Lancet Microbe最新文献

{"title":"Genomic reconstruction of an azole-resistant Candida parapsilosis outbreak and the creation of a multi-locus sequence typing scheme: a retrospective observational and genomic epidemiology study.","authors":"Phillip J T Brassington, Frank-Rainer Klefisch, Barbara Graf, Roland Pfüller, Oliver Kurzai, Grit Walther, Amelia E Barber","doi":"10.1016/j.lanmic.2024.07.012","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.07.012","url":null,"abstract":"<p><strong>Background: </strong>Fluconazole-resistant Candida parapsilosis has emerged as a significant health-care-associated pathogen with a propensity to spread patient to patient and cause nosocomial outbreaks, similar to Candida auris. This study investigates a long-lasting outbreak of fluconazole-resistant C parapsilosis that was initially detected in December, 2018, and January, 2019, and officially declared in November, 2019; lasted multiple years; and involved several health-care centres in Berlin, Germany.</p><p><strong>Methods: </strong>In this retrospective, observational, and genomic epidemiology study, we used whole-genome sequencing (WGS) of isolates sent by German health-care facilities and laboratories to the National Reference Center for Invasive Fungal Infections (Jena, Germany) for antifungal susceptibility testing between Jan 1, 2016, and Dec 31, 2022. We included all potential outbreak samples (ie, isolates originating from Berlin that were resistant to fluconazole and voriconazole but susceptible to posaconazole) and all non-outbreak isolates that originated from outside of Berlin and were resistant to at least one azole. We also included a number of non-outbreak isolates from outside Berlin that were susceptible or resistant to azoles so that the total study dataset included a matching amount of outbreak and non-outbreak samples from Germany. We used admission and discharge records for patients involved in the outbreak and constructed a network of patient transfers in time and space. We used WGS data for included samples, complemented with WGS data for global samples obtained from the National Center for Biotechnology Information Sequence Read Archive, to construct single-nucleotide variant (SNV)-based phylogeny and perform SNV distance-based analyses. Additionally, we used the whole genomic dataset to identify loci with high discriminatory power to establish a multi-locus sequence typing (MLST) strategy for C parapsilosis.</p><p><strong>Findings: </strong>We identified 38 clonal, azole-resistant isolates of C parapsilosis causing 33 cases of invasive infection during a 2018-22 outbreak in multiple hospitals in Berlin. We also sequenced the genomes of 37 non-outbreak isolates. WGS revealed that outbreak strains were separated by a mean of 36 SNVs (SD 20), whereas outbreak strains differed from outgroup samples from Berlin and other regions of Germany by a mean of 2112 SNVs (828). Temporal and genomic reconstruction of the outbreak cases indicated that transfer of patients between health-care facilities was probably responsible for the persistent reimportation of the drug-resistant clone and subsequent person-to-person transmission. German outbreak strains were closely related to strains responsible for an outbreak in Canada and to isolates from Kuwait, Türkiye, and South Korea. Including the outbreak clone, we identified three distinct azole-resistant lineages carrying ERG11 Y132F in Germany. We identified four 750 bp loci","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"100949"},"PeriodicalIF":20.9,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142669013","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":"Reassessing the role of butyrate-producing bacteria in infection risk.","authors":"Rajesh Parsanathan","doi":"10.1016/j.lanmic.2024.101036","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.101036","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101036"},"PeriodicalIF":20.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640068","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":"Variability of Mycobacterium tuberculosis lipid body content in sputum and its implications for treatment response.","authors":"Mohamed Imath, Viswanathan Sathyanathan, Suresh Velayudam, R A M Jainaf Nachiya","doi":"10.1016/j.lanmic.2024.101024","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.101024","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101024"},"PeriodicalIF":20.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640070","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":"Therapeutics for Nipah virus disease: a systematic review to support prioritisation of drug candidates for clinical trials.","authors":"Xin Hui S Chan, Ilsa L Haeusler, Bennett J K Choy, Md Zakiul Hassan, Junko Takata, Tara P Hurst, Luke M Jones, Shanghavie Loganathan, Elinor Harriss, Jake Dunning, Joel Tarning, Miles W Carroll, Peter W Horby, Piero L Olliaro","doi":"10.1016/j.lanmic.2024.101002","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.101002","url":null,"abstract":"<p><p>Nipah virus disease is a bat-borne zoonosis with person-to-person transmission, a case-fatality rate of 38-75%, and well recognised potential to cause a pandemic. The first reported outbreak of Nipah virus disease occurred in Malaysia and Singapore in 1998, which has since been followed by multiple outbreaks in Bangladesh and India. To date, no therapeutics or vaccines have been approved to treat Nipah virus disease, and only few such candidates are in development. In this Review, we aim to assess the safety and efficacy of the therapeutic options (monoclonal antibodies and small molecules) for Nipah virus disease and other henipaviral diseases to support prioritisation of drug candidates for further evaluation in clinical trials. At present, sufficient evidence exists to suggest trialling 1F5, m102.4, and remdesivir (alone or in combination) for prophylaxis and early treatment of Nipah virus disease. In addition to well designed clinical efficacy trials, in-vivo pharmacokinetic-pharmacodynamic studies are needed to optimise the selection and dosing of therapeutic candidates in animal challenge and natural human infection.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101002"},"PeriodicalIF":20.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644707","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":"Using demographics of patients to inform treatment of shigellosis in England.","authors":"Lewis C E Mason, Daniel Richardson, Hannah Charles, Ian Simms, Holly D Mitchell, Rohini Manuel, Gauri Godbole, Claire Jenkins, Kate S Baker","doi":"10.1016/j.lanmic.2024.101026","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.101026","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101026"},"PeriodicalIF":20.9,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640069","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":"Impact of vaccines in reducing antimicrobial resistance.","authors":"Timothy Jesudason","doi":"10.1016/j.lanmic.2024.101040","DOIUrl":"10.1016/j.lanmic.2024.101040","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101040"},"PeriodicalIF":20.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142630081","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":"Performance of stool-based molecular tests and processing methods for paediatric tuberculosis diagnosis: a systematic review and meta-analysis.","authors":"Lucía Carratalà-Castro, Shilzia Munguambe, Belén Saavedra-Cervera, Petra de Haas, Alexander Kay, Olivier Marcy, Pamela Nabeta, Willy Ssengooba, Elisabetta Ghimenton-Walters, Sozinho Acácio, Maryline Bonnet, Joanna Ehrlich, Andrew R DiNardo, Anca Vasiliu, Christoph Lange, Sabine Hermans, Anna M Mandalakas, Elisa López-Varela, Alberto L García-Basteiro","doi":"10.1016/j.lanmic.2024.100963","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.100963","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;There has been a global pursuit to improve the diagnosis of tuberculosis in young children by applying diagnostic methods on accessible biospecimens such as stool. We aimed to conduct a systematic review on the accuracy of stool-based molecular tests for tuberculosis diagnosis in children and to assess the impact of the available pre-processing methods and other design characteristics.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;In this systematic review and meta-analysis, we evaluated studies in children younger than 16 years with presumptive tuberculosis that were published in English, Spanish, French, and Portuguese from Jan 1, 2000, to May 3, 2024, in MEDLINE, Embase, and Embase Classic, comparing the molecular detection of Mycobacterium tuberculosis DNA in stool with microbiological tests on other samples or a clinical diagnosis. We did not exclude studies based on geographical location, sample size, or study design if they were reporting primary data. Two independent reviewers (LC-C and SM) screened titles, abstracts, and full-text articles for eligibility and extracted data on study characteristics, study population, and diagnostic performance. If information relevant to the main analysis was not reported in the article, the corresponding authors were contacted. Point estimates and 95% CIs were calculated for sensitivity and specificity for each study and for the different molecular tests (Xpert MTB/RIF, Xpert Ultra MTB/RIF [Cepheid, Sunnyvale, CA, USA], and other tests) versus a reference standard (culture only, any bacteriological confirmation, and tuberculosis case definition). Sensitivity and specificity were stratified by the stool processing method. We also quantified the additionality of stool Xpert Ultra tests for tuberculosis bacteriological confirmation. The protocol was registered with PROSPERO, CRD42022341514.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Findings: &lt;/strong&gt;A total of 4521 records were identified through the database search, one record was identified from an article bibliography, and 67 studies were retained for full-text reading. 39 studies were included in the qualitative synthesis, 35 of which were included in the meta-analyses. When using any bacteriological confirmation from a respiratory sample as the reference standard, stool Xpert sensitivity was 0·60 (95% CI 0·48-0·71), stool Xpert Ultra sensitivity was 0·73 (0·63-0·81), and sensitivity was 0·44 (0·29-0·60) for other in-house molecular methods combined. When using tuberculosis case definition as the reference standard, stool Xpert sensitivity was 0·23 (0·11-0·41), stool Xpert Ultra sensitivity was 0·38 (0·22-0·56), and sensitivity was 0·17 (0·09-0·23) for other in-house molecular methods. The addition of stool Xpert Ultra increased bacteriological confirmation of tuberculosis by 38·6% overall. Further, the utilisation of centrifuge-free simplified methods improved the sensitivity of stool Xpert Ultra when using any bacteriological confirmation as a reference stand","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"100963"},"PeriodicalIF":20.9,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640067","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":"Yellow fever breakthrough infections after yellow fever vaccination: a systematic review and meta-analysis.","authors":"Jenny L Schnyder, Bache E Bache, Matthijs R A Welkers, René Spijker, Frieder Schaumburg, Abraham Goorhuis, Martin P Grobusch, Hanna K de Jong","doi":"10.1016/j.lanmic.2024.06.004","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.06.004","url":null,"abstract":"<p><strong>Background: </strong>Yellow fever vaccination is considered to provide effective long-term immunity. However, yellow fever breakthrough infections in vaccinated patients have been reported. In this systematic review and meta-analysis we aimed to identify and summarise all documented symptomatic yellow fever breakthrough infections in the literature occurring less than 10 years and 10 years or more after primary yellow fever vaccination.</p><p><strong>Methods: </strong>We searched MEDLINE (Ovid), Embase (Ovid), and Global Index Medicus for records published between Jan 1, 1936 (introduction of yellow fever vaccination) and June 16, 2023. We included prospective and retrospective cohort studies, case series and reports, and epidemiological reports from national and international health organisations reporting symptomatic yellow fever among individuals vaccinated 30 days or more before symptom onset. We excluded cases vaccinated less than 30 days before symptom onset. The primary outcome for the meta-analysis was the proportions of vaccinees among virologically confirmed and probable cases of yellow fever (IgM seroconversion without seroconversion to other flaviviruses). Risk of bias was assessed with an adapted version of the Newcastle-Ottawa Scale. Records of moderate or good quality (probable or confirmed yellow fever diagnosis with documented proof of previous vaccination) were included for random-effects meta-analysis. This systematic review and meta-analysis is registered with PROSPERO, number CRD42023450205.</p><p><strong>Findings: </strong>After reviewing 1975 records, 37 records reported a total of 6951 yellow fever cases, of which 537 were vaccinated. 31 records were of low quality. Nine confirmed and 24 probable cases with proof of previous yellow fever vaccination were identified, all from Brazil. Confirmed cases were vaccinated 3 months to 3 years before symptom onset; of these patients two fell severely ill and died. The pooled proportion of verified yellow fever breakthrough infections among probable and confirmed cases was 3% (95% CI 1-19%). No confirmed yellow fever breakthrough infections were identified occurring 10 years or more after yellow fever vaccination.</p><p><strong>Interpretation: </strong>Yellow fever breakthrough infections documented in literature are rare, and not necessarily more common 10 years or more after primary yellow fever vaccination. This finding suggests that a single dose of yellow fever vaccination is sufficient to provide lifelong protective immunity against symptomatic yellow fever.</p><p><strong>Funding: </strong>None.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"100937"},"PeriodicalIF":20.9,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142630084","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":"Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis.","authors":"Olivo Miotto, Alfred Amambua-Ngwa, Lucas N Amenga-Etego, Muzamil M Abdel Hamid, Ishag Adam, Enoch Aninagyei, Tobias Apinjoh, Gordon A Awandare, Philip Bejon, Gwladys I Bertin, Marielle Bouyou-Akotet, Antoine Claessens, David J Conway, Umberto D'Alessandro, Mahamadou Diakite, Abdoulaye Djimdé, Arjen M Dondorp, Patrick Duffy, Rick M Fairhurst, Caterina I Fanello, Anita Ghansah, Deus S Ishengoma, Mara Lawniczak, Oumou Maïga-Ascofaré, Sarah Auburn, Anna Rosanas-Urgell, Varanya Wasakul, Nina F D White, Alexandria Harrott, Jacob Almagro-Garcia, Richard D Pearson, Sonia Goncalves, Cristina Ariani, Zbynek Bozdech, William L Hamilton, Victoria Simpson, Dominic P Kwiatkowski","doi":"10.1016/j.lanmic.2024.07.004","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.07.004","url":null,"abstract":"<p><strong>Background: </strong>The population structure of the malaria parasite Plasmodium falciparum can reveal underlying adaptive evolutionary processes. Selective pressures to maintain complex genetic backgrounds can encourage inbreeding, producing distinct parasite clusters identifiable by population structure analyses.</p><p><strong>Methods: </strong>We analysed population structure in 3783 P falciparum genomes from 21 countries across Africa, provided by the MalariaGEN Pf7 dataset. We used Principal Coordinate Analysis to cluster parasites, identity by descent (IBD) methods to identify genomic regions shared by cluster members, and linkage analyses to establish their co-inheritance patterns. Structural variants were reconstructed by de novo assembly and verified by long-read sequencing.</p><p><strong>Findings: </strong>We identified a strongly differentiated cluster of parasites, named AF1, comprising 47 (1·2%) of 3783 samples analysed, distributed over 13 countries across Africa, at locations over 7000 km apart. Members of this cluster share a complex genetic background, consisting of up to 23 loci harbouring many highly differentiated variants, rarely observed outside the cluster. IBD analyses revealed common ancestry at these loci, irrespective of sampling location. Outside the shared loci, however, AF1 members appear to outbreed with sympatric parasites. The AF1 differentiated variants comprise structural variations, including a gene conversion involving the dblmsp and dblmsp2 genes, and numerous single nucleotide polymorphisms. Several of the genes harbouring these mutations are functionally related, often involved in interactions with red blood cells including invasion, egress, and erythrocyte antigen export.</p><p><strong>Interpretation: </strong>We propose that AF1 parasites have adapted to some unidentified evolutionary niche, probably involving interactions with host erythrocytes. This adaptation involves a complex compendium of interacting variants that are rarely observed in Africa, which remains mostly intact despite recombination events. The term cryptotype was used to describe a common background interspersed with genomic regions of local origin.</p><p><strong>Funding: </strong>Bill & Melinda Gates Foundation.</p>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"100941"},"PeriodicalIF":20.9,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142630078","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":"Burden of infectious diseases in Sudan.","authors":"Priya Venkatesan","doi":"10.1016/j.lanmic.2024.101035","DOIUrl":"https://doi.org/10.1016/j.lanmic.2024.101035","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":" ","pages":"101035"},"PeriodicalIF":20.9,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142630010","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}