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