Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens
Abstract
:1. Introduction
2. Microbial Diagnostic Microarrays (MDMs)
2.1. Selection of Diagnostic Markers
2.2. Probe Selection
2.3. Selection of DNA Amplification/Labeling Methods
2.4. Selection of the Assay Format
3. Application of Microbial Diagnostic Microarrays for Pathogen Detection in Food, Environmental and Water Samples
3.1. 16S rRNA Gene-Based MDMs
3.2. MDMs Based on Alternative Marker Genes
3.3. MDMs for Typing of Microorganisms
4. Conclusions
4.1. Specificity and Informational Content
4.2. Sensitivity
4.3. Issues of Live/Dead Differentiation
4.4. Development of the Comprehensive Analytical Chain
Acknowledgements
References and Notes
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Appendix
Reference | Targeted organisms | Marker gene | Probes | Amplification | Specificity tests | Sensitivity tests | Proof-of-principle | Comments | ||
---|---|---|---|---|---|---|---|---|---|---|
Detection MDMs | ||||||||||
Wang et al., 2007 | [ 20] | food-borne | 16S rRNA, invA, virA | short oligonucleotides | PCR | only inclusivity test | 10−103 cfu / g food | +/− (bacterial isolates from food) | resolution problem on species level2nd array ( invA + virA) needed for differentiation of E. coli/Shigella spp. and Salmonella spp. | |
Lee et al., 2008 | [ 21] | water-borne (38 species, 4 genera, and 1 family) | 16S rRNA | short oligonucleotides | PCR | only in-silico test | 103 cfu (absolute) and 1% (relative) | + (wastewater samples) | resolution problem on species level | |
Cremonesi et al., 2009 | [ 23] | food-borne (diary products)(15 bacterial groups) | 16S rRNA | LDR probes | PCR | inclusivity + limited exclusivity test | 6−12 fg gDNA pre-PCR | + (milk samples) | SNP differentiation through LDR approach | |
Wang et al., 2009 | [ 24] | food-borne (powder infant formula)(10 pathogenic bacteria) | ITS, wzy | short oligonucleotides | duplex PCR | inclusivity + exclusivity test | 0.001−0.1 ng gDNA pre-PCR1−10 cfu / 25 g PIF (with biological pre-enrichment) | +(powder infant formula samples) | comprehensive in vitro validation | |
Maynard et al., 2005 | [ 25] | water-borne | 16S rRNA, cpn60, wecE | short oligonucleotides | PCR (3 rnx) | incomplete inclusivity test | 0.1% (corresponding to 104 genomes) | +/− (spiked wastewater gDNA samples) | ||
Kostic et al., 2010 | [ 26] | food- and water-borne | gyrB | short oligonucleotides | PCR | inclusivity + exclusivity test | 104 cfu (absolute) and 0.1% (relative)1−10 cfu / 25 g food (with biological pre-enrichment) | +(spiked food and water samples) | SNP differentiation through SSELO method | |
Wilson et al., 2002 | [ 30] | 18 pathogenic organisms(11 bacteria, 5 RNA viruses, 2 eukaryotes) | 142 unique diagnostic regions | short oligonucleotides | multiplex PCR + RT-PCR | inclusivity test | 10 fg gDNA pre-PCR2.5% relative | +/− (spiked air gDNA samples) | high density microarray (>50000 probes) | |
Miller et al., 2009 | [ 31] | food- and water-borne(12 pathogenic bacteria) | 35 virulence and marker genes | short oligonucleotides | multiplex PCRs (5 rnx, 9- to 10-plex) | inclusivity test | 0.1−0.01% | +/− (spiked water gDNA samples) | highly redundant probe set (1−5 genes / pathogen; 8−35 probes / gene) | |
Kim et al., 2008 | [ 32] | food-borne(11 pathogenic bacteria) | pathogen specific DNA-regions (identified by comparative genomics) | long oligonucleotides | WGA | inclusivity + exclusivity test | n.d. | n.d. | only one diagnostic region/pathogen | |
Detection/Typing MDMs | ||||||||||
Call et al., 2001 | [ 28] | E. coli O157:H7 | eaeA , hylA , stx1 , stx2 | short oligonucleotides | multiplex PCR | inclusivity + limited exclusivity test | 10 fg gDNA pre-PCR2.4 × 109 copies of PCR product~100 cfu | + (spiked chicken carcass rinsates) | ||
Sergeev et al., 2004 | [ 29] | Listeria spp., Campylobacter spp., S. aureus, C. perfringens | iap, glyA, fur, ste genes, CPT genes | short oligonucleotides | PCR (8 rnx) | only inclusivity test | n.d. | n.d. | ||
Peterson et al., 2010 | [ 33] | 43 pathogenic bacteria | 113 virulence genes, 227 antimicrobial resistance genes, metal resistance genes, horizontally transferrable elements | long oligonucleotides | WGA | limited inclusivity test (only 7 targeted organisms) | 109 cfu/g (absolute)103 cfu/g (with biological pre-enrichment) | +/− (spiked manure samples) | only one probe/genehighly complex hybridization patterns | |
Suo et al., 2009 | [ 34] | E. coli O157:H7, Salmonella spp., L. monocytogenes, C. jejuni | 14 virulence genes | long oligonucleotides | multiplex PCR (14-plex) | inclusivity test | 0.1 pg gDNA pre-PCR | + (meat samples) | only one probe/gene | |
Berthet et al., 2008 | [ 35] | 42 viruses + 50 bacterial species | 229 pathogenicity and virulence genes, 390 antimicrobial resistance genes | short oligonucleotides | WGA | incomplete | one genome copy (absolute)>0.01% (relative) | +/− (one wound sample) | high density Affymetrix array (2.56 million probes) | |
Typing MDMs | ||||||||||
Anjum et al., 2007 | [ 36] | E. coli pathotyping | virulence and bacteriocin genes | short oligonucleotides | linear | inclusivity test | n.d. | clinical isolates (55/63 typeable) | ArrayTube platform | |
Bruant et al., 2006 | [ 37] | E. coli pathotyping | virulence and antimicrobial resistance genes | long oligonucleotides | WGA | inclusivity test | n.d. | screening of river waters (Hamelin et al. , 2007, [ 33 ]) | ||
Ballmer et al., 2007 | [ 39] | E. coli serotyping | wzx, wzy, fliC | short oligonucleotides | linear | inclusivity test (sensitivity 96%, specificity 90%) | 106 genome copies | n.d. | 24/118 O-antigens and 47/53 H-antigens | |
Huehn et al., 2009 | [ 40] | Salmonella spp. typing | functional genes | long oligonucleotides | WGA | inclusivity test | n.d. | typing of 4,12:d:- isolates | ||
Wattiau et al., 2008a,b | [ 42,43] | Salmonella spp. serotyping | undisclosed genomic loci | LDR probes | multiplex PCR | n.d. | n.d. | performance studies (754 and 443 isolates) | commercial productresults not corresponding to Kauffmann-White scheme | |
Tankouo-Sandjong et al., 2008a | [ 44] | Salmonella spp. serotyping | atpD, gyrB, fliC, fljB | short oligonucleotides | PCR (4 rnx) | inclusivity test | 103 cfu (absolute)1 cfu/25 g food (with biological pre-enrichment) | panel of blind samples | parallel typing of mixed cultures possible | |
Friedrich et al., 2010 | [ 8] | Enterobacteriaceae typing | pathogroup specific DNA-regions (identified by comparative genomics) | long oligonucleotides | WGA | inclusivity test | n.d. | clinical isolates | complex data analysis algorithms | |
Call et al., 2003 | [ 45] | antimicrobial resistance | tet, blaTEM-1 | PCR amplicons | nick-translation | inclusivity + exclusivity test | n.d. | n.d. | ||
Peretten et al., 2005 | [ 46] | antimicrobial resistance (Gram-positive) | 90 antimicrobial resistance genes | short oligonucleotides | linear | inclusivity(125/137 probes tested) | n.d. | n.d. | SNP differentiation not possible | |
Batchelor et al., 2008 | [ 47] | antimicrobial resistance (Gram-negative) | 47 antimicrobial resistance genes | short oligonucleotides | linear | inclusivity | n.d. | clinical isolates | discrepancy phenotype vs. genotype |
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Kostić, T.; Sessitsch, A. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens. Microarrays 2012, 1, 3-24. https://doi.org/10.3390/microarrays1010003
Kostić T, Sessitsch A. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens. Microarrays. 2012; 1(1):3-24. https://doi.org/10.3390/microarrays1010003
Chicago/Turabian StyleKostić, Tanja, and Angela Sessitsch. 2012. "Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens" Microarrays 1, no. 1: 3-24. https://doi.org/10.3390/microarrays1010003