A1 Refereed original research article in a scientific journal
Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020 : a prospective cohort study
Authors: Thorpe, Harry A; Pesonen, Maiju; Corbella, Marta; Pesonen, Henri; Gaiarsa, Stefano; Boinett, Christine J; Tonkin-Hill, Gerry; Mäklin, Tommi; Pöntinen, Anna K; MacAlasdair, Neil; Gladstone, Rebecca A; Arredondo-Alonso, Sergio; Kallonen, Teemu; Jamrozy, Dorota; Lo, Stephanie W; Chaguza, Chrispin; Blackwell, Grace A; Honkela, Antti; Schürch, Anita C; Willems, Rob J L; Merla, Cristina; Petazzoni, Greta; Feil, Edward J; Cambieri, Patrizia; Thomson, Nicholas R; Bentley, Stephen D; Sassera, Davide; Corander, Jukka
Publisher: Elsevier
Publication year: 2024
Journal: Lancet microbe
Journal name in source: The Lancet. Microbe
Journal acronym: Lancet Microbe
Article number: 100890
Volume: 5
Issue: 10
eISSN: 2666-5247
DOI: https://doi.org/10.1016/S2666-5247(24)00113-7
Web address : https://doi.org/10.1016/S2666-5247(24)00113-7
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/457674387
Background: Nosocomial infections pose a considerable risk to patients who are susceptible, and this is particularly acute in intensive care units when hospital-associated bacteria are endemic. During the first wave of the COVID-19 pandemic, the surge of patients presented a significant obstacle to the effectiveness of infection control measures. We aimed to assess the risks and extent of nosocomial pathogen transmission under a high patient burden by designing a novel bacterial pan-pathogen deep-sequencing approach that could be integrated with standard clinical surveillance and diagnostics workflows.
Methods: We did a prospective cohort study in a region of northern Italy that was severely affected by the first wave of the COVID-19 pandemic. Inpatients on both ordinary and intensive care unit (ICU) wards at the San Matteo hospital, Pavia were sampled on multiple occasions to identify bacterial pathogens from respiratory, nasal, and rectal samples. Diagnostic samples collected between April 7 and May 10, 2020 were cultured on six different selective media designed to enrich for Acinetobacter baumannii, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae, and DNA from each plate with positive growth was deep sequenced en masse. We used mSWEEP and mGEMS to bin sequencing reads by sequence cluster for each species, followed by mapping with snippy to generate high quality alignments. Antimicrobial resistance genes were detected by use of ARIBA and CARD. Estimates of hospital transmission were obtained from pairwise bacterial single nucleotide polymorphism distances, partitioned by within-patient and between-patient samples. Finally, we compared the accuracy of our binned Acinetobacter baumannii genomes with those obtained by single colony whole-genome sequencing of isolates from the same hospital.
Findings: We recruited patients from March 1 to May 7, 2020. The pathogen population among the patients was large and diverse, with 2148 species detections overall among the 2418 sequenced samples from the 256 patients. In total, 55 sequence clusters from key pathogen species were detected at least five times. The antimicrobial resistance gene prevalence was correspondingly high, with key carbapenemase and extended spectrum ß-lactamase genes detected in at least 50 (40%) of 125 patients in ICUs. Using high-resolution mapping to infer transmission, we established that hospital transmission was likely to be a significant mode of acquisition for each of the pathogen species. Finally, comparison with single colony Acinetobacter baumannii genomes showed that the resolution offered by deep sequencing was equivalent to single-colony sequencing, with the additional benefit of detection of co-colonisation of highly similar strains.
Interpretation: Our study shows that a culture-based deep-sequencing approach is a possible route towards improving future pathogen surveillance and infection control at hospitals. Future studies should be designed to directly compare the accuracy, cost, and feasibility of culture-based deep sequencing with single colony whole-genome sequencing on a range of bacterial species.
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Funding information in the publication:
This research was funded in part by the Wellcome Trust Grant number 206194. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. Additional funding was obtained from the European Research Council (grant 742158, JC, HAT, HP), Academy of Finland Flagship programme (JC, AH), Trond Mohn Foundation (BATTALION grant, JC, AKP, RAG, NM), Research Council of Norway (grant 2999131 JC, GT-H).