Early Release
Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.
Volume 31, Supplement—April 2025
Supplement
- SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA
- Integrating Genomic Data into Public Health Surveillance for Multidrug-Resistant Organisms, Washington, United States
- Using Genomic Epidemiology to Estimate Pathogen Burden in a Population
- Pathogen Genomics in Public Health Practice: a Decade of Partnerships and Progress
- Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance
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Leveraging a Strategic Public–Private Partnership to Launch an Airport-Based Pathogen Monitoring Program to Detect Emerging Health Threats
Airport-based pathogen monitoring is a critical tool that can contribute to early detection and characterization of existing and new pathogen threats. A novel public–private partnership between an airport spa group, a biotech company, and the Centers for Disease Control and Prevention was instrumental in establishing a multimodal pathogen genomic surveillance program at US international airports. That public–private partnership addressed critical challenges that neither party could overcome independently, resulting in the development and deployment of a scalable, flexible early warning system for pathogen detection and public health monitoring.
- Genomic Epidemiology and Phylodynamic Modelling of an Outbreak of Multidrug Resistant Shigella sonnei, San Francisco Bay Area, California, USA, 2023–2024
- Genomic Characterization of Escherichia coli O157:H7 Associated with Multiple Sources, United States
- Successful Transition to Whole-Genome Sequencing and Bioinformatics to Identify Invasive Streptococcus Drug Resistance, Alaska, USA, 2019–2021
- Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States
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Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA
Highly pathogenic avian influenza A(H5N1) virus has caused a multistate outbreak among US dairy cattle, spreading across 16 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk samples from 20 states for methods development, we found that H5N1 virus concentrations by digital PCR strongly correlated with quantitative PCR cycle threshold values; digital PCR exhibited greater sensitivity. Metagenomic sequencing after hybrid selection was best for higher concentration samples, whereas amplicon sequencing performed best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to perform monthly testing of bulk milk samples from all dairy cattle farms in Massachusetts, USA, which remain negative to date. The methods, workflow, and recommendations described provide a framework for others aiming to conduct H5N1 surveillance efforts.
- Advanced Molecular Detection Improves Public Health Response to Infectious Diseases
- Respiratory Virus Detection and Sequencing from Negative SARS-CoV-2 Rapid Antigen Tests
- Effects of Decentralized Sequencing on National Listeria monocytogenes Genomic Surveillance, Australia, 2016–2023
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Strategies and Opportunities to Improve Community Health through Advanced Molecular Detection and Genomic Surveillance of Infectious Diseases
Advanced molecular detection (AMD) refers to the integration of next-generation sequencing, epidemiologic, and bioinformatics data to drive public health actions. As new AMD technologies emerge, it is critical to ensure those methods are used in communities that are most affected by disease-induced illness and death. We describe strategies and opportunities for using AMD approaches to improve health in those communities, which include improving access to pathogen sequencing, increasing data linkages, and using pathogen sequencing for those diseases where sequencing technologies can provide the best health outcome. Such strategies can help address and prevent differences in health outcomes in various populations, such as rural and tribal communities, persons with underlying health issues, and other populations that experience higher risks for infectious disease.
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Real-Time Use of Mpox Genomic Surveillance, King County, Washington, USA, 2022–2024
A monkeypox virus genomic surveillance pilot began in King County, Washington, USA, during the 2022 outbreak. Genomic surveillance proved critical in determining local versus international exposure of a case where no known exposures were identified by interview, illustrating the value of genomics in case investigation and public health practice.
- The NGS Quality Initiative and Challenges for Next-Generation Sequencing Technology in Clinical and Public-Health Laboratories
Volume 31, Number 5—May 2025
Synopses
- Comprehensive Survival Analysis of Patients with Alveolar Echinococcosis, University Hospital Zurich, 1973–2022
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Outbreak of Marburg Virus Disease, Equatorial Guinea, 2023
In February 2023, the government of Equatorial Guinea declared an outbreak of Marburg virus disease. We describe the response structure and epidemiologic characteristics, including case-patient demographics, clinical manifestations, risk factors, and the serial interval and timing of symptom onset, treatment seeking, and recovery or death. We identified 16 laboratory-confirmed and 23 probable cases of Marburg virus disease in 5 districts and noted several unlinked chains of transmission and a case-fatality ratio of 90% (35/39 cases). Transmission was concentrated in family clusters and healthcare settings. The median serial interval was 18.5 days; most transmission occurred during late-stage disease. Rapid isolation of symptomatic case-patients is critical in preventing transmission and improving patient outcomes; community engagement and surveillance strengthening should be prioritized in emerging outbreaks. Further analysis of this outbreak and a One Health surveillance approach can help prevent and prepare for future potential spillover events.
- Features of Invasive Aspergillosis Caused by Aspergillus flavus, France, 2012–2018
Research
- Nationwide Observational Case-Control Study of Risk Factors for Aerococcus Bloodstream Infections, Sweden
- Post-Exposure Antibiotic Therapy in Goats Infected with Burkholderia pseudomallei
- Powassan Virus and Eastern Equine Encephalitis Virus Seroprevalence in Endemic Areas, United States, 2019–2020
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Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023
We used metagenomic next-generation sequencing (mNGS) to investigate an outbreak of Fusarium solani meningitis in US patients who had surgical procedures under spinal anesthesia in Matamoros, Mexico, during 2023. Using a novel method called metaMELT (metagenomic multiple extended locus typing), we performed phylogenetic analysis of concatenated mNGS reads from 4 patients (P1–P4) in parallel with reads from 28 fungal reference genomes. Fungal strains from the 4 patients were most closely related to each other and to 2 cultured isolates from P1 and an additional case (P5), suggesting that all cases arose from a point source exposure. Our findings support epidemiologic data implicating a contaminated drug or device used for epidural anesthesia as the likely cause of the outbreak. In addition, our findings show that the benefits of mNGS extend beyond diagnosis of infections to public health outbreak investigation.
- Detection of SARS-CoV-2 Reinfections Using Anti-Nucleocapsid Antibody Boosting
- Highly Pathogenic Avian Influenza A(H5N1) Outbreak in Endangered Cranes, Izumi Plain, Japan, 2022–23
Dispatches
- Self-Reported SARS-CoV-2 Infections among National Blood Donor Cohort, United States, 2020–2022
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Recent and Forecasted Increases in Coccidioidomycosis Incidence Linked to Hydroclimatic Swings, California, USA
In 2023, California reported near–record high coccidioidomycosis cases after a dramatic transition from drought to heavy precipitation. Using an ensemble model, we forecasted 12,244 cases statewide during April 1, 2024–March 31, 2025, a 62% increase over cases reported 2 years before and on par with case counts for 2023.
- Tropheryma whipplei Infections, Mexico, 2019–2021
- High Prevalence of Influenza D Virus Infection in Swine, Northern Ireland
- Orthomarburgvirus, Paramyxovirus, and Orthonairovirus Co-Infections in Egyptian Rousette Bats, Uganda and Sierra Leone
- Venezuelan Equine Encephalitis, Peruvian Amazon, 2020
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Influenza A(H1N1)pdm09 Virus with Reduced Susceptibility to Baloxavir, Japan, 2024
Influenza A(H1N1)pdm09 virus carrying an I38N substitution was detected in an untreated teenager in Japan. The I38N mutant virus exhibited reduced susceptibility to baloxavir but remained susceptible to neuraminidase inhibitors and showed reduced growth capability. Monitoring antiviral drug susceptibility of influenza viruses is necessary to aid public health planning and clinical recommendations.
- Oral Transmission of L-type Bovine Spongiform Encephalopathy in Cynomolgus Macaques to Evaluate Zoonotic Potential
- Clade Ia Monkeypox Virus Linked to Sexual Transmission, Democratic Republic of the Congo, August 2024
- Rapid Transmission and Divergence of Sequence Type 80 Vancomycin-Resistant Enterococcus faecium, China
- Molecular Detection of Histoplasma in Bat-Inhabited Tunnels of Camino de Hierro Tourist Route, Spain
Research Letters
- Emergence of Feline Sporotrichosis near Brazil Border, Argentina, 2023–2024
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Clinical and Epidemiologic Characteristics of Mpox Cases, Dominican Republic, July 2022–February 2023
During July 2022–February 2023, mpox was confirmed in 71 of 283 suspected cases in the Dominican Republic; 32.4% of patients were women, and 22.5% children <10 years of age. We found differences in transmission compared with global trends, emphasizing the need for continued surveillance, diagnostics, and public health interventions.
- Increase in Pneumonia-associated Attendances to Emergency Departments in Northern Italy, June–October 2024
- Autochthonous Leishmania (Viannia) lainsoni in Dog (Canis familiaris), Rio de Janeiro State, Brazil, 2023
- Case Report of Aerococcus urinae Tricuspid Valve Endocarditis
- Unexpected Schistosome Zoonotic and Hybrid Egg Excretion Patterns, Mangochi District, Malawi, 2024
- Napoleon Bonaparte, A Possible Case of Trench Fever
- Molecular Epidemiology of St. Louis Encephalitis Virus, São Paulo State, Brazil, 2016–2018
- Trichophyton indotineae Infection, Sao Paulo, Brazil, 2024
Etymologia
- Emayella augustorita [em″-ǝ-yel′-ǝ aw-gōōst′-ō-rē″-tǝ]
Corrections
Volume 31, Number 6—June 2025
Synopsis
- Clinical Manifestations, Risk Factors, and Disease Burden of Rickettsiosis, Cambodia, 2007–2020
Research
- Long-Term Clinical Outcomes of Adults Hospitalized for COVID-19 Pneumonia
- Prospective Multicenter Surveillance of Helicobacter pylori and Non–H. pylori Helicobacter Infections during Medical Checkups, Japan, 2022
- Safety and Immunogenicity of Poultry Vaccine for Protecting Critically Endangered Avian Species against Highly Pathogenic Avian Influenza Virus, USA
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