Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool.

Christy-Lynn Peterson,David Alexander,Eduardo Taboada,Jessica Forbes,Aleisha R Reimer,Julie Chih-Yu Chen,Morag Graham,Natalie Knox,Matthew Walker,Dillon O R Barker,Jennifer Ali,Heather Adam

doi:10.3390/microorganisms10020441

Abstract

Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.

Highlights

IntroductionWhat would be an ideal, modern approach for gastroenteritis diagnosis?
While in this bacterial enteric pathogens, there is potential to further leverage metagenome sequence study we focused on detecting bacterial enteric pathogens, there is potential to further results for detection of other DNA-based organisms and in silico antimicrobial resistance leverage metagenome sequence results for detection of other DNA-based organisms and (AMR) prediction, which would result in further cost efficiencies
Considering that the vast proportion of sequence acquired from a clinical specimen is not derived from the pathogen of interest, there is still a considerable cost to metagenomics sequencing

Summary

Introduction

What would be an ideal, modern approach for gastroenteritis diagnosis? For acute care clinical laboratories, the ideal approach must be rapid, cost-effective, and accurately detect infections (and co-infections) due to common, rare, and emerging enteric pathogens. Testing must provide actionable antimicrobial susceptibility information, as well as subtyping data to support identification, surveillance, and investigation of outbreaks caused by contaminated food or water. Traditional, culture-based methods are cost-effective, but testing algorithms can be complicated, and turnaround times are typically more than 24 h.

Methods

Results

Conclusion