Stool Pathogens Research Articles

Trends and antibiotic susceptibility patterns of diarrhoeal pathogens - experience over 14 years in southern India.

Introduction. Enteric pathogens contribute significantly to morbidity in a developing country such as India. Early and prompt diagnosis of diarrhoeal diseases can reduce the mortality rate, particularly in children. The pattern of sensitivity to antimicrobials for the common pathogens can vary from time to time. The present study was conducted to study the pathogen distribution and antimicrobial susceptibility pattern during the study period (January 2010 to December 2023). Hypothesis/gap statement. Studying the changing trend in the antimicrobial sensitivity pattern of diarrhoeal pathogens over a decade can help to plan future treatment options. Aim. This study was undertaken to provide insights into the changing pattern of pathogen distribution and antimicrobial susceptibility for enteric pathogens over 14 years. Methods. A retrospective observational cohort analysis was conducted on all the stool pathogens isolated from the samples received in the microbiology department of a tertiary care hospital from 2010 to 2023. The demographic details, stool microscopy, culture reports, and antimicrobial susceptibility patterns were noted. Results. A total of 18 336 stool specimens were received in the microbiology laboratory between January 2010 and December 2023, of which 1354 specimens had diarrhoeal pathogens grown in culture. Out of these 1354 specimens, 591 (44%) had Salmonella, 471 (35%) Shigella, 181 (13%) Vibrio cholerae, and 80 (6%) Aeromonas species. Among these pathogens, susceptibility to ceftriaxone was seen in 93% (552 isolates) of Salmonella species, 89% (420 isolates) of Shigella species, and 95% (171 isolates) of Vibrio cholerae; 91% (73 isolates) of Aeromonas species were susceptible to chloramphenicol. Some major parasites were also observed on microscopy. Conclusion. Timely diagnosis of diarrhoeal pathogens can be life-saving for patients at the extremes of age, i.e. in children and the elderly. Pathogens can exhibit a changing susceptibility pattern to antibiotics, which should be regularly observed to plan future therapy.

Precautionary findings on the utilization of FilmArray® to detect human astroviruses in fecal and sewage samples

The FilmArray® Gastrointestinal (GI) Panel is a modern, sensitive, and comprehensive stool testing technique for identifying common gastrointestinal pathogens, including viruses, bacteria, and parasites. Its increasing demand is due to ease of operation and automation. Pathogens, particularly viruses, undergo constant genetic evolution. For instance, human astrovirus (HAstV), which causes gastroenteritis in children, the elderly, and immune-compromised individuals, can be identified by the GI Panel. HAstV has evolved into several clades, including the classic (HAstV1-8), novel Melbourne (MLB1-3), and Virginia (VA1-5) clades. This study investigated whether the GI Panel accurately detects all HAstV clades. A total of 12 stool and three sewage water (SW) samples were selected post-confirmation of distinct HAstV strains using conventional RT-PCR and sequence-based genotyping for reassessment by the GI Panel. The GI Panel accurately detected the classic HAstV in stool and SW samples. However, our results confirm the GI Panel's inability to detect the novel MLB (MLB1-3) and VA (VA2) clades in fecal samples, raising the possibility of false-negative results in HAstV testing. Although the GI Panel is useful for identifying a variety of gastrointestinal pathogens in stool and SW samples in a single test, our findings highlight the need to exercise caution when interpreting HAstV results from the GI Panel.

Positive pathogens in stool could predict the clinical outcomes of sepsis-associated acute kidney injury in critical ill patient

In this study, we sought to evaluate the influence of positive pathogens in stool (PPS) on clinical outcomes in critical ill patients with Sepsis-associated acute kidney injury (S-AKI) from intensive care unit. Our sample consisted of 7338 patients, of whom 752 (10.25%) had PPS. We found that the presence of Clostridium difficile (C. difficile) and protists in stool samples was correlated with survival during hospitalization, as well as 30-day and 90-day survival. Interestingly, there was no significant difference in overall survival and 30-day in-hospital survival between the PPS group and the negative pathogens in stool (NPS) control group. However, the cumulative incidence of 90-day infection-related mortality was significantly higher in the PPS group (53 vs. 48%, P = 0.022), particularly in patients with C. difficile in their stool specimens. After adjusting for propensity scores, the results also have statistical significance. These findings suggest that PPS may affect the 90-days survival outcomes of S-AKI, particularly in patients with C. difficile and protists in their stool samples. Further research is warranted to further explore these associations.

Is detection of enteropathogens and human or animal faecal markers in the environment associated with subsequent child enteric infections and growth: an individual participant data meta-analysis

Quantifying contributions of environmental faecal contamination to child diarrhoea and growth faltering can illuminate causal mechanisms behind modest health benefits in recent water, sanitation, and hygiene (WASH) trials. We aimed to assess associations between environmental detection of enteropathogens and human or animal microbial source tracking markers (MSTM) and subsequent child health outcomes. In this individual participant data meta-analysis we searched we searched PubMed, Embase, CAB Direct Global Health, Agricultural and Environmental Science Database, Web of Science, and Scopus for WASH intervention studies with a prospective design and concurrent control that measured enteropathogens or MSTM in environmental samples, or both, and subsequently measured enteric infections, diarrhoea, or height-for-age Z-scores (HAZ) in children younger than 5 years. We excluded studies that only measured faecal indicator bacteria. The initial search was done on Jan 19, 2021, and updated on March 22, 2023. One reviewer (AM) screened abstracts, and two independent reviewers (AM and RT) examined the full texts of short-listed articles. All included studies include at least one author that also contributed as an author to the present Article. Our primary outcomes were the 7-day prevalence of caregiver-reported diarrhoea and HAZ in children. For specific enteropathogens in the environment, primary outcomes also included subsequent child infection with the same pathogen ascertained by stool testing. We estimated associations using covariate-adjusted regressions and pooled estimates across studies. Data from nine published reports from five interventions studies, which included 8603 children (4302 girls and 4301 boys), were included in the meta-analysis. Environmental pathogen detection was associated with increased infection prevalence with the same pathogen and lower HAZ (ΔHAZ -0·09 [95% CI -0·17 to -0·01]) but not diarrhoea (prevalence ratio 1·22 [95% CI 0·95 to 1·58]), except during wet seasons. Detection of MSTM was not associated with diarrhoea (no pooled estimate) or HAZ (ΔHAZ -0·01 [-0·13 to 0·11] for human markers and ΔHAZ -0·02 [-0·24 to 0·21] for animal markers). Soil, children's hands, and stored drinking water were major transmission pathways. Our findings support a causal chain from pathogens in the environment to infection to growth faltering, indicating that the lack of WASH intervention effects on child growth might stem from insufficient reductions in environmental pathogen prevalence. Studies measuring enteropathogens in the environment should subsequently measure the same pathogens in stool to further examine theories of change between WASH, faecal contamination, and health. Given that environmental pathogen detection was predictive of infection, programmes targeting specific pathogens (eg, vaccinations and elimination efforts) can environmentally monitor the pathogens of interest for population-level surveillance instead of collecting individual biospecimens. The Bill & Melinda Gates Foundation and the UK Foreign and Commonwealth Development Office.

High-Throughput, Nondestructive, and Biosafe Method to Accurately Quantify Water Content in Human Fecal Samples by Benchtop 1H TD-NMR Analysis for Downstream Bioanalytical and Clinical Uses.

Water or moisture content in human stool samples is an important parameter for bioanalytical and clinical purposes. For bioanalytical use, accurate quantitation of water content in stool can provide the extent of dilution within the stool sample which can further be used for absolute quantitation of various stool based biomarkers. For clinical use, water or moisture content in stool is an important indicator of gastrointestinal health, and its accurate determination can enable quantitative assessment of the Bristol Stool Form Scale. In general, accurate determination of water content of stool samples is cumbersome, low-throughput process and is prone to harmful stool pathogens biocontamination, sample cross-contamination using techniques such as gravimetry and karl fischer titration. Here, we report a novel user-friendly high-throughput method to quantitatively and accurately measure the overall water content in human fecal samples nondestructively and biocontained in a closed tube using benchtop a 1H time domain nuclear magnetic resonance analyzer. We used gravimetry and measurement of various bile acid metabolites in stool to verify the accuracy and robustness of the water content measurement using this technique.

Fecal calprotectin level is nonlinearly associated with GI pathogen detection in patients with and without inflammatory bowel disease.

Fecal calprotectin (FCP) is used to monitor inflammatory bowel disease (IBD) activity and can also be elevated in gastrointestinal infections. Our study's objective was to quantify the relationship between FCP levels and lab-confirmed infections in people with and without IBD. We performed a cross-sectional study at a tertiary-care center of all encounters during which FCP and gastrointestinal pathogen polymerase-chain reaction (GI PCR) panel testings were conducted. Using non-parametric tests and quantile regression, we compared the FCP levels by IBD status and pathogen detection. There were 3,347 encounters with FCP and GI PCR testings from 2,780 unique individuals between 1 August 2016 and 17 February 2022. Overall, 54.4% had IBD (n = 1,819). Pathogens were detected in 744 encounters (22.2%), and the detection rate did not differ by IBD status. Median FCP without IBD was significantly elevated when a pathogen was detected (64 vs 41 mg/kg, P = 0.0003, normal ≤50.0 mg/kg), but FCP with IBD was not significantly elevated when a pathogen was detected (299 vs 255 mg/kg, P = 0.207). In quantile regression adjusted for age and IBD, pathogen detection was only significantly associated with higher FCP in the lower two quartiles, though IBD remained significantly associated with higher FCP at all levels (P > 0.001). Pathogen detection by GI PCR is associated with elevated FCP, though this relationship is nonlinear and varies by IBD status. Our findings indicate that FCP may be an adjunct to, but not a substitute for, stool pathogen testing.

Prevalence of Enteric Infections in Patients on Immune Checkpoint Inhibitors and Impact on Management and Outcomes.

Stool pathogen testing is recommended as part of the initial evaluation for patients with new-onset diarrhea on immune checkpoint inhibitors (ICIs), yet its significance has not been well-studied. We aimed to determine the impact of multiplex gastrointestinal (GI) pathogen PCR testing on the clinical course and use of immunosuppressive therapy in patients who develop diarrhea on ICIs. This retrospective cohort included individuals who underwent GI pathogen panel PCR for diarrhea on ICIs at Memorial Sloan Kettering between 7/2015 and 7/2021. The primary outcome was use of immunosuppressive therapy for suspected immunotherapy-related enterocolitis (irEC). Secondary outcomes included diarrhea severity and endoscopic and histologic disease patterns. Among 521 ICI-treated patients tested for GI pathogens, 61 (11.7%) had a positive PCR. Compared to patients without detectable infections, patients with infections had more frequent grades 3-4 diarrhea (37.7% vs. 19.6%, P < .01) and colitis (39.3% vs. 14.7%, P < .01). However, patients with infections did not have higher rates of persistent or recurrent diarrhea and were less likely to receive steroids (P < .01) and second-line immunosuppressive agents (P = .03). In 105 patients with lower endoscopy, similar trends were observed and no differences in endoscopic severity or histologic patterns were noted between groups. GI infections in ICI-treated patients presenting with diarrhea are linked to more severe but self-limited clinical presentations and may be optimally treated with observation and supportive care alone. Routine and timely stool pathogen testing may help avert unnecessary empiric immunosuppression for suspected irEC, which has been linked to blunted antitumor responses and numerous adverse effects.

Manufacturing Processes of a Purified Microbiome Therapeutic Reduce Risk of Transmission of Potential Bacterial Pathogens in Donor Stool.

Although fecal microbiota transplant has been used to prevent recurrent Clostridioides difficile infection (rCDI), documented pathogen transmission highlight inherent safety risks of minimally-processed stool. We describe manufacturing processes for fecal microbiota spores, live (VOWSTTM; VOS, formerly SER-109), a microbiota-based oral therapeutic of Firmicutes spores. Bacterial inactivation kill curves were obtained after ethanol exposure for four model organisms spiked into process intermediates. Bacterial log reduction factors ranged from 6.5 log10 to 7.4 log10 and lysis of spiked organisms occurred rapidly within 30 seconds. These experiments demonstrate substantial and rapid inactivation of representative organisms, supporting the potential benefit of VOS manufacturing processes to mitigate risk.

Flat nodular lymphoid hyperplasia resembling "apple tree branches" in the colon.

A 19-year-old woman with a history of adjustment disorder presented with abdominal pain, bloating, and chronic diarrhea. Colonoscopy revealed multiple flat whitish areas, less than 3 mm in diameter, diffusely distributed throughout the entire colon and rectum. These findings were prominent under narrow-band imaging (NBI) ([Fig. 1 a]) and more difficult to distinguish with white-light imaging ([Fig. 1 b]). The flat areas and the surrounding superficial vessels were described in the report as resembling “apple tree branches” ([Video 1]). Inspection of the terminal ileum was unremarkable, and esophagogastroduodenoscopy was unrevealing. Histologic examination of the colonic biopsy specimens showed nodules of benign lymphoid tissue with enlarged germinal centers and an intact mantle zone, consistent with a diagnosis of nodular lymphoid hyperplasia (NLH) ([Fig. 2]). Laboratory investigations and fecal calprotectin were within normal limits. Stool pathogen testing was negative. The patient was diagnosed with irritable bowel syndrome (IBS) and diffuse flat NLH.

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...

Development and validation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecular system

PCR-based enteric multiplex panels represent a rapid and reliable alternative to conventional “classical” phenotypic stool diagnostics. The aim of this study was to establish a laboratory-developed non-commercial multiplex Real-Time-PCR panel for the detection of the most important bacterial stool pathogens, Salmonella spp., Shigella spp., Yersinia enterocolitica/ pseudotuberculosis and Campylobacter jejuni/coli. on the “open” cobas omni Utility Channel (UC) of the cobas 6800 system (Roche). The aim was to replace the laborious phenotypical stool diagnostics with a high throughput Real-Time PCR method. The respective primers and probes were designed to cover conserved genomic regions of the pathogens and validated using Ultramer oligonucleotides, positive stool material and reference strains. To further validate the multiplex PCR-assay, the following parameters were evaluated: analytical-sensitivity and -specificity, cross-reactivity, linearity and inter- and intra-assay variance as well as limit of detection (LOD). In addition a retrospective analysis of culture positive and negative samples from daily routine was performed using 745 native stool samples.The Gastro assay was linear over a 5-log-unit and within the expected dynamic range with amplification efficiencies ranging from 94.6% to 120%. In addition, all targets showed excellent coefficients of repeatability (≤ 1.11%), intermediate precision (≤ 1.02%) and total variance (≤ 1.39%). In terms of analytical sensitivity the assay demonstrated detection limits ranging from 7.83 copies per reaction to 14.4 copies per reaction. The assay showed excellent agreement with culture methods (>95%) and a 100% sensitivity and specificity after resolution of discrepant results.The multiplex-PCR assay provides a comprehensive, rapid and sensitive alternative to conventional methods for the detection of the major bacterial stool pathogens in diagnostic laboratories.

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.

Diagnostic value of serum procalcitonin and C-reactive protein in discriminating between bacterial and nonbacterial colitis: a retrospective study.

Differentiating between bacterial and nonbacterial colitis remains a challenge. We aimed to evaluate the value of serum procalcitonin (PCT) and C-reactive protein (CRP) in differentiating between bacterial and nonbacterial colitis. Adult patients with three or more episodes of watery diarrhea and colitis symptoms within 14 days of a hospital visit were eligible for this study. The patients' stool pathogen polymerase chain reaction (PCR) testing results, serum PCT levels, and serum CRP levels were analyzed retrospectively. Patients were divided into bacterial and nonbacterial colitis groups according to their PCR. The laboratory data were compared between the two groups. The area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. In total, 636 patients were included; 186 in the bacterial colitis group and 450 in the nonbacterial colitis group. In the bacterial colitis group, Clostridium perfringens was the commonest pathogen (n=70), followed by Clostridium difficile toxin B (n=60). The AUC for PCT and CRP was 0.557 and 0.567, respectively, indicating poor discrimination. The sensitivity and specificity for diagnosing bacterial colitis were 54.8% and 52.6% for PCT, and 52.2% and 54.2% for CRP, respectively. Combining PCT and CRP measurements did not increase the discrimination performance (AUC, 0.522; 95% confidence interval, 0.474-0.571). Neither PCT nor CRP helped discriminate bacterial colitis from nonbacterial colitis.

Characteristics of infections and their risk factors in children with biliary atresia

BackgroundChildren with biliary atresia (BA) may experience various infections (e.g., cholangitis, bacteremia, and viral respiratory infections (VRI)) throughout their disease course. This study aimed to identify and describe these infections and their risk factors for development in children with BA. MethodsThis retrospective observational study identified infections in children with BA using predefined criteria, including VRI, bacteremia with and without central line (CL), bacterial peritonitis, positive stool pathogens, urinary tract infections, and cholangitis. Infections were identified until liver transplant, death or last follow-up with native liver. Infection-free survival was estimated by Kaplan-Meier analysis. Logistic regression was used to estimate odds of infection per clinical characteristics. Cluster analysis was performed to identify patterns of infection development. Results48 of 65 (73.8%) children had ≥1 infection during their disease course (mean length of follow up: 40.2 months). Cholangitis (n = 30) and VRI (n = 21) were most common. Nearly half (45%) of all infections developed within 3-months of Kasai hepatoportoenterostomy. Kasai performed ≥45 days of life was associated with 3.5-fold increased risk of any infection (95% CI 1.2–11.4). Risk of VRI was inversely related to platelet count at 1-month post-Kasai (OR 0.5, 0.19–0.99). Cluster analysis of infectious patterns identified three unique cohorts of patients based on their infection history: no/few infections (n = 18), mostly cholangitis (n = 20) or mixed infections (n = 27). ConclusionVariability of infection risk exists amongst children with BA. Age at Kasai and platelet count are risk factors for future infections, suggesting that patients with more severe disease are at greater risk. Cirrhosis associated immune deficiency may exist in chronic pediatric liver disease and should be the subject of future investigations in order to optimize outcomes.

Stool biomarkers as measures of enteric pathogen infection in infants from Addis Ababa informal settlements.

Frequent enteric infections in children may be an important cause of growth faltering; however, we do not fully understand the mechanisms by which pathogen infections and the physiological responses to these infections result in poorer growth. Commonly used protein fecal biomarkers (anti-alpha trypsin, neopterin, and myeloperoxidase) provide broad immunological information on an inflammatory response; however, they do not provide information on non-immune processes (e.g., gut integrity) that may be important indicators of chronic end states such as environmental enteric dysfunction (EED). To explore how additional biomarkers will better inform which physiological pathways (both immune and non-immune) are impacted by pathogen exposure we added to the traditional panel of 3 protein fecal biomarkers 4 novel fecal mRNA transcript biomarkers (sucrase isomaltase, caudal homeobox 1, S100A8, and mucin 12) and analyzed stool samples from infants living in informal settlements in Addis Ababa, Ethiopia. To test how this expanded biomarker panel captures distinct pathogen exposure processes we used two different scoring systems. First, we used a theory-based approach to assign each biomarker to specific physiological attributes based on prior understanding of each biomarker. Second, we used data reduction methods to categorize biomarkers and then assign physiological attributes to those categories. We used linear models to examine the association between the derived biomarker scores (based on mRNA and protein levels) and stool pathogen gene counts to determine pathogen specific effects on gut physiology and immune responses. Inflammation scores were positively associated with Shigella and enteropathogenic E.Coli (EPEC) infection, while gut integrity scores were negatively associated with Shigella, EPEC and, shigatoxigenic E.coli (STEC) infection. Our expanded panel of biomarkers hold promise as tools to measure systemic outcomes of enteric pathogen infection. mRNA biomarkers complement established protein biomarkers by providing important cell-specific physiological and immunological consequences of pathogen carriage that can lead to chronic end states such as EED.

Infections and nutrient deficiencies during infancy predict impaired growth at 5 years: Findings from the MAL-ED study in Pakistan.

Socio-economic, nutritional, and infectious factors have been associated with impaired infant growth, but how the presence of these factors during infancy affects growth around 5 years is not well understood. This secondary analysis of the MAL-ED cohort included 277 children from Pakistan for whom socio-demographic, breastfeeding, complementary foods, illness, nutritional biomarkers, stool pathogens and environmental enteropathy indicators between 0 and 11 months were recorded. We used linear regression models to analyze associations of these indicators with height-for-age (HAZ), weight-for-age (WAZ) and weight-for-height (WLZ) at 54-66 months (~5 years), and Poisson regression with robust standard errors to estimate risk ratios for stunting and underweight ~5 years, controlling for gender, first available weight, and income. Among the 237 infants followed longitudinally and evaluated at about 5 years of age, exclusive breastfeeding was short (median = 14 days). Complementary feeding started before 6 months with rice, bread, noodles, or sugary foods. Roots, dairy products, fruits/vegetables, and animal-source foods were provided later than recommended (9-12 months). Anemia (70.9%), deficiencies in iron (22.0%), zinc (80.0%), vitamin A (53.4%) and iodine (13.3%) were common. Most infants (>90%) presented with diarrhea and respiratory infections in their first year. At ~5 years, low WAZ (mean-1.91 ± 0.06) and LAZ (-2.11 ± 0.06) resulted in high prevalence of stunting (55.5%) and underweight (44.4%) but a relatively low rate of wasting (5.5%). While 3.4% had concurrent stunting and wasting ~5 years, 37.8% of children had coexisting stunting and underweight. A higher income and receiving formula or dairy products during infancy were associated with a higher LAZ ~5 years, but infant's history of hospitalizations and more respiratory infections were associated with lower LAZ and higher risk of stunting ~5 years. Infants' intake of commercial baby foods and higher serum-transferrin receptors were associated with higher WAZ and lower risk of underweight ~5 years. Presence of Campylobacter and fecal neopterin >6.8 nmol/L in the first year were associated with increased risk of underweight ~5 years. Growth indicators ~5 years were associated with poverty, inappropriate complementary feeding, and infections during the first year of life, which supports the early start of public health interventions for preventing growth delay ~5 years.

P894 Diagnostic yield of routine stool pathogen tests during the relapse of Inflammatory Bowel Disease

Abstract Background To make the diagnosis of Inflammatory bowel disease (IBD) flare, it is traditionally necessary to exclude infectious colitis, including bacteria and parasites. Furthermore, Infectious colitis prevalence varies between geographic areas of the world. It has been a routine clinical practice of sending broad stool testing and cultures to the laboratory before starting targeted therapy for IBD flare. The purpose of this study is to examine the yield of stool testing in adult patients with inflammatory bowel disease flare. Methods It is a retrospective study. We reviewed the medical records of the admitted patients with IBD flare at Mount Sinai Hospital, Toronto, Canada between October 2018, and August 2019. We used a computer-generated list of patients admitted with a diagnosis of IBD. We excluded patients with no confirmed diagnosis of IBD or admitted for reasons other than IBD flare. A number of variables were recorded, such as the patient's demographics, concurrent and previous IBD therapy, steroid use, presenting symptoms, vital signs, and the results of the initial laboratory investigation Results This study included 96 adult patients admitted with IBD flare. A total of ninety-four of our samples were tested for C. difficile at the time of admission. Only 9.4% were positive for C. difficile. Six of them had ulcerative colitis and three had Crohn’s disease. The percentage of patients evaluated with stool cultures was 86%, while the percentage of patients evaluated for ova and parasites was 51% at the time of patient admission. Only 34% of the population had colonic biopsies stained for Cytomegalovirus (CMV) of which 74% had ulcerative colitis. None of the stool cultures nor CMV tests were positive in our population. The risk of acquiring C difficile infection was not significantly correlated with the patient's disease phenotype, the biological therapy they were receiving, or their smoking history. In our sample, clinical tests and routine laboratory tests did not predict infectious colitis. The CRP level, as well as the neutrophil and eosinophil counts, were not associated with positive C. difficile infection. Conclusion In IBD flare, we did not routinely identify pathogens besides C difficile. Aside from areas where bacterial or parasitic infections are prevalent, routine stool testing with cultures and parasites has a low yield.

Evaluation of Diagnostic Performance of Bd Max Ebp Assay in Patients with Diarrheal Illness

Objective: Detection of the etiological agents in patients with acute diarrhea is challenging due to a wide variety of pathogens. The aim of this study is to evaluate the diagnostic performance of BD Max Enteric Bacterial Pathogens (EBP) PCR assay in patients with diarrheal illness. Methods: Between 1 January 2014 and 31 May 2015, stool samples from pediatric or adult patients with diarrhea submitted for routine analysis of bacterial stool pathogens were included in the study. We compared the BD Max EBP PCR assay to culture for the detection of Salmonella spp., Shigella spp., Campylobacter jejuni, and Campylobacter coli and an EIA for Shiga toxins 1 and 2. Discordant results were adjudicated by either antigen detection methods or Film array GI Panel. Results: When coinfections were excluded, the positive percent agreement values for the BD Max EBP assay (PPA) was 100% and negative percent agreement (NPA) was between 98.0%-99.7%, when compared with culture and EIA. After discrepant analysis, the PPA values for the BD Max EBP assay was 100% and NPA was between 99.5%-100%. Conclusion: The BD Max EBP assay showed a high correlation rate with conventional and molecular methods for the detection of stool pathogens.

1996. Association between Multiplex Polymerase Chain Reaction Stool Diagnostic Testing and Pathogen Detection, Healthcare Resource Use, and Cost Among Adult Outpatients Treated in United States Hospitals for Acute Infectious Gastroenteritis

Abstract Background Multiplex polymerase chain reaction (PCR) gastroenteritis testing panels simultaneously detect multiple pathogens with rapid turnaround, allowing more accurate and timely diagnosis and treatment. This retrospective observational study assessed the association between stool test type (i.e., multiplex PCR panel with &amp;lt; 12 target pathogens [PCR&amp;lt; 12], multiplex PCR panel with ≥ 12 target pathogens [PCR12], traditional work-up [TW]) and healthcare resource use (HRU), cost, and diagnostic yield in adult outpatients treated in U.S. hospitals for acute infectious gastroenteritis (AIG). Methods Using large geographically diverse PINC AI Healthcare Database data from January 1, 2016–June 30, 2021, we analyzed adults (≥ 18-years) with an AIG diagnosis and stool test performed during an outpatient visit. Pathogen analysis was performed in those with microbiology data available. Results Among 36,787 patients, TW was most often performed (57.0%), followed by PCR12 (30.2%) and PCR&amp;lt; 12 (12.8%). Patients with PCR12 were more likely younger, Hispanic/Latino, and uninsured, and less likely socially vulnerable compared to TW (all p&amp;lt; 0.01, Table 1). PCR12 was more common in patients from large (500+ beds), teaching, urban hospitals in the Midwest, compared to patients with TW (all p&amp;lt; 0.01, Table 2). Patients with PCR12 were more likely to have a history of transplantation or HIV/AIDS (both p&amp;lt; 0.01). PCR12 was associated with a higher mean index visit cost (by $101) but lower mean 30-day follow-up cost (by $130) than TW (Table 3). Patients with PCR12 had lower 30-day AIG-related admission risk than TW (1.7% vs. 2.7% p&amp;lt; 0.01). Among 8,451 patients with microbiology data, PCR12 was associated with fewer stool tests per patient (mean:1.61 vs. 1.26), faster turnaround time (mean: 6.3 vs. 25.7 hours) and less likelihood of receiving in-hospital antibiotics (39.4% vs. 47.1%, all p&amp;lt; 0.01) than TW. A higher percentage of patients with PCR12 had a target pathogen detected (73.1%) compared to PCR&amp;lt; 12 (63.6%) or TW (45.4%, p&amp;lt; 0.01). Table 1.Patient characteristics of hospital-based infectious gastroenteritis outpatients during January 1, 2016 - June 30, 2021, stratified by type of stool testTable 2.Clinical and hospital characteristics of hospital-based infectious gastroenteritis outpatients during January 1, 2016 - June 30, 2021, stratified by type of stool testTable 3.Outcomes of hospital-based infectious gastroenteritis outpatients during January 1, 2016 - June 30, 2021, stratified by the type of stool test Conclusion PCR12 multiplex panels were associated with lower 30-day follow-up cost and risk of IG-related hospitalization. PCR12 was also associated with less secondary testing, reduced in-hospital antibiotic use, faster turnaround, and increased diagnostic yield compared to TW. Disclosures Rena Moon, MD, MPH, Premier Inc: Employee Tammy C. Bleak, PharmD, MSc, bioMerieux: Employee of bioMerieux Ning Rosenthal, MD, PhD, MPH, Premier Inc: Employee|Premier Inc: Stocks/Bonds Brianne Couturier, PhD, bioMerieux: Employee of bioMerieux Rachael Hemmert, MSPH, bioMerieux: Employee of bioMerieux Tristan T. Timbrook, PharmD, bioMerieux: Employee of bioMerieux Harold Brown, MBA, MHA, Premier Inc: Employee Ferric C. Fang, MD, bioMerieux: Advisor/Consultant.

Respiratory and diarrhoeal pathogens in Malawian children hospitalised with diarrhoea and association with short-term growth: A prospective cohort study

Background: Pneumonia and diarrhoea are the leading causes of childhood mortality and morbidity worldwide. The gut-lung axis is associated with disease, and these common infections, especially the parasite Cryptosporidium, are associated with malnutrition. We sought to evaluate the association of respiratory and gastrointestinal (GI) pathogens with short-term growth among children hospitalised with diarrhoeal disease. Methods: In this sub-study, we followed 27 children (two-24 months) who tested positive for Cryptosporidium spp. for eight weeks with two weekly sampling of the respiratory and GI tract. Respiratory and stool pathogens were detected using quantitative molecular methods. Nutritional outcomes were assessed as length-for-age (LAZ), weight-for-length (WLZ) and weight-for-age (WAZ) z-scores. Changes over the study period were compared using repeated analysis of variance and mixed effects model analysis. Results: In this period,104 sputum and stool samples were collected. All stool samples had at least one pathogen detected, with an average of 5.1 (SD 2.1) stool pathogens, compared to 84% of the sputum samples with an average 3.5 (SD 1.8). Diarrhoeagenic E. coli were the most common stool pathogens (89%), followed by Cryptosporidium (57.6%) and Adenovirus pan (41%). In sputum, Streptococcus pneumoniae was the most prevalent pathogen (84%), followed by hinovirus (56%) and Moraxella catarrhalis (50%). There was a significant change in WAZ over the follow-up period. Children who had ≥3 GI pathogens had significantly a lower LAZ mean score at enrolment (-1.8 [SD 1.4]) and across the follow-up period. No relationship between respiratory pathogens and short-term growth was observed. Out of 49 sputum samples that had ≥3 pathogens, 42 (85%) concurrent stool samples had ≥3 GI pathogens. Conclusions: Among young children hospitalised with diarrhoea, multiple GI and respiratory pathogens were prevalent over an eight-week follow-up period. The presence of more GI, but not respiratory, pathogens was significantly associated with reduced short-term growth.