Harry A Thorpe PhD , Maiju Pesonen PhD , Marta Corbella MSc , Henri Pesonen DSc , Stefano Gaiarsa PhD , Christine J Boinett PhD , Gerry Tonkin-Hill PhD , Tommi Mäklin PhD , Anna K Pöntinen PhD , Neil MacAlasdair PhD , Rebecca A Gladstone PhD , Sergio Arredondo-Alonso PhD , Teemu Kallonen PhD , Dorota Jamrozy PhD , Stephanie W Lo PhD , Chrispin Chaguza PhD , Grace A Blackwell PhD , Prof Antti Honkela PhD , Anita C Schürch PhD , Prof Rob J L Willems , Prof Jukka Corander PhD
{"title":"2020 年春季意大利医院内细菌病原体的泛病原体深度测序:一项前瞻性队列研究。","authors":"Harry A Thorpe PhD , Maiju Pesonen PhD , Marta Corbella MSc , Henri Pesonen DSc , Stefano Gaiarsa PhD , Christine J Boinett PhD , Gerry Tonkin-Hill PhD , Tommi Mäklin PhD , Anna K Pöntinen PhD , Neil MacAlasdair PhD , Rebecca A Gladstone PhD , Sergio Arredondo-Alonso PhD , Teemu Kallonen PhD , Dorota Jamrozy PhD , Stephanie W Lo PhD , Chrispin Chaguza PhD , Grace A Blackwell PhD , Prof Antti Honkela PhD , Anita C Schürch PhD , Prof Rob J L Willems , Prof Jukka Corander PhD","doi":"10.1016/S2666-5247(24)00113-7","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><div>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.</div></div><div><h3>Methods</h3><div>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 <em>Acinetobacter baumannii, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus,</em> and <em>Streptococcus pneumoniae</em>, 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 <em>Acinetobacter baumannii</em> genomes with those obtained by single colony whole-genome sequencing of isolates from the same hospital.</div></div><div><h3>Findings</h3><div>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 <em>Acinetobacter baumannii</em> 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.</div></div><div><h3>Interpretation</h3><div>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.</div></div><div><h3>Funding</h3><div>Wellcome Trust, European Research Council, Academy of Finland Flagship program, Trond Mohn Foundation, and Research Council of Norway.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9000,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study\",\"authors\":\"Harry A Thorpe PhD , Maiju Pesonen PhD , Marta Corbella MSc , Henri Pesonen DSc , Stefano Gaiarsa PhD , Christine J Boinett PhD , Gerry Tonkin-Hill PhD , Tommi Mäklin PhD , Anna K Pöntinen PhD , Neil MacAlasdair PhD , Rebecca A Gladstone PhD , Sergio Arredondo-Alonso PhD , Teemu Kallonen PhD , Dorota Jamrozy PhD , Stephanie W Lo PhD , Chrispin Chaguza PhD , Grace A Blackwell PhD , Prof Antti Honkela PhD , Anita C Schürch PhD , Prof Rob J L Willems , Prof Jukka Corander PhD\",\"doi\":\"10.1016/S2666-5247(24)00113-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><div>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. 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Diagnostic samples collected between April 7 and May 10, 2020 were cultured on six different selective media designed to enrich for <em>Acinetobacter baumannii, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus,</em> and <em>Streptococcus pneumoniae</em>, 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. 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Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study
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.
Funding
Wellcome Trust, European Research Council, Academy of Finland Flagship program, Trond Mohn Foundation, and Research Council of Norway.
期刊介绍:
The Lancet Microbe is a gold open access journal committed to publishing content relevant to clinical microbiologists worldwide, with a focus on studies that advance clinical understanding, challenge the status quo, and advocate change in health policy.