Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101135
Fergus W Hamilton , Tom Parks , Gabriele Pollara
{"title":"Altered IL-6 signalling and risk of tuberculosis–Authors’ reply","authors":"Fergus W Hamilton , Tom Parks , Gabriele Pollara","doi":"10.1016/j.lanmic.2025.101135","DOIUrl":"10.1016/j.lanmic.2025.101135","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101135"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051031","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}
Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101157
Sandhya Dhawan MSc , Atalay G Muluneh MPH , Wirichada Pan-gnum PhD , C Raina MacIntyre PhD , Kathrin Summermatter PhD , Stuart D Blacksell PhD
{"title":"Risk factors and mitigation strategies of laboratory-acquired infections in research and clinical laboratories worldwide: a systematic review","authors":"Sandhya Dhawan MSc , Atalay G Muluneh MPH , Wirichada Pan-gnum PhD , C Raina MacIntyre PhD , Kathrin Summermatter PhD , Stuart D Blacksell PhD","doi":"10.1016/j.lanmic.2025.101157","DOIUrl":"10.1016/j.lanmic.2025.101157","url":null,"abstract":"<div><div>Laboratory-acquired infections and accidental pathogen escapes from laboratory settings pose biosafety risks, affecting laboratory personnel, the scientific community, the general public, animal populations, and the environment. This systematic review compares reports of laboratory-acquired infections and accidental pathogen escapes from laboratory settings in research and clinical laboratories between 2000 and 2024, identifying key risk factors. A total of 250 reports documenting 712 human cases of laboratory-acquired infections were analysed. Research laboratories reported 276 infections and eight fatalities, whereas clinical laboratories accounted for 227 infections and five deaths. Needlestick injuries and ineffective use of personal protective equipment or containment measures were major risk factors in both settings. Research laboratories frequently reported inadequate decontamination techniques, whereas improper sample handling techniques often occurred in clinical laboratories. Given that most causes of laboratory-acquired infections are unknown or under-reported, these data can inform coordinated efforts to strengthen biosafety oversight, incident reporting, and risk management to reduce biosafety lapses and ensure long-term laboratory operations.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101157"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561538","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}
Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101130
Jian-Te Lee , Ya-Li Hu , Wei-Liang Shih , Luan-Yin Chang
{"title":"Age-stratified seroprevalence of enterovirus D68 and the need for cohort studies in children","authors":"Jian-Te Lee , Ya-Li Hu , Wei-Liang Shih , Luan-Yin Chang","doi":"10.1016/j.lanmic.2025.101130","DOIUrl":"10.1016/j.lanmic.2025.101130","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101130"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044383","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}
Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101122
Joseline M Velasquez-Reyes BS , Beau Schaeffer SM , Scott R Curry MD MS , Victoria Overbeck MPH , Cole Sher-Jan BS , Bradford P Taylor PhD , Jacquelyn Turcinovic PhD , Krutika Kuppalli MD , John H Connor PhD , William P Hanage PhD
{"title":"Characterisation of a persistent SARS-CoV-2 infection lasting more than 750 days in a person living with HIV: a genomic analysis","authors":"Joseline M Velasquez-Reyes BS , Beau Schaeffer SM , Scott R Curry MD MS , Victoria Overbeck MPH , Cole Sher-Jan BS , Bradford P Taylor PhD , Jacquelyn Turcinovic PhD , Krutika Kuppalli MD , John H Connor PhD , William P Hanage PhD","doi":"10.1016/j.lanmic.2025.101122","DOIUrl":"10.1016/j.lanmic.2025.101122","url":null,"abstract":"<div><h3>Background</h3><div>People who are immunocompromised can develop persistent SARS-CoV-2 infections. Several viral mutations accumulated during the course of such persistent infections have also been observed in prominent variants of concern (VOCs). Here, we characterise persistent infection and viral evolution of SARS-CoV-2 lasting more than 750 days in a person with advanced HIV-1 infection.</div></div><div><h3>Methods</h3><div>Between March, 2021, and July, 2022, eight clinical specimens were collected from a person living with HIV, neither receiving antiretroviral therapy nor virally suppressed, and presumed to have been initially infected with SARS-CoV-2 in mid-May, 2020. Viral RNA was extracted from each swab and an amplicon-based sequencing approach was used for genomic analysis of SARS-CoV-2. Variable sites were characterised at the consensus and subconsensus levels, and phylogenetic tools were applied to analyse viral evolution. Publicly available SARS-CoV-2 sequences from GenBank were leveraged to contextualise our sequenced samples and identify any potential evidence of transmission.</div></div><div><h3>Findings</h3><div>Genomes formed a monophyletic cluster in the B.1 lineage. 68 consensus and 67 subconsensus single nucleotide variants were observed over the course of infection. The intrahost clock rate remained similar to that of the interhost rate in contemporaneous community sequences (6·74 × 10<sup>–4</sup> [95% credible interval 5·05 × 10<sup>–4</sup> to 8·54 × 10<sup>–4</sup>] substitutions per site per year <em>vs</em> 6·11 × 10<sup>–4</sup> [5·54 × 10<sup>–5</sup> to 6·66 × 10<sup>–4</sup>]). Mutations grouped into two distinct subpopulations present throughout infection. 10 non-synonymous mutations in the spike protein gene were at positions in common with those defining the omicron lineage (BA.1 or BA.2), of which nine were present before November, 2021. Nine of 18 substitutions present throughout infection were rare in online databases, suggesting a lack of long transmission chains descending from this individual.</div></div><div><h3>Interpretation</h3><div>Convergent SARS-CoV-2 evolution, both in and outside the spike protein, observed in this study suggests parallels with the evolutionary process leading to emergence of the omicron VOC. The inferred absence of onward infections might indicate a loss of transmissibility during adaptation to a single host. Our results underscore the importance of appropriate treatment to cure persistent SARS-CoV-2 infections and monitoring them to understand how mutations contribute to viral adaptation.</div></div><div><h3>Funding</h3><div>National Institute of General Medical Sciences of the National Institutes of Health, Centers for Disease Control and Prevention, the National Institute of Allergy and Infectious Diseases, MassCPR, and Morris Singer Foundation.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101122"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709399","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}
Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101153
Tiffeney Mann MSc , Stephanie Minnies PhD , Rishi K Gupta PhD , Byron W P Reeve PhD , Georgina Nyawo PhD , Zaida Palmer MSc , Charissa Naidoo PhD , Prof Anton Doubell MMed PhD , Alfonso Pecoraro MMed PhD , Thadathilankal-Jess John MBChB , Pawel Schubert MPhil , Claire J Calderwood MRCP , Aneesh Chandran PhD , Prof Grant Theron PhD , Prof Mahdad Noursadeghi PhD
{"title":"Blood RNA biomarkers and C-reactive protein for triage of adult patients with tuberculosis lymphadenitis and pericarditis in South Africa: a single-centre, prospective, observational, diagnostic accuracy study","authors":"Tiffeney Mann MSc , Stephanie Minnies PhD , Rishi K Gupta PhD , Byron W P Reeve PhD , Georgina Nyawo PhD , Zaida Palmer MSc , Charissa Naidoo PhD , Prof Anton Doubell MMed PhD , Alfonso Pecoraro MMed PhD , Thadathilankal-Jess John MBChB , Pawel Schubert MPhil , Claire J Calderwood MRCP , Aneesh Chandran PhD , Prof Grant Theron PhD , Prof Mahdad Noursadeghi PhD","doi":"10.1016/j.lanmic.2025.101153","DOIUrl":"10.1016/j.lanmic.2025.101153","url":null,"abstract":"<div><h3>Background</h3><div>Data on the diagnostic accuracy of blood RNA biomarker signatures for extrapulmonary tuberculosis are scarce. We aimed to address this question among people investigated for tuberculosis lymphadenitis and tuberculosis pericarditis.</div></div><div><h3>Methods</h3><div>This prospective, observational, diagnostic accuracy study was done at a tertiary hospital in Cape Town, South Africa. We enrolled consecutive symptomatic adults (aged 18 years or older) with presumptive tuberculosis lymphadenitis (Jan 25, 2017, to Oct 9, 2019) or tuberculosis pericarditis (Nov 24, 2016, to Oct 28, 2019). We used microbiological testing of samples from the site of disease as the reference standard. We evaluated the diagnostic accuracy of seven previously reported blood RNA signatures by area under the receiver operating characteristic curve (AUROC) and sensitivity and specificity at prespecified thresholds using two SDs above the mean of a healthy reference control group, benchmarked against blood C-reactive protein and WHO target product profile for a tuberculosis triage test. Decision curve analysis was used to evaluate clinical utility of the best-performing blood RNA signature and C-reactive protein.</div></div><div><h3>Findings</h3><div>The pooled cohort included 440 individuals, 374 of whom (275 with lymphadenitis and 99 with pericarditis) had at least one microbiological test from the site of disease, blood C-reactive protein, and RNA measurements available and were included in the analysis. 181 (48%) participants were female and 193 (52%) were male. The diagnostic accuracy of blood RNA signatures was similar across patients with lymphadenitis and pericarditis. In pooled analysis of both cohorts, all RNA signatures had similar discrimination, with AUROC point estimates ranging from 0·77 (95% CI 0·72–0·82) to 0·82 (0·77–0·86), and greater than that of C-reactive protein (0·61 [0·56–0·67]). The best-performing signature (Roe3) did not meet the WHO target product profile benchmark for a triage test. At the prespecified threshold, Roe3 had 78% (95% CI 72–83) sensitivity and 69% (62–75) specificity; C-reactive protein at a threshold of 10 mg/L had 83% (77–87) sensitivity and 35% (29–43) specificity. In this setting, decision curve analysis showed that Roe3 offered greater net benefit than other approaches for services aiming to reduce the number needed to investigate with confirmatory testing to fewer than four to identify each individual with tuberculosis.</div></div><div><h3>Interpretation</h3><div>Our results suggest RNA biomarkers show better accuracy and clinical utility than C-reactive protein to trigger confirmatory tuberculosis testing in patients with tuberculosis lymphadenitis and tuberculosis pericarditis, but still fall short of the WHO target product profile for tuberculosis triage tests.</div></div><div><h3>Funding</h3><div>South African Medical Research Council, European and Developing Countries Clinical Trials Partnersh","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101153"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660736","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}
Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101105
Eloise Williams MBBS , Soo Jen Low PhD , Georgina L Pollock PhD , Mona L Taouk BSc , Jacqueline Prestedge BSc , Benjamin P Howden PhD , Eric P F Chow PhD , Christopher K Fairley PhD , Kate L Seib PhD , James S McCarthy MD , Shivani Pasricha PhD , Deborah A Williamson PhD
{"title":"Selecting candidate Neisseria gonorrhoeae strains for oropharyngeal gonorrhoea human challenge: a genomics-based analysis of clinical isolates","authors":"Eloise Williams MBBS , Soo Jen Low PhD , Georgina L Pollock PhD , Mona L Taouk BSc , Jacqueline Prestedge BSc , Benjamin P Howden PhD , Eric P F Chow PhD , Christopher K Fairley PhD , Kate L Seib PhD , James S McCarthy MD , Shivani Pasricha PhD , Deborah A Williamson PhD","doi":"10.1016/j.lanmic.2025.101105","DOIUrl":"10.1016/j.lanmic.2025.101105","url":null,"abstract":"<div><h3>Background</h3><div><em>Neisseria gonorrhoeae</em> is a human pathogen of major public health importance due to its increasing global prevalence and antimicrobial resistance (AMR). Evidence suggests that oropharyngeal infection plays a key role in <em>N gonorrhoeae</em> transmission and AMR; however, our understanding of oropharyngeal gonorrhoea pathogenesis is poor. A controlled human infection model (CHIM) for oropharyngeal gonorrhoea will improve understanding of infection and accelerate urgently needed novel gonorrhoea prevention and therapeutic strategies. As the first step in the development of this CHIM, we describe a systematic approach to CHIM strain selection that leverages genomics and clinical data.</div></div><div><h3>Methods</h3><div>In this genomics-based analysis, we applied a systematic <em>N gonorrhoeae</em> challenge strain selection strategy incorporating genomic and clinical data to a primary dataset of clinical isolates of <em>N gonorrhoeae</em> collected from adult patients in Victoria, Australia, between Jan 1 and Dec 31, 2017, and July 1, 2019, and June 30, 2021. This selection strategy used clinical, phenotypic, and genomic characteristics to define a set of eight criteria that aimed to ensure the contemporary global clinical relevance of the candidate strains; select strains that would be applicable for the assessment of current and future gonorrhoea vaccines; and maximise participant safety by reducing the risk of disseminated gonococcal infection and clinically significant AMR. We applied these criteria to our primary dataset to generate a panel of potential challenge strains. From this final dataset of potential challenge strains, we predetermined that we would select up to ten isolates to proceed to the next stage of detailed phenotypic characterisation for final <em>N gonorrhoeae</em> CHIM strain selection.</div></div><div><h3>Findings</h3><div>5881 isolates comprised the primary dataset. After application of the selection criteria, most of the isolates (5795 [98·6%] of 5881) were excluded, mostly due to having clinically significant AMR and poor contemporary global clinical relevance. The remaining 86 <em>N gonorrhoeae</em> challenge strain candidates comprised five multilocus sequence types and six <em>N gonorrhoeae</em> multiantigen sequence types, many of which were represented by a single isolate. Of these 86 strains, five isolates were selected to maximise coverage of the phylogenetically distinct groups within the 86 candidate challenge strains and ensure representation of strains collected from various anatomical sites.</div></div><div><h3>Interpretation</h3><div>We transparently describe a novel, systematic, and rational genomics-based strategy for oropharyngeal gonorrhoea CHIM strain selection that improves the efficiency and transparency of CHIM strain selection and enables identification of contemporary and clinically relevant potential challenge strains. A final <em>N gonorrhoeae</em> challeng","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101105"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144627394","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}
Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101154
Mahan Ghafari DPhil , Steven A Kemp PhD , Matthew Hall PhD , Joseph Clarke MSc , Luca Ferretti PhD , Laura Thomson MRes , Ruth Studley BSc , The COVID-19 Infection Survey Group , The COVID-19 Genomics UK (COG-UK) Consortium , Prof Ann Sarah Walker PhD , Tanya Golubchik PhD , Katrina Lythgoe PhD
{"title":"SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study","authors":"Mahan Ghafari DPhil , Steven A Kemp PhD , Matthew Hall PhD , Joseph Clarke MSc , Luca Ferretti PhD , Laura Thomson MRes , Ruth Studley BSc , The COVID-19 Infection Survey Group , The COVID-19 Genomics UK (COG-UK) Consortium , Prof Ann Sarah Walker PhD , Tanya Golubchik PhD , Katrina Lythgoe PhD","doi":"10.1016/j.lanmic.2025.101154","DOIUrl":"10.1016/j.lanmic.2025.101154","url":null,"abstract":"<div><h3>Background</h3><div>Persistent SARS-CoV-2 infections in hospitalised immunocompromised individuals are known to facilitate accelerated within-host viral evolution, potentially contributing to the emergence of highly divergent variants. However, little is known about the evolutionary dynamics and transmission risks of persistent infections in the general population. We aimed to characterise the within-host evolution of SARS-CoV-2 during persistent infections identified through a large community surveillance study.</div></div><div><h3>Methods</h3><div>We used data from the Office for National Statistics COVID-19 Infection Survey (ONS-CIS), a large-scale, longitudinal, population-based surveillance study conducted in the UK from April, 2020, to March, 2023. For this analysis, we focused on infections with high viral load (cycle threshold ≤30) and available genome sequences, from seven major SARS-CoV-2 lineages (alpha, delta, BA.1, BA.2, BA.4, BA.5, and XBB). ONS-CIS participants were randomly selected from the general population and tested regularly by RT-PCR, regardless of symptoms. We defined persistent infections as those with sustained or rebounding high viral RNA titres for 26 days or longer. We examined associated host characteristics and used raw sequence data to identify de novo mutations and estimate within-host synonymous and non-synonymous evolutionary rates across the SARS-CoV-2 genome.</div></div><div><h3>Findings</h3><div>Between Nov 2, 2020, and March 21, 2023, we identified 576 persistent infections with at least two sequences, including 11 alpha, 106 delta, 102 BA.1, 204 BA.2, 16 BA.4, 133 BA.5, and 4 XBB. Persistent infections were more common in males than females (p<0·0001) and individuals older than 60 years (p=0·0027). The median within-host genome-wide evolutionary rate was 7·9 × 10<sup>−4</sup> substitutions per site per year (IQR 7·0–9·0 × 10<sup>–4</sup>), with high inter-individual variability driven largely by non-synonymous mutations, particularly in the N-terminal and receptor-binding domains of the spike protein. Longer infection duration was associated with higher evolutionary rates, while no associations were found with age, sex, vaccination status, previous infection, or virus lineage. We found no clear evidence of transmission beyond the first month of infection in any of the 84 persistent infections lasting 56 days or longer. In total, we identified 379 recurrent mutations, including many with known or predicted negative fitness effects and low prevalence at the population level, as well as de novo reversions to the Wuhan-Hu-1 reference sequence, which were likely under positive selection within those individuals.</div></div><div><h3>Interpretation</h3><div>This study highlights the heterogeneous nature of within-host SARS-CoV-2 evolution in individuals with persistent infection in the community. Notably, a small subset of persistent infections with high viral loads underwent accelerated viral evolutio","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101154"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769181","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}
Lancet MicrobePub Date : 2025-09-01DOI: 10.1016/j.lanmic.2025.101205
Frances V Ue , Paul E Sax
{"title":"Clinical and public health implications of persistent SARS-CoV-2 infection in a person with HIV disease","authors":"Frances V Ue , Paul E Sax","doi":"10.1016/j.lanmic.2025.101205","DOIUrl":"10.1016/j.lanmic.2025.101205","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 9","pages":"Article 101205"},"PeriodicalIF":20.4,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709400","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}