Detection Of Enteric Pathogens Research Articles

Multiplex PCR detection of enteric pathogens in a community-based birth cohort in Ecuador: comparison of xTAG-GPP and TaqMan array card assays.

We compared the performance of two multiplex platforms, Luminex xTAG Gastrointestinal Pathogen PanelⓇ and TaqMan Array Card, against a panel of 14 enteric pathogen targets in a community-based birth cohort in Ecuador. We found high levels of agreement and similar prevalence estimates across most pathogens.

Enteric Pathogen Detection Using Multiplex PCR Assay in Kidney Transplant Recipients with Diarrhea-Retrospective Before-After Study.

Diarrhea is a frequent complication after kidney transplantation, however the etiology is often not identified. Multiplex PCR assays may increase the detection of diarrheal pathogens among kidney transplant recipients (KTRs), leading to improved management. This was a retrospective before-after study, conducted in a high-volume transplant center. In September 2017, multiplex PCR assay was introduced. We reviewed all hospitalized KTRs with diarrhea during 1/2015-8/2017 (pre-GI PCR, n = 111) and 9/2017-12/2021 (GI PCR, n = 159) and followed them for 3years. We performed univariate and multivariate analysis for predictors of pathogen identification, introducing the study period as an independent variable. Among 270 hospitalized KTRs with diarrhea, 64 (24%) had an identified diarrheal pathogen. The proportion of KTRs with an identified pathogen increased from 20% (13/64) in the pre-GI PCR to 80% (51/64) post GI PCR (p < 0.01). Of 51 KTRs with an identified pathogen in the post GI PCR, 44 (86%) were diagnosed using GI PCR. GI PCR was more likely used in younger KTRs with more recent transplantation and higher creatinine level at admission. The most common non-C. difficile diarrheal pathogens in the post-GI PCR cohort were enteropathogenic Escherichia coli (n = 23, 58%), norovirus (n = 11, 28%), and Campylobacter (n = 11, 28%). Implementing GI PCR significantly increased the detection and identification of GI pathogens (odds ratio [OR] = 21, CI 95% 10-44; p < 0.001). Infectious etiologies of diarrhea were identified in a higher proportion of KTRs after the implementation of GI PCR. This emphasizes the importance of integrating this diagnostic tool into diarrhea workup in KTRs.

Detection of enteric pathogens in foal faecal samples submitted to a UK laboratory between 2019 and 2023

Detection of enteric pathogens in foal faecal samples submitted to a <scp>UK</scp> laboratory between 2019 and 2023

NLRP1B allele 2 does not respond to Val-boro-Pro (VbP) in intestinal epithelial cells

The intestinal mucosa must balance tolerance to commensal microbes and luminal antigens with rapid detection of enteric pathogens in order to maintain homeostasis. This balance is facilitated through the regulation of epithelial layer integrity by innate immune receptors. Certain NOD-like receptors (NLRs) expressed in intestinal epithelial cells, including NLRC4 and NLRP9B, form inflammasomes that protect against pathogens by activating caspase-1 to cause extrusion of infected cells. NLRP1B is a murine NLR encoded by five alleles of a highly polymorphic gene homologous to human NLRP1. NLRP1B forms inflammasomes in response to a variety of pathogens that cause intestinal infections, but it has almost exclusively been studied in immune cells and has not been characterized in cells of the intestinal epithelium. Here, we show that Nlrp1b allele 2 is expressed in ileal and colonic organoids derived for C57BL/6J mice, while the related gene Nlrp1a was not expressed. Nlrp1b was upregulated by interleukin-13 in organoids and by the protozoan Tritrichomonas muris in vivo, suggesting that NLRP1B may be involved in defense against enteric parasites. Surprisingly, while Val-boro-Pro (VbP) activated C57BL/6J-derived bone marrow-derived macrophages, which expressed both Nlrp1a and Nlrp1b, it did not activate intestinal organoids of the same genotype. We furthermore did not detect Nlrp1b in organoids derived from Balb/cJ mice, which express a different allele than the one expressed in C57BL/6J mice. Together, our results suggest that NLRP1B may have an allele-dependent function in murine IECs whose regulation is distinct from that of macrophages, and that the response to VbP might be exclusively driven by NLRP1A in C57BL/6J mice.

Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance

Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance

An integrated FoodNet in North East India: fostering one health approach to fortify public health

BackgroundFood safety is a critical factor in promoting public health and nutrition, especially in developing countries like India, which experience several foodborne disease outbreaks, often with multidrug-resistant pathogens. Therefore, implementing regular surveillance of enteric pathogens in the human-animal-environment interface is necessary to reduce the disease burden in the country.ObjectiveTo establish a network of laboratories for the identification of major food and waterborne pathogens prevailing in the northeast region of India through integrated surveillance of animal, food, human, and environment and investigate the antimicrobial susceptibility pattern of the pathogens of public health significance.MethodsThe Indian Council of Medical Research (ICMR) has identified FoodNet laboratories; based on their geographical location, inclination to undertake the study, preparedness, proficiency, and adherence to quality assurance procedures, through an 8-step process to systematically expand to cover the Northeastern Region (NER) with comprehensive diagnostic capacities for foodborne pathogens and diarrhea outbreak investigations. Network initiated in the NER given the unique food habits of the ethnic population.FindingsThis surveillance network for foodborne enteric pathogens was established in Assam, Arunachal Pradesh, Tripura, and Sikkim, and expanded to other four states, i.e., Manipur, Mizoram, Meghalaya, and Nagaland, thereby covering the entire NER by including nine medical and three veterinary centers. All these centers are strengthened with periodic training, technical support, funding, capacity building, quality assurance, monitoring, centralized digital data management, and website development.ResultsThe ICMR-FoodNet will generate NER-specific data with close to real-time reporting of foodborne disease and outbreaks, and facilitate the updating of food safety management protocols, policy reforms, and public health outbreak response. During 2020-2023, 13,981 food samples were tested and the detection of enteric pathogens ranged from 3 to 4%. In clinical samples, the detection rate of the pathogens was high in the diarrheal stools (8.9%) when 3,107 samples were tested. Thirteen outbreaks were investigated during the study period.ConclusionFoodborne diseases and outbreaks are a neglected subject. Given the frequent outbreaks leading to the deaths of children, it is crucial to generate robust data through well-established surveillance networks so that a strong food safety policy can be developed for better public health.

Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance

BackgroundSyndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers.MethodsA multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens.ResultsOverall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons.ConclusionsThe adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.

Enteric Aeromonas Infection: a Common Enteric Bacterial Infection with a Novel Infection Pattern Detected in an Australian Population with Gastroenteritis.

Aeromonas species are emerging human enteric pathogens. However, they are currently not routinely detected in many diagnostic laboratories, and information regarding Aeromonas enteric infections detected using molecular methods is lacking. Here, we investigated the detection of Aeromonas species and four other enteric bacterial pathogens in 341,330 fecal samples from patients with gastroenteritis processed in a large Australian diagnostic laboratory between 2015 and 2019. These enteric pathogens were detected using quantitative real-time PCR (qPCR) methods. Furthermore, we compared the qPCR cycle threshold (CT) values obtained from fecal samples that tested positive for Aeromonas only by molecular detection with those of samples that tested positive by both molecular detection and bacterial isolation methods. Aeromonas species were found to be the second most common bacterial enteric pathogens among patients with gastroenteritis. We observed a unique pattern of three infection peaks for Aeromonas, which correlated with the age of the patients. Aeromonas species were the most common enteric bacterial pathogens in children younger than 18 months. Fecal samples that tested positive for Aeromonas only by molecular detection had significantly higher CT values than fecal samples that tested positive by both molecular detection and bacterial culture. In conclusion, our findings reveal that Aeromonas enteric pathogens exhibit an age-related three-peak infection pattern, distinguishing them from other enteric bacterial pathogens. Moreover, the high rate of Aeromonas enteric infection discovered in this study suggests that Aeromonas species should be routinely tested in diagnostic laboratories. Our data also show that combining qPCR with bacterial culture can enhance the detection of enteric pathogens. IMPORTANCE Aeromonas species are emerging human enteric pathogens. However, these species are currently not routinely detected in many diagnostic laboratories, and no studies have reported the detection of Aeromonas enteric infection using molecular methods. We investigated the presence of Aeromonas species and four other enteric bacterial pathogens in 341,330 fecal samples from patients with gastroenteritis using quantitative real-time PCR (qPCR) methods. Interestingly, we discovered that Aeromonas species were the second most common bacterial enteric pathogens in patients with gastroenteritis, exhibiting a novel infection pattern compared to those of other enteric pathogens. Furthermore, we found that Aeromonas species were the most prevalent enteric bacterial pathogens in children aged 6 to 18 months. Our data also revealed that qPCR methods exhibit higher sensitivity in detecting enteric pathogens compared to that of bacterial culture alone. Moreover, combining qPCR with bacterial culture enhances the detection of enteric pathogens. These findings emphasize the importance of Aeromonas species in public health.

Long-term impacts of an urban sanitation intervention on enteric pathogens in children in Maputo city, Mozambique: study protocol for a cross-sectional follow-up to the Maputo Sanitation (MapSan) trial 5 years postintervention

IntroductionWe previously assessed the effect of an onsite sanitation intervention in informal neighbourhoods of urban Maputo, Mozambique on enteric pathogen detection in children after 2 years of follow-up (Maputo Sanitation...

Giardia Detection and Codetection With Other Enteric Pathogens in Young Children in the Vaccine Impact on Diarrhea in Africa (VIDA) Case-Control Study: 2015–2018

Giardia has been associated with reduced risk of diarrhea in children in low-resource settings, but the mechanism underlying this association is unknown. To assess whether Giardia may shape colonization or infection with other enteric pathogens and impact associations with diarrhea, we examined Giardia and enteric pathogen codetection among children <5 years old in Kenya, The Gambia, and Mali as part of the Vaccine Impact on Diarrhea in Africa study. We tested for Giardia and other enteric pathogens using enzyme-linked immunosorbent assays and real-time polymerase chain reaction (PCR) on stool, respectively. We evaluated associations between Giardia and enteric pathogen detection using multivariable logistic regression models separately for children with moderate-to-severe diarrhea (MSD, cases) and free of diarrhea (controls). Among 11 039 enrolled children, Giardia detection was more common among controls (35%) than cases (28%, P < .001). Campylobacter coli/jejuni detection was associated with Giardia in controls in The Gambia (adjusted odds ratio [aOR] [95% confidence interval {CI}]: 1.51 [1.22‒1.86]) and cases across all sites (1.16 [1.00‒1.33]). Among controls, the odds of astrovirus (1.43 [1.05‒1.93]) and Cryptosporidium spp. (1.24 [1.06‒1.46]) detection were higher among children with Giardia. Among cases, the odds of rotavirus detection were lower in children with Giardia in Mali (.45 [.30‒.66]) and Kenya (.31 [.17‒.56]). Giardia was prevalent in children <5 years old and was associated with detection of other enteric pathogens, with differing associations in cases versus controls and by site. Giardia may affect colonization or infection by certain enteric pathogens associated with MSD, suggesting an indirect mechanism of clinical impact.

Exploring Survey-Based Water, Sanitation, and Animal Associations With Enteric Pathogen Carriage: Comparing Results in a Cohort of Cases With Moderate-to-Severe Diarrhea to Those in Controls in the Vaccine Impact on Diarrhea in Africa (VIDA) Study, 2015–2018

The magnitude of pediatric enteric pathogen exposures in low-income settings necessitates substantive water and sanitation interventions, including animal feces management. We assessed associations between pediatric enteric pathogen detection and survey-based water, sanitation, and animal characteristics within the Vaccine Impact on Diarrhea in Africa case-control study. In The Gambia, Kenya, and Mali, we assessed enteric pathogens in stool of children aged <5 years with moderate-to-severe diarrhea and their matched controls (diarrhea-free in prior 7 days) via the TaqMan Array Card and surveyed caregivers about household drinking water and sanitation conditions and animals living in the compound. Risk ratios (RRs) and 95% confidence intervals (CIs) were calculated using modified Poisson regression models, stratified for cases and controls and adjusted for age, sex, site, and demographics. Bacterial (cases, 93%; controls, 72%), viral (63%, 56%), and protozoal (50%, 38%) pathogens were commonly detected (cycle threshold <35) in the 4840 cases and 6213 controls. In cases, unimproved sanitation (RR, 1.56; 95% CI, 1.12-2.17), as well as cows (RR, 1.61; 95% CI, 1.16-2.24) and sheep (RR, 1.48; 95% CI, 1.11-1.96) living in the compound, were associated with Shiga toxin-producing Escherichia coli. In controls, fowl (RR, 1.30; 95% CI, 1.15-1.47) were associated with Campylobacter spp. In controls, surface water sources were associated with Cryptosporidium spp., Shigella spp., heat-stable toxin-producing enterotoxigenic E. coli, and Giardia spp. Findings underscore the importance of enteric pathogen exposure risks from animals alongside more broadly recognized water and sanitation risk factors in children.

Environmental and behavioural exposure pathways associated with diarrhoea and enteric pathogen detection in 5-month-old, periurban Kenyan infants: a cross-sectional study

ObjectivesThe aim of this study was to test whether household environmental hygiene and behavioural conditions moderated associations between diarrhoea and enteric pathogen detection in infants 5 months of age in...

Network-wide analysis of the Serosep EntericBio Gastro Panel 2 for the detection of enteric pathogens in Public Health Wales microbiology laboratories.

Introduction. A retrospective data analysis of 34 months (spanning 2016-2020) of 961573 diagnostic results obtained before and after nucleic acid amplification testing (NAAT) implementation, across the Public Health Wales microbiology network.Hypothesis / Gap Statement. This is the first network-wide analysis of the implementation of enteric NAAT in diagnostic microbiology.Aim. To assess the outcome of replacing microscopy and bacterial culture with NAAT as the primary test in the diagnosis of: Campylobacter spp., Salmonella sp., Shigella spp., Shiga toxin-producing Escherichia coli (STEC), Cryptosporidium spp. and Giardia duodenalis infections.Methodology. Following NAAT introduction, bacterial culture was performed as a secondary test, to provide further information from NAAT positive samples for epidemiological purposes. Primary detection rates and overall bacterial culture rates were calculated for each target pathogen using both testing regimes (Stage I) including a comparison of in-patient and out-patient diagnoses (Stage II).Results. Stage I analysis showed that the primary detection rate significantly increased for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0151), Shigella spp. (P<0.0001), STEC (P<0.0001), Cryptosporidium spp. (P<0.0001) and Giardia duodenalis (P<0.0001) when using NAAT compared to microscopy or bacterial culture. A significant decrease was seen in the overall rate of Campylobacter spp. isolation by bacterial culture (P<0.0001), whilst other targets remained unaffected. Stage II analysis showed that NAAT positive out-patient samples were more likely to be supplemented by a positive bacterial culture than NAAT positive in-patient samples for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0004) and STEC (P=0.0039). However, Shigella spp. was more frequently isolated from NAAT positive in-patient samples (P=0.0005). A notable increase was seen for G. duodenalis detection from in-patient samples (P=0.0002). Reference laboratory data showed the NAAT assay can detect at least 53 serotypes of STEC but may not be able to detect some of the rarer species of Cryptosporidium seen in human infections.Conclusion. The implementation of NAAT has significantly increased the primary detection rate of all target enteric pathogens in Wales and information gleaned previously from direct culture is largely unaffected.

Only Low Effects of Water Filters on the Enteric Carriage of Gastrointestinal Pathogen DNA in Colombian Indigenous People.

Water filtration is a common strategy of water sanitation in resource-poor tropical settings. Here, we assessed the intermediate term effect of this preventive procedure including specific filter-related as well as general hygiene training on the molecular detection of enteric pathogens in stool samples from Colombian Indigenous people. From a total of 89 individuals from an Indigenous tribe called Wiwa, stool samples were assessed by real-time PCR for enteropathogenic microorganisms prior to the implementation of water filtration-based infection prevention. Three years after the onset of the preventive strategy, a follow-up assessment was performed. A significantly beneficial effect of water filtration could be shown for Ascaris spp. only (p = 0.035) and a tendency (p = 0.059) for Hymenolepis nana. No hints for effects on the gastrointestinal shedding of Giardia duodenalis, Entamoeba histolytica, Cryptosporidium spp., Campylobacter spp., Shigella spp./enteroinvasive Escherichia coli, Necator americanus, Strongyloides stercoralis, Trichuris trichiura, and Taenia spp. were seen. In conclusion, the study indicates that water filtration can only be an element of a multi-modal hygiene concept to reduce enteric pathogen carriage in inhabitants of resource-poor tropical settings in spite of tendencies of beneficial effects.

Characterization of Enteric Disease in Children by Use of a Low-Cost Specimen Preservation Method.

ABSTRACTDiarrhea is a leading cause of death in children under five. Molecular methods exist for the rapid detection of enteric pathogens; however, the logistical costs of storing stool specimens limit applicability. We sought to demonstrate that dried specimens preserved using filter paper can be used to identify diarrheal diseases causing significant morbidity among children in resource-constrained countries. A substudy was nested into cholera surveillance in Cameroon. Enrollment criteria included enrollment between 1 August 2016 and 1 October 2018, age of <18 years, availability of a stool specimen, and having three or more loose stools within 24 h with the presence of dehydration and/or blood. A total of 7,227 persons were enrolled, of whom 2,746 met enrollment criteria and 337 were included in this analysis using the enteric TaqMan array card. Bacterial pathogens were compared to severity of diarrhea, age, and sex, among other variables. One hundred seven were positive for enterotoxigenic Escherichia coli, of which 40.2% (n = 43) had heat-labile enterotoxin (LT) and the heat-stable enterotoxin STh, 19.6% (n = 21) had LT and the heat-stable enterotoxin STp, and 49.5% (n = 53) had LT only. Major colonization factors (CFs) were present in 43.9% of enterotoxigenic E. coli (ETEC)-positive patients. Ninety-six were positive for Shigella, of whom 14 (14.6%) reported dysentery. Model-derived quantitative cutoffs identified 116 (34.4%) with one highly diarrhea-associated pathogen and 16 (4.7%) with two or more. Shigella and rotavirus were most strongly associated with diarrhea in children with mixed infections. Dried-filter-paper-preserved specimens eliminate the need for frozen stool specimens and will facilitate enteric surveillance and contribute to the understanding of disease burden, which is needed to guide vaccine development and introduction. This study confirms rotavirus, Shigella, and ETEC as major contributors to pediatric diarrheal disease in two regions of Cameroon.

Improved diagnosis of gastrointestinal infections using a semi-automated multiplex real-time PCR for detection of enteropathogens.

Introduction. The identification of enteropathogens is critical for the clinical management of patients with suspected gastrointestinal infection. The FLOW multiplex PCR system (FMPS) is a semi-automated platform (FLOW System, Roche) for multiplex real-time PCR analysis.Hypothesis/Gap Statement. FMPS has greater sensitivity for the detection of enteric pathogens than standard methods such as culture, biochemical identification, immunochromatography or microscopic examination.Aim.The diagnostic performance of the FMPS was evaluated and compared to that of traditional microbiological procedures.Methodology. A total of 10 659 samples were collected and analysed over a period of 7 years. From 2013 to 2018 (every July to September), samples were processed using standard microbiological culture methods. In 2019, the FMPS was implemented using real-time PCR to detect the following enteropathogens: Shigella spp., Salmonella spp., Campylobacter spp., Giardia intestinalis, Entamoeba histolytica, Blastocystis hominis, Cryptosporidum spp., Dientamoeba fragilis, adenovirus, norovirus and rotavirus. Standard microbiological culture methods (2013-2018) included stool culture, microscopy and immunochromatography.Results. A total of 1078 stool samples were analysed prospectively using the FMPS from July to September (2019): bacterial, parasitic and viral pathogens were identified in 15.3, 9.71 and 5.29 % of cases, respectively. During the same period of 6 years (2013-2018), the proportion of positive identifications using standard microbiological methods from 2013 to 2018 was significantly lower. A major significant recovery improvement was observed for all bacteria species tested: Shigella spp./enteroinvasive Escherichia coli (EIEC) (P <0.05), Salmonella spp. (P <0.05) and Campylobacter spp. (P <0.05). Marked differences were also observed for the parasites G. intestinalis, Cryptosporidium spp. and D. fragilis.Conclusion. These results support the value of multiplex real-time PCR analysis for the detection of enteric pathogens in laboratory diagnosis with outstanding performance in identifying labile micro-organisms. The identification of unsuspected micro-organisms for less specific clinical presentations may also impact on clinical practice and help optimize patient management.

Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils.

Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n = 49) and control (n = 51) compounds during baseline (preintervention) and after 24 months (postintervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 18 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated gene target in 91% (163/179) of soils and a median of 3 (IQR = 1, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of detecting ≥1 pathogen gene by 15% (adjusted prevalence ratio, aPR = 0.85; 95% CI: 0.70, 1.0) and the total number of pathogens by 35% (aPR = 0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24 months following the introduction of new latrines.

Associations between enteric pathogen carriage and height-for-age, weight-for-age and weight-for-height in children under 5 years old in urban Dhaka, Bangladesh.

Nutritional factors and infectious agents may contribute to paediatric growth deficits in low- and middle-income countries; however, the contribution of enteric pathogens is only beginning to be understood. We analysed the stool from children <5 years old from an open cohort, cluster-randomised controlled trial of a point-of-collection water chlorinator in urban Bangladesh. We compared the presence/absence of 15 enteric pathogens detected via multiplex, molecular methods in the stool with concurrent Z-scores/Z-score cut-offs (-2 standard deviations (s.d.)) for height-for-age (HAZ/stunting), weight-for-age (WAZ/underweight) and weight-for-height (WHZ/wasting), adjusted for sociodemographic and trial-related factors, and measured caregiver-reported diarrhoea. Enteric pathogen prevalence in the stool was high (88% had ≥1 enteric pathogen, most commonly Giardia spp. (40%), Salmonella enterica (33%), enterotoxigenic E. coli (28%) and Shigella spp. (27%)) while reported 7-day diarrhoea prevalence was 6%, suggesting high subclinical infection rates. Many children were stunted (26%) or underweight (24%). Adjusted models suggested Giardia spp. detection was associated with lower HAZ (-0.22 s.d., 95% CI -0.44 to 0.00; prevalence ratio for stunting: 1.39, 95% CI 0.94-2.06) and potentially lower WAZ. No pathogens were associated with reported diarrhoea in adjusted models. Giardia spp. carriage may be associated with growth faltering, but not diarrhoea, in this and similar low-income settings. Stool-based enteric pathogen detection provides a direct indication of previous exposure that may be useful as a broader endpoint of trials of environmental interventions.

Stool-Based Pathogen Detection Offers Advantages as an Outcome Measure for Water, Sanitation, and Hygiene Trials.

.Most health impact trials of water, sanitation, and hygiene use caregiver-reported diarrhea in children as the primary outcome; this measure is known to be subject to considerable bias, especially when used in unblinded trials. Detection of enteric pathogens in stool or fecal waste via multiplex molecular methods may offer advantages over—and is complementary to—caregiver-reported diarrhea because these measures are objective, on the causal pathway from exposures of interest to disease outcomes, and increasingly feasible in high-burden countries.

Evaluation of the Vibrant DNA microarray for the high-throughput multiplex detection of enteric pathogens in clinical samples

ABSTRACTBackgroundRapid detection of a wide range of etiologic agents is essential for appropriate treatment and control of gastrointestinal (GI) infections. A variety of microbial species including bacteria, viruses, parasites, and fungi have been recognized as diarrheagenic enteric pathogens. However, multiplex testing of various targets in a single reaction needs further improvement because of its limitation in species and throughput.ResultsThis study aims at developing and evaluating a DNA microarray-based qualitative multiplexed polymerase chain reaction (PCR) assay, Vibrant GI pathogen panel (GPP), for simultaneous detection of 27 enteric GI pathogenic targets (16 bacteria, 5 viruses, 4 parasites, and 2 fungi) directly from stool specimens. Limits of detection ranged from 102 to 104 cells/mL for bacteria, 102 to 103 cells/mL for parasites, 102 to 103 RNA copies/mL for viruses, and 102 to 103 cells/mL for fungi. Performance characteristics were determined using 27 Quantitative Genomic DNAs, 212 spiked stool specimens, 1067 clinical and archived stool specimens. Overall sensitivity was 95.9% (95% CI 92.4–98.1) and specificity was 100% (95% CI 99.9–100). Polymicrobial detections contained either two or three organisms was 20.2% (35/173) of positive clinical specimens and 3.3% (35/1055) of all clinical specimens.ConclusionThe Vibrant GPP is a comprehensive, high-throughput, and rapid DNA microarray to provide etiologic diagnosis of GI infections in the laboratory setting.