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Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review 整合基因组和空间分析来描述结核病传播:范围综述。
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2025.101094
Yu Lan PhD , Isabel Rancu , Melanie H Chitwood PhD , Benjamin Sobkowiak PhD , Kate Nyhan MLS , Prof Hsien-Ho Lin ScD , Chieh-Yin Wu MS , Barun Mathema PhD , Tyler S Brown MD , Prof Caroline Colijn PhD , Joshua L Warren PhD , Prof Ted Cohen DPH
{"title":"Integrating genomic and spatial analyses to describe tuberculosis transmission: a scoping review","authors":"Yu Lan PhD ,&nbsp;Isabel Rancu ,&nbsp;Melanie H Chitwood PhD ,&nbsp;Benjamin Sobkowiak PhD ,&nbsp;Kate Nyhan MLS ,&nbsp;Prof Hsien-Ho Lin ScD ,&nbsp;Chieh-Yin Wu MS ,&nbsp;Barun Mathema PhD ,&nbsp;Tyler S Brown MD ,&nbsp;Prof Caroline Colijn PhD ,&nbsp;Joshua L Warren PhD ,&nbsp;Prof Ted Cohen DPH","doi":"10.1016/j.lanmic.2025.101094","DOIUrl":"10.1016/j.lanmic.2025.101094","url":null,"abstract":"<div><div>Tuberculosis remains a leading cause of infection-related mortality, and efforts to reduce its incidence have been hindered by an incomplete understanding of local <em>Mycobacterium tuberculosis</em> transmission dynamics. Advances in pathogen sequencing and spatial analysis have created new opportunities to map <em>M tuberculosis</em> transmission patterns more precisely. In this scoping review, we searched for studies combining pathogen genetics and location data to analyse the spatial patterns of <em>M tuberculosis</em> transmission and identified 142 studies published between 1994 and 2024. Secular changes in genetic methods were observed, with genome sequencing approaches largely replacing lower-resolution genotyping methods since 2020. The included studies addressed four primary research questions: how are tuberculosis cases and <em>M tuberculosis</em> transmission clusters geographically distributed; do spatially concentrated <em>M tuberculosis</em> clusters exist, and where are these areas located; when spatial concentration occurs, what host, pathogen, or environmental factors contribute to these patterns; and do identifiable relationships exist between the spatial proximity of tuberculosis cases and the genetic similarity of the <em>M tuberculosis</em> isolates infecting these individuals? Collectively, in this Review, we examined the available study data, evaluated the analytical requirements for addressing these questions, and discussed opportunities and challenges for future research. We found that the integration of spatial and genomic data can inform a detailed understanding of local <em>M tuberculosis</em> transmission patterns, but improved study designs and new analytical methods to address gaps in sampling completeness and to integrate additional movement data are needed to fully realise the potential of these tools.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101094"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144024431","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}
引用次数: 0
Diagnostic and phylogenetic perspectives of the 2023 Murray Valley encephalitis virus outbreak in Australia: an observational study 2023年澳大利亚默里谷脑炎病毒爆发的诊断和系统发育观点:一项观察性研究
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2025.101089
Annaleise R Howard-Jones DPhil , Jackie E Mahar PhD , Kate Proudmore MBBS , Grace I Butel-Simoes MD , John-Sebastian Eden PhD , Matthew J Neave PhD , Patrick Mileto (Hons) BSc , Linda Hueston PhD , Kevin Freeman BSc , Justin Ellem (Hons) BMedSci , Leon Caly PhD , Chisha Sikazwe PhD , Avram Levy PhD , Ashmitha Thomas MBBS , Carmel Taylor BSc , Nina Kurucz MSc , Kirsten Smyth MPHTM , Amy Jennison PhD , Peter Moore PhD , Rose Wright MPhil , Jen Kok PhD
{"title":"Diagnostic and phylogenetic perspectives of the 2023 Murray Valley encephalitis virus outbreak in Australia: an observational study","authors":"Annaleise R Howard-Jones DPhil ,&nbsp;Jackie E Mahar PhD ,&nbsp;Kate Proudmore MBBS ,&nbsp;Grace I Butel-Simoes MD ,&nbsp;John-Sebastian Eden PhD ,&nbsp;Matthew J Neave PhD ,&nbsp;Patrick Mileto (Hons) BSc ,&nbsp;Linda Hueston PhD ,&nbsp;Kevin Freeman BSc ,&nbsp;Justin Ellem (Hons) BMedSci ,&nbsp;Leon Caly PhD ,&nbsp;Chisha Sikazwe PhD ,&nbsp;Avram Levy PhD ,&nbsp;Ashmitha Thomas MBBS ,&nbsp;Carmel Taylor BSc ,&nbsp;Nina Kurucz MSc ,&nbsp;Kirsten Smyth MPHTM ,&nbsp;Amy Jennison PhD ,&nbsp;Peter Moore PhD ,&nbsp;Rose Wright MPhil ,&nbsp;Jen Kok PhD","doi":"10.1016/j.lanmic.2025.101089","DOIUrl":"10.1016/j.lanmic.2025.101089","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;An outbreak of Murray Valley encephalitis virus (MVEV), the largest since 1974, was observed in Australia between Jan 1 and July 31, 2023. This study aims to characterise the utility of diagnostic platforms, testing algorithms, and genomic characteristics of MVEV to facilitate a comprehensive framework for MVEV testing and surveillance in the outbreak setting.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;In this observational study, we assessed flavivirus diagnostics for all patients with suspected Murray Valley encephalitis in Australia from Jan 1 to July 31, 2023. We included all patients with confirmed Murray Valley encephalitis, probable Murray Valley encephalitis, or acute unspecified flavivirus infection using the Communicable Diseases Network Australia case definition. Cases were excluded if an alternative diagnosis was identified. We collected blood, serum, cerebrospinal fluid, brain tissue, urine, or a combination of these samples, as appropriate and at the discretion of the treating clinician. We conducted multimodal diagnostic testing, which included flavivirus-specific serological and nucleic acid amplification testing. Metagenomic next-generation sequencing, including next-generation deep sequencing, target-enrichment, and targeted amplification, was conducted on human and representative mosquito-derived samples obtained from established mosquito population surveillance programmes for phylogenetic analysis.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Findings&lt;/h3&gt;&lt;div&gt;27 patients with encephalitis were assessed for MVEV between Jan 1, 2023, and July 31, 2023, 23 (85%) of whom fulfilled national case definitions for confirmed Murray Valley encephalitis. Patient ages ranged from 6 weeks to 83 years (median 62·0 years [IQR 31·0-67·5]) and patients were mostly male (21 [78%] male patients and six [22%] female patients). Incidence varied widely by geographical region and was highest in the Northern Territory (32·0 per 1 000 000 population). Diagnostic specimen collection generally occurred promptly (median 6·0 days [IQR 4·0–14·5] from symptom onset to diagnostic specimen collection). In seven patients, case assignation relied on convalescent serum samples to assess for seroconversion or an appropriate rise in antibody titre (to four times the initial value or greater), or both. MVEV-specific IgM was detectable in serum samples of 17 (81%) of 21 patients tested by day 7 and MVEV IgG or total antibody (TAb) were detected in 18 (100%) of 18 patients tested by day 30. MVEV-specific IgM (or TAb) and MVEV RNA were detected in cerebrospinal fluid collected within 14 days of symptom onset in nine (39%) of 23 patients and seven (28%) of 25 patients, respectively. Phylogenetic analysis revealed two circulating MVEV genotypes, G1A and G2, in mosquitoes and humans in 2023. In southeast Australia, only G1A was detected and probably introduced from enzootic foci in northern Australia.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Interpretation&lt;/h3&gt;&lt;div&gt;This study provides a compr","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101089"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144477175","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}
引用次数: 0
Hepatitis B virus resistance to nucleos(t)ide analogue therapy: WHO consultation on questions, challenges, and a roadmap for the field 乙型肝炎病毒对核苷类似物治疗的耐药性:世卫组织就该领域的问题、挑战和路线图进行磋商。
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2025.101076
Sheila F Lumley PhD MRCP , Jolynne Mokaya PhD , Tongai G Maponga PhD , Prof Anna Kramvis PhD , Prof Geoffrey Dusheiko FRCP , Prof William Irving PhD , Marion Delphin PhD , Khadija Said Mohammed MSc , Louise O Downs FRCPath , Elizabeth Waddilove MSc , Motswedi Anderson PhD , Prof Collins Iwuji MBBS MD , Nokukhanya Msomi MBChB PhD , Ponsiano Ocama MD PhD , Prof Saeed Hamid FRCP , Danjuma Adda MPH , Rachel Halford , Kenneth Kabagambe MPH , Kimberley S M Benschop PhD , Seth Inzaule PhD , Prof Philippa C Matthews PhD FRCPath
{"title":"Hepatitis B virus resistance to nucleos(t)ide analogue therapy: WHO consultation on questions, challenges, and a roadmap for the field","authors":"Sheila F Lumley PhD MRCP ,&nbsp;Jolynne Mokaya PhD ,&nbsp;Tongai G Maponga PhD ,&nbsp;Prof Anna Kramvis PhD ,&nbsp;Prof Geoffrey Dusheiko FRCP ,&nbsp;Prof William Irving PhD ,&nbsp;Marion Delphin PhD ,&nbsp;Khadija Said Mohammed MSc ,&nbsp;Louise O Downs FRCPath ,&nbsp;Elizabeth Waddilove MSc ,&nbsp;Motswedi Anderson PhD ,&nbsp;Prof Collins Iwuji MBBS MD ,&nbsp;Nokukhanya Msomi MBChB PhD ,&nbsp;Ponsiano Ocama MD PhD ,&nbsp;Prof Saeed Hamid FRCP ,&nbsp;Danjuma Adda MPH ,&nbsp;Rachel Halford ,&nbsp;Kenneth Kabagambe MPH ,&nbsp;Kimberley S M Benschop PhD ,&nbsp;Seth Inzaule PhD ,&nbsp;Prof Philippa C Matthews PhD FRCPath","doi":"10.1016/j.lanmic.2025.101076","DOIUrl":"10.1016/j.lanmic.2025.101076","url":null,"abstract":"<div><div>In this Review, we summarise outputs from a multidisciplinary consultation convened by WHO between July 11 and 13, 2023, to discuss hepatitis B virus (HBV) drug resistance (HBVDR). Treatment of chronic HBV infection with highly effective nucleos(t)ide analogue agents, tenofovir and entecavir, is a crucial intervention that supports the global goal of elimination of HBV infection as a public health threat. The risk of HBVDR as a threat to treatment outcomes is currently considered low from a public health perspective; however, drug resistance can influence individual outcomes, particularly among those who are treatment-experienced. We highlight the need to develop appropriate prevention, monitoring, and surveillance approaches for HBVDR, to support investment in the global scale-up of HBV diagnosis and treatment. Recommendations for the HBVDR field will ultimately be incorporated into a WHO integrated Global Action Plan for drug-resistant HIV, viral hepatitis, and priority sexually transmitted infections.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101076"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144062749","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}
引用次数: 0
Efficacy, safety, pharmacokinetics, and associated microbiome changes of ibezapolstat compared with vancomycin in adults with Clostridioides difficile infection: a phase 2b, randomised, double-blind, active-controlled, multicentre study ibezapolstat与万古霉素在成人艰难梭菌感染中的疗效、安全性、药代动力学和相关微生物组变化:一项2b期、随机、双盲、主动对照的多中心研究。
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2025.101126
Taryn A Eubank PharmD , Jinhee Jo PharmD , M Jahangir Alam PhD , Khurshida Begum PhD , Jacob K McPherson PharmD , ThanhPhuong M Le PharmD , Thomas D Horvath PhD , Sigmund J Haidacher BS , Eugene C Poggio PhD , Rong Lin MD , Corinne Seng Yue PhD , Murray P Ducharme PharmD , Georges Koudssi BS , Julie Mercier BS , Jeffrey D Alder PhD , Michael H Silverman MD , Prof Kevin W Garey PharmD
{"title":"Efficacy, safety, pharmacokinetics, and associated microbiome changes of ibezapolstat compared with vancomycin in adults with Clostridioides difficile infection: a phase 2b, randomised, double-blind, active-controlled, multicentre study","authors":"Taryn A Eubank PharmD ,&nbsp;Jinhee Jo PharmD ,&nbsp;M Jahangir Alam PhD ,&nbsp;Khurshida Begum PhD ,&nbsp;Jacob K McPherson PharmD ,&nbsp;ThanhPhuong M Le PharmD ,&nbsp;Thomas D Horvath PhD ,&nbsp;Sigmund J Haidacher BS ,&nbsp;Eugene C Poggio PhD ,&nbsp;Rong Lin MD ,&nbsp;Corinne Seng Yue PhD ,&nbsp;Murray P Ducharme PharmD ,&nbsp;Georges Koudssi BS ,&nbsp;Julie Mercier BS ,&nbsp;Jeffrey D Alder PhD ,&nbsp;Michael H Silverman MD ,&nbsp;Prof Kevin W Garey PharmD","doi":"10.1016/j.lanmic.2025.101126","DOIUrl":"10.1016/j.lanmic.2025.101126","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;&lt;em&gt;Clostridioides difficile&lt;/em&gt; infection is a common health-care-associated and community-acquired disease with few antibiotic treatment options. We aimed to assess the safety, efficacy, pharmacokinetics, and associated microbiome changes of ibezapolstat, an antibiotic that inhibits the PolC-type DNA polymerase III α subunit C, versus vancomycin for the treatment of &lt;em&gt;C difficile&lt;/em&gt; infection in adults.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;This was a phase 2b, randomised, double-blind, active-controlled study conducted at 15 centres, primarily outpatient clinics and hospitals, in the USA. Adults aged 18–90 years, with signs and symptoms of &lt;em&gt;C difficile&lt;/em&gt; infection and a positive toxin stool test were recruited. Participants were randomly assigned (1:1) with block assignment by study site using an interactive web response system to receive oral ibezapolstat (450 mg twice daily) or oral vancomycin (125 mg every 6 h) for 10 days. Masking was achieved by over-encapsulation of both study drugs (ibezapolstat and vancomycin) and placebo into identically sized capsules. Participants were excluded if they had received more than 24 h of treatment with oral vancomycin, fidaxomicin, or metronidazole for the current episode of &lt;em&gt;C difficile&lt;/em&gt; infection before the first dose of study drug or any other antibacterial therapy within 48 h, had had more than three episodes of &lt;em&gt;C difficile&lt;/em&gt; infection in the previous 12 months, or had had more than one previous episode in the past 3 months (excluding the current episode). The primary efficacy endpoint was initial clinical cure maintained for at least 48 h after the end of treatment. All individuals with &lt;em&gt;C difficile&lt;/em&gt; infection who met inclusion and exclusion criteria, were randomly assigned, and were administered at least one dose of study drug were included in the efficacy analysis. The safety and tolerability of ibezapolstat was assessed in all individuals who were administered at least one dose of study drug. This study is registered with &lt;span&gt;&lt;span&gt;ClinicalTrials.gov&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;, &lt;span&gt;&lt;span&gt;NCT04247542&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Findings&lt;/h3&gt;&lt;div&gt;Between March 12, 2021, and Oct 27, 2023, 39 individuals were assessed for eligibility, 32 of whom were recruited and randomly assigned to ibezapolstat (n=18) or vancomycin (n=14). Two participants were excluded from the efficacy analysis: one participant in the ibezapolstat group withdrew consent before receiving the study drug and another was identified after random assignment as having an exclusion criterion. The primary efficacy analysis included 16 participants in the ibezapolstat group and 14 in the vancomycin group; 24 (80%) participants were female and six (20%) were male. 15 (94%) of 16 participants in the ibezapolstat group had initial clinical cure compared with 14 (100%) of 14 participants in the vancomycin group (treatment difference −6·3%","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101126"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295104","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}
引用次数: 0
The cost of blood cultures: a barrier to diagnosis in low-income and middle-income countries 血液培养成本:中低收入国家诊断的障碍。
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2025.101125
Peter Hyland , Jan Jacobs , Liselotte Hardy
{"title":"The cost of blood cultures: a barrier to diagnosis in low-income and middle-income countries","authors":"Peter Hyland ,&nbsp;Jan Jacobs ,&nbsp;Liselotte Hardy","doi":"10.1016/j.lanmic.2025.101125","DOIUrl":"10.1016/j.lanmic.2025.101125","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101125"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744214","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}
引用次数: 0
Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics 新生儿肠道菌群与2岁前严重病毒性下呼吸道感染之间关系的研究:一项宏基因组学出生队列研究
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2024.101072
Cristina Garcia-Mauriño MD PhD , Yan Shao PhD , Ada Miltz PhD , Trevor D Lawley PhD , Prof Alison Rodger MBBS PhD , Prof Nigel Field MB PhD
{"title":"Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics","authors":"Cristina Garcia-Mauriño MD PhD ,&nbsp;Yan Shao PhD ,&nbsp;Ada Miltz PhD ,&nbsp;Trevor D Lawley PhD ,&nbsp;Prof Alison Rodger MBBS PhD ,&nbsp;Prof Nigel Field MB PhD","doi":"10.1016/j.lanmic.2024.101072","DOIUrl":"10.1016/j.lanmic.2024.101072","url":null,"abstract":"<div><h3>Background</h3><div>Early-life gut microbiota affects immune system development, including the lung immune response (gut–lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs).</div></div><div><h3>Methods</h3><div>The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother–baby pairs between Jan 1, 2016, and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2 years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs.</div></div><div><h3>Findings</h3><div>3305 (95%) of the 3476 BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564 born vaginally and 518 born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2·0 years (IQR 1·4–2·9). Most babies were born at term (996 [92%] ≥37 weeks gestational age and 1070 [99%] &gt;35 weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0·92 [95% CI 0·85–0·99]; Shannon Index adjusted HR 0·57 [0·33–0·98]; and Simpson Index adjusted HR 0·36 [0·11–1·20]). Three microbiota clusters were identified. Cluster 1 had a mixed composition and cluster 2 was dominated by <em>Bifidobacterium breve</em>, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3 was found only in vaginally born babies and was dominated by <em>Bifidobacterium longum</em>. Having cluster 1 (mixed) or cluster 2 (<em>B breve</em> dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (<em>B longum</em> dominated; cluster 1 [mixed] 3·05 [1·25–7·41] and cluster 2 [<em>B breve</em> dominated] 2·80 [1·06–7·44]).</div></div><div><h3>Interpretation</h3><div>We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in youn","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101072"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250239","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}
引用次数: 0
Centrifuge-free stool processing methods for Xpert MTB/RIF Ultra tuberculosis diagnosis in children in Uganda and Zambia: an observational, prospective, diagnostic accuracy study 乌干达和赞比亚儿童MTB/RIF超结核诊断的无离心粪便处理方法:一项观察性、前瞻性、诊断准确性研究。
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2024.101055
Manon Lounnas PhD , Eden Ngu Masama MPH , Samuel Beneteau MSc , Kunda Kasakwa MSc , Rodney Kaitano MSc , Pamela Nabeta MD , Morten Ruhwald PhD , Petra De Haas BSc , Edine W Tiemersma PhD , Bwendo Nduna MMed , Mark P Nicol PhD , Sara Eyangoh PhD , Eric Wobudeya MD , Juliet Mwanga-Amumpaire PhD , Chishala Chabala MMed , Olivier Marcy PhD , Maryline Bonnet PhD
{"title":"Centrifuge-free stool processing methods for Xpert MTB/RIF Ultra tuberculosis diagnosis in children in Uganda and Zambia: an observational, prospective, diagnostic accuracy study","authors":"Manon Lounnas PhD ,&nbsp;Eden Ngu Masama MPH ,&nbsp;Samuel Beneteau MSc ,&nbsp;Kunda Kasakwa MSc ,&nbsp;Rodney Kaitano MSc ,&nbsp;Pamela Nabeta MD ,&nbsp;Morten Ruhwald PhD ,&nbsp;Petra De Haas BSc ,&nbsp;Edine W Tiemersma PhD ,&nbsp;Bwendo Nduna MMed ,&nbsp;Mark P Nicol PhD ,&nbsp;Sara Eyangoh PhD ,&nbsp;Eric Wobudeya MD ,&nbsp;Juliet Mwanga-Amumpaire PhD ,&nbsp;Chishala Chabala MMed ,&nbsp;Olivier Marcy PhD ,&nbsp;Maryline Bonnet PhD","doi":"10.1016/j.lanmic.2024.101055","DOIUrl":"10.1016/j.lanmic.2024.101055","url":null,"abstract":"<div><h3>Background</h3><div>WHO recommends Xpert MTB/RIF Ultra (Ultra) for stool testing for tuberculosis diagnosis in children. Stool processing requires removal of debris and PCR inhibitors, frequently by using centrifugation, which can be an implementation barrier for low-income and middle-income countries (LMICs). We evaluated the diagnostic accuracy of Ultra on stool using three centrifuge-free processing methods, the simple one-step (SOS), stool processing kit (SPK), and the optimised sucrose flotation (OSF) methods against a microbiological reference standard (MRS).</div></div><div><h3>Methods</h3><div>In this observational, prospective, multicountry, diagnostic accuracy study, we collected two respiratory samples and two stool samples in children younger than 15 years with presumptive tuberculosis in one hospital in Uganda and two hospitals in Zambia for Ultra testing and culture (on respiratory samples only). We defined positive MRS as positive culture or Ultra on respiratory sample and negative MRS as two negative respiratory samples by either culture or Ultra. We assessed the perception of the laboratory operators of test ease-of-use using a self-administered questionnaire at all sites. This study is registered with <span><span>ClinicalTrials.gov</span><svg><path></path></svg></span> (<span><span>NCT04203628</span><svg><path></path></svg></span>) and the Pan African Clinical Trial Registry (PACTR202006814433059).</div></div><div><h3>Findings</h3><div>Of the 216 children enrolled between Jan 13, 2020, and Dec 31, 2021, 215 were included in the study and of these 104 (48·4%) were female and 211 (51·6%) were male, the median age was 1·8 years (IQR 1·1–4·8), 68 (31·6%) were HIV positive, and 38 (17·7%) were MRS positive. For one or both stool samples, depending on availability, the sensitivity of stool Ultra against MRS was 69·7% (95% CI 51·3–84·4) for SOS, 69·7% (51·3–84·4) for SPK, and 73·5% (55·6–87·1) for OSF (McNemar test p&gt;0·6 for all), with a specificity above 96% for all methods. The SOS stool method was considered the easiest by six of seven operators because it required least manipulation and no additional reagents.</div></div><div><h3>Interpretation</h3><div>Centrifuge-free stool processing methods could improve access to microbiological diagnosis of tuberculosis in LMICs. These results contributed to the WHO endorsement of the SOS and OSF methods.</div></div><div><h3>Funding</h3><div>UNITAID.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101055"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144508827","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}
引用次数: 0
Defining the serotypes of SARS-CoV-2 subvariants up to December, 2024 确定截至2024年12月SARS-CoV-2亚型的血清型。
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2025.101124
Pei Du , Jiajing Li , Tianxiang Kong , Bin Lu , Ruiqi Li , George Fu Gao , Qihui Wang
{"title":"Defining the serotypes of SARS-CoV-2 subvariants up to December, 2024","authors":"Pei Du ,&nbsp;Jiajing Li ,&nbsp;Tianxiang Kong ,&nbsp;Bin Lu ,&nbsp;Ruiqi Li ,&nbsp;George Fu Gao ,&nbsp;Qihui Wang","doi":"10.1016/j.lanmic.2025.101124","DOIUrl":"10.1016/j.lanmic.2025.101124","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101124"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040079","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}
引用次数: 0
Fungal Update: Mycology 2025 真菌更新:真菌学2025。
IF 20.4 1区 生物学
Lancet Microbe Pub Date : 2025-08-01 DOI: 10.1016/j.lanmic.2025.101152
Elena Dalla Vecchia
{"title":"Fungal Update: Mycology 2025","authors":"Elena Dalla Vecchia","doi":"10.1016/j.lanmic.2025.101152","DOIUrl":"10.1016/j.lanmic.2025.101152","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"6 8","pages":"Article 101152"},"PeriodicalIF":20.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041760","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}
引用次数: 0
Beyond bacteria: a multikingdom ecological perspective on neonatal gut and severe viral lower respiratory tract infection risk. 超越细菌:新生儿肠道和严重病毒性下呼吸道感染风险的多领域生态学观点。
IF 20.9 1区 生物学
Lancet Microbe Pub Date : 2025-07-17 DOI: 10.1016/j.lanmic.2025.101202
Jiaqi Wang, Zengguo Cao, Xuemin Jin
{"title":"Beyond bacteria: a multikingdom ecological perspective on neonatal gut and severe viral lower respiratory tract infection risk.","authors":"Jiaqi Wang, Zengguo Cao, Xuemin Jin","doi":"10.1016/j.lanmic.2025.101202","DOIUrl":"https://doi.org/10.1016/j.lanmic.2025.101202","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101202"},"PeriodicalIF":20.9,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676095","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}
引用次数: 0
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