Early Release

Synopses

• Clinical Manifestations, Risk Factors, and Disease Burden of Rickettsiosis, Cambodia, 2007–2020
  G. C. Kelly et al.
• Multicenter Retrospective Study of Spiroplasma ixodetis Infantile Cataract in 8 Countries in Europe
  L. Van Os et al.
• Genomic Surveillance of a Climate Amplified Cholera Outbreak, Malawi, 2022–2023
  L. Chabuka 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. View Abstract

  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 × 10⁴ 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.

• Characterization of Adult and Pediatric Healthcare-Associated and Community-Associated Clostridioides difficile Infections, Canada, 2015–2022
  T. Du et al.
• Force of Infection Model for Estimating Time to Dengue Virus Seropositivity among Expatriate Populations, Thailand
  E. Rapheal et al.
• Genesis and Spread of Novel Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Genotype EA-2023-DG Reassortant, Western Europe
  S. Van Borm et al.
• Emergence of Oropouche Virus in Espírito Santo State, Brazil, 2024
  E. Delatorre et al.
• High Genetic Diversity of Histoplasma in the Amazon Basin, 2006-2017
  T. Ly 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.
• Cadaveric Human Growth Hormone–Associated Creutzfeldt-Jakob Disease with Long Latency Period, United States
  A. S. Ribeiro et al.
• Use of Oral Flea Preventative to Control Rickettsia typhi–Infected Fleas on Reservoir Opossums, Galveston, Texas, USA, 2023–2024
  L. S. Blanton and A. Villasante-Tezanos
• Global Prevalence of Nitroimidazole-Refractory Giardiasis, 2008–2020
  K. A. Ydsten et al.
• Three Cases of Human Babesiosis, Italy, 2017–2020
  C. Sepulcri et al.
• Characterization of OXA-204 Carbapenemase in a Clinical Isolate of Pseudomonas guariconensis
  N. Jaidane et al.
• High Prevalence of Artemisinin-Resistant Plasmodium falciparum Kelch13 R622i and Hrp2/3 Deleted Parasites in South-Eastern Sudan
  M. L’Episcopia et al.
• A One Health Approach to Investigating Cache Valley Virus, Arkansas, USA, July 2023
  A. Carpenter 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.
• Nosocomial Transmission of Plasmodium falciparum Malaria, Spain, 2024
  M. L. Romero et al.
• Molecular Detection of Wesselsbron Virus in Dromedary Camel, Borana Zone, Ethiopia, 2024
  Z. I. Hassan et al.
• Aedes aegypti Mosquito Detection at Bus Stations, Bogota, Colombia, 2023–2024
  A. V. Gomez et al.
• Rapid Subcutaneous Migration of Dirofilaria repens in Facial Tissue, Italy
  M. Carbonara et al.
• Avian Influenza A(H5N1) Isolated from Dairy Farm Worker, Michigan
  N. Brock et al. View Abstract

  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.

Letter

• A Pictorial Human Case of “Furious Rabies”
  C. E. Rupprecht and A. C. Jackson

• 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.
• 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.

• 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.

• 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.

• Respiratory Virus Detection and Sequencing from SARS-CoV-2–Negative Rapid Antigen Tests
  E. Jules et al. View Abstract

  Genomic epidemiology offers insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 rapid antigen tests to identify a wide range of respiratory viruses and generate full genome sequences. This process offers a streamlined mechanism for broad respiratory virus genomic surveillance.

• The Next-Generation Sequencing Quality Initiative and Challenges in Clinical and Public Health Laboratories
  B. Cherney et al. View Abstract

  The Next-Generation Sequencing (NGS) Quality Initiative addresses laboratory challenges faced when performing NGS by developing tools and resources to build a robust quality management system. Here, we illustrate how those products support laboratories in navigating complex regulatory environments and quality-related challenges while implementing NGS effectively in an evolving landscape.

• A Decade of Partnerships and Progress in Pathogen Genomics in Public Health Practice
  D. MacCannell et al.
• Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance
  K. R. Florek et al. View Abstract

  Bioinformatic software containerization, the process of packaging software that encapsulates an application together with all necessary dependencies to simplify installation and use, has improved the deployment and management of next-generation sequencing workflows in both clinical and public health laboratories. Containers have increased next-generation sequencing workflow reproducibility and broadened their usage across different laboratories. We highlight the value of the State Public Health Bioinformatics community’s containerized software repository during the COVID-19 pandemic.

• Integrating Genomic Data into Public Health Surveillance for Multidrug-Resistant Organisms, Washington, USA
  L. Torres et al. View Abstract

  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: Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. 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.

• An Advanced Molecular Detection Roadmap for Nonlaboratorians
  J. N. Ricaldi et al. View Abstract

  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.

• Detection and Tracking of SARS-CoV-2 Lineages through National Wastewater Surveillance System Pathogen Genomics
  D. J. Feistel et al. View Abstract

  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.

• SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA
  I. E. Emmen et al. View Abstract

  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 >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.

• Large-Scale Genomic Analysis of SARS-CoV-2 Omicron BA.5 Emergence, United States
  K. Pham et al. View Abstract

  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.

Research

• Estimation of Incubation Period for Oropouche Virus Disease among Travel-Associated Cases, 2024–2025
  S. J. Guagliardo et al. View Abstract

  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.

Dispatches

• Human Infections by the Novel Zoonotic Species Corynebacterium silvaticum, Germany
  A. Berger et al.
• Multisystemic Disease and Septicemia Caused by Presumptive Burkholderia pseudomallei in American Quarter Horse
  J. J. Thornton et al.

Research Letter

• Fatal Acute Hypoxemic Respiratory Failure Caused by Burkholderia thailandensis, People’s Republic of China
  P. Zhang et al.