Organism Techniques Used Reference Comments Diarrheagenic Escherichia coli (DEC) Multiplex real time PCR 17728475 The real-time PCR assay considerably reduces the high false-positive rate from the use of serotyping alone and thus it is suggested that serogrouping-based methods are inadequate for the identification of DEC isolates although they are useful for the identification of a limited number of serogroups Diarrheagenic Escherichia coli (DEC) Isolation culture; biochemical identification and serotyping methods 22177306 The population distribution temporal distribution and serotype distribution of the pathogenic bacteria were analyzed by descriptive statistical methods. Escherichia coli (EPEC) Fluorescentactin staining test using localised antisera 8904439 Strains identified as EPEC by commercial antisera may possess potential virulence properties and suggest that O grouping is still a useful diagnostic tool for presumptive identification of diarrheagenic E. coli in clinical laboratories. Escherichia coli (EPEC) Serological and PCR-based methods 17887989 Molecular detection by the eae-PCR followed by serotyping and virutyping is useful for monitoring trends in EPEC infections and to discover their possible reservoirs. Escherichia coli (EPEC) FAS assays and PCR 16490272 The possession of EPEC-related O and H antigens is no longer deemed an essential characteristic of true pathogenic EPEC strains emphasising the importance of routinely screen for virulence markers in E. coli strains isolated from foods. Escherichia coli (EPEC) Immunomagnetic separation 20378282 The method combining both enrichment periods with direct plating and IMS followed by plating yielded a detection limit of 20-90 cfu/25 g. But if only certain serotypes have to be investigated the protocol can be simplified. Escherichia coli (EPEC) PCR-based detection 19284162 Based on the virulence genotype identified the prevalence of atypical EPEC (eae+) was higher than of typical EPEC (eae+ bfpA+) and typical EPEC identification was restricted to children. Escherichia coli (EPEC) Serotyping 15558161 serotyping is a reliable method for those serotypes that correspond to clones. Escherichia coli (EPEC) PFGE 16914645 PFGE patterns suggests the prevailing clonal diversity among EPEC strains isolated from children with diarrhoea in Montevideo. Escherichia coli (EPEC) PCR-RFLP 21861008 The multiplex PCR assay was found to be rapid and reliable in comparison to serological test; especially when screening the large number of isolates. Escherichia coli (EPEC) qRT-PCR 22028433 EPEC load measured by qRT-PCR is higher in diarrheal than in healthy children. qRT-PCR may be useful to study the relationship between disease and colonization in settings of endemicity. Escherichia coli (STEC) PCR 21317253 Simple diagnostic test might be applicable in hospital service laboratories or public health laboratories to test strains isolated from stools of patients suffering from diarrhea. Escherichia coli (STEC) ProSpecT Shiga toxin E. coli Microplate assay 15071021 ProSpecT assay is sensitive and specific for the detection of Shiga toxins 1 and 2 in stool and has potentially significant clinical impact for the individual patient and public health Escherichia coli (STEC) Enzyme immunoassay (EIA) 8874070;21186994 EIA is easy to perform and time efficient and can be recommended as a screening test for non-O157 STEC in children with diarrhea. Escherichia coli (STEC) Enzyme-linked immunosorbent assays (ELISAs) ; direct immunofluorescent filter techniques 10880188 The primary use of these procedures is therefore to identify food and faecal samples that possibly contain O157 STEC. Escherichia coli (STEC) PCR 17317110 screening for STEC will allow the detection of STEC O26 O111 O145 and non-sorbitol-fermenting O157 but most strains (in this study 74.3%) from other serotypes will be missed. Escherichia coli (STEC) Multiplex polymerase chain reaction (PCR) 15992278 Multiplex PCR was an effective tool for characterizing STEC pathogenic profiles and distinguished STEC O157:H7 from other STEC Escherichia coli (STEC) Enzyme-linked immunosorbent assays (ELISAs) 10880188 The primary use of these procedures is therefore to identify food and faecal samples that possibly contain O157 STEC. Escherichia coli (STEC) Immunomagnetic separation 18045431 Incorporating tellurite into an E. coli O157 detection strategy may select for the subset of E. coli O157 that contains the Shiga-toxin genes. Escherichia coli (STEC) Enzyme-linked fluorescent immunoassay using (VIDAS) and polymerase chain reaction (PCR) 18234025 wide distribution of STEC in ruminant herds which represent an important reservoir for strains that pose a potential risk for human infections. Escherichia coli (STEC) Media enrichment 18767974 enrichment for STEC has been a critical step in any successful protocol for their detection Escherichia coli (STEC) Immunomagnetic separation (IMS)- slide agglutination (SA); PCR and DNA probes 12904221 IMS-SA is a sensitive method for detecting specific E. coli serogroups. Escherichia coli (STEC) Immunomagnetic separation 18045431 The combination of 6-h enrichment in Gram-negative broth containing vancomycin cefixime and cefsuludin large volume IMS and selective plating on TCA maximized STEC O157 recovery from naturally contaminated cattle faecal specimens. Escherichia coli (STEC) Real-time PCR test 22239032;21317253 This simple diagnostic test might be applicable in hospital service laboratories or public health laboratories to test strains isolated from stools of patients suffering from diarrhea. Escherichia coli (STEC) conventional culture methods and polymerase chain reaction (PCR) 19052337 PCR on enrichment cultures gave better results Escherichia coli (EHEC) O157:H7 Multiplex PCR assay 17685340 It had better overall performance for enrichment of cold- and freeze-stressed E. coli O157:H7 Escherichia coli (EHEC) O157:H7 Real-time PCR assays 15992285;15726961;15726961;14572231 The real-time PCR assays for detection of E. coli O157:H7 were specific sensitive and rapid. Escherichia coli (EHEC) O157:H7 VIDAS ultra performance E. coli test (ECPT UP) ;PCR 21219756 The primer specificity of the RT-PCR assay and the highly specific phage ligand used in the VIDAS ECPT UP for target recognition enabled the detection of low levels of E. coli O157:H7 Escherichia coli (EHEC) O157:H7 Immunomagnetic separation 10050682 The sensitivity of the immuno-kits appeared to be similar to the IMS-plating methods but the specificity was lower. Escherichia coli (EHEC) O157:H7 Polymerase chain reaction (PCR) assays. 17803865 PCR for Campylobacter Salmonella and E. coli O157 is potentially very successful in identifying pathogens possibly detecting more than the number currently reported using culture Escherichia coli (EHEC) O157:H7 PCR 20847380;14572231 Efficacy of enrichment broths in the recovery of freeze-injured Escherichia coli O157:H7 in inoculated ground beef by PCR. Escherichia coli (EHEC) O157:H7 Double polymerase chain reaction (PCR) 19103121 The established assay in this study based on oligonucleotide microarray to detect the seven pathogenic bacteria has many advantages such as convenient rapid accurate stable and high flux which is suitable for clinical specimen examination and epidemiological field investigation. Escherichia coli (EHEC) Gene profiling 21689465 The OI-122 encoded nleB gene was found to be most closely associated with Cluster 1 strains and may serve as a diagnostic tool for the identification of virulent EHEC and EPEC seropathotypes Escherichia coli (EHEC) Serological and PCR-based methods 17887989 Molecular detection by the eae-PCR followed by serotyping and virutyping is useful for monitoring trends in EHEC infections and to discover their possible reservoirs. Escherichia coli (ETEC) multiplex real-time PCR 18399125;19733452 The multiplex real-time PCR assay can detect invA elt ipaH simultaneously in a single reaction moreover it can detect for virulence genes in strains of Salmonella ETEC and Shigella or EIEC and screen these pathogens in fecal specimens from patients with diarrhea with a high specificity. Escherichia coli (ETEC) PCR or hybridization assays "19733452 " This method was suitable for a sensitive qualitative detection of O149 E. coli Salmonella enterica 7-plex PCR-Luminex assay 22075596 This multiplex PCR-Luminex assay enables sensitive specific and quantitative detection of the major bacterial causes of gastroenteritis. Salmonella enterica PCR assay 21855409;15184531;21175956 The new real-time multiplex PCR provides reliable results within a short time and might be useful as an additional diagnostic tool whenever time is important in the diagnosis of enteropathogenic bacteria. Salmonella enterica multiplex real-time PCR 18399125;20622219 The multiplex real-time PCR assay can detect invA elt ipaH simultaneously in a single reaction moreover it can detect for virulence genes in strains of Salmonella and screen these pathogens in fecal specimens from patients with diarrhea with a high specificity. Salmonella enterica duplex real-time SYBR Green LightCycler PCR (LC-PCR) assay with DNA extraction 14605150 The rapid amplification and reliable detection of specific genes of greater than 10(5) food- or waterborne pathogenic bacteria per g in samples should facilitate the diagnosis and management of food- or waterborne outbreaks. Salmonella enterica The robotic detection 22056326 The robotic detection platform assessed here represents a sensitive high-throughput tool for key pathogens linked to infectious diarrhoea in humans. This platform requires little molecular biological expertise and is well suited to various diagnostic facilities and settings. Salmonella enterica Isolation culture biochemical identification and serotyping methods 22177306 The population distribution temporal distribution and serotype distribution of the pathogenic bacteria were analyzed by descriptive statistical methods. Salmonella enterica Microarray analysis 21406379 Salmonella is an intracellular pathogen we suggest that increased apoptosis may be a mechanism by which the probiotic culture reduces Salmonella infection. Salmonella enterica Reverse Dot blot method 19469006 The hybridization results indicated that the improved RDB assay developed was a reliable method for the detection of intestinal pathogen in fecal samples. Salmonella enterica Kirby-Bauer method 19403206 A multidrug-resistant Salmonella strain was recovered from feces of a traveler to Egypt. The antimicrobial susceptibility test to 12 antimicrobial agents was performed with the Kirby-Bauer method Salmonella enterica MALDI-TOF-MS 19239002 The detection and identification of foodborne pathogenic bacteria by MALDI-TOF-MS is of good characteristics of stability and reproducibility. It is a powerful tool in detecting and identifying foodborne pathogenic bacteria. Salmonella enterica pyrosequencing 18324428 pyrosequencing approach proved to have significant reliability and provided a fast and effective method for clinical diagnosis. Shigella species PCR assays 20519461;5184531;18990527 Paired with reflexive culture of stools testing positive this should provide an improvement in care for patients with acute infectious diarrheal disease. Shigella species Multiplex real-time PCR 18399125 The multiplex real-time PCR assay can detect invA elt ipaH simultaneously in a single reaction moreover it can detect for virulence genes in strains of Shigella and screen these pathogens in fecal specimens from patients with diarrhea with a high specificity. Shigella species Duplex real-time SYBR Green LightCycler PCR (LC-PCR) assay with DNA extraction 14605150 The rapid amplification and reliable detection of specific genes of greater than 10(5) food- or waterborne pathogenic bacteria per g in samples should facilitate the diagnosis and management of food- or waterborne outbreaks. Shigella species Isolation culture biochemical identification and serotyping methods 22177306 "The detected rate of pathogenic bacteria showed evident seasonal variations, with a peak from July to October" Shigella species Reverse Dot blot method 19469006 The hybridization results indicated that the improved RDB assay developed was a reliable method for the detection of intestinal pathogen in fecal samples. Yersinia enterocolitica Duplex real-time SYBR Green LightCycler PCR (LC-PCR) assay with DNA extraction 14605150 The rapid amplification and reliable detection of specific genes of greater than 10(5) food- or waterborne pathogenic bacteria per g in samples should facilitate the diagnosis and management of food- or waterborne outbreaks. Yersinia enterocolitica cold-enrichment culture; antibiogram test 19554973 Pathogenicity of the isolated Yersinia was determined. Antibodies to Y. enterocolitica were raised for rapid Yersinia detection in the stool. Yersinia enterocolitica Reverse Dot blot method 19469006 The hybridization results indicated that the improved RDB assay developed was a reliable method for the detection of intestinal pathogen in fecal samples. Yersinia enterocolitica microarray technique 18834908 "microarray technique s an attractive diagnostic tool for rapidly and simultaneously identifying multiple pathogens in clinical practice, especially in patients with infectious diarrhea." Yersinia enterocolitica DNA microarray 18834908;21046348 DNA microarray was used successfully to identify the causative agents in clinical stool samples from patients with food-borne enteritis. Campylobacter jejuni ELISA; multiplex PCR assays 22075596 This multiplex PCR-Luminex assay enables sensitive specific and quantitative detection of the major bacterial causes of gastroenteritis. Campylobacter jejuni One-tube PCR assay 21855409;20519461;15184531 The new real-time multiplex PCR provides reliable results within a short time and might be useful as an additional diagnostic tool whenever time is important in the diagnosis of enteropathogenic bacteria. Campylobacter jejuni The robotic detection 22056326 The robotic detection platform assessed here represents a sensitive high-throughput tool for key pathogens linked to infectious diarrhoea in humans. This platform requires little molecular biological expertise and is well suited to various diagnostic facilities and settings. Vibrio parahaemolyticus Duplex real-time SYBR Green LightCycler PCR (LC-PCR) assay with DNA extraction 14605150 The rapid amplification and reliable detection of specific genes of greater than 10(5) food- or waterborne pathogenic bacteria per g in samples should facilitate the diagnosis and management of food- or waterborne outbreaks. Vibrio parahaemolyticus Isolation culture biochemical identification and serotyping methods 22177306 The population distribution temporal distribution and serotype distribution of the pathogenic bacteria were analyzed by descriptive statistical methods. Vibrio cholerae SYBR-Green-based real-time PCR 22268636 Estimation of relative pathogen load by real-time PCR indicated that the inability of conventional culture-dependent methods to detect the pathogens was related to lower colony-forming units of the pathogen. Vibrio cholerae Serotyping 21215109 Non-O1/non-O139 Vibrio cholerae have diversified serotypes causing certain infection rate among the population in this region. These bacteria exist extensively in external environment and they are the potential hazard to the citizens. Vibrio cholerae DNA loop-mediated isothermal amplification (LAMP) 20518355;19861266;19874480 LAMP assay established is a sensitive rapid and simple tool for detecting Vibrio cholerae and will facilitate the surveillance for its control. Vibrio cholerae Reverse Dot blot method 19469006 The hybridization results indicated that the improved RDB assay developed was a reliable method for the detection of intestinal pathogen in fecal samples. Clostridium difficile Xpert® CD assays Xpert® CD/Epi (Cepheid; CA) 22278839 The Xpert CD and Xpert CD/Epi assays were the most sensitive rapid and easy to use assays for the detection of toxigenic CD in stool specimens. Clostridium difficile Enzyme immunoassays (EIAs) 21741114 A national laboratory survey of diagnostic methods and testing protocols for the diagnosis of CDI is simple and inexpensive and could act as the first step towards implementing national standardized criteria for optimal diagnosis of CDI. Clostridium difficile ELISA 20049303 Identification of the etiological agent of diarrhea in a patient with AIDS is very important as it can help in the institution of appropriate therapy and the reduction of morbidity and mortality in these patients. Clostridium difficile Loop-Mediated Isothermal Amplification; PCR; EIA 22189114 In the era of rapid molecular-based tests for toxigenic C. difficile toxin enzyme immunoassays (EIAs) should no longer be considered the standard of care. Clostridium difficile Real-time PCR method (direct stool PCR [DPCR]) 19923482 A three-step algorithm in which DPCR is used to analyze GDH EIA-positive toxin EIA-negative specimens provides a convenient and specific alternative with rapid results for 87.7% of specimens. Rotavirus Enzyme immunoassay;RT-PCR 15861888;22175547 Demographic and epidemiological data were collected and specimens were tested for rotavirus via enzyme immunoassay. Genotyping was performed via reverse transcriptase polymerase chain reaction. Rotavirus Reverse transcription polymerase chain reaction (RT-PCR) 15627523;21866637 Rotavirus is one of the major etiological agents of viral diarrhea among infants in Chengdu. G1 was the dominant type G in Chengdu. G1P[8] was the predominant type of G/P dominance combination. Rotavirus Seeplex DV assay 21775550 Seeplex DV assay is sensitive specific convenient and reliable for the simultaneous detection of several viral pathogens directly in specimens from patients with gastroenteritis. Rotavirus Enzyme immunoassay (EIA) 22030330 ntroduction of effective and available rotavirus vaccines could substantially affect worldwide deaths attributable to diarrhoea with EIAs or polyacrylamide gel electrophoresis. Rotavirus Latex agglutination (LA); immunochromatography (ICG); polyacrylamide gel electrophoresis (PAGE) and negative staining electron microscopy (ME) tests 21340294 The data showed similar electropherotypes and genotypes G P and NSP4 of the inland wild circulating strains of RV. Rotavirus Reverse transcription loop-mediated isothermal amplification (RT-LAMP) 21286798;21127872;20799985;20160420 A reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detection of porcine epidemic diarrhea virus (PEDV). Rotavirus Multiplex reverse transcription PCR Luminex assay 21256076 This one-step nucleic acid-based assay enables rapid sensitive and specific detection of the major viral causes of gastroenteritis. The quantitation yielded by the assay is informative for clinical research particularly in the context of mixed infections. Rotavirus Multiplex reverse transcription PCR 15158068 This novel multiplex RT-PCR is an attractive technique for the rapid specific and cost-effective laboratory diagnosis of non-rotavirus acute gastroenteritis. Rotavirus multiplex polymerase chain reaction assay was 21349292 The new multiplex PCR is useful as a rapid and cost effective diagnostic tool for the detection of major pathogenic viruses causing diarrhea. Norovirus Conventional reverse transcription-polymerase chain reaction (Con RT-PCR) 15911433 The assay has good precision sensitivity and specificity and is cost-effective as a routine diagnostic test. Norovirus Reverse transcriptase-polymerase chain reactions (RT-PCR) " 18680645;19109464;16606447;17063517;20305012;18680654;19109464 " The one-tube multiplex RT real-time PCR using a minor groove binder-DNA probe for GI is a fast specific sensitive and cost-effective tool for the detection of norovirus infections in both mass outbreaks and sporadic cases. Norovirus Multiplex reverse transcription PCR 15158068 This novel multiplex RT-PCR is an attractive technique for the rapid specific and cost-effective laboratory diagnosis of non-rotavirus acute gastroenteritis. Norovirus TaqMan real-time reverse transcription (RT)-PCR assays 16597869;15812014 The TaqMan methods have proven useful in assisting scientists in public health and diagnostic laboratories report findings quickly to outbreak management teams. Cryptosporidium parvum ELISA 20049303 Identification of the etiological agent of diarrhea in a patient with AIDS is very important as it can help in the institution of appropriate therapy and the reduction of morbidity and mortality in these patients. Cryptosporidium parvum Co-agglutination test 21296078 Co-A test proved to be simple and suitable tool for detecting microsporidial antigen in different specimens and did not need sophisticated equipment. It is very practical under field or rural conditions and in poorly equipped clinical laboratories. Cryptosporidium parvum MT-PCR assays 21048004 MT-PCR must be considered the diagnostic methods of choice for enteric protozoan parasites. Entamoeba histolytica enzyme-linked immunosorbent assay (ELISA) 22450915 the presence of leukocytes and erythrocytes and Entamoeba and Giardia trophozoite and cysts were examined Entamoeba histolytica conventional and real-time PCR 17630338 The incorporation these technologies into the diagnostic laboratory will lead to a better understanding of the public health problem and measures to control the disease. Entamoeba histolytica PCR and enzyme immunoassays 18367563 The E. histolytica PCR was found to be both sensitive and specific for the detection and differentiation of the E complex Giardia lamblia enzyme-linked immunosorbent assay (ELISA) 22450915 the presence of leukocytes and erythrocytes and Entamoeba and Giardia trophozoite and cysts were examined.