Nicole Brock, Joanna A. Pulit-Penaloza, Jessica A. Belser, Claudia Pappas, Xiangjie Sun, Troy J. Kieran, Hui Zeng, Juan A. De La Cruz, Yasuko Hatta, Han Di, C. Todd Davis, Terrence M. Tumpey, Taronna R. Maines
{"title":"Avian Influenza A(H5N1) Isolated from Dairy Farm Worker, Michigan","authors":"Nicole Brock, Joanna A. Pulit-Penaloza, Jessica A. Belser, Claudia Pappas, Xiangjie Sun, Troy J. Kieran, Hui Zeng, Juan A. De La Cruz, Yasuko Hatta, Han Di, C. Todd Davis, Terrence M. Tumpey, Taronna R. Maines","doi":"10.3201/eid3106.250386","DOIUrl":"https://doi.org/10.3201/eid3106.250386","url":null,"abstract":"<p>Influenza A(H5N1) viruses have been detected in US dairy cow herds since 2024. We assessed the pathogenesis, transmission, and airborne release of A/Michigan/90/2024, an H5N1 isolate from a dairy farm worker in Michigan, in the ferret model. Results show this virus caused airborne transmission with moderate pathogenicity, including limited extrapulmonary spread, without lethality.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"44 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dorian J. Feistel, Rory Welsh, Jeffrey Mercante, Miguella Mark-Carew, Jason Caravas, Arun Boddapati, Samantha Sevilla, Matthew H. Seabolt, Dhwani Batra, Suchitra Chavan, Shatavia Morrison, Jesse Yoder, Hannah Long, Satvik Mishra, Benjamin Lorentz, Andi Dhroso, Iryna V. Goraichuk, Seonghye Jeon, Daniel M. Cornforth
{"title":"Detection and Tracking of SARS-CoV-2 Lineages through National Wastewater Surveillance System Pathogen Genomics","authors":"Dorian J. Feistel, Rory Welsh, Jeffrey Mercante, Miguella Mark-Carew, Jason Caravas, Arun Boddapati, Samantha Sevilla, Matthew H. Seabolt, Dhwani Batra, Suchitra Chavan, Shatavia Morrison, Jesse Yoder, Hannah Long, Satvik Mishra, Benjamin Lorentz, Andi Dhroso, Iryna V. Goraichuk, Seonghye Jeon, Daniel M. Cornforth","doi":"10.3201/eid3113.241411","DOIUrl":"https://doi.org/10.3201/eid3113.241411","url":null,"abstract":"<p>We conducted retrospective analysis of the emergence of the SARS-CoV-2 JN.1 variant in US wastewater during November 2023–July 2024 using Aquascope, a bioinformatics pipeline for the National Wastewater Surveillance System. This study highlights the value of open-source bioinformatics tools in tracking pathogen variants for public health monitoring.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"26 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jessica N. Ricaldi, J. Todd Parker, Nathelia Barnes, Hannah Turner, Scott Santibañez
{"title":"An Advanced Molecular Detection Roadmap for Nonlaboratorians","authors":"Jessica N. Ricaldi, J. Todd Parker, Nathelia Barnes, Hannah Turner, Scott Santibañez","doi":"10.3201/eid3113.241506","DOIUrl":"https://doi.org/10.3201/eid3113.241506","url":null,"abstract":"<p>This article, aimed at nonlaboratorians such as healthcare providers, public health professionals, and policymakers, provides basic concepts and terminology to enable better understanding of other manuscripts in this advanced molecular detection journal supplement. This article focuses on 3 aspects of advanced molecular detection: pathogen genomics, bioinformatics, and public health application, while providing additional resources for understanding.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"44 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elie Ishara-Nshombo, Anushri Somasundaran, Alessandra Romero-Ramirez, Konstantina Kontogianni, Daniel Mukadi-Bamuleka, Marithé Mukoka-Ntumba, Emile Muhindo-Milonde, Hugues Mirimo-Nguee, Jacob Parkes, Yusra Hussain, Susan Gould, Christopher T. Williams, Dominic Wooding, Juvenal Nkeramahame, Mikaela Watson, Hayley E. Hardwick, Malcolm G. Semple, John Kenneth Baillie, Jake Dunning, Thomas E. Fletcher, Thomas Edwards, Devy M. Emperador, Hugo Kavunga-Membo, Ana Isabel Cubas-Atienzar
{"title":"Diagnostic Accuracy of 3 Mpox Lateral Flow Assays for Antigen Detection, Democratic Republic of the Congo and United Kingdom","authors":"Elie Ishara-Nshombo, Anushri Somasundaran, Alessandra Romero-Ramirez, Konstantina Kontogianni, Daniel Mukadi-Bamuleka, Marithé Mukoka-Ntumba, Emile Muhindo-Milonde, Hugues Mirimo-Nguee, Jacob Parkes, Yusra Hussain, Susan Gould, Christopher T. Williams, Dominic Wooding, Juvenal Nkeramahame, Mikaela Watson, Hayley E. Hardwick, Malcolm G. Semple, John Kenneth Baillie, Jake Dunning, Thomas E. Fletcher, Thomas Edwards, Devy M. Emperador, Hugo Kavunga-Membo, Ana Isabel Cubas-Atienzar","doi":"10.3201/eid3106.250166","DOIUrl":"https://doi.org/10.3201/eid3106.250166","url":null,"abstract":"<p>The ongoing outbreaks of mpox highlight the urgent need for a rapid and low-cost diagnostic test to accurately detect and control this emerging disease. We estimated the analytical sensitivity using viral culture of the monkeypox virus clade IIb lineage and clinical diagnostic performance of 3 antigen detection rapid diagnostic tests (Ag-RDT) by using skin swab samples and upper-respiratory swab samples from mpox patients in the Democratic Republic of the Congo and the United Kingdom. The analytical limit of detection was 1.0 × 10<sup>4</sup> plaque-forming units/mL, fulfilling World Health Organization recommendations. Specificity of the 3 Ag-RDTs was 100%, but sensitivity was estimated at 0.00%–15.79% using skin samples and 0.00% using respiratory samples. None of the 3 Ag-RDTs reached the World Health Organization’s target clinical sensitivity, and we do not recommend them as diagnostic or screening tools for suspected mpox cases. Accurate Ag-RDTs for mpox diagnosis remain urgently needed.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"35 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isla E. Emmen, William C. Vuyk, Andrew J. Lail, Sydney Wolf, Eli J. O’Connor, Rhea Dalvie, Maansi Bhasin, Aanya Virdi, Caroline White, Nura R. Hassan, Alex Richardson, Grace VanSleet, Andrea Weiler, Savannah Rounds-Dunn, Kenneth Van Horn, Marc Gartler, Jane Jorgenson, Michael Spelman, Sean Ottosen, Nicholas R. Minor, Nancy Wilson, Thomas C. Friedrich, David H. O’Connor
{"title":"SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA","authors":"Isla E. Emmen, William C. Vuyk, Andrew J. Lail, Sydney Wolf, Eli J. O’Connor, Rhea Dalvie, Maansi Bhasin, Aanya Virdi, Caroline White, Nura R. Hassan, Alex Richardson, Grace VanSleet, Andrea Weiler, Savannah Rounds-Dunn, Kenneth Van Horn, Marc Gartler, Jane Jorgenson, Michael Spelman, Sean Ottosen, Nicholas R. Minor, Nancy Wilson, Thomas C. Friedrich, David H. O’Connor","doi":"10.3201/eid3113.241192","DOIUrl":"https://doi.org/10.3201/eid3113.241192","url":null,"abstract":"<p>In the United States, SARS-CoV-2 genomic surveillance initially relied almost entirely on residual diagnostic specimens from nucleic acid amplification–based tests. However, use of those tests waned after the end of the COVID-19 Public Health Emergency on May 11, 2023. In Dane County, Wisconsin, we partnered with local- and state-level public health agencies and the South Central Library System to continue genomic surveillance by obtaining SARS-CoV-2 genome sequences from freely available community rapid antigen tests (RATs). During August 15, 2023–February 29, 2024, we received 227 RAT samples, from which we generated 127 sequences with >10× depth of coverage for <span>></span>90% of the SARS-CoV-2 genome. In a subset of tests, lower cycle threshold values correlated with sequence success. Our results demonstrated that collecting and sequencing results from RATs in partnership with community sites is a practical approach for sustaining SARS-CoV-2 genomic surveillance.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"18 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kien Pham, Chrispin Chaguza, Rafael Lopes, Ted Cohen, Emma Taylor-Salmon, Melanie Wilkinson, Volha Katebi, Nathan D. Grubaugh, Verity Hill
{"title":"Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States","authors":"Kien Pham, Chrispin Chaguza, Rafael Lopes, Ted Cohen, Emma Taylor-Salmon, Melanie Wilkinson, Volha Katebi, Nathan D. Grubaugh, Verity Hill","doi":"10.3201/eid3113.240981","DOIUrl":"https://doi.org/10.3201/eid3113.240981","url":null,"abstract":"<p>The COVID-19 pandemic has been marked by continuous emergence of novel SARS-CoV-2 variants. Questions remain about the mechanisms with which those variants establish themselves in new geographic areas. We performed a discrete phylogeographic analysis on 18,529 sequences of the SARS-CoV-2 Omicron BA.5 sublineage sampled during February–June 2022 to elucidate emergence of that sublineage in different regions of the United States. The earliest BA.5 sublineage introductions came from Africa, the putative variant origin, but most were from Europe, matching a high volume of air travelers. In addition, we discovered extensive domestic transmission between different US regions, driven by population size and cross-country transmission between key hotspots. We found most BA.5 virus transmission within the United States occurred between 3 regions in the southwestern, southeastern, and northeastern parts of the country. Our results form a framework for analyzing emergence of novel SARS-CoV-2 variants and other pathogens in the United States. </p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"43 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Features of Invasive Aspergillosis Caused by Aspergillus flavus, France, 2012-2018.","authors":"Lise Bertin-Biasutto,Olivier Paccoud,Dea Garcia-Hermoso,Blandine Denis,Karine Boukris-Sitbon,Olivier Lortholary,Stéphane Bretagne,Maud Gits-Muselli,Raoul Herbrecht,Valérie Letscher-Bru,François Danion,Sophie Cassaing,Florent Morio,Céline Nourrisson,Marc Pihet,Milène Sasso,Guillaume Desoubeaux,Marie-Fleur Durieux,Julie Bonhomme,Elisabeth Chachaty,Taieb Chouaki,Nicole Desbois-Nogard,Alexandre Alanio,Jean-Pierre Gangneux,Fanny Lanternier","doi":"10.3201/eid3105.241392","DOIUrl":"https://doi.org/10.3201/eid3105.241392","url":null,"abstract":"Invasive aspergillosis (IA) caused by Aspergillus flavus remains poorly described. We retrospectively analyzed 54 cases of IA caused by A. flavus reported in France during 2012-2018. Among cases, underlying IA risk factors were malignancy, solid organ transplantation, and diabetes. Most (87%, 47/54) infections were localized, of which 33 were pleuropulmonary and 13 were ear-nose-throat (ENT) infection sites. Malignancy (70% [23/33]) and solid organ transplantation (21% [7/33]) were the main risk factors in localized pulmonary infections, and diabetes mellitus was associated with localized ENT involvement (61.5%, [8/13]). Fungal co-infections were frequent in pulmonary (36%, 12/33) but not ENT IA (0 cases). Antifungal monotherapy was prescribed in 45/50 (90%) cases, mainly voriconazole (67%, 30/45). All-cause 30-day case-fatality rates were 39.2% and 90-day rates were 47.1%, and rates varied according to risk factor, IA site, and fungal co-infections. Clinicians should remain vigilant for A. flavus and consider it in the differential diagnosis for IA.","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"48 1","pages":"896-905"},"PeriodicalIF":11.8,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143897336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sarah Anne J. Guagliardo, Stacey Martin, Carolyn V. Gould, Rebekah Sutter, Daniel Jacobs, Kevin O’Laughlin, Ralph Huits, Concetta Castilletti, J. Erin Staples
{"title":"Estimation of Incubation Period for Oropouche Virus Disease among Travel-Associated Cases, 2024–2025","authors":"Sarah Anne J. Guagliardo, Stacey Martin, Carolyn V. Gould, Rebekah Sutter, Daniel Jacobs, Kevin O’Laughlin, Ralph Huits, Concetta Castilletti, J. Erin Staples","doi":"10.3201/eid3107.250468","DOIUrl":"https://doi.org/10.3201/eid3107.250468","url":null,"abstract":"<p>Determining the incubation period of Oropouche virus disease can inform clinical and public health practice. We analyzed data from 97 travel-associated cases identified by the Centers for Disease Control and Prevention (n = 74) or the GeoSentinel Network (n = 13) and 10 cases from published literature. Using log-normal interval-censored survival analysis, we estimated the median incubation period to be 3.2 (95% CI 2.5–3.9) days. Symptoms developed by 1.1 (95% CI 0.6–1.5) days for 5% of patients, 9.7 (95% CI 6.9–12.5) days for 95% of patients, and 15.4 (95% CI 9.6–21.3) days for 99% of patients. The estimated incubation period range of 1–10 days can be used to assess timing and potential source of exposure in patients with Oropouche symptoms. For patients with symptom onset >2 weeks after travel, clinicians and public health responders should consider the possibility of local vectorborne transmission or alternative modes of transmission.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"48 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Laura Marcela Torres, Jared Johnson, Audrey Valentine, Audrey Brezak, Emily C. Schneider, Marisa D’Angeli, Jennifer Morgan, Claire Brostrom-Smith, Chi N. Hua, Michael Tran, Darren Lucas, Joenice Gonzalez De Leon, Drew MacKellar, Philip Dykema, Kelly J. Kauber, Allison Black
{"title":"Integrating Genomic Data into Public Health Surveillance for Multidrug-Resistant Organisms, Washington, USA","authors":"Laura Marcela Torres, Jared Johnson, Audrey Valentine, Audrey Brezak, Emily C. Schneider, Marisa D’Angeli, Jennifer Morgan, Claire Brostrom-Smith, Chi N. Hua, Michael Tran, Darren Lucas, Joenice Gonzalez De Leon, Drew MacKellar, Philip Dykema, Kelly J. Kauber, Allison Black","doi":"10.3201/eid3113.241227","DOIUrl":"https://doi.org/10.3201/eid3113.241227","url":null,"abstract":"<p>Mitigating antimicrobial resistance (AMR) is a public health priority to preserve antimicrobial treatment options. The Washington State Department of Health in Washington, USA, piloted a process to leverage longitudinal genomic surveillance on the basis of whole-genome sequencing (WGS) and a genomics-first cluster definition to enhance AMR surveillance. Here, we outline the approach to collaborative surveillance and describe the pilot using 6 carbapenemase-producing organism outbreaks of 3 species: <em>Pseudomonas aeruginosa</em>, <em>Acinetobacter baumannii</em>, and <em>Klebsiella pneumoniae.</em> We also highlight how we applied the approach to an emerging outbreak. We found that genomic and epidemiologic data define highly congruent outbreaks. By layering genomic and epidemiologic data, we refined linkage hypotheses and addressed gaps in traditional epidemiologic surveillance. With the accessibility of WGS, public health agencies must leverage new approaches to modernize surveillance for communicable diseases.</p>","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"148 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143872692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Duncan MacCannell, Bronwyn MacInnis, Scott Santibanez, Margaret A. Honein, Wendi Kuhnert, Christopher Braden
{"title":"A Decade of Partnerships and Progress in Pathogen Genomics in Public Health Practice","authors":"Duncan MacCannell, Bronwyn MacInnis, Scott Santibanez, Margaret A. Honein, Wendi Kuhnert, Christopher Braden","doi":"10.3201/eid3113.241670","DOIUrl":"https://doi.org/10.3201/eid3113.241670","url":null,"abstract":"Partnerships and Progress in Pathogen Genomics","PeriodicalId":11595,"journal":{"name":"Emerging Infectious Diseases","volume":"74 1","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143872656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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