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Abstract Background Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms. Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. This study aims to determine the ability to routinely apply mNGS testing, in comparison to traditional culture or polymerase chain reaction (PCR) based tests, for the identification of causal pathogens for gastrointestinal infections. Results The performance of mNGS, PCR and microscopy, culture and sensitivity (MCS) assays was established using 2,619 prospectively collected faecal samples from patients with symptomology indicative of infectious gastroenteritiss. Commonly experienced pathogens including Aeromonas spp, Campylobacter spp, Salmonella spp and Giardia spp, in single and co-infected patients, were used to establish test outcomes. When testing for these organisms, using the combined result from either or both PCR and MCS testing as the comparator, the mNGS assay had clinically acceptable sensitivity (89.2–100%). Further, the mNGS assay detected 14 additional enteropathogens, that were either not detected or not tested, by initial PCR/MCS testing. Conclusions The advantage of mNGS compared to other syndromic testing systems is the broad range of detectable targets and the ability to interrogate samples without clinician informed or assay specific bias. With the development of newer sequencing assays, it is now feasible to test for a wide range of target organisms in a sample using a single mNGS test. Overall, the mNGS based approach enabled pathogen detection that was comparable to conventional diagnostics and was shown to have the potential to be extended for the detection of many pathogens and genes of clinical interest. In conclusion, the mNGS assay offers an easy, sample to answer workflow with rapid detection of enteropathogens and has the potential to improve diagnosis, therapy and infection control precautions.

Abstract Background Healthcare-associated infections pose a potentially fatal threat to patients worldwide and Staphylococcus aureus is one of the most common causes of healthcare-associated infections. S. aureus is a common commensal pathogen and a frequent cause of bacteremia, with studies demonstrating that nasal and blood isolates from single patients match more than 80% of the time. Here we report on a contemporary collection of colonizing isolates from those with methicillin-resistant S. aureus (MRSA) bloodstream infections to evaluate the diversity within hosts, and detail the clinical features associated with concomitant nasal colonization. Methods Swabs of the bilateral anterior nares were obtained from patients diagnosed with MRSA bacteremia. A single colony culture from the blood and an average of 6 colonies from the nares were evaluated for MRSA growth. For the nares cultures, we typed multiple isolates for staphylococcal protein A (spa) and derived the clonal complexes. Demographic and clinical data were obtained retrospectively from the electronic medical record system and analysed using univariate and multivariable regression models. Results Over an 11-month period, 68 patients were diagnosed with MRSA bloodstream infection, 53 were swabbed, and 37 (70%) were colonized with MRSA in the anterior nares. We performed molecular typing on 213 nasal colonies. Spa types and clonal complexes found in the blood were also detected in the nares in 95% of the cases. We also found that 11% of patients carried more than one clone of MRSA in the nares. Male sex and history of prior hospitalization within the past 90 days increased odds for MRSA colonization. Conclusion The molecular epidemiological landscape of colonization in the setting of invasive disease is diverse and defining the interplay between colonization and invasive disease is critical to combating invasive MRSA disease.

Matthew M. Hernandez and Ana S. Gonzalez-Reiche and colleagues report evidence of SARSCoV-2 infections in respiratory pathogen-negative nasopharyngeal specimens collected in New York, which date back to over one month before the first officially documented case in the state. The findings provide insights in to the origins of the virus in New York.

Abstract Background Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology. Methods We developed the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT) to automate integration of genomic and medical record data for rapid detection and tracing of nosocomial outbreaks. To demonstrate its capabilities, we applied PathoSPOT to complete genome surveillance data of 197 MRSA bacteremia cases from two hospitals during a 2-year period. Results PathoSPOT identified 8 clonal clusters encompassing 33 patients (16.8% of cases), none of which had been recognized by standard practices. The largest cluster corresponded to a prolonged outbreak of a hospital-associated MRSA clone among 16 adults, spanning 9 wards over a period of 21 months. Analysis of precise timeline and location data with our toolkit suggested that an initial exposure event in a single ward led to infection and long-term colonization of multiple patients, followed by transmissions to other patients during recurrent hospitalizations. Conclusions We demonstrate that PathoSPOT genomic surveillance enables the detection of complex transmission chains that are not readily apparent from epidemiological data and that contribute significantly to morbidity and mortality, enabling more effective intervention strategies.