Lancet Microbe最新文献

{"title":"Promoting sustainable national action to tackle antimicrobial resistance: a proposal to develop an antimicrobial resistance accountability index","authors":"Michael Anderson , Hans Henri P Kluge , Danilo Lo Fo Wong , Robb Butler , Elias Mossialos","doi":"10.1016/j.lanmic.2024.100997","DOIUrl":"10.1016/j.lanmic.2024.100997","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100997"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356164","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":"Human cases of avian influenza A(H5) in the USA","authors":"Priya Venkatesan","doi":"10.1016/j.lanmic.2024.100978","DOIUrl":"10.1016/j.lanmic.2024.100978","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100978"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146581","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":"Global and regional genetic diversity of HIV-1 in 2010–21: systematic review and analysis of prevalence","authors":"Malavika Nair BA ,&nbsp;Lucy Gettins MSc ,&nbsp;Matthew Fuller BA ,&nbsp;Shona Kirtley MSc ,&nbsp;Prof Joris Hemelaar DPhil","doi":"10.1016/S2666-5247(24)00151-4","DOIUrl":"10.1016/S2666-5247(24)00151-4","url":null,"abstract":"<div><h3>Background</h3><div>The extensive global genetic diversity of HIV-1 poses a major challenge to HIV vaccine development. We aimed to determine recent estimates of and changes in the global and regional distributions of HIV-1 genetic variants.</div></div><div><h3>Methods</h3><div>We conducted a systematic literature review by searching PubMed, Embase, Global Health, and CINAHL for studies containing country-specific HIV-1 subtyping data, published between Jan 1, 2010 and Sep 16, 2022. The proportions of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in each country were weighted by UNAIDS estimates of the numbers of people living with HIV (PLHIV) in each country to obtain regional and global prevalence estimates of HIV-1 subtypes, CRFs, and URFs with 95% CIs for the time periods 2010–15 and 2016–21. The protocol is registered with PROSPERO, CRD42017067164.</div></div><div><h3>Findings</h3><div>We obtained 1044 datasets, containing HIV-1 subtyping data from 653 013 PLHIV from 122 countries in 2010–2021. In 2016–2021, subtype C accounted for 50·4% (95% CI 50·2–50·7; n=18 570 462 of 36 823 798) of global HIV infections, subtype A for 12·4% (12·2–12·6; n=4 571 250), subtype B for 11·3% (11·1–11·5; n=4 157 686), subtype G for 2·9% (2·9–3·0; n=1 083 568), subtype D for 2·6% (2·5–2·7; n=945 815), subtype F for 0·9% (0·8–0·9; n=316 724), CRFs for 15·1% (14·9–15·3; n=5 564 566), and URFs for 2·0% (1·9–2·1; n=733 374). Subtypes H, J, and K each accounted for 0·1% or less of infections. Compared with 2010–15, we observed significant (p&lt;0·0001) increases in global proportions of subtype A (0·9%, 95% CI 0·7 to 1·1) and subtype C (3·4%, 3·0 to 3·7) and decreases in subtype D (–0·5%, –0·6 to –0·4), subtype G (–0·8%, –1·0 to –0·7), CRFs (–1·0%, –1·3 to –0·8), and URFs (–1·8%, –1·9 to –1·7), with no changes for subtypes B and F. The global proportion of infections attributed to recombinants decreased from 21·6% (95% CI 21·4 to 21·7; n=7 099 252 of 32 622 808) in 2010–15 to 19·3% (19·1 to 19·5; n=7 094 694 of 36 823 798) in 2016–21 (–2·3%, 95% CI –2·6 to –2·0; p&lt;0·0001). Regional distributions of HIV-1 variants were complex and evolving, with global trends in the prevalence of HIV-1 variants supported by trends across the regions.</div></div><div><h3>Interpretation</h3><div>Global and regional HIV-1 genetic diversity are complex and continue to evolve. Continued and improved surveillance of HIV-1 variants remains vital for HIV vaccine development and implementation.</div></div><div><h3>Funding</h3><div>None.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100912"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142298320","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":"The future of large language models in fighting emerging outbreaks: lights and shadows","authors":"Alberto Rizzo ,&nbsp;Enrico Mensa ,&nbsp;Andrea Giacomelli","doi":"10.1016/j.lanmic.2024.07.017","DOIUrl":"10.1016/j.lanmic.2024.07.017","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100954"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879577","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":"Effects of doxycycline post-exposure prophylaxis for prevention of sexually transmitted infections on gonorrhoea prevalence and antimicrobial resistance among men who have sex with men in the USA: a modelling study","authors":"Emily Reichert MSc ,&nbsp;Prof Yonatan H Grad MD PhD","doi":"10.1016/S2666-5247(24)00168-X","DOIUrl":"10.1016/S2666-5247(24)00168-X","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;Doxycycline post-exposure prophylaxis (PEP) has been shown to be efficacious for the prevention of bacterial sexually transmitted infections, but resistance implications for &lt;em&gt;Neisseria gonorrhoeae&lt;/em&gt; remain unknown. We aimed to use a mathematical model to investigate the anticipated impact of doxycycline PEP on the burden of gonorrhoea and antimicrobial resistance dynamics in men who have sex with men (MSM) in the USA.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;Using a deterministic compartmental model, characterising gonorrhoea transmission in a US MSM population comprising three sexual activity groups defined by annual partner turnover rates, we introduced doxycycline PEP at various uptake levels (10–90%) among those with high sexual activity. Infections were stratified by symptom status and resistance profile (ie, susceptible, ceftriaxone-resistant, tetracycline-resistant, or dual-resistant), with ceftriaxone the treatment for active infection. As resistance to tetracycline, not doxycycline, is monitored and reported nationally, we used this as a proxy for doxycycline PEP resistance. We compared the 20-year prevalence, incidence rates, and cumulative incidence of gonococcal infection, resistance dynamics (time to 5% prevalence of ceftriaxone resistance, 5% prevalence of dual resistance, and 84% prevalence of tetracycline resistance), and antibiotic consumption with baseline (ie, no doxycycline PEP).&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Findings&lt;/h3&gt;&lt;div&gt;Uptake of doxycycline PEP resulted in substantial reductions in the prevalence and incidence of gonorrhoea, but accelerated the spread of tetracycline resistance. The maximum reduction in prevalence over 20 years compared with no uptake ranged from 40·3% (IQR 15·3–83·4) with 10% doxycycline PEP uptake to 77·4% (68·4–84·9) with 90% uptake. Similarly, the maximum reduction in the incidence rate ranged from 38·6% (14·1–83·6) with 10% uptake to 77·6% (68·1–84·7) with 90% uptake. Cumulative gonococcal infections were reduced by a median of 14·5% (IQR 8·4–21·6) with 10% uptake and up to 46·2% (26·5–59·9) with 90% uptake after 5 years, and by 6·5% (3·4–13·0) with 10% uptake and 8·7% (4·3–36·2) with 90% uptake by 20 years. In almost all scenarios explored, doxycycline PEP lost clinical effectiveness (defined as 84% prevalence of tetracycline resistance) within the 20-year period, but its lifespan ranged from a median of 12·1 years (IQR 9·9–15·7) with 10% uptake to 1·6 years (1·3–1·9) with 90% uptake. Doxycycline PEP implementation had minimal impact on extending the clinical lifespan of ceftriaxone monotherapy (5·0 years [IQR 4·0–6·2]), with the median time to 5% prevalence of resistance ranging from 4·8 years (3·9–6·0) for 90% uptake to 5·0 years (4·1–6·2) for 10% uptake. Similarly, the median time to 5% prevalence of dual resistance to ceftriaxone and tetracycline ranged from 4·8 years (3·9–6·0) for 90% uptake to 5·8 years (4·8–7·4) for 10% uptake. Median decrease in ceftriaxone consumptio","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100926"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142394171","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":"Detection of dengue virus and chikungunya virus in wastewater in Portugal: an exploratory surveillance study","authors":"Sílvia Monteiro PhD ,&nbsp;Raquel Pimenta MSc ,&nbsp;Filipa Nunes MSc ,&nbsp;Mónica V Cunha PhD ,&nbsp;Ricardo Santos PhD","doi":"10.1016/S2666-5247(24)00150-2","DOIUrl":"10.1016/S2666-5247(24)00150-2","url":null,"abstract":"<div><h3>Background</h3><div>The global distribution and prevalence of arboviral diseases have increased in recent years, driven by factors such as climate change, biodiversity loss, globalisation, and urbanisation. These diseases are often underestimated due to uneven surveillance and unreported asymptomatic cases. Current surveillance relies on vector and clinical surveillance. In this study, we aimed to explore wastewater-based surveillance (WBS) as an additional tool for dengue virus (DENV) and chikungunya virus (CHIKV) tracking.</div></div><div><h3>Methods</h3><div>In this exploratory surveillance study, WBS was done at eleven wastewater treatment plants in three regions in Portugal (North, Lisboa and Vale do Tejo, and south). Using quantitative RT-PCR, we quantified in raw wastewater the RNA concentrations of DENV and CHIKV (non-structural viral protein 1 [<em>nsP1</em>] and envelope protein [<em>E1</em>] genes) once every 2 weeks for a period of 11 months, between May 16, 2022, and April 19, 2023. Results were normalised with crAssphage (concentration of target viral RNA divided by the concentration of crAssphage DNA) and provided as median normalised viral load. Prevalence (proportion of positive samples) and viral quantities were summarised for the total sampling period, by calendar month, and by seasons.</div></div><div><h3>Findings</h3><div>273 samples were collected from 11 wastewater treatment plants situated across the North (n=75 samples), Lisboa and Vale do Tejo (n=98), and south (n=100) regions of Portugal. DENV was detected in 68 (25%) of 273 samples, with a median viral load of 1·1 × 10^–4 (IQR 3·2 × 10^–5 to 8·0 × 10^–4). CHIKV was detected in 30 (11%) of 273 samples, with median viral loads of 3·1 × 10^–4 (1·6 × 10^–4 to 6·4 × 10^–4; <em>nsP1</em> gene) and 7·8 × 10^–4 (4·2 × 10^–4 to 2·0 × 10^–³; <em>E1</em> gene). The pattern of occurrence of CHIKV was similar between regions whereas slight differences were found for DENV. When combining results for the three studied regions, DENV prevalence and viral load had two seasonal peaks (summer and winter) and CHIKV prevalence and viral load had a single peak during March and April of 2023.</div></div><div><h3>Interpretation</h3><div>This study highlights the potential of WBS as a potent tool for gauging the epidemiological landscape of DENV and CHIKV in Portugal, where autochthonous cases have not yet been detected. WBS could serve as an additional element to conventional surveillance approaches, especially in areas where real-time clinical surveillance data are scarce or delayed.</div></div><div><h3>Funding</h3><div>EU Emergency Support Instrument and Fundação para a Ciencia e Tecnologia.</div></div>","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100911"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142298318","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":"Reappraising Cladophialophora bantiana phaeohyphomycosis in France: retrospective nation-based study","authors":"Prof Olivier Lortholary MD ,&nbsp;Dea Garcia-Hermoso PhD ,&nbsp;Aude Sturny-Leclère PhD ,&nbsp;Karine Sitbon MD ,&nbsp;Céline Nourrisson PharmD ,&nbsp;Valérie Letscher-Bru PharmD ,&nbsp;Nicole Desbois-Nogard MD ,&nbsp;Prof Ferouze Bani-Sadr MD ,&nbsp;Frédéric Bastides MD ,&nbsp;Prof Boris Bienvenu MD ,&nbsp;Camille Cordier PharmD ,&nbsp;Anne Coste MD ,&nbsp;François Danion MD ,&nbsp;Tristan Dégot MD ,&nbsp;David Delarbre MD ,&nbsp;Arnaud Fekkar PharmD ,&nbsp;Christophe Garcie PharmD ,&nbsp;Cyril Garrouste MD ,&nbsp;Maud Gits-Muselli MD ,&nbsp;Emilie Guemas PharmD ,&nbsp;Prof Guillaume Desoubeaux MD","doi":"10.1016/S2666-5247(24)00139-3","DOIUrl":"10.1016/S2666-5247(24)00139-3","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;&lt;em&gt;Cladophialophora bantiana&lt;/em&gt; is one of the most virulent phaeohyphomycetes, typically causes non-angiogenic single (or sometimes multiple) cystic brain lesions, and has resulted in a mortality rate of up to 70%. Most &lt;em&gt;C bantiana&lt;/em&gt; cases are described either in a series of isolated reports or in very small cohorts. The aim of this retrospective nation-based study was to share the data on &lt;em&gt;C bantiana&lt;/em&gt; phaeohyphomycosis cases reported in France and French overseas territories over the past two decades to improve understanding of this disease.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;Patients with &lt;em&gt;C bantiana&lt;/em&gt; infection were processed through the active surveillance programme of invasive fungal infections launched by the National Reference Center for Mycoses and Antifungals, Institut Pasteur (Paris, France), and the French Surveillance Network of Invasive Fungal Infections, which involved 29 hospitals from mainland France and overseas French territories. Only proven and probable cases of infection, according to the revised and updated consensus definitions from the European Organization for Research and Treatment of Cancer and Mycoses Study Group, were included in the study. Patients were diagnosed or confirmed, or both, using a polyphasic approach at the Institut Pasteur between 2002 and 2022. Patients were separated into two groups: those with CNS involvement and those with no CNS involvement. The primary outcome was the survival rate.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Findings&lt;/h3&gt;&lt;div&gt;A total of 23 patients with a &lt;em&gt;C bantiana&lt;/em&gt; invasive infection were included during the study period (Jan 1, 2002, to Dec 31, 2022). The median age was 56 years in the CNS involvement group and 65 years in the non-CNS involvement group. Until 2021, the annual number of cases varied between zero and two, with six cases observed in 2022, the warmest year recorded in France since 1900. CNS involvement was observed in 15 (65%) patients, including three disseminated cases; skin and soft tissue involvement in seven (30%) patients and an isolated lung infection in one case. Diabetes was observed in five patients, and any immunodepression factor was observed in 14 (61%) of 23 patients. When considering only patients with CNS involvement, 9-month survival appeared higher in patients who underwent exeresis or large drainage (three [75%] of four patients &lt;em&gt;vs&lt;/em&gt; three [27%] of 11 patients; p=0·24) and significantly higher in those treated for 2 or more weeks with triple antifungal therapy (liposomal amphotericin B plus posaconazole and flucytosine; seven [78%] of nine patients &lt;em&gt;vs&lt;/em&gt; one [17%] of six patients; p=0·040). Two patients were treated with excision surgery alone (one patient with success, and the other patient lost to follow-up).&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Interpretation&lt;/h3&gt;&lt;div&gt;This study shows that the clinical presentations and underlying medical conditions of &lt;em&gt;C bantiana&lt;/em&gt; infections are more diverse than previ","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100907"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142477431","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":"Leveraging genomic surveillance for public health: insights from Latin America","authors":"William Calero-Cáceres ,&nbsp;José Luis Balcázar","doi":"10.1016/S2666-5247(24)00159-9","DOIUrl":"10.1016/S2666-5247(24)00159-9","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100919"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474689","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":"Changing epidemiological patterns in human avian influenza virus infections","authors":"Mei Kang ,&nbsp;Hai-peng Li ,&nbsp;Jia Tang ,&nbsp;Xin-yu Wang ,&nbsp;Li-fang Wang ,&nbsp;Guy Baele ,&nbsp;Jia-tao Lou ,&nbsp;Philippe Lemey ,&nbsp;Shuo Su","doi":"10.1016/S2666-5247(24)00158-7","DOIUrl":"10.1016/S2666-5247(24)00158-7","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100918"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565571","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":"Enhancing public health strategies for dengue control: insights and recommendations for comprehensive management in tropical regions","authors":"Man Sun ,&nbsp;Huan Zhou","doi":"10.1016/j.lanmic.2024.07.013","DOIUrl":"10.1016/j.lanmic.2024.07.013","url":null,"abstract":"","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 11","pages":"Article 100950"},"PeriodicalIF":20.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898624","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}