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. Author manuscript; available in PMC: 2012 Oct 1.
Published in final edited form as: Curr Opin Infect Dis. 2011 Oct;24(5):464–471. doi: 10.1097/QCO.0b013e32834aa13a

Table 1.

Selected PCR methods for the detection of diarrheagenic enteropathogens

Pathogen Type Pathogen(s) detected Assay Type(s) Comments Reference
Bacteria Vibrio cholera Conventional, dip stick, PCR, multiplex PCR Cholera suspect stools did not grow cholera but were PCR positive, potentially due to inactivation by phage. [18]
Clostridium difficile Cepheid Gene Xpert (PCR), EIA/cytotoxin neutralization Excellent sensitivity and specificity of PCR vs. the predicate EIA followed by cytotoxin neutralization test [19]
Campylobacter jejuni; Campylobacter coli PCR, real-time PCR, commercial EIA Low sensitivity of culture was between vs. molecular (60% vs. 90%) [20]
Shiga Toxigenic E. coli Real-time PCR after enrichment culture Large public health study showing utility of PCR on submitter broths. [21]
Diarrheagenic E. coli Multiplex PCR + Gel analysis Nine virulence genes targeted over two PCRs and gel analysis; 100% specificity and limit of detection of 104 CFU/mL for tested strains. [22]
Diarrheagenic E. coli Multiplex real-time PCR + melt curve analysis Multiplexed real-time PCR targeting eight virulence genes; reported 99% sensitivity and 100% specificity for recognized diarrheagenic and non-diarrheagenic laboratory strains [23]
Diarrheagenic E. coli Multiplex real-time PCR + melt curve analysis Validation of assay presented in reference [23]; finding of 98% sensitivity and 100% specificity [24]
Salmonella Enrichment culture; real-time PCR Enrichment culture-based PCR was more sensitive than routine bacterial culture alone [25]
Campylobacter spp. 16S rRNA PCR PCR methods used detected Campylobacter in 38% of “no diagnosis” samples [26]
Diarrheagenic E. coli Multiplex PCR + Gel analysis Scheme of 4 multiplexed PCRs to detect 14 E. coli genes. [27]
Salmonella enterica, Campylobacter jejuni Real-time PCR In a prospective study of 2,067 stool samples, use of real-time PCR as a screening method provided a 15% to 18% increase in the pathogen detection rate [28]
Diarrheagenic E. coli Multiplex PCR This multiplex PCR is simultaneously detects six pathotypes of E. coli on pooled isolates. [29]
Virus Norovirus GI, GII, and GIV Real-Time PCR Quantitative method for all 3 Norovirus genogroups. [30]
Rotavirus A and C, adenovirus, norovirus GI and GII, sapovirus, astrovirus, Aichi virus, parechovirus, enterovirus Multiplex PCR Multiplex PCR plus gel method to detect 10 diarrhea-causing viruses. [31]
Adenovirus, Astrovirus, Norovirus GI and GII, Rotavirus, Sapovirus Multiplex PCR with bead-based detection Multiplex PCR plus Luminex-bead based detection method provides similar sensitivity and quantitation as the real-time PCR method. [32]
Adenovirus, Rotavirus Real-time PCR, latex agglutination, electron microscopy PCR methods resulted in increases of 111–175% versus latex agglutination, or electron microscopy. [33]
Rotavirus qRT-PCR vs. ELISA RT-PCR detected several additional infections beyond ELISA however these were subclinical and of low qRT-PCR Ct so a Ct cutoff was recommended. [34]
Norovirus qRT-PCR qRT-PCR Ct cutoff can be used to attribute norovirus to diarrhea cases vs. controls. [35]*
Norovirus RT-PCR with HRM Can distinguish genotype by HRM [36]
Adenovirus, astrovirus, enterovirus, norovirus, parechovirus, rotavirus, sapovirus Real-time PCR Detection of causative agent increased from 49% using conventional methods to 97% using real-time PCR. [37]
Rotavirus Real-time PCR Quantitative real-time PCR was able to detect 28% more rotavirus infections than EIA [38]
Parasite Ancyclostoma, Necator americanus, Ascaris lubricoides, Strongyloides stercoralis Real-time PCR Detected a pathogen in ~62% of samples vs. ~8% by microscopy [39]
Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, Giardia intestinalis Multiplex real-time PCR, singleplex real-time PCR, microscopy 15% of samples tested were positive under either of the PCR methods whereas only 8% of samples were positive by microscopy. [40]
Cryptosporidium spp., Giardia intestinalis, Entamoeba histolytica, Ancylostoma duodenale, Ascaris lubricoides, Necator americanus, Strongyloides stercoralis Multiplex PCR + Bead-based detection Multiplex assay for seven intestinal parasites offered 83–100% sensitivity/specificity vs. the real time assays. [41]
Multiple enteropathogens Campylobacter spp., Salmonella spp., EAEC, EPEC, enterotoxigenic Clostridium perfringens, Cryptosporidium spp., Giardia spp PCR, microscopy, bacterial cultures, immunoassays PCR was able to detect a disease agent in 41% of samples compared to only 15% with conventional methods [17]
norovirus, rotavirus, sapovirus, Campylobacter spp., Salmonella spp., EAEC, Cryptosporidium spp., Giardia spp. Real-time PCR In 4,627 samples tested, use of PCR increased detection of an enteropathogen versus conventional methods from 53% to 75% in cases and 19% to 42% in controls. [10]**
Campylobacter jejuni, EIEC, Giardia lambia, Salmonella enteric, Shigella, STEC Multiplex real-time PCR on broths and direct stool In screening a total of 28,185 specimens, the pathogen detection rate was 19.2% using MSA versus 6.4% using conventional culture methods. [42]**

Note: References in this table are limited to those describing detection of human pathogens