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. 2011 Oct 14;1(1):3–24. doi: 10.3390/microarrays1010003

Table 1.

Overview of microbial diagnostic microarrays developed for food and water analysis (n.d. = not defined).

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