagar

7. Results
Epidemiology, ICAR-IVRI, Izatnagar
Characteristics Healthy (n=128) UTI (n=161)
Microbial load in urine <3.33×103 cfu/ mL >6000 (1.2×104 ± 6.02×103) cfu/ mL
Fungi in urine Candida krusei 1 and C. albicans
1
C. albicans 2, C. catenulata 1, C.
tropicalis 1, C. parapsiplosis 1, C.
gulliermondii 1
Bacteria in urine 88 types, in 64 urine samples
only single type of bacteria, 34,
13, 3, 11, 2 and 1 sample had 2,
3, 4, 5, 6 and seven types of
microbes, respectively.
90 types, 73 samples had only single
type of bacteria, 49, 29, 3, 4, 1
sample had 2, 3, 4, 5, 6 and 7 types
of bacteria, respectively.
The most common types of
Bacteria
E. coli (26), S. aureus (22), S.
haemolyticus (19), Enterococcus
faecalis (11), S. epidermidis (11),
E. faecium (7), S. delphinii (7)
E. coli (52), E. faecalis (22), S.
epidermidis (20), S. haemolyticus
(17), K. pneumoniae (13), P.
agglomerans (13), Raoultella
terrigena (8)
Exclusively detected bacteria 39 species, Mammaliicoccus
sciuri (3) and Staphylococcus
cohnii ssp. urealyticus (3),
Aeromonas media, A. trota
41 species, most common types
Alcaligenes faecalis (6),
Acinetobacter indicus (4) and
Streptococcus pyogenes (3).

8. Epidemiology, ICAR-IVRI, Izatnagar
Characteristics Healthy (n=128) UTI (n=161)
Significantly more
common
M. sciuri, S. aureus, S.
delphini, S. intermedius, S.
cohnii
A. faecalis, E. coli, K. pneumoniae
Maximum 7 types of
microbes detected in a
single sample
1 (Staphylococcus auricularis,
S. aureus, Lysinibacillus
sphaericus, Paenibacillus
amylolyticus, Streptococcus
milleri, S. cohnii ssp. cohnii,
Geobacillus
stearothermophilus)
2 (E. coli, Staphylococcus xylosus, A.
faecalis, S. capitis ssp. capitis, Citrobacter
freundii, E. faecalis, E. faecium;
S. epidermidis, Rhizopus spp., Micrococcus
luteus, S. haemolyticus, Pluralibacter
gergoviae, A. faecalis, S. aureus
49 types of Bacteria
were detected in both
types of samples, The
most common ones
detected in more than
10 samples
E. faecalis, E. coli, S. aureus, S.
epidermidis, S. haemolyticus
E. faecalis, E. coli, K. pneumoniae ssp.
pneumoniae, P. agglomerans, S.
epidermidis, S. haemolyticus

9. 39 Microbes exclusively detected in urine of apparently
healthy people (Pathogens, Opportunists pathogens, probiotic or not harmful bacteria)
• Two from 3 samples each: Mammaliicoccus sciuri, Staphylococcus cohnii ssp. urealyticus (Both are opportunistic
pathogens of humans, Sands et al., 2022; Wanden et al., 2002)
• Seven from two samples each: Brevibacillus brevis (Mahdi et al, 2012), Paenibacillus amylolyticus (Thakur et al.,
2022; Wnzler et al., 2015), , Staphylococcus felis (Sips et al., 2023), S. kloosii, S. schleiferi ssp. coagulans, S. simulans
(von Eiff et al, 2002), Streptococcus defactivus (Singh, 2022).
• Thirty from one sample each: Aeromonas bestiarum, A. media, A. trota (Pessoa et al., 2022), Bacillus
anthracoides (Turnbull et al., 1979), B. circulans, B. coaglulans (Elshaghabee et al., 2017), B. subtilis (Fernández-No et al., 2011),
Brevibacillus laterosporus (Liu et al., 2024), Candida krusei (Jamiu et al., 2021), Citrobacter amalonaticus (Mullineaux-
Sanders et al., 2021; Suwansrinon et al., 2005), Comamonas testosterone (Tsui et al., 2011), Enterococcus dispar (Goel et al.,
2016), Enterococcus durans (Pieniz et al., 2014; Toc et al., 2022), E. raffinosus (Toc et al., 2022), Escherichia
vulneris (Jain et al., 2016), Hafnia alvei (Ionescu et al., 2022), Kocuria varians (Tsai et al., 2010), Leclercia adecarboxylata
(Zavet et al., 2021), Lysinibacillus sphaericus (Wnzler et al., 2015), Paenibacillus alvei (DeLeon and Welliver et al., 2016),
Providencia haembachae (Naveed et al., 2022), P. stuartii (Liu et al., 2020), Roseomonas rosae (Ioannou et al., 2020),
Staphylococcus carnosus (Rosenstein et al., 2009), S. sacchrolyticus (Wang et al., 2020), S. saprophyticus (Hovelius and
Mårdh, 1984), Streptococcus phocae (Numberger et al., 2024), Virgibacillus pantothenticus (Zhao et al., 2021),
Xenorhabdus poinarii (Sajnaga et al., 2018; Singh et al., 2015).
• Many of the bacteria detected in healthy people’s urine have also been reported in urine of
apparently healthy animals (Singh et al., 2022)
Epidemiology, ICAR-IVRI, Izatnagar

10. 41 Microbes exclusively detected in urine of UTI cases
• From 6 samples: Alcaligenes faecalis
• From four samples: Acinetobacter indicus
• From three samples: Streptococcus pyogenes
• From two samples each: Acinetobacter variabilis, Bacillus mycoides, Moraxella osloensis,
Streptococcus agalactiae
• From one sample each: Acinetobacter baumannii, A. schindleri, Actinobacillus equeli, A.
seminist, Aerococcus viridans, Aeromonas eucranophila, A. hydrophila, A. schubertii, Budvicia
aquatica, Candida catenulate, Candida gulliermondii, Candida parapsiplosis, C. tropicalis Biovar
urealyticus, Edwardsiella hoshiniae, E. ictalurid, Enterococcus durans, Enterobacter taylorae,
Flavobacterium aquatile, F. branchiophilum, Gardnerella spp., Gemella haemolysans, Kluyvera
intermedia, Morganella morganii, Proteus penneri, Pseudomonas fluorescens, P. stutzeri,
Rhizopus spp., Serratia odorifera, Staphylococcus capitis ssp. urealyticus, S. caseolyticus, S.
equorum, Streptococcus adjacens, S. equi ssp. zooepidemicus, S. mitis, Vibrio alginolyticus
• They are potentially pathogenic and similar causes of Urogenital tract infections have been
reported in animals also, Singh, 2015; 2019.
Epidemiology, ICAR-IVRI, Izatnagar

11. 49 Microbes detected in urine of both UTI cases and
apparently healthy people
• From ≥10 samples each: Escherichia coli (78), Staphylococcus haemolyticus (36), Enterococcus faecalis (33),
Staphylococcus epidermidis (31), Staphylococcus aureus (27), Pantoea agglomerans (17), Enterococcus faecium
(14), Klebsiella pneumoniae ssp. pneumoniae (14), Staphylococcus capitis ssp. capitis (13), Streptococcus milleri
(13), Raoultella terrigena (12), Aerococcus sanguinicola (10) (Singh, 2019; 2022, Singh et al., 2024).
• From eight samples each: Micrococcus luteus (Tsai et al., 2010), Proteus mirabilis, Pseudomonas aeruginosa,
Staphylococcus delphini (Singh et al., 2024)
• From seven samples each: Proteus vulgaris, Staphylococcus lugdunensis (Singh, 2022, Singh et al., 2024)
• From six samples each: Acinetobacter calcoaceticus (Lynch et al., 2022), Staphylococcus arlettae, S. cohnii ssp.
cohnii, S. intermedius (Singh, 2022, Singh et al., 2024)
• From five samples each: Alcaligenes denitrificans (Morrison and Boyce, 1986), Enterococcus solitarius (a feacal
bacteria, Collins et al., 1989), Geobacillus stearothermophilus (a soil bacteria, Kotzekidou, 2014), Staphylococcus
chromogenes (Singh, 2022, Singh et al., 2024), S. xylosus (a commensal on skin, Clifford and Pritchett-Corning, 2012)
• From four samples each: Acinetobacter lwoffii (Wong et al., 2017), Aerococcus suis, Citrobacter freundii, Erwinia
mallotivora, Escherichia fergusonii, Pseudomonas pseudoalcaligenes, Staphylococcus caprae, Staphylococcus
hominis, Streptococcus porcinus (Singh, 2019; 2022; Singh et al., 2024)
• From three samples each: Candida albicans, Cronobacter universalis, Enterococcus pseudoavium, Serratia
plymuthica, Staphylococcus warneri, (All potentially pathogenic, Singh et al., 2015; 2024); Xenorhabdus bovienii
(Sajnaga et al., 2018; Singh et al., 2015).
• From two samples each: Aerococcus viridans (Ezechukwu et al., 2019), Aeromonas caviae, Bacillus cereus,
Enterococcus gallinarum, Mammaliicoccus lentus (Sands et al., 2022).
• Pectobacterium chrysanthemi (Durate et al., 2000), Pluralibacter gergoviae (Rueda and Steling, 2023),
Staphylococcus hyicus (Kirk et al., 2022)
Epidemiology, ICAR-IVRI, Izatnagar

12. Epidemiology, ICAR-IVRI, Izatnagar
Characteristics Healthy (n=128) UTI (n=161)
G +ve bacteria were more
resistant to
Nitrofurantoin, Piperacillin,
Piperacillin + Tazobactam
Lemongrass oil, Amikacin, Cefepime,
Cefoperazone, Cefotaxime, Cefotaxime+
clavulanic acid, Ceftazidime, Ceftazidime +
clavulanic acid, Ceftriaxone, Ceftriaxone +
tazobactam, Cefoperazone + sulbactam,
Chloramphenicol, Ciprofloxacin, Cotrimoxazole,
Gentamicin, Imipenem, Meropenem,
Tetracycline, Vancomycin
G -ve bacteria were more
resistant to
Lemongrass oil Carvacrol, Cinnamldehyde, Cinnamon oil, thyme
oil, Lemongrass oil, Amikacin, Amoxicillin,
Amoxicillin + clavulanic acid, Ampicillin,
Azithromycin, Cefepime, Cefoperazone,
Cefotaxime, Cefotaxime+ clavulanic acid,
Ceftazidime, Ceftazidime + clavulanic acid,
Ceftriaxone, Ceftriaxone + tazobactam,
Cefoperazone + sulbactam, Chloramphenicol,
Ciprofloxacin, Colistin, Cotrimoxazole,
Gentamicin, Imipenem, Meropenem,
Tetracycline

13. Epidemiology, ICAR-IVRI, Izatnagar
Characteristics Healthy (n=128) UTI (n=161)
Gram +ve bacteria
were more often (p,
<0.01) resistant
than Gram -ve
bacteria.
Ajowan oil, Carvacrol,
Cinnamledehyde,
Cinnamon oil, Holy basil
oil, Thyme oil, Amikacin,
Gentamicin
Ajowan oil, Cinnamledehyde,
Cinnamon oil , Holy basil oil,
Cefotaxime+ clavulanic acid
Gram +ve bacteria
were more often (p,
<0.01) susceptible
than Gram -ve
bacteria.
Lemongrass oil,
Doxycycline,
Erythromycin,
Nitrofurantoin
Sandalwood oil, Amoxicillin +
clavulanic acid, Amoxicillin,
Ampicillin + sulbactam, Ampicillin,
Azithromycin, Ceftriaxone,
Doxycycline, Erythromycin,
Nitrofurantoin, Piperacillin,
Piperacillin + Tazobactam,
Tetracycline

14. Epidemiology, ICAR-IVRI, Izatnagar
MDR and
Cephalosporin
resistance was more
common in
G -ve bacteria than in G +ve bacteria
G –ve bacteria than G +ve bacteria from UTI cases
G +ve and G -ve bacteria from UTI cases than from healthy people
Multiple herbal
antimicrobial drug
resistance was more
common among
No difference among G +ve/ G-ve bacteria irrespective of source of
isolation
Carbapenem resistance
was more common in
G -ve bacteria than in G +ve bacteria
G +ve and G -ve bacteria from UTI cases than from healthy people
ESBL Producers were
more common among
G -ve bacteria than in G +ve bacteria
G –ve bacteria than G +ve bacteria from UTI cases
G -ve bacteria from UTI cases than from healthy people

15. Most commonly used antimicrobials for UTI
treatment and their comparative efficacy
Antimicrobial More resistant than
Nitrofurantoin G –ve bacteria than G +ve bacteria both from UTI cases and
healthy people
G +ve bacteria from UTI cases than from healthy people
Amoxicillin + clavulanic acid G –ve bacteria from UTI cases than from healthy people
Doxycycline G –ve bacteria than G +ve bacteria both from UTI cases and
healthy people
Ceftriaxone, Ciprofloxacin
Cotrimoxazole, Gentamicin
Meropenem
G –ve and G +ve bacteria from UTI cases than from healthy
people
Epidemiology, ICAR-IVRI, Izatnagar

16. Best antimicrobials for selected bacteria from UTI cases
Epidemiology, ICAR-IVRI, Izatnagar
Bacteria 10 best antimicrobials
Escherichia coli
(20)
Tigecycline, Cefotaxime + clavulanic acid, Meropenem, Imipenem, Nitrofurantoin,
Chloramphenicol, Colistin, Ceftazidime + Clavulanic acid, Gentamicin, Amikacin
Staphylococcus
epidermidis (4)
Cefotaxime + clavulanic acid, Tigecycline, Imipenem, Nitrofurantoin, Ceftazidime +
Clavulanic acid, Ceftazidime, Cefotaxime, Ceftriaxone + Tazobactam, Ceftriaxone,
Doxycycline
Staphylococcus
haemolyticus (4)
Tigecycline, Nitrofurantoin, Imipenem, Chloramphenicol, Meropenem, Cefotaxime +
clavulanic acid, Cefoperazone + sulbactam, Cefoperazone, Cefepime, Ceftriaxone +
Tazobactam, Nitrofurantoin not effective
Acinetobacter
indicus (3)
Cotrimoxazole, Gentamicin, Amikacin, Aztreonam, Meropenem, Imipenem,
Cefoperazone, Cephoperazone + sulbactam, Nitrofurantoin not effective
Enterococcus
faecalis (3)
Tigecycline, Ampicillin + sulbactam, Ampicillin, Imipenem, Cefotaxime+ clavulanic acid,
Meropenem, Nitrofurantoin, Piperacillin, Piperacillin Tazobactam, Doxycycline
Escherichia.
fergusonii (3)
Ceftazidime + Clavulanic acid, Imipenem, Tigecycline, Cefotaxime + clavulanic acid,
Ceftriaxone, Ceftriaxone + Tazobactam, Cefepime, Cefoperazone, Cefoperazone +
sulbactam, Nitrofurantoin
Klebsiella
pneumoniae (3)
Tigecycline, Cefotaxime + clavulanic acid, Meropenem, Chloramphenicol, Cefepime,
Gentamicin, Amikacin, Imipenem, Ceftriaxone + Tazobactam, Ceftriaxone,
Nitrofurantoin not effective

17. The most effective antibiotics in UTI and Health
Epidemiology, ICAR-IVRI, Izatnagar
On bacteria from UTI case, % isolates inhibited % of bacterial isolates inhibited from healthy people
Tigecycline, 86.54
Cefotaxime + clavulanic acid, 81.89
Imipenem, 78.42
Meropenem, 77.05
Cefepime, 64.60
Chloramphenicol, 64.52
Piperacillin Tazobactam, 63.85
Ceftriaxone + Tazobactam, 63.31
Nitrofurantoin, 62.88
Vancomycin, 60.87
Colistin, 59.89
Gentamicin, 59.36
Ceftriaxone, 58.77
Amikacin, 58.56
Doxycycline, 57.56
Cefotaxime+ clavulanic acid, 97.77
Imipenem, 97.26
Meropenem, 96.95
Tigecycline, 96.72
Chloramphenicol, 88.99
Ceftazidime + Clavulanic acid, 88.00
Gentamicin, 83.33
Amikacin, 83.33
Cotrimoxazole, 81.31
Ceftriaxone + Tazobactam, 80.06
Ceftriaxone, 80.06
Cefepime, 79.62
Vancomycin, 79.61
Cefotaxime, 79.27
Cephoperazone + sulbactam, 76.14
Commonly used antimicrobials for treatment of UTI: Nitrofurantoin, Co-
trimoxazole, Ciprofloxacin, Amoxicillin + clavulanate, Cephalexin, Ceftriaxone,
Meropenem (Sinha A, Aster Medical Centre, Doha) are no more the best antimicrobials for treatment of
UTI.

18. Antimicrobial efficacy (% of isolates inhibited) of Herbal
antimicrobials on microbes isolated from human urine
Epidemiology, ICAR-IVRI, Izatnagar
Herbal Antimicrobials
Microbes from urine of
UTI cases Healthy humans
Ajowan oil 90.43 91.34
Thyme oil 86.65 86.87
Holy basil oil 82.37 84.18
Carvacrol 80.35 78.81
Lemongrass oil 77.08 80.30
Cinnamledehyde 64.23 59.10
Citral 50.88 54.33
Cinnamon oil 42.57 43.88
Sandalwood oil 33.50 34.63

19. Conclusions
• The line between eubiotic (healthy) and dysbiotic (UTI) status microbiota of urine is
highly blurred as most of the common pathogens causing UTI could be detected in both
types of samples.
• Urine of some of the healthy people may have bacteria with probiotic potential and may
be responsible for Eubiosis (Colella et al., 2023; Kawalec and Zwoli´nska, 2022).
• Bacteria with probiotics potential were rarely detectable in urine of UTI cases.
• On the basis of urobiome analysis (unless pathotyping and total microbial loads is
detected), it is not possible to predict the cause of dysbiosis (UTI) as 50 similar type of
microbes were detected in urine of both healthy and sick human.
• Though total count of bacteria in urine samples of UTI cases was always more than 6000
cfu/ mL, CFU count may be high in urine of some of the healthy people too, thus one
should be careful in interpreting the bacteruria as UTI.
• In most of the cases of UTI more than one type of microbes were detected and all may not
be the cause of UTI, thus to conduct the antimicrobial susceptibility testing (AST) for
UTI cases one should be careful to because results may be erroneous when pure cultures
are not used for AST.
Epidemiology, ICAR-IVRI, Izatnagar

20. • The most effective antimicrobials on bacteria detected in urine of UTI cases were even
more detrimental on microbes present in healthy state, a wrong selection of antimicrobial
is destined to cause dysbiosis (Chesca et al., 2022; Mironov et al., 2021; Singh et al,
2024).
• The commonly used antimicrobials including the high end carbapenem antibiotics to treat
UTI cases were not effective on more than 78% cases, thus AST in UTI cases is the must
to be practiced.
• Of the most commonly recommended antimicrobials for UTI treatment (Nitrofurantoin,
Co-trimoxazole, Ciprofloxacin, Amoxicillin + clavulanate, Cephalexin, Ceftriaxone,
Meropenem), some (Co-trimoxazole, Ciprofloxacin, Amoxicillin + clavulanate,
Cephalexin) were not in the 15 most effective antimicrobials detected to inhibit bacteria
detected in 60% of the cases, thus it may be recommended that the priority list of
antimicrobials for UTI therapeutics needs revision, at least regionally.
• More systematic studies are needed to understand urobiome in health and disease
targeting detection of pathotypes/ virotypes / genotypes / biotypes/ clonotypes to make
any potential use of microbiome studies.
• Herbal antimicrobials being very effective (ajowan oil and thyme oil were more effective
than the most effective antibiotic tigecycline) against bacteria isolated from urine,
however had no significant difference in their efficacy on G +ve/ G-ve bacteria
irrespective of source of isolation, thus seems to be a double edged sword, further we
need to develop delivery system for those effective herbals to the site of the infection.
Epidemiology, ICAR-IVRI, Izatnagar

21. Acknowledgements and thanks
to:
1. The Director, ICAR-IVRI for providing
necessary funds to conduct the study.
2. All the clinicians those referred the UTI
urine samples for AST.
3. All the healthy people who consented to
provide their urine samples.
4. All the staff and students in Clinical
Epidemiology laboratory those helped at
many fronts during the study.
5. Organizers of the “Infection-24” for
waiving off the registration fee and last
minute changes requested.
6. All the audience specially those took
interest in the presentation.
Epidemiology, ICAR-IVRI, Izatnagar

22. Relevant References
• Ajose DJ, Oluwarinde BO, Abolarinwa TO et al. (2022). Combating bovine mastitis in the dairy sector in an era of antimicrobial resistance: ethno-veterinary
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