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Impact of Culture-Independent Diagnostic Testing on Recovery of Enteric Bacterial Infections.

ABSTRACT: Background:Culture-independent diagnostic tests (CIDTs) are increasingly used to identify enteric pathogens. However, foodborne illness surveillance systems have relied upon culture confirmation to estimate disease burden and identify outbreaks through molecular subtyping. This study examined the impacts of CIDT and estimated costs for culture verification of Shigella, Salmonella, Shiga toxin-producing Escherichia coli (STEC), and Campylobacter at the Tennessee Department of Health Public Health Laboratory (PHL). Methods:This observational study included laboratory and epidemiological surveillance data collected between years 2013-2016 from patients with the reported enteric illness. We calculated pathogen recovery at PHL based on initial diagnostic test type reported at the clinical laboratory. Adjusted prevalence ratios (PRs) and 95% confidence intervals (CIs) were estimated with modified Poisson regression. Estimates of cost were calculated for pathogen recovery from CIDT-positive specimens compared to recovery from culture-derived isolates. Results:During the study period, PHL received 5553 specimens from clinical laboratories from patients with the enteric illness. Pathogen recovery was 57% (984/1713) from referred CIDT-positive stool specimens and 95% (3662/3840) from culture-derived isolates (PR, 0.61 [95% CI, .56-.66]). Pathogen recovery from CIDT-positive specimens varied based on pathogen type: Salmonella (72%), Shigella (64%), STEC (57%), and Campylobacter (26%). Compared to stool culture-derived isolates, the cost to recover pathogens from 100 CIDT-positive specimens was higher for Shigella (US $6192), Salmonella (US $18373), and STEC (US $27783). Conclusions:Pathogen recovery was low from CIDT-positive specimens for enteric bacteria. This has important implications for the current enteric disease surveillance system, outbreak detection, and costs for public health programs.

SUBMITTER: Imdad A

PROVIDER: S-EPMC6248818 | biostudies-other | 2018 Jun

REPOSITORIES: biostudies-other

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Impact of Culture-Independent Diagnostic Testing on Recovery of Enteric Bacterial Infections.

Imdad Aamer A Retzer Fiona F Thomas Linda S LS McMillian Marcy M Garman Katie K Rebeiro Peter F PF Deppen Stephen A SA Dunn John R JR Woron Amy M AM

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20180601 12

<h4>Background</h4>Culture-independent diagnostic tests (CIDTs) are increasingly used to identify enteric pathogens. However, foodborne illness surveillance systems have relied upon culture confirmation to estimate disease burden and identify outbreaks through molecular subtyping. This study examined the impacts of CIDT and estimated costs for culture verification of Shigella, Salmonella, Shiga toxin-producing Escherichia coli (STEC), and Campylobacter at the Tennessee Department of Health Publi ...[more]

PMID: 29293941

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Project description:After stool culture was replaced by an enteric bacterial panel (EBP) at the Johns Hopkins Hospital (JHH), many EBPs were ordered >3 days after admission (EBP >3 days) with low yield. To reduce unnecessary testing, a hard stop for ordering EBP >3 days was established with the option to override the restriction. The present study retrospectively evaluates the usefulness of overriding that restriction. A retrospective chart review was performed on all patients with an EBP >3 days at the JHH from November 2021 to October 2022. The override provided only one new diagnosis of Salmonella infection in a patient who developed diarrhea within 3 days of admission but was not tested by EBP until day 5. There were no positive EBPs >3 days in patients without diarrhea or who developed diarrhea >3 days after admission (diarrhea >3 days). Most patients with requests to override the restriction were also tested for Clostridioides difficile. All patients positive for C. difficile received treatment and their C. difficile positive test resulted >1 day before the EBP was run. There were no differences in yield in patients >65 years of age with significant comorbidities or associated with neutropenia, leukocytosis, human immunodeficiency virus status, or lactoferrin positivity. There were no positive tests in patients receiving stool softeners within the previous 48 hours of testing. Overriding the hard stop should not be approved in patients without diarrhea or with diarrhea >3 days, who received stool softeners within the previous 48 hours or have not been tested for more common causes of hospital-acquired diarrhea.IMPORTANCETesting for enteric bacterial pathogens in patients hospitalized for more than 3 days is almost always inappropriate. Our study validates the utility of the 3-day rule and the use of clinical decision support tools to decrease unnecessary testing of enteropathogenic bacteria other than C. difficile. Overriding the restriction was very low yield. Our study highlights the importance of diagnostic stewardship and further refines the criteria for allowing providers to override the restriction while monitoring the impact of the interventions.

Project description:In the central plains of North America, the beetle family Silphidae comprised two subfamilies, Silphinae and Nicrophorinae, differentiated by reproductive behaviors. Silphinae, known as carrion beetles, feed on carrion and fly larvae and produce free-living larvae that receive no parental care. Adult Nicrophorinae, known as burying beetles, prepare a vertebrate carcass into a brood ball and provide biparental care to their offspring. Preparation of a brood ball involves coating the carcass in antimicrobial oral and anal secretions. These secretions contain a community of microbes, referred to as the secretion microbiome, which inhibit carcass microbe succession, preventing normal decomposition. Here, the secretion microbiomes of five species of Nicrophorinae and two species of Silphinae, both sampled from Oklahoma, with additional Nicrophorinae from Nebraska, were characterized using culture-independent analyses to understand and decipher factors shaping diversity and community structure. We identify the core secretion microbiome across Silphidae and show that, while the host subfamily, secretion type, and collection locality had no significant effect on the bacterial community alpha diversity, these factors significantly influenced bacterial community structure. Global and local tests of phylogenetic associations identified 14 genera with phylogenetic signals to the host subfamily and species. Description of the bacterial communities present in silphid secretions furthers our understanding of how these beetles interact with microbes for carcass nutrient processing. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials.IMPORTANCEThe manuscript explores the secretion bacterial community of carrion and burying beetles of the central plains of North America. A core secretion microbiome of 11 genera is identified. The host subfamily, secretion type, and collection locality significantly affects the secretion microbiome. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials.

Dataset Information

Impact of Culture-Independent Diagnostic Testing on Recovery of Enteric Bacterial Infections.

Publications

Impact of Culture-Independent Diagnostic Testing on Recovery of Enteric Bacterial Infections.

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