Lancet Microbe最新文献

{"title":"Genomic cluster formation among invasive group A streptococcal infections in the USA: a whole-genome sequencing and population-based surveillance study.","authors":"Yuan Li, Joy Rivers, Saundra Mathis, Zhongya Li, Sopio Chochua, Benjamin J Metcalf, Bernard Beall, Lesley McGee","doi":"10.1016/S2666-5247(24)00169-1","DOIUrl":"https://doi.org/10.1016/S2666-5247(24)00169-1","url":null,"abstract":"<p><strong>Background: </strong>Clusters of invasive group A streptococcal (iGAS) infection, linked to genomically closely related group A streptococcal (GAS) isolates (referred to as genomic clusters), pose public health threats, and are increasingly identified through whole-genome sequencing (WGS) analysis. In this study, we aimed to assess the risk of genomic cluster formation among iGAS cases not already part of existing genomic clusters.</p><p><strong>Methods: </strong>In this WGS and population-based surveillance study, we analysed iGAS case isolates from the Active Bacterial Core surveillance (ABCs), which is part of the US Centers for Disease Control and Prevention's Emerging Infections Program, in ten US states from Jan 1, 2015, to Dec 31, 2019. We included all residents in ABCs sites with iGAS infections meeting the case definition and excluded non-conforming GAS infections and cases with whole-genome assemblies of the isolate containing fewer than 1·5 million total bases or more than 150 contigs. For iGAS cases we collected basic demographics, underlying conditions, and risk factors for infection from medical records, and for isolates we included emm types, antimicrobial resistance, and presence of virulence-related genes. Two iGAS cases were defined as genomically clustered if their isolates differed by three or less single-nucleotide variants. An iGAS case not clustered with any previous cases at the time of detection, with a minimum trace-back time of 1 year, was defined as being at risk of cluster formation. We monitored each iGAS case at risk for a minimum of 1 year to identify any cluster formation event, defined as the detection of a subsequent iGAS case clustered with the case at risk. We used the Kaplan-Meier method to estimate the cumulative incidence of cluster formation events over time. We used Cox regression to assess associations between features of cases at risk upon detection and subsequent cluster formation. We developed a random survival forest machine-learning model based on a derivation cohort (random selection of 50% of cases at risk) to predict cluster formation risk. This model was validated using a validation cohort consisting of the remaining 50% of cases at risk.</p><p><strong>Findings: </strong>We identified 2764 iGAS cases at risk from 2016 to 2018, of which 656 (24%) formed genomic clusters by the end of 2019. Overall, the cumulative incidence of cluster formation was 0·057 (95% CI 0·048-0·066) at 30 days after detection, 0·12 (0·11-0·13) at 90 days after detection, and 0·16 (0·15-0·18) at 180 days after detection. A higher risk of cluster formation was associated with emm type (adjusted hazard ratio as compared with emm89 was 2·37 [95% CI 1·71-3·30] for emm1, 2·72 [1·82-4·06] for emm3, 2·28 [1·49-3·51] for emm6, 1·47 [1·05-2·06] for emm12, and 2·21 [1·38-3·56] for emm92), homelessness (1·42 [1·01-1·99]), injection drug use (2·08 [1·59-2·72]), residence in a long-term care facility (1·78 [1·29-2·45]), and ","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142477425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epidemiology of periportal fibrosis and relevance of current Schistosoma mansoni infection within the context of repeated mass drug administration in rural Uganda: a population-based, cross-sectional study.","authors":"Seun Anjorin, Betty Nabatte, Simon Mpooya, Benjamin Tinkitina, Christopher K Opio, Narcis B Kabatereine, Goylette F Chami","doi":"10.1016/j.lanmic.2024.07.007","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.07.007","url":null,"abstract":"<p><strong>Background: </strong>WHO guidelines for schistosomiasis-related morbidity control and elimination rely on current infection as a proxy indicator for morbidity. We evaluated these guidelines within the context of repeated mass drug administration and periportal fibrosis attributable to chronic intestinal schistosomiasis.</p><p><strong>Methods: </strong>We examined 1442 households randomly sampled from 38 villages in Buliisa, Pakwach, and Mayuge districts of Uganda within the SchistoTrack cohort. Periportal fibrosis was diagnosed in 2834 individuals aged 5-90 years using ultrasound and image patterns C-F from the Niamey protocol. Schistosoma mansoni status and intensity were diagnosed by Kato-Katz microscopy and point-of-care circulating cathodic antigen tests. Schistosome infection, co-infections, and comorbidities were examined as exposures for periportal fibrosis. Multivariable logistic regressions were run with SEs clustered by household.</p><p><strong>Findings: </strong>Between Jan 6 and Feb 3, 2022, 342 (12·1%) of 2834 participants were diagnosed with periportal fibrosis. By Kato-Katz microscopy, 1229 (43·4%) of 2834 participants were infected. 1863 (65·7%) of 2834 participants had trace positive point-of-care circulating cathodic antigen tests, which was higher than prevalence by Kato-Katz microscopy, and 1158 (40·9%) of 2834 participants had trace negative point-of-care circulating cathodic antigen tests. Individual schistosome status, intensity, and prevalence of heavy intensity infections of less than 1% and less than 5% were not correlated with periportal fibrosis likelihood or village prevalence. Periportal fibrosis likelihood linearly increased with age from age 5 years to age 25 years, non-linearly increased from age 26 years to age 45 years, attenuated or remained unchanged from age 46 years to age 60 years, and steadily decreased past 60 years of age. History of liver diseases, HIV, and ultrasound-detected chronic hepatitis or early cirrhosis-like disease were associated with more than two-times increased periportal fibrosis likelihood.</p><p><strong>Interpretation: </strong>WHO guidelines reliant on current schistosome status and intensity are uninformative for identifying probable cases or communities with periportal fibrosis. History of HIV and underlying chronic hepatitis or early cirrhosis-like disease are risk factors that could be investigated for periportal fibrosis surveillance and management.</p><p><strong>Funding: </strong>NDPH Pump Priming Fund, Wellcome Trust, John Fell Fund, Robertson Foundation, and UK Research and Innovation Engineering and Physical Sciences Research Council.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142477424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pandemic risk characterisation of zoonotic influenza A viruses using the Tool for Influenza Pandemic Risk Assessment (TIPRA).","authors":"Reina Yamaji, Wenqing Zhang, Akiko Kamata, Cornelia Adlhoch, David E Swayne, Dmitriy Pereyaslov, Dayan Wang, Gabriele Neumann, Gounalan Pavade, Ian G Barr, Malik Peiris, Richard J Webby, Ron A M Fouchier, Sophie Von Dobschütz, Thomas Fabrizio, Yuelong Shu, Magdi Samaan","doi":"10.1016/j.lanmic.2024.100973","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.100973","url":null,"abstract":"<p><p>A systematic risk assessment approach is essential for evaluating the relative risk of influenza A viruses (IAVs) with pandemic potential. To achieve this, the Tool for Influenza Pandemic Risk Assessment (TIPRA) was developed under the Global Influenza Programme of WHO. Since its release in 2016 and update in 2020, TIPRA has been used to assess the pandemic risk of 11 zoonotic IAVs across ten evaluation rounds. Notably, A(H7N9), A(H9N2), and A(H5) clade 2.3.4.4 viruses were re-evaluated owing to changes in epidemiological characteristics or virus properties. A(H7N9) viruses had the highest relative risk at the time of assessment, highlighting the importance of continuous monitoring and reassessment as changes in epidemiological trends within animal and human populations can alter risk profiles. The knowledge gaps identified throughout the ten risk assessments should help to guide the efficient use of resources for future research, including surveillance. The TIPRA tool reflects the One Health approach and has proven crucial for closely monitoring virus dynamics in both human and non-human populations to enhance preparedness for potential IAV pandemics.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142477429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wastewater monitoring of human and avian influenza A viruses in Northern Ireland: a genomic surveillance study.","authors":"Andrew J Lee, Stephen Carson, Marina I Reyne, Andrew Marshall, Daniel Moody, Danielle M Allen, Pearce Allingham, Ashley Levickas, Arthur Fitzgerald, Stephen H Bell, Jonathan Lock, Jonathon D Coey, Cormac McSparron, Behnam F Nejad, Evan P Troendle, David A Simpson, David G Courtney, Gisli G Einarsson, James P McKenna, Derek J Fairley, Tanya Curran, Jennifer M McKinley, Deirdre F Gilpin, Ken Lemon, John W McGrath, Connor G G Bamford","doi":"10.1016/S2666-5247(24)00175-7","DOIUrl":"https://doi.org/10.1016/S2666-5247(24)00175-7","url":null,"abstract":"<p><strong>Background: </strong>Influenza A viruses (IAVs) are significant pathogens of humans and other animals. Although endemic in humans and birds, novel IAV strains can emerge, jump species, and cause epidemics, like the latest variant of H5N1. Wastewater-based epidemiology (WBE) has been shown capable of detecting human IAVs. We aimed to assess whether whole-genome sequencing (WGS) of IAVs from wastewater is possible and can be used to discriminate between circulating strains of human and any non-human IAVs, such as those of avian origin.</p><p><strong>Methods: </strong>Using a pan-IAV RT-quantitative PCR assay, six wastewater treatment works (WWTWs) across Northern Ireland were screened from Aug 1 to Dec 5, 2022. A nanopore WGS approach was used to sequence RT-qPCR-positive samples. Phylogenetic analysis of sequences relative to currently circulating human and non-human IAVs was performed. For comparative purposes, clinical data (PCR test results) were supplied by The Regional Virus Laboratory, Belfast Health and Social Care Trust (Belfast, Northern Ireland, UK).</p><p><strong>Findings: </strong>We detected a dynamic IAV signal in wastewater from Sept 5, 2022, onwards across Northern Ireland, which did not show a clear positive relationship with the clinical data obtained for the region. Meta (mixed strain) whole-genome sequences were generated from wastewater samples displaying homology to only human and avian IAV strains. The relative proportion of IAV reads of human versus avian origin differed across time and sample site. A diversity in subtypes and lineages was detected (eg, H1N1, H3N2, and several avian). Avian segment 8 related to those found in recent H5N1 clade 2.3.4.4b was identified.</p><p><strong>Interpretation: </strong>WBE affords a means to monitor circulating human and avian IAV strains and provide crucial genetic information. As such, WBE can provide rapid, cost-effective, year-round One Health surveillance to help control IAV epidemic and pandemic-related threats. However, optimisation of WBE protocols are necessary to ensure observed wastewater signals not only correlate with clinical case data, but yield information on the wider environmental pan-influenz-ome.</p><p><strong>Funding: </strong>Department of Health for Northern Ireland.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142477433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implementing a national programme of pathogen genomics for public health: the Australian Pathogen Genomics Program (AusPathoGen).","authors":"Jessica R Webb, Patiyan Andersson, Eby Sim, Alireza Zahedi, Angela Donald, Tuyet Hoang, Anne E Watt, Jessica E Agius, Celeste M Donato, Max L Cummins, Tehzeeb Zulfiqar, Son Nghiem, Chantel Lin, Dimitrios Menouhos, Lex E X Leong, Rob Baird, Karina Kennedy, Louise Cooley, David Speers, Chuan Kok Lim, Joep de Ligt, Angeline Ferdinand, Katie Glass, Martyn D Kirk, Steven P Djordjevic, Clare Sloggett, Kristy Horan, Torsten Seemann, Vitali Sintchenko, Amy V Jennison, Benjamin P Howden","doi":"10.1016/j.lanmic.2024.100969","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.100969","url":null,"abstract":"<p><p>Delivering large-scale routine pathogen genomics surveillance for public health is of considerable interest, although translational research models that promote national-level implementation are not well defined. We describe the development and deployment of the Australian Pathogen Genomics Program (AusPathoGen), a comprehensive national partnership between academia, public health laboratories, and public health agencies that commenced in January, 2021. Successfully establishing and delivering a national programme requires inclusive and transparent collaboration between stakeholders, defined and clear focus on public health priorities, and support for strengthening national genomics capacity. Major enablers for delivering such a programme include technical solutions for data integration and analysis, such as the genomics surveillance platform AusTrakka, standard bioinformatic analysis methods, and national ethics and data sharing agreements that promote nationally integrated surveillance systems. Training of public health officials to interpret and act on genomic data is crucial, and evaluation and cost-effectiveness programmes will provide a benchmark and evidence for sustainable investment in genomics nationally and globally.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mpox genomics in outbreak control: challenges and limitations.","authors":"Kathryn Edenborough, Ammar Aziz, Nicola Sexton-Oates, Ivana Savic, Eike Steinig, Brendan Quinn, Mihaela Ivan, Alicia Arnott, Leon Caly, Chuan Kok Lim","doi":"10.1016/j.lanmic.2024.100999","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.100999","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibody mechanisms of protection against malaria in RTS,S-vaccinated children: a post-hoc serological analysis of phase 2 trial","authors":"Liriye Kurtovic PhD ,&nbsp;Gaoqian Feng PhD ,&nbsp;Alessia Hysa MBSc ,&nbsp;Ali Haghiri PhD ,&nbsp;Katherine O’Flaherty PhD ,&nbsp;Bruce D Wines PhD ,&nbsp;Rebeca Santano PhD ,&nbsp;Laura D’Andrea PhD ,&nbsp;Prof Heidi E Drummer PhD ,&nbsp;Prof P Mark Hogarth PhD ,&nbsp;Prof Jahit Sacarlal PhD ,&nbsp;Prof Freya J I Fowkes DPhil ,&nbsp;Prof Julie A Simpson PhD ,&nbsp;Prof Carlota Dobaño PhD ,&nbsp;Prof James G Beeson PhD","doi":"10.1016/S2666-5247(24)00130-7","DOIUrl":"10.1016/S2666-5247(24)00130-7","url":null,"abstract":"<div><h3>Background</h3><div>The RTS,S malaria vaccine is currently recommended for children aged 5–6 months in regions with moderate-to-high <em>Plasmodium falciparum</em> transmission. However, vaccination only confers 55% efficacy over 12 months and wanes within 18 months. The immunological mechanisms of RTS,S-mediated immunity are poorly understood; therefore, we aimed to identify antibody response types associated with protection against malaria in children vaccinated with RTS,S.</div></div><div><h3>Methods</h3><div>In this post-hoc analysis, we evaluated antibody responses in 737 children aged 1–4 years vaccinated with RTS,S in a phase 2b clinical trial conducted in Mozambique in 2003. We evaluated all available samples collected from children 30 days after the three-dose vaccination schedule at study month 3 (M3; n=737 available of 803 children allocated to receive RTS,S). For comparison, we tested a subset of samples collected before vaccination at study month 0 (M0; n=50) and from children in the control vaccine group (M0 n=25; M3 n=99). We quantified the induction of antibodies to different regions of the vaccine antigen that function by fixing serum complement proteins and binding to Fcγ receptors (FcγRs; FcγRI, FcγRIIa, and FcγRIII) expressed on immune cells as potential mechanisms of immunity.</div></div><div><h3>Findings</h3><div>Functional antibody responses to the C-terminal region of the vaccine antigen, circumsporozoite protein (CSP), were associated with a reduced risk of malaria (C1q p=0·0060, FcγRIIa p=0·014, and FcγRIII p=0·019). These associations remained significant in male participants when the analyses were stratified by sex (C1q p=0·012, FcγRI p=0·023, FcγRIIa p=0·0070, and FcγRIII p=0·0080). IgA to the central repeat (p=0·0010) and C-terminal (p=0·0040) regions of CSP were also associated with protection. We show that IgA can bind FcαRI and mediate opsonic phagocytosis using a serum pool and monoclonal antibodies. Multiparameter analysis using machine-learning methods suggest that IgA, complement fixation, and FcγRI binding were most predictive of protection against malaria (hazard ratio &lt;1) and suggested that associations differed between male and female participants.</div></div><div><h3>Interpretation</h3><div>We provide evidence that functional antibody responses mediated by IgG and IgA are associated with protection against malaria in young children vaccinated with RTS,S, and suggest potential differences in the correlates of immunity between males and females. These findings reveal new avenues that could be used to achieve malaria vaccines with higher efficacy.</div></div><div><h3>Funding</h3><div>National Health and Medical Research Council, Australia, and Thrasher Research Fund.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rare in the country, not in the community: Chagas disease in the Latin American diaspora","authors":"Natalie Elkheir ,&nbsp;David A J Moore","doi":"10.1016/j.lanmic.2024.100982","DOIUrl":"10.1016/j.lanmic.2024.100982","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142298323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study","authors":"Harry A Thorpe PhD ,&nbsp;Maiju Pesonen PhD ,&nbsp;Marta Corbella MSc ,&nbsp;Henri Pesonen DSc ,&nbsp;Stefano Gaiarsa PhD ,&nbsp;Christine J Boinett PhD ,&nbsp;Gerry Tonkin-Hill PhD ,&nbsp;Tommi Mäklin PhD ,&nbsp;Anna K Pöntinen PhD ,&nbsp;Neil MacAlasdair PhD ,&nbsp;Rebecca A Gladstone PhD ,&nbsp;Sergio Arredondo-Alonso PhD ,&nbsp;Teemu Kallonen PhD ,&nbsp;Dorota Jamrozy PhD ,&nbsp;Stephanie W Lo PhD ,&nbsp;Chrispin Chaguza PhD ,&nbsp;Grace A Blackwell PhD ,&nbsp;Prof Antti Honkela PhD ,&nbsp;Anita C Schürch PhD ,&nbsp;Prof Rob J L Willems ,&nbsp;Prof Jukka Corander PhD","doi":"10.1016/S2666-5247(24)00113-7","DOIUrl":"10.1016/S2666-5247(24)00113-7","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;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.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;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 &lt;em&gt;Acinetobacter baumannii, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus,&lt;/em&gt; and &lt;em&gt;Streptococcus pneumoniae&lt;/em&gt;, 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 &lt;em&gt;Acinetobacter baumannii&lt;/em&gt; genomes with those obtained by single colony whole-genome sequencing of isolates from the same hospital.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Findings&lt;/h3&gt;&lt;div&gt;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 &lt;em&gt;Acinetobacter baumannii&lt;/em&gt; 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.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early warning COVID-19 outbreak in long-term care facilities using wastewater surveillance: correlation, prediction, and interaction with clinical and serological statuses","authors":"Xiaoli Pang PhD ,&nbsp;Bonita E Lee MD ,&nbsp;Tiejun Gao PhD ,&nbsp;Rhonda J Rosychuk PhD ,&nbsp;Linnet Immaraj PhD ,&nbsp;Judy Y Qiu PhD ,&nbsp;Jiabi Wen MS ,&nbsp;Nathan Zelyas MD ,&nbsp;Krista Howden DACVPM ,&nbsp;Janelle Wallace MPh ,&nbsp;Eleanor Risling MD ,&nbsp;Lorie A Little MD ,&nbsp;John Kim PhD ,&nbsp;Heidi Wood PhD ,&nbsp;Alyssia Robinson BA ,&nbsp;Michael Parkins MD ,&nbsp;Casey R J Hubert PhD ,&nbsp;Kevin Frankowski MS ,&nbsp;Steve E Hrudey Dsc [Eng] ,&nbsp;Christopher Sikora MD","doi":"10.1016/S2666-5247(24)00126-5","DOIUrl":"10.1016/S2666-5247(24)00126-5","url":null,"abstract":"<div><h3>Background</h3><div>The unprecedented COVID-19 pandemic has highlighted the strategic value of wastewater-based surveillance (WBS) of SARS-CoV-2. This multisite 28-month-long study focused on WBS for older residents in 12 long-term care facilities (LTCFs) in Edmonton (AB, Canada) by assessing relationships between COVID-19, WBS, and serostatus during the pandemic.</div></div><div><h3>Methods</h3><div>Wastewater samples collected two to three times per week were tested for SARS-CoV-2 using RT-quantitative PCR. The serostatus of antibodies was examined using immunoassays. The data of clinical COVID-19 outbreaks based on extensive testing were obtained from local public health officials. Analyses included calculating correlations between 7-day rolling averages for WBS and COVID-19 cases and investigating whether WBS led or lagged confirmed outbreaks using a multinomial test.</div></div><div><h3>Findings</h3><div>Wastewater results correlated well with clinical COVID-19 infections and outbreaks at participating LTCFs. 1058 (36·0%) of 2936 collected wastewater samples were SARS-CoV-2 positive, compared with 1247 people (resident n=671, staff n=572, and unknown n=4) reporting positive test results of 21 673 clinical samples assessed (5·8%). WBS led clinical testing in 32 (60·4%) confirmed outbreaks, which was significantly different from WBS lagged (12 outbreaks [22·6%, 95% CI 11·3–33·7]). Non-detection of WBS SARS-CoV-2 served as a negative predictor for outbreaks. WBS results attested protective immunity in vaccinated individuals before the omicron wave. A parallel increase in the proportions of positive WBS SARS-CoV-2 and anti-nucleocapsid antibodies underlined that omicron was an immunity-evading variant despite high seropositivity of neutralising antibodies after multiple doses of vaccine.</div></div><div><h3>Interpretation</h3><div>Implementation of WBS could enable targeted clinical investigations and improve cost-effectiveness of COVID-19 outbreak management in LTCFs. WBS and serostatus provided informed dynamic changes of infections and immunity. Critical evidence was that LTCF WBS is an effective early warning system to support rapid public health outbreak management and protect vulnerable older populations.</div></div><div><h3>Funding</h3><div>Canadian Immunity Task Force for COVID-19 and Alberta Health.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":null,"pages":null},"PeriodicalIF":20.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142056886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}