Early Release

Supplement

• SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA
  I. E. Emmen et al.
• Integrating Genomic Data into Public Health Surveillance for Multidrug-Resistant Organisms, Washington, United States
  L. Torres et al.
• Pathogen Genomics in Public Health Practice: a Decade of Partnerships and Progress
  D. MacCannell et al.
• Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance
  K. R. Florek et al.
• Leveraging a Strategic Public–Private Partnership to Launch an Airport-Based Pathogen Monitoring Program to Detect Emerging Health Threats
  C. R. Friedman et al. View Abstract

  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
  T. Lloyd et al.
• Genomic Characterization of Escherichia coli O157:H7 Associated with Multiple Sources, United States
  J. S. Wirth et al.
• Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States
  K. Pham et al.
• Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA
  E. Stachler et al. View Abstract

  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
  J. N. Ricaldi et al.
• Respiratory Virus Detection and Sequencing from Negative SARS-CoV-2 Rapid Antigen Tests
  E. Jules et al.
• Effects of Decentralized Sequencing on National Listeria monocytogenes Genomic Surveillance, Australia, 2016–2023
  P. Andersson et al.
• Strategies and Opportunities to Improve Community Health through Advanced Molecular Detection and Genomic Surveillance of Infectious Diseases
  J. Moore et al. View Abstract

  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.

• The NGS Quality Initiative and Challenges for Next-Generation Sequencing Technology in Clinical and Public-Health Laboratories
  B. Cherney et al.
• Lessons from 5 Years of Routine Whole-Genome Sequencing for Epidemiologic Surveillance of Shiga Toxin–Producing Escherichia coli, France, 2018–2022
  G. Jones et al.
• Nationwide Implementation of HIV Molecular Cluster Detection by Centers for Disease Control and Prevention and State and Local Health Departments, United States
  A. France et al.
• Genomic Epidemiology for Estimating Pathogen Burden in a Population
  W. Porter et al. View Abstract

  The role of genomics in outbreak response and pathogen surveillance has expanded and ushered in the age of pathogen intelligence. Genomic surveillance enables detection and monitoring of novel pathogens; case clusters; and markers of virulence, antimicrobial resistance, and immune escape. We can leverage pathogen genomic diversity to estimate total pathogen burden in populations and environments, which was previously challenging because of unreliable data. Pathogen genomics might allow pathogen burdens to be estimated by sequencing even a small percentage of cases. Deeper genomic epidemiology analyses require multidisciplinary collaboration to ensure accurate and actionable real-time pathogen intelligence.

• 16S Ribosomal RNA Gene PCR and Sequencing of Normally Sterile Body Fluids and Tissues for Pediatric Infection Diagnosis, United States, 2020-2023
  G. Li et al.
• Successful Transition to Whole-Genome Sequencing and Bioinformatics to Identify Invasive Streptococcus spp. Drug Resistance, Alaska, USA
  K. M. Miernyk et al. View Abstract

  The Centers for Disease Control and Prevention’s Arctic Investigations Program evaluated whole-genome sequencing (WGS) workflows and bioinformatics pipelines developed by the Centers’ Streptococcus Laboratory. We compared WGS-based antimicrobial drug resistance predictions with phenotypic testing for group B (n = 130) and group A (n = 217) Streptococcus and Streptococcus pneumoniae (n = 293). Isolates were collected in Alaska during January 2019–February 2021. We also included a historical phenotypically nonsusceptible subset. Concordances between phenotypic testing and WGS predictions were 99.9% (895/896) for group B Streptococcus, 100% (1,298/1,298) for group A Streptococcus, and 99.98% (3,516/3,517) for S. pneumoniae. Common resistance determinants were ermTR, ermB, and mef for macrolides, tetM for tetracyclines, and gyrA and parC for levofloxacin. S. pneumoniae trimethoprim/sulfamethoxazole nonsusceptibility was associated with folP gene insertions and folA mutations. In 2022, the Arctic Investigations Program transitioned Streptococcus spp. workflows to WGS, enabling more rapid monitoring and prevention of invasive disease.

• Real-Time Use of Monkeypox Virus Genomic Surveillance, King County, Washington, USA, 2022–2024
  K. M. Lau et al. View Abstract

  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.

Synopses

• Comprehensive Survival Analysis of Patients with Alveolar Echinococcosis, University Hospital Zurich, 1973–2022
  A. Deibel et al.
• Outbreak of Marburg Virus Disease, Equatorial Guinea, 2023
  S. Ngai et al. View Abstract

  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
  L. Bertin-Biasutto et al.

Research

• Nationwide Observational Case-Control Study of Risk Factors for Aerococcus Bloodstream Infections, Sweden
  J. Walles et al.
• Post-Exposure Antibiotic Therapy in Goats Infected with Burkholderia pseudomallei
  R. A. Bowen et al.
• Powassan Virus and Eastern Equine Encephalitis Virus Seroprevalence in Endemic Areas, United States, 2019–2020
  H. Padda et al.
• Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023
  C. Y. Chiu et al. View Abstract

  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
  E. Grebe et al.
• Highly Pathogenic Avian Influenza A(H5N1) Outbreak in Endangered Cranes, Izumi Plain, Japan, 2022–23
  M. Esaki et al. View Abstract

  During the 2022–23 winter season, >1,500 endangered cranes, including hooded crane (Grus monacha) and white-naped crane (Grus vipio), were found debilitated or dead in the Izumi Plain, Japan. Most of the cranes, particularly those collected in November, were infected with highly pathogenic avian influenza (HPAI) H5N1 viruses; virus shedding was higher from the trachea than from the cloaca. The isolation rate from the cranes’ roost water was not markedly higher than that of previous seasons, suggesting that the viruses might be more effectively transmitted among cranes via the respiratory route than through feces. Most wild bird–derived H5N1 isolates were phylogenetically distinct from viruses isolated on nearby chicken farms, indicating limited relationship between the wild bird and chicken isolates. Serologic analyses suggested that herd immunity had little effect on outbreak subsidence. This study deepens our understanding of the circumstances surrounding the unexpected HPAI outbreaks among these endangered cranes.

• Exponential Clonal Expansion of 5-Fluorocytosine–Resistant Candida tropicalis and New Insights into Underlying Molecular Mechanisms
  N. Abou-Chakra et al.

Dispatches

• Self-Reported SARS-CoV-2 Infections among National Blood Donor Cohort, United States, 2020–2022
  B. R. Spencer et al. View Abstract

  SARS-CoV-2 case surveillance in the United States did not distinguish first infections from reinfections. In a large blood donor cohort, self-reported first infections and reinfections during 2020–2022 mirrored public health case count surveillance, and reinfection incidence peaked in 2022. Blood donor data could aid in SARS-CoV-2 and emerging infectious disease surveillance.

• Recent and Forecasted Increases in Coccidioidomycosis Incidence Linked to Hydroclimatic Swings, California, USA
  S. K. Camponuri et al. View Abstract

  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
  J. Delgado-de la Mora et al.
• High Prevalence of Influenza D Virus Infection in Swine, Northern Ireland
  P. Lagan and K. Lemon
• Co-Infections with Orthomarburgviruses, Paramyxoviruses, and Orthonairoviruses in Egyptian Rousette Bats, Uganda and Sierra Leone
  B. R. Amman et al. View Abstract

  We report 1.3% (19/1,511) of Egyptian rousette bats (ERBs) in Uganda and Sierra Leone were co-infected with different combinations of Marburg, Sosuga, Kasokero, or Yogue viruses. To prevent infection by those viruses, we recommend avoiding ERB-populated areas, avoiding ERBs and ERB-contaminated objects, and thoroughly washing harvested fruits before consumption.

• Venezuelan Equine Encephalitis, Peruvian Amazon, 2020
  M. Piche-Ovares et al. View Abstract

  We screened 1,972 febrile patients from the Peruvian Amazon in 2020–2021 for Venezuelan equine encephalitis virus (VEEV). Neutralizing antibody detection rate was 3.9%; 2 patients were PCR positive. Genome identity compared with VEEV subtype ID strains was 97.6%–98.1%. Evidence for purifying selection and ancestry ≈54 years ago corroborated VEEV endemicity.

• Influenza A(H1N1)pdm09 Virus with Reduced Susceptibility to Baloxavir, Japan, 2024
  E. Takashita et al. View Abstract

  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.

• Administration of L-type Bovine Spongiform Encephalopathy to Macaques to Evaluate Zoonotic Potential
  M. Imamura et al. View Abstract

  We administered L-type bovine spongiform encephalopathy prions to macaques to determine their potential for transmission to humans. After 75 months, no clinical symptoms appeared, and prions were undetectable in any tissue by Western blot or immunohistochemistry. Protein misfolding cyclic amplification, however, revealed prions in the nerve and lymphoid tissues.

• Clade Ia Monkeypox Virus Linked to Sexual Transmission, Democratic Republic of the Congo, August 2024
  J. Makangara-Cigolo et al.
• Rapid Transmission and Divergence of Vancomycin-Resistant Enterococcus faecium Sequence Type 80, China
  L. Li et al. View Abstract

  We investigated genomic evolution of vancomycin-resistant Enterococcus faecium (VREF) during an outbreak in Shenzhen, China. Whole-genome sequencing revealed 2 sequence type 80 VREF subpopulations diverging through insertion sequence–mediated recombination. One subpopulation acquired more antimicrobial resistance and carbohydrate metabolism genes. Persistent VREF transmission underscores the need for genomic surveillance to curb spread.

• Molecular Detection of Histoplasma in Bat-Inhabited Tunnels of Camino de Hierro Tourist Route, Spain
  J. García-Martín et al. View Abstract

  We detected Histoplasma capsulatum in 2 bat-inhabited tunnels of a tourist route in northern Spain. This finding confirms that the geographic distribution of this fungal pathogen is wider than previously thought. Our results highlights the need for surveillance and assessment of the potential infection risk for workers and visitors.

Research Letters

• Emergence of Feline Sporotrichosis near Brazil Border, Argentina, 2023–2024
  K. Vizcaychipi et al.
• Clinical and Epidemiologic Characteristics of Mpox Cases, Dominican Republic, July 2022–February 2023
  R. Paulino-Ramirez et al. View Abstract

  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.

• Increased Pneumonia-Related Emergency Department Visits, Northern Italy
  S. Villa et al. View Abstract

  An increase in pneumonia-related emergency department visits was observed in Lombardy, northern Italy, during June–October 2024. Viral causes appear insufficient to explain the increase, suggesting a bacterial cause. Mycoplasma pneumoniae and Bordetella pertussis emerged as possible causes when other surveillance systems were consulted, but the reasons behind this trend remain unknown.

• Autochthonous Leishmania (Viannia) lainsoni in Dog, Rio de Janeiro State, Brazil, 2023
  I. da Silva Santos et al. View Abstract

  In Brazil, Leishmania (Leishmania) infantum causes canine visceral leishmaniasis; the primary vector is the Lutzomyia longipalpis sand fly. We describe a case of canine visceral leishmaniasis caused by Leishmania (Viannia) lainsoni in a dog from Barra Mansa municipality, Rio de Janeiro state. Better specificity of serologic diagnostic techniques is needed for diagnoses.

• Case Report of Aerococcus urinae Tricuspid Valve Endocarditis, New York, USA
  T. Siam et al. View Abstract

  We report a case of a 61-year-old man in New York, USA, who had recurrent Aerococcus urinae endocarditis that first involved his native and then his bioprosthetic tricuspid valve. We demonstrate that a complicated A. urinae endocarditis case can be successfully treated with single-agent antimicrobial drug therapy and surgery.

• Unexpected Schistosome Zoonotic and Hybrid Egg Excretion Patterns, Mangochi District, Malawi, 2024
  A. M. O’Ferrall et al.
• Napoleon Bonaparte—A Possible Case of Trench Fever
  É. Faure View Abstract

  In 1799, Napoleon Bonaparte reported having a recurrent febrile illness that initially subsided for 4 days and then had multiple relapses of similar duration. A speculative diagnosis of trench fever would be supported by poor hygiene conditions, prolonged exposure to cold, and the presence of lice in Napoleon’s barracks environment.

• Molecular Epidemiology of St. Louis Encephalitis Virus, São Paulo State, Brazil, 2016–2018
  G. Caleiro et al.
• Trichophyton indotineae Infection, Sao Paulo, Brazil, 2024
  J. N. de Almeida et al.

Etymologia

• Emayella augustorita [em″-ǝ-yel′-ǝ aw-goost′-ō-rē″-tǝ]
  C. Partin

Corrections

• Correction: Vol. 31, No. 3
• Correction: Vol. 31, No. 3
• Correction: Vol. 31, No. 2

Synopsis

• Clinical Manifestations, Risk Factors, and Disease Burden of Rickettsiosis, Cambodia, 2007–2020
  G. C. Kelly et al.

Research

• Long-Term Clinical Outcomes of Adults Hospitalized for COVID-19 Pneumonia
  I. O. Rosas et al.
• Prospective Multicenter Surveillance of Helicobacter pylori and Non–H. pylori Helicobacter Infections during Medical Checkups, Japan, 2022
  K. Tokunaga et al.
• Safety and Immunogenicity of Poultry Vaccine for Protecting Critically Endangered Avian Species against Highly Pathogenic Avian Influenza Virus, United States
  T. E. Katzner et al. View Abstract

  In 2023, an outbreak of highly pathogenic avian influenza occurred among critically endangered California condors (Gymnogyps californianus), and >21 died. We evaluated safety, immunogenicity, vaccination strategies, and correlates of antibody response of an influenza vaccine for poultry in black vultures (Coragyps atratus) and then California condors. We noted differences in antibody titers between vaccinated and unvaccinated birds (vultures p<0.004; condors p­<0.02) but no adverse effects of vaccination. All vaccinated vultures and 80% of vaccinated condors showed maximum measured antibody response within the published range associated with survival of vaccinated and virally challenged chickens. We noted weak evidence of higher antibody responses for birds given two 0.5-mL vaccines versus those given one 1-mL vaccine but no correlation between antibody titers and sex for either species or between antibody titers and bone lead concentrations in vultures. Our results prompted initiation of a vaccination program for condors that could reduce spread of this disease among highly threatened species.

• Diagnostic Accuracy of 3 Mpox Lateral Flow Assays for Antigen Detection, Democratic Republic of the Congo and United Kingdom
  E. Ishara-Nshombo et al.
• Characterization of Adult and Pediatric Healthcare-Associated and Community-Associated Clostridioides difficile Infections, Canada, 2015–2022
  T. Du et al.

Dispatches

• Negligible Neutralization of Influenza A(H5N1) Virus by Quadrivalent Seasonal Vaccines, United Kingdom, 2021–2024
  P. Stevenson-Leggett et al.
• Mycoplasma arginini Cellulitis, Tenosynovitis, and Arthritis in a Kidney Transplant Recipient, Slovenia, 2024
  T. Vivoda et al.

Research Letters

• Baylisascaris procyonis Roundworm in Common Raccoons, Mexico
  A. Gómez-Sánchez et al.
• Highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus isolated from a dairy farm worker in Michigan transmits through the air in a ferret model
  N. Brock et al.