Profiling Hospital-Acquired Pathogens and Antibiotic Resistance Genes Webinar

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Profiling hospital-acquired pathogens and antibiotic resistance
genes
Miranda Hanson-Baseler, Ph.D.
Miranda.Hanson-Baseler@qiagen.com

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Legal disclaimer
2
• QIAGEN products shown here are intended for molecular biology
applications. These products are not intended for the diagnosis,
prevention or treatment of a disease.
• For up-to-date licensing information and product-specific
disclaimers, see the respective QIAGEN kit handbook or user
manual. QIAGEN kit handbooks and user manuals are available
at www.QIAGEN.com or can be requested from QIAGEN
Technical Services or your local distributor.
Hospital Acquired Infection

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Agenda
Introduction to the microbiome
Technologies for microbial analysis
Hospital-acquired infections
Antibiotic resistance
QIAGEN’s microbial qPCR products
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Agenda
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Microbiome: Definition and background
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“The microbiome is defined as the collective genomes of the
microbes (composed of bacteria, bacteriophage, fungi, protozoa,
and viruses) that live inside and on the human body.”
-NIH, 2012
Microbiota refers to the collection of microbial organisms that
inhabits a certain environment
Metagenomics is the study of the collective genomes of
microorganisms from a sample without cultivation (Lederberg and
McCray 2001, The NIH HMP Working Group)
What does “microbiome” mean?
Kuczynski et al. Nature Reviews Genetics 13, 47-58 (January 2012)

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Human Microbiome Project
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Microorganisms cluster by body site
Cataloguing efforts by the NIH
Human Microbiome Project
suggest:
• ~10,000 organisms live with us
• ~ 8 ×106 genes in this “second
genome”
Identifying microbiota in healthy
individuals revealed:
• Different body sites have
unique communities
• Race, age, gender, weight or
ethnicity have an effect
1 Hoffmann A.R., et al. “The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals.” Vet Pathol. 2015
2 http://commonfund.nih.gov/hmp/index
3 Structure, function and diversity of the health human microbiome. The Human Microbiome Project Consortium. Nature, 486, 207-214 (14 June 2012). doi: 10.1038/nature11234

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Human microbiota and disease
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Gut
• Intestinal infections
• Obesity
• Inflammatory Bowel Disease
Airway
• Pneumonia and other respiratory infections
• Chronic Obstructive Pulmonary Disease
• Cystic Fibrosis
Urogenital
• Bacterial vaginosis
• Urinary Tract Infections
• Sexually Transmitted Disease
Blood
• Sepsis/bloodstream infections
Oral
• Periodontitis
• Gingivitis
http://commonfund.nih.gov/hmp/index

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Agenda
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Agenda
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Technologies to analyze microbial communities
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• Culture
• Gene cloning (Pan 16S rRNA) and Sanger sequencing
• Microarray
• MALDI
• Next generation sequencing
• 16S rRNA sequencing
• Whole genome sequencing
• qPCR - target dependent
• 16S rRNA gene
• Other relevant gene (antibiotic resistance gene, virulence
factor gene)

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Limitations of current pathogen detection methods
• Time consuming
• (Involve multiple steps, 5-7 days)
• Cannot identify all pathogens
• Majority are non-culturable
• Culture conditions are different
• Require extensive microbiological training
and expertise
• Varying protocols for identification
• Waste generation
11Hospital Acquired Infection

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Rapid
• Detection in less than 3 hours
• Amenable to routine testing
Sensitive
• Can detect low copy numbers
Standardized
• Automated protocols
• Stable chemical design
Specific
• Only detects target sequence
Benefits of real-time PCR for detection of microorganisms

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Agenda
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Agenda
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Hospital-acquired infections (HAIs)
• Also called nosocomial or healthcare-associated infections
• CDC: Infections that patients acquire during the course of receiving treatment for other
conditions, or acquired by healthcare workers while performing their duties in healthcare
settings
• Infection was NOT present nor incubating at time of admission
3 main contributing factors of HAIs
1. Agent: Variety of microorganisms (viruses, bacteria,
fungi and parasites)
2. Host factors: Suppressed immune system
3. Environment: Transmission of pathogens between
staff and patients and among patients
Hospital Acquired Infection 15

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Sources of infection
1. Exogenous: Outside the body
• Caused by organisms acquired by exposure to hospital personnel, medical devices or hospital
environment
2. Endogenous: By normal human flora
• Caused by organisms that are present as a part of the normal flora of the patient
• Organisms which are harmless in one site can be pathogenic when transferred to another site
• Bacteria from other patients, visitors, hospital personnel
• Contamination from medical equipment
• Ventilation ducts, bacteria from outside
Modes of transmission:
• Contact
• Airborne
• Oral route
• Parenteral route
• Vector borne

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Steps to infections
1. Source of microorganism
• Infected person or other sources
2. Method of transmission
• Medical instruments/devices, hands, clothing, sneezing, coughing, etc.
3. Point of entry
• Orifices, mucus membranes, skin
4. Susceptible host
• Immunocompromised; low resistance to infection

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Pathogens that cause HAIs
Majority of HAIs in the U.S. are caused by “ESKAPE” pathogens:
Enterococcus faecium
Staphylococcus aureus
Klebsiella sp.
Acinetobacter baumannii
Pseudomonas aeruginosa
Enterobacter sp.
Viruses:
• Blood borne infections – HBV, HCV, HIV
• Rubella, varicella, SARS
Fungi:
• Candida
• Aspergillus

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Types of HAIs
Urinary tract infections
• Very common
• ~80% of infections are associated with use of bladder catheter
Sepsis (blood stream infections)
• Represent small proportion of HAIs
• High fatality rates
Respiratory infections
• Cough, purulent sputum, infiltrate on chest x-ray
• Pneumonia
Intestinal infections
• Mostly caused by Clostridium difficile which is linked to 14,000 deaths in the U.S per year
• Symptoms range from diarrhea to life-threatening inflammation of the colon
Surgical site infections
• Usually acquired during an operation
• Purulent discharge, abscess, spreading cellulitis at surgical site within a month after the operation

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Urinary tract infections: Microbial identification or profiling
Urinary Tract Infections Microbial DNA qPCR Array
• Research tool used to screen for pathogenic bacteria from the urogenital tract
• Quickly detects the presence of pathogenic microorganisms from urine, urogenital swabs or other samples
that originate from the urogenital tract
• Can be used to monitor the frequency of various urinary tract infections in epidemiology research studies
• Contains assays for the following bacterial pathogens, designed to target the 16S rRNA gene:
• Streptococcus agalactiae
• Pseudomonas aeruginosa
• Morganella morganii
• Escherichia coli
• Enterococcus faecium
• Enterococcus faecalis
• Burkholderia cepacia
• Aerococcus urinae
• Acinetobacter baumannii

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Sepsis: Microbial identification or profiling
Sepsis Microbial DNA qPCR Array
• Research tool used to screen for pathogenic bacteria and fungi associated with bloodstream infections
• Quickly detects the presence of pathogenic bacteria from sepsis-associated samples such as blood, blood
culture or isolated bacterial colonies
• Can be used to monitor the frequency of sepsis-related microbial infections in epidemiology research
studies
• Contains 89 assays for the following bacterial pathogens, designed to target the 16S rRNA gene:
Actinobacteria: Bifidobacterium longum, Brevibacterium casei, Corynebacterium diphtheriae, Kocuria kristinae, Leifsonia aquatica, Micrococcus luteus,
Nocardia farcinica, Propionibacterium acnes, Streptomyces bikiniensis, Streptomyces griseus
Bacteriodetes: Bacteroides fragilis, Prevotella bivia, Prevotella intermedia, Prevotella melaninogenica
Firmicutes: Aerococcus viridans, Bacillus anthracis, Bacillus cereus, Bacillus licheniformis, Butyrivibrio fibrisolvens, Clostridium perfringens, Clostridium
sordellii, Enterococcus faecalis, Enterococcus faecium, Erysipelothrix rhusiopathiae, Exiguobacterium aurantiacum, Geobacillus stearothermophilus,
Paenibacillus larvae, Paenibacillus macerans, Paenibacillus thiaminolyticus, Pediococcus acidilactici, Pediococcus pentosaceus, Staphylococcus aureus,
Staphylococcus epidermidis, Staphylococcus saprophyticus, Streptococcus agalactiae, Streptococcus anginosus, Streptococcus mitis, Streptococcus
mutans, Streptococcus oralis, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus salivarius, Streptococcus sanguinis, Weissella confusa
Fusobacteria: Fusobacterium mortiferum, Fusobacterium necrophorum, Fusobacterium nucleatum, Fusobacterium varium
Proteobacteria: Achromobacter xylosoxidans, Acinetobacter baumannii, Acinetobacter calcoaceticus, Aeromonas hydrophila, Aeromonas sobria,
Alcaligenes faecalis, Brevundimonas diminuta, Brevundimonas vesicularis, Burkholderia cepacia, Burkholderia mallei, Citrobacter freundii, Desulfovibrio
desulfuricans, Enterobacter cloacae, Escherichia coli, Haemophilus influenzae, Hafnia alvei, Helicobacter pylori, Methylobacterium fujisawaense,
Methylobacterium zatmanii, Morganella morganii, Neisseria meningitidis, Ochrobactrum anthropi, Pantoea agglomerans, Plesiomonas shigelloides,
Proteus mirabilis, Pseudomonas aeruginosa, Rahnella aquatilis, Ralstonia pickettii, Stenotrophomonas maltophilia, Vibrio cholerae, Vibrio
parahaemolyticus, Vibrio vulnificus, Yersinia enterocolitica, Yersinia pestis
Fungi: Aspergillus flavus, Aspergillus fumigatus, Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis.
Antibiotic Resistance Marker: mecA.
Virulence Factors: lukF, spa.

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Respiratory infections: Microbial identification or profiling
Respiratory Tract Infections Microbial DNA qPCR Array
• Research tool used to screen for pathogenic bacteria and fungi from air-way derived samples
• Quickly detects the presence of pathogenic bacteria or fungi from bronchoalveolar lavage fluid, sputum or
other samples that originate from the lung or airway
• Can be used to monitor the frequency of various respiratory infections in epidemiology research studies
• Contains assays for the following bacterial pathogens, designed to target the 16S rRNA gene:
• Acinetobacter baumannii
• Acinetobacter calcoaceticus
• Actinobacillus hominis
• Aspergillus flavus
• Aspergillus fumigatus
• Bacillus anthracis
• Bordetella parapertussis
• Burkholderia cepacia
• Burkholderia gladioli
• Burkholderia mallei
• Chlamydia trachomatis
• Chlamydophila pneumoniae
• Chlamydophila psittaci
• Clostridium sordellii
• Corynebacterium
diphtheriae
• Coxiella burnetii
• Francisella tularensis
• Haemophilus influenzae
• Legionella pneumophila
• Moraxella catarrhalis
• Mycobacterium africanum
• Mycobacterium avium
• Mycobacterium kansasii
• Mycobacterium tuberculosis
• Mycoplasma pneumoniae
• Neisseria meningitidis
• Nocardia asteroides
• Peptostreptococcus
anaerobius
• Pneumocystis jirovecii
• Prevotella bivia
• Prevotella oris
• Proteus mirabilis
• Pseudomonas aeruginosa
• Rhodococcus equi
• Stenotrophomonas
maltophilia
• Streptobacillus moniliformis
• Streptococcus agalactiae
• Streptococcus pneumoniae
• Streptococcus pyogenes
• Yersinia pestis
• Staphylococcus aureus

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Intestinal infections: Microbial identification or profiling
Intestinal Infections Microbial DNA qPCR Array
• Research tool used to screen for pathogenic bacteria from gut-derived samples
• Quickly detects the presence of pathogenic bacteria in stool or other samples that originate from the gut
and are associated with intestinal infections or gastroenteritis
• Can be used to monitor the frequency of intestinal infections in epidemiology research studies
• Contains 45 assays for the following bacterial pathogens, designed to target the 16S rRNA gene:
Actinobacteria: Mycobacterium avium, Mycobacterium intracellulare.
Bacteriodetes: Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides vulgatus.
Firmicutes: Acidaminococcus fermentans, Anaerococcus lactolyticus, Anaerostipes caccae, Anaerotruncus colihominis, Bacillus cereus, Blautia
hydrogenotrophica, Brevibacillus brevis, Butyricicoccus pullicaecorum, Clostridium difficile, Clostridium perfringens, Clostridium septicum, Enterococcus
casseliflavus, Enterococcus faecalis, Enterococcus faecium, Enterococcus italicus, Listeria monocytogenes, Staphylococcus aureus, Streptococcus
agalactiae, Streptococcus pyogenes, Streptococcus suis.
Proteobacteria: Aeromonas hydrophila, Aeromonas sobria, Campylobacter jejuni, Campylobacter fetus, Campylobacter upsaliensis, Citrobacter freundii,
Enterobacter cloacae, Francisella tularensis, Helicobacter cinaedi, Helicobacter fennelliae, Helicobacter pylori, Morganella morganii, Plesiomonas
shigelloides, Shigella dysenteriae, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, Yersinia enterocolitica, Yersinia pestis.
Verrucomicrobia: Akkermansia muciniphila
Intestinal Infections 2 Microbial DNA qPCR Array (11 assays)
• Aeromonas hydrophila
• Plesiomonas shigelloides
• Yersinia enterocolitica
• Blastocystis hominis
• Campylobacter spp.
• Cryptosporidium spp.
• Dientamoeba fragilis
• Entamoeba histolytica
• Giardia intestinalis
• Salmonella spp.
• ipaH

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Agenda
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Antibiotic-resistant genes: How can we take control?
• CDC estimates: Causes sickness in 2 million people and 23,000 deaths per year
• March 2015, Obama Administration Releases National Action Plan to Combat
Antibiotic-Resistant Bacteria1
• June 2015, The National Cattlemen’s Beef Association participated in the White House
Forum on Antibiotic Stewardship2
1) https://www.whitehouse.gov/the-press-office/2015/03/27/fact-sheet-obama-administration-releases-national-action-plan-combat-ant
2) https://www.beefusa.org/newsreleases1.aspx?NewsID=4966

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The rise of the superbugs
• Antibiotics have been in use for the last 80 years
• Prevalent use has led microbes to adapt to them, eliminating
their effectiveness
• Superbugs carry several resistance genes and are multi-antibiotic-resistance microbes
(MRSA, VRSA, CRE)
• Acquire resistance genes by a transfer of DNA from a bacterium already resistant (transformation,
conjugation or transduction) or through a genetic mutation that helps the bacteria survive
• Genetic mutations can enable bacteria to:
• Express efflux systems that remove the drug from the cells (A)
• Produce antibiotic-inactivating enzymes like carbapenemase (B)
• Modify the drug’s target site or activate an alternative metabolic pathway (C)

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Beta-lactam resistance
• Beta-lactams belong to a family of antibiotics characterized by a beta-lactam ring
• Penicillins, cephalosporins, clavans, cephamycins and carbapenems
• Resistance to beta-lactams is primarily due to the hydrolysis of the antibiotic by a
beta-lactamase
• Mutations resulting in the modification of PBPs (penicillin binding proteins) or
cellular permeability can lead to resistance [e.g, methicillin resistance in
Staphylococcus aureus (MRSA)]
• These genes are classified as groups based on function and classes based on
sequence similarity

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Aminoglycoside resistance
• Aminoglycosides are characterized by the presence of an aminocyclitol ring linked to
aminosugars in their structure
• Resistance genes encode for aminoglycoside acetyltransferases, adenyltransferases and
phosphotransferases
• Streptomycin, kanamyin, tobramycin, amikacin
• Bactericidal activity is attributed to the irreversible binding to the ribosomes
• Have a broad antimicrobial spectrum
• Active against aerobic and facultative aerobic Gram-negative bacilli and some Gram-positive
bacteria
• 3 mechanisms of resistance: Ribosome alteration, decreased permeability and inactivation of
drugs by aminoglycoside modifying enzymes

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Tetracycline resistance
• Tetracyclines inhibit the bacterial growth by stopping protein synthesis
• Tetracycline, doxycycline, minocycline
• Most common antibiotic resistance encountered
• 3 different mechanisms of resistance have been identified
• Tetracycline efflux
• Ribosome protection
• Tetracycline modification

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Macrolide, lincosamide and streptogramin resistance
• Macrolides inhibit protein synthesis by stimulating dissociation of the peptidyl-tRNA molecule
from the ribosomes during elongation
• Erythromycin, clarithromycin, azithromycin
• Intrinsic resistance is due to low permeability of outer membrane protein
• Drug inactivation and active efflux may also occur

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Quinolone and fluoroquinolone resistance
• Quinolones and fluoroquinolones have diverse molecular mechanisms
• Altering DNA topology
• Performing enzymatic modifications
• Acting as drug efflux pumps
• Ciprofloxacin, gemifloxacin, moxifloxacin

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Colistin-resistant bacteria in the U.S.
• Researchers at the Walter Reed Army Institute of Research and the
Walter Reed National Military Medical Center tested drug-resistant E.coli
bacteria isolated from U.S. patients
• Identified first instance of mcr-1-mediated colistin resistance in the U.S.
• Sample collected from a woman treated for a UTI
• mcr-1 is located on a plasmid that is capable of easily moving between
bacterial species
• Plasmid: an independent, circular, self-replicating DNA molecule that carries only
a few genes
McGann, P. et al. (2016) Escherichia coli Harboring mcr-1 and blaCTX-M on a Novel IncF Plasmid: First report of mcr-1 in the USA. Antimicrob.
Agents Chemother. 60, 6.

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Antibiotic resistance genes from food and fertilizer sources
Antibiotic resistance genes in our food supply?
• One potential source of acquiring antibiotic
resistance genes is through the food-supply
• Both livestock and feed may acquire
antibiotic resistant bacteria through different
mechanisms
• Food can be exposed to antibiotic resistant
bacteria through fertilizer originating from
waste-water treatment plants. This, in
addition to increasing administration of
antibiotics to livestock can lead to food as
being a potential source of antibiotic
resistant genes
• This may then lead to horizontal gene
transfer to pathogenic enteropathogens
leading to drug resistance in humans,
therefore highlighting the importance of
surveillance and prevention of antibiotic
resistant genes in food

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Antibiotic Resistance Genes Microbial DNA qPCR Array
• Research tool used for the detection and relative profiling of antibiotic resistance
genes
• Quickly detects the presence of antibiotic resistance genes that may be present in
isolated bacterial colonies, bacteria from blood culture, metagenomic samples or
other sample types
• Contains assays for 87 antibiotic resistance genes belonging to aminoglycoside,
β-lactam, erythromycin, fluoroquinolone, macrolide-lincosamide-streptogramin B,
tetracycline, vancomycin, and multidrug resistance classifications

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Antibiotic Resistance Gene Screening Microbial qPCR Array

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Microbial PCR array method
Genomic DNA from stool samples was extracted using a QIAGEN QIAamp® DNA Stool Mini Kit.
500 ng of genomic DNA from stool samples were mixed with microbial qPCR probe mastermix and
microbe-free water. This mixture was then uniformly dispensed into a 96-well PCR plate containing dried-
down primers and 5’-hydrolysis probes for each of the antibiotic resistance genes tested.
Each PCR plate was run on a Roche LightCycler 480 using the
following cycling conditions:
After the PCR run, raw CT values were exported to the microbial qPCR analysis software to detect the presence of antibiotic
resistance genes. The identification criteria were as follows: CT<32 was identified as positive, CT>35 was identified as
negative and a 32<CT<35 was inconclusive. In addition, the control assay PPC (Positive PCR Control) had to have a
CT=22±2 to show that the PCR instrument and mastermix performed properly and there were no PCR inhibitors in the
sample.

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Screening of sewage samples and gut microbiota

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Validation of specificity for PCR array by pyrosequencing

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Screening using Antibiotic Resistance Genes qPCR Array

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Summary
• Microbial qPCR arrays are a collection of sensitive and specific qPCR assays for the
detection of antibiotic resistance genes from both bacterial isolates and metagenomic
samples
• Detection of 87 antibiotic resistance genes can be performed simultaneously in one 3-hour
PCR run
• ermB and mefA were found in all meat and stool samples suggesting that acquisition of
these antibiotic resistance genes may come from consumption of meat
• The Antibiotic Resistance Gene Microbial PCR Array is an effective tool for monitoring
potential outbreaks of antibiotic resistant bacteria, detection in food samples and potential
sources of fertilizer, and identifying new sources of antibiotic resistance genes

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In the literature: Antibiotic Resistance Genes Microbial DNA qPCR Array
Vandini, A. et al. (2014) Hard surface biocontrol in hospitals using microbial-based cleaning
products. PLoS One. 9, 9.
• Determined the efficacy of a probiotic-based cleaning procedure by assessing the presence and survival
of a number of bacteria responsible for HAIs
• Study conducted in 3 different hospitals with ~20,000 microbial surface samples
• Used the ARG Microbial DNA qPCR Array to analyze bacillus strains used in the cleaning products and
on different isolates from the various hospital settings
• Conclusion: Probiotic-based cleaning procedure is more effective in lowering the number of HAI-related
microorganisms on surfaces, when compared to conventional cleaning products.

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Han, X-M. et al. (2015) Impacts of reclaimed water irrigation on soil antibiotic resistome in urban
parks of Victoria, Australia. Environmental Pollution. 211.
• Determined the impact of reclaimed water irrigation on the patterns of antibiotic resistance genes and
the soil bacteria community
• Used the ARG Microbial DNA qPCR Array to identify antibiotic resistance genes in 12 urban parks with
and without reclaimed water irrigation
• Conclusion: Irrigation of urban parks with reclaimed water could have an effect on the abundance,
diversity and composition of a wide variety of soil antibiotic resistance genes of clinical relevance

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Agga, G.E. et al. (2015) Antimicrobial-resistant bacterial populations and antimicrobial
resistance genes obtained from environments impacted by livestock and municipal waste. PLoS
One. 10, 7.
• Compared antimicrobial-resistant bacteria and antimicrobial resistance genes from environments
associated with municipal sewage treatment plant runoff, cattle feedlot runoff ponds, swine waste
lagoons and environments with minimal direct fecal impact
• Liquid and solid samples were collected and tested for antibiotic resistance genes using the ARG
Microbial DNA qPCR array
• Conclusion: Antimicrobial-resistant bacteria and antimicrobial resistance genes exist in cattle, human
and swine waste streams, but a higher diversity of ARGs are present in treated human waste
discharged fro municipal wastewater treatment plants than in livestock environments

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Agenda
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Overview of QIAGEN’s Microbial qPCR products
Microbiology: From identification to characterization
16S rRNA gene
- Conserved region - Variable region
Microbial qPCR assays and arrays for identification and profiling use probes and
primers against 16srRNA variable region.
Content: Largest microbiome portfolio; experimentally verified 580 assays
Custom: Select 8 to 384 microbial species for simultaneous detection/profiling
Control: Integrated controls ensure reliability of results
Sensitivity: Can detect as low as 10 copy numbers; data available

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Microbial DNA qPCR Array: Pre-printed assays profile up to 90 different species/genes
PCR plates (either 96-well or 384-well) are pre-printed with primers
and probes.
Each numbered well is a separate assay that tests the same sample.
Integrated control assays:
• Host assays detect genomic DNA to test sample collection
• Pan A/C is a pan- Aspergillus/Candida assay that detects
the presence of fungal rRNA
• PanB1 and PanB2 detect bacterial 16S rRNA to determine
bacterial load in the sample
• PPC is a positive PCR control reaction that tests if the PCR
reactions failed from PCR inhibitors from the sample, etc.

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Layout of a Microbial DNA qPCR Array: Different arrays have different number of assays and
samples

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Microbial DNA qPCR Arrays and Assays
Profile or identify the presence of microbial DNA (from bacteria, fungi, virus, protist, antibiotic resistance
and virulence factors)
Identification experiment answers the following question:
Are any of these microbes or genes present in the sample?
• Must be compared against a known negative sample
• Run NTC as one sample
• Answers are Yes or No
Profiling experiment answers the following question:
Have the amounts of any of these microbes or genes changed?
• Must be compared against a reference sample
• Answers are fold change

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Sample to Insight: Microbial qPCR Assays and Arrays
QIAsymphony/QIAcube/QIAcube HT QIAgility Rotor-Gene Q
DNA
Isolation
Assays
and Arrays
Data
Analysis
• QIAamp DNA Microbiome
Kit
• Mericon Bacteria Kit
• QIAamp UCP Pathogen
Mini Kit
• QIAamp DNA Stool Mini
Kit
• QIAamp UCP
PurePathogen Blood Kit
• QIAamp DNA Mini Kit
• MagAttract HMW kit
• Microbial DNA
qPCR Arrays
• Microbial DNA
qPCR Assay Kits
• Microbial DNA
qPCR Assays
• Microbial qPCR
Multi-Assay Kits
• Custom Microbial
DNA qPCR Arrays
• GeneGlobe Data
Analysis Center
Sample Insight

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Microbial NGS (microbiome/pathogen): QIAGEN Tools
Sample
Disruption
Sample
Preparation
Library
construction
NGS run Data analysis
Validation by
PCR
• TissueLyserII;
TissueLyser LT;
TissueRuptor
• Pathogen Lysis
Tubes
• QIAamp DNA
Microbiome Kit
(human
microbiome NGS)
• QIAamp UCP
Pathogen Mini Kit
(If depletion of
human gDNA is
not necessary)
• MagAttract HMW
DNA Kit (For
genome finishing,
starting with
culture)
• Repli-g Single Cell
Kit (Limited
primary sample
material)
• QIAamp Fast DNA
Stool Mini Kit (If
inhibitors are
present)
Data Analysis Software
• CLC Bio
Genomics
workbench
• Microbial Genome
Finishing module
Predesigned & custom
arrays / assays for
verification and
focused microbiome
analyses
• Microbial DNA
qPCR Arrays
• Microbial DNA
qPCR Multi-Assay
Kits
• Microbial DNA
qPCR Assay Kits
• Microbial DNA
qPCR Assays
• QC assays kits to detect
species specific gDNA
and microbial DNA:
o Pan bacteria, Pan
fungal, Pan
aspergillus,
hgDNA, mgDNA
etc.
• QIAseq FX DNA Library
Kit
(ILMN)
• GeneRead DNA Library
Prep Kits
(Life, ILMN)
• GeneRead Size
Selection Kit
• GeneRead Library
Quant System

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Want to stay up-to-date?
Visit the Biomarker Insights Blog for NGS, PCR,
Liquid Biopsy, Microbiome updates and more
biomarkerinsights.qiagen.com/
@QIAGENscience
Follow us:
QIAGEN Life Sciences
QIAGENscience

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Agenda
Questions
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6

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Thank you for coming
Any questions?
Contact us
Telephone: 888-503-3187
Email: brcsupport@QIAGEN.com
qiawebinars@QIAGEN.com

Profiling Hospital-Acquired Pathogens and Antibiotic Resistance Genes Webinar

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