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Methods to Detect Microbes in the Environment ENVR 133


Gene-specific RFLP for polymorphisms in rRNA genes (rDNA) ... Image courtesy of O.D. 'Chip' Simmons, III. 35. Cryptosporidium parvum: ... – PowerPoint PPT presentation

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Title: Methods to Detect Microbes in the Environment ENVR 133

Methods to Detect Microbes in the
EnvironmentENVR 133 Part 2
  • Mark D. Sobsey

Detection of Pathogens by Detection and
Amplification of Nucleic Acids
  • Nucleic Acid Hybridization potentially very
    useful, but
  • (i) high detection limits (about 100-1000 genomic
    targets or more)
  • (ii) large sample volumes impractical for most
    hybridization protocols without further
  • (iii) hybridization reaction failures (false
  • and ambiguities (false positives) due to
    sample-related interferences and non-specific
    reactions, and
  • (iv) uncertainties about whether positive
    reactions are truly indicative of infectious

Some Methods for Molecular Genetic Detection
Typing of Microbes
Progress in Detection of Environmental Pathogens
by Nucleic Acid Hybridization
  • Cons early 1990s
  • High detection limits (gt1000 genomic targets)
  • Sample volumes too large without concentration
  • False (-) and false () due to sample
  • Uncertain if positive reactions truly indicate
    infectious pathogens
  • Pros late 1990s
  • Confirm identity of PCR and RT-PCR products
  • Oligoprobe hybridization
  • Detect PCR products as they are generated
  • Labeled primers
  • Simultaneously genotype many gene targets with
    multiple probes
  • Reverse Line Blot Hybridization Assay

Agarose Gel Electrophoresis
  • Separate nucleic acid fragments in an agarose gel
  • Resolves small DNA molecules 0.1 to 50 kb
  • agarose determines resolution of DNA size
  • 0.3 w/v resolves 5 to 50 kb
  • 2 w/v resolves 0.1 to 2 kb
  • Resolving large molecules (up to 500 kb) requires
    specialized methods
  • Pulse-field gel electrophoresis (PFGE)

DNA marker ladder
Specific DNA fragment
Direct Detection of Viruses and Other Microbes by
Nucleic Acid Amplification
  • For viruses not growing in lab hosts
  • Detect directly by in-vitro amplification of
    their nucleic acids
  • PCR (DNA viruses) or RT-PCR (RNA viruses)
  • Amplify nucleic acids (105-106 times)
  • Detect by oligoprobe hybridization
  • OR
  • Amplify nucleic acids and detect in real-time by
    fluorescent signal as primers are incorporated
    during amplification
  • Taqman PCR with LightCycler

Nucleic Acid Amplification - PCR
Example RT-PCR and Oligoprobe Detection of
Enteroviruses in Water
  • Filter
  • Elute
  • Precipitate
  • Extract RNA
  • RT-PCR
  • Oligoprobe
  • (10 ul sample)

Real-Time PCR and Quantitative Fluorogenic
  • Molecular beacon. Several 5' bases form base
    pairs with several 3' bases reporter and
    quencher in close proximity.
  • If reporter is excited by light, its emission is
    absorbed by quencher no fluorescence is
  • Detection of PCR product by molecular beacon.
  • Beacon binds to PCR product and fluoresces when
    excited by the appropriate ? of light.
  • Fluorescence proportional to PCR product

Real-Time, Multiplex RT-PCRHepatitis A Virus
(HAV) and Enteroviruses (EV)
  • Fluorescent probes to simultaneously detect HAV
    and EV (CVB3).
  • HAV and EV primer pairs gave predicted 244 and
    145-bp products.
  • Detect lt10 genomic RNA copies
  • Evaluated for virus detection in spiked water
  • Fluorogenic reporter probes (FAM- and
    ROX-labeled) specifically detected HAV or
    enterovirus, respectively.
  • No amplified products from viruses not belong to
    these group.

1 2 3 4 5 6 7 8
1. Std, 100 bp fragments 2. CVB3 , 145 bp 3.
negative control 4. HAV, 244 bp 5.negative
control 6. CVB3 and HAV 7.negative control 8.
Std, 100 bp fragments
Assessing DNA Polymorphisms to Detect and
Characterize Specific Bacteria
  • Molecular methods used to group or type bacteria
    based on genomic homogeniety or diversity
  • Identifies groups of closely-related isolates
    (presumed to arise from a common ancestor in the
    same chain of transmission) and divergent,
    epidemiologically unrelated isolates arising from
    independent sources.
  • Restriction fragment length polymorphisms
    variable and distinct size fragments of DNA
    detected by cutting DNA at unique sites using
    specific restriction endonucleases
  • Macrorestriction analysis
  • Ribotyping cutting DNA amplifies from 16S
    ribosomal RNA
  • Restriction analysis of virulence-associated
  • Arbitrary-primed PCR (Randomly Amplified
    Polymorphic DNA)

Restriction Endonucleases used in Molecular
Restriction Fragment Polymorphisms
  • Variations in DNA sequences are manifest as
    changes in some recognition sites for specific
    restriction endonuclease enzymes
  • Alters size and number of DNA fragments obtained
    from restriction enzyme digestion of chromosomal
  • Whole genomic DNA macrorestriction analysis
  • Specific gene(s) ribotyping (rRNA operons)

Example Macrorestriction Analysis of E. coli
RFLP Analysis Procedure
  • Isolate chromosomal DNA
  • Digest DNA with restriction endonuclease
  • Agarose gel electrophoresis
  • Macrorestriction analysis
  • Southern blotting and hybridization
  • Transfer DNA from gel to membrane (cellulose or
  • Hybridize with labeled probe to gene of interest
  • e.g., rDNA
  • Ribotype

DNA from electrophoresed gel (left) is
transferred to membrane filter by contact and DNA
on membrane is hybridized with specific probe(s)
  • Gene-specific RFLP for polymorphisms in rRNA
    genes (rDNA)
  • Identify rDNA fragments from electrophoresed
    chromosomal restriction digests by Southern
  • Use specific restriction enzymes with good
    discrimination abilities to generate restriction
    patterns from rDNA
  • rRNA is found in all bacteria
  • Some sequences are highly conserved and are
    common in broad groups (genera) can identify
    genus as first step with broad rRNA probe
  • rDNA has less but sufficient variability compared
    to other genes to type specific species and
    strains of related bacteria

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RFLP of Other Genes
  • Species-specific genes as targets for RFLP
  • Virulence genes
  • Toxins
  • Pili
  • Flagellar genes
  • Outer membrane protein genes

Arbitrarily-Primed PCR (Randomly Amplified
Polymorphic DNA or RAPID)
  • Identifies strain-specific variations in DNA
  • Use arbitrarily-chosen primers pairs (10- to
    20-mers) to amplify chromosomal DNA under
    non-stringent conditions
  • Variations in DNA sequences of different strains
    will give differences in numbers and sizes of
    their PCR products
  • Provides a unique DNA fingerprint
  • Limited number of patterns or groups per species
    of bacterium
  • Problems in reproducability and interpretation
    have occurred

Repetitive Element-PCR (Rep-PCR)
  • PCR amplify specific fragments of chromosomal DNA
    lying between known repeat motifs of the
  • Use two outwardly directed primers for the repeat
    element at high stringency to generate unique DNA
    products that are strain-specific.

Detecting Active or Viable Pathogens Using
Nucleic Acid Targets
  • Detect short-lived nucleic acids present in only
    viable/infectious microbes
  • ribosomal RNA
  • messenger RNA
  • genomic RNA of viruses (large amplicons)
  • Detect pathogen nucleic acid by fluorescent
    in-situ hybridization (FISH)
  • applied to bacteria, protozoan cysts and oocysts,
    as well as viruses in infected cell cultures
  • (see pictures in later slides)

Infectious Microbe Detection by Nucleic Acid
Target RNA (viral RNA or mRNA)
  • Viruses (and other microbes) growing slowly or
    without visible signs of growth
  • Detect rapidly by amplification of nucleic acids
    produced in cells or by vial nucleic acids in
    host cells
  • Integrated cell culture-PCR (or RT-PCR) for
  • mRNA in viable cells

Reverse transcribe ?
Polymerase Chain Reaction Amplification (PCR)
Nucleic acids in cells or in virus-infected
infected cells
Detecting Infectious Viruses by Direct Nucleic
Acid Analysis - A Functional Approach
  • Direct nucleic acid analysis alone does not
    assure detection of infectious viruses
  • Nucleic acid still present in inactivated viruses
    or free in the sample (water, etc.)
  • Infectious viruses have intact surface
    chemistries (epitopes) that react with host cells
    to initiate virus infection
  • The presence of functional surface epitopes for
    binding to cell receptors is evidence of virus

Infectious Non-infectious Nucleic acid
Cell Receptor
In Out
Virus Capture Plus RT-PCR to Detect Infectious
Viruses - The sCAR System
  • The cell receptor gene for Coxsackieviruses and
    Adenoviruses has been cloned and expressed,
    producing a soluble protein receptor, sCAR
  • Expressed, purified and bound sCAR to solid
    phases to capture infectious Coxsackieviruses
    from environmental samples
  • The nucleic acid of the sCAR-captured viruses is
    RT-PCR amplified for detection and quantitation

Application of sCAR with Para-Magnetic Beads for
Virus Particle Capture and then RT-PCR
sCAR purification
Covalent coupling to paramagnetic beads
Culture media sCAR produced
Blocking post-coupling
NA extraction
Sample containing viruses
Virus Particle
Blocking protein
Amine Terminated Support Magnetic Bead
BioSpheres(Biosource) Pre-coated to provide
available amine groups for covalent coupling of
proteins or other ligands by glutaraldehyde-mediat
ed coupling method
Ligand Capture of CVB3 Followed by
RT-PCR (Magnetic Bead-sCAR-CVB3)
Ligand capture
Bead control
Ligand capture capture of CVB3 with magnetic
beads coupled with purified sCAR Bead control
Reaction of CVB3 with BSA coated magnetic bead
Magnetic Bead BioSpheres (Amine Terminated
Support) Viral RNA extraction QIAamp kit
Microbe Nucleic Acid Detection by DNA Microarrays
or Gene Chip Technology
  • Generate/obtain DNA complimentary to genes
    (sequences) of interest
  • 1000s of different ones
  • Apply tiny quantities of each different one onto
    solid surfaces at defined positions
  • gene chip or DNA microarray
  • Isolate or amplify target NA of interest and
    label with a fluorescent probe
  • Apply sample NA to the gene chip surface
  • Sample NA binds to specific DNA probes on chip
    surface wash away unbound NA
  • Detect bound DNA or RNA by fluorescence after
    laser excitation
  • Analyze hybridization data using imaging systems
    and computer software

Fluorescing Gene Chip or DNA Microarray
Microscopic Detection of Pathogens Still Widely
Used in Clinical Diagnostic Microbiology
C. parvum oocysts 5 um diam. Acid fast stain of
fecal preparation
Microscopic and Imaging Detection of Pathogens
  • Still widely used for parasites and bacteria
  • Specific staining and advanced imaging to
    distinguish target from non-target organisms
  • Differential interference contrast microscopy
  • Confocal laser microscopy
  • Distinguish infectious from non-infectious
  • Combine with infectivity, viability or activity
  • Overcome sample size limitation due to presence
    of non-target particles
  • Flow cytometry and other advanced imaging
  • Advanced imaging methods require expensive

Fluorescent In Situ Hybridization - FISH
  • Bacteria of the target group are red
  • Other bacteria are blue
  • (artificial colors)

FISH DAPI-stained Bacteria Incubated with INT
(Tetrazolium Salt)
  • Enhanced image with artificial colors.
  • Blue DAPI stain
  • Red INT grains indicate respiratory active

Cryptosporidium parvumDifferential Interference
Contrast Microscopy
Image courtesy of O.D. Chip Simmons, III
Cryptosporidium parvum Microscopic Analysis of
NC field isolate
Differential Interference Contrast
DAPI stain
Images courtesy of O.D. Chip Simmons, III
Pathogen Detection by Biochemical Methods
  • Enzymatic activities unique to target microbe
  • Signature Biolipid Analysis
  • Detection of unique biolipids by
    gas-chromatography, mass spectrometry and other
    advanced organic analytical methods
  • Extract and purify from cells
  • Analyze
  • Other biochemical markers unique to a specific
    pathogen or class of pathogens.

Summary - Detecting and Quantifying Microbes in
the Environment
  • Get representative samples
  • Recover the microbes from the samples
  • may have to separate, concentrate and purify
  • very low numbers lots of other similar objects
    and other stuff (interferences)
  • Analyze for the recovered microbes
  • observe and count them - microscopy/imaging
  • culture them on media or in live hosts
  • detect them as antigens (immunoassays)
  • detect their genetic material (nucleic acid
  • detect their unique or characteristic chemical
    properties or other properties (e.g., antibiotic

Future Directions in Microbial Detection in the
  • Rapid and Sensitive Pathogen Detection Methods
  • Molecular detection for real-time or near
    real-time monitoring of pathogens (BT agents,
  • Real-time PCR
  • Couple with methods to selectively recover and
    detect potentially infectious microbes
  • Enrich for virulence genes of microbes in
    environmental media - early warning/alerts system
  • Nucleic acid microarrays (gene chips) for 1000s
    at a time
  • Culture plus molecular or immunodetection
  • Detect pathogen nucleic acids or antigens early
    in microbial proliferation in culture