Early Release

Synopses

• Comprehensive Survival Analysis of Alveolar Echinococcosis Patients, University Hospital Zurich, Zurich, Switzerland, 1973–2022
  A. Deibel et al. View Abstract

  Alveolar echinococcosis (AE) is a zoonotic disease of increasing concern worldwide. Before benzimidazole drug therapy, 10-year death rates were 90% without surgical resection. In unresectable patients, long-term benzimidazole therapy is highly effective in stabilizing the disease course. We performed a retrospective study of 334 AE patients treated at the University Hospital Zurich, Zurich, Switzerland, during 1973–2022. Annual diagnoses increased over time, and more cases were detected by chance at earlier stages. Ninety patients died, mostly from causes unrelated to AE. Relative survival of AE patients compared with the population of Switzerland demonstrated a steady decrease 5 years after diagnosis. Patient age at diagnosis was the primary variable associated with overall survival. In a propensity-score matched survival analysis, early curative surgery was associated with overall improvement but not AE-specific survival. We conclude that survival of patients with AE is limited by non-AE causes and that early curative surgery does not improve AE-specific survival.

• 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

• Medscape CME Activity
  Nationwide Observational Case–Control Study of Risk Factors for Aerococcus Bloodstream Infections, Sweden
  J. Walles et al. View Abstract

  Risk factors for developing bloodstream infections (BSIs) caused by Aerococcus bacteria remain insufficiently examined. In this nationwide case–control study in Sweden, 19 of 23 clinical microbiological laboratories identified patients who had aerococcal BSIs during 2012–2016. We compared each of those index patients with 4 controls matched for age, sex, and county of residence. Overall, 588 episodes of aerococcal BSI occurred over 39.6 million person-years, corresponding to an average incidence of 1.48/100,000 person-years (95% CI 1.37–1.60/100,000 person-years). Most infections developed in men >65 years of age. Aerococcal BSI was associated with neurologic (adjusted odds ratio 2.89 [95% CI 2.26–3.70]) and urologic (adjusted odds ratio 2.15 [95% CI 1.72—2.68]) conditions and previous hospitalization or infection treatment. Our findings support the previously observed predilection for aerococcal BSIs developing in elderly men with urinary tract disorders. Awareness of Aerococcus spp. in patients, especially elderly men, will be needed to manage invasive infections.

• Postexposure Antimicrobial Drug Therapy in Goats Infected with Burkholderia pseudomallei
  R. A. Bowen et al. View Abstract

  Infection with Burkholderia pseudomallei, the causative agent of melioidosis, occurs by exposure to the organism in soil or water. There is concern for B. pseudomallei use as a potential bioweapon and as an exposure hazard in diagnostic laboratories processing samples or cultures containing the bacterium. The optimal strategies for treatment and postexposure prophylaxis are inadequately developed. This study used goats to evaluate 3 antimicrobial drug treatment regimens for postexposure therapy because they are a species naturally susceptible to B. pseudomallei infection. Goats were infected by percutaneous inoculation, and antimicrobial drug therapies were initiated 48 hours later. Widespread infection with abscess formation in multiple organs developed in untreated goats and goats treated with either amoxicillin/clavulanate or sulfamethoxazole/trimethoprim. In contrast, treatment with the combination of all 4 antimicrobial drugs might have eradicated the infection. Our findings suggest combination therapy with those 4 antimicrobial drugs may be useful for postexposure prophylaxis in humans.

• Powassan and Eastern Equine Encephalitis Virus Seroprevalence in Endemic Areas, United States, 2019–2020
  H. Padda et al. View Abstract

  Powassan virus (POWV) and Eastern equine encephalitis virus (EEEV) are regionally endemic arboviruses in the United States that can cause neuroinvasive disease and death. Recent identification of EEEV transmission through organ transplantation and POWV transmission through blood transfusion have increased concerns about infection risk. After historically high numbers of cases of both viruses were reported in 2019, we conducted a seroprevalence survey using blood donation samples from selected endemic counties. Specimens were screened for virus-specific neutralizing antibodies, and population seroprevalence was estimated using weights calibrated to county population census data. For POWV, median county seroprevalence in 4 states was 0.84%, ranging from 0% (95% CI 0%–2.28%) to 11.5% (95% CI 0.82%–40.9%). EEEV infection was identified in a single county (estimated seroprevalence 1.62% [95% CI 0.04%–8.75%]). Although seroprevalence estimates in sampled areas were generally low, additional investigation of higher-prevalence areas could inform risk for transmission from asymptomatic blood and organ donors.

• 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 Nucleocapsid Antibody Boosting
  E. Grebe et al. View Abstract

  More than 85% of US adults had been infected with SARS-CoV-2 by the end of 2023. Continued serosurveillance of transmission and assessments of correlates of protection require robust detection of reinfections. We developed a serologic method for identifying reinfections in longitudinal blood donor data by assessing nucleocapsid (N) antibody boosting using a total immunoglobulin assay. Receiver operating characteristic curve analysis yielded an optimal ratio of >1.43 (sensitivity 87.1%, specificity 96.0%). When prioritizing specificity, a ratio of >2.33 was optimal (sensitivity 75.3%, specificity 99.3%). In donors with higher anti-N reactivity levels before reinfection, sensitivity was reduced. Sensitivity could be improved by expanding the dynamic range of the assay through dilutional testing, from 38.8% to 66.7% in the highest reactivity group (signal-to-cutoff ratio before reinfection >150). This study demonstrated that longitudinal testing for N antibodies can be used to identify reinfections and estimate total infection incidence in a blood donor cohort.

• 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. View Abstract

  In 2022, we initiated systematic 5-fluorocytosine susceptibility testing of Candida spp. isolates in Denmark; we observed a bimodal MIC distribution in C. tropicalis, with MICs >16 mg/L in half the isolates. This study investigates the epidemiology and molecular mechanisms of 5-fluorocytosine resistance in C. tropicalis. We analyzed 104 C. tropicalis isolates from 3 time periods, alongside 353 C. albicans and 227 C. glabrata isolates from 2022. We determined MICs using EUCAST E.Def 7.3. Sequencing of FCY2 (purine-cytosine permease), FCY1 (cytosine deaminase), FUR1 (uracil phosphoribosyl transferase), and URA3 (orotidine-5′-phosphate decarboxylase) genes revealed FCY2 alterations—E49X (30/32), Q7X (1/32), and K6NfsX10 (1/32)—in resistant C. tropicalis strains. We found a URA3 alteration, K177E, in both susceptible and resistant strains. Microsatellite genotyping showed that all C. tropicalis isolates with E49X were clonally related. The marked increase in resistance, driven by the clonal spread of E49X, necessitates further research into virulence and environmental factors.

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. View Abstract

  Whipple’s disease is rarely diagnosed in Latin America. We describe 2 patients with Tropheryma whipplei infection diagnosed in Mexico during 2019–2021. Diagnoses were confirmed by histopathology, electron microscopy, immunohistochemistry, and DNA amplification and sequencing analysis of the 16S rRNA gene. Clinicians should be aware of T. whipplei infection and associated syndromes.

• High Prevalence of Influenza D Virus Infection in Swine, Northern Ireland
  P. Lagan and K. Lemon View Abstract

  We detected influenza D virus in multiple swine herds in Northern Ireland. Whole-genome sequencing showed several circulating genotypes and novel mutations in the receptor-binding site and esterase domains of the hemagglutinin-esterase fusion protein. Transmission routes of influenza D virus to swine remain to be clarified but could be direct or indirect.

• 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. View Abstract

  Several concurrent mpox outbreaks are ongoing in the Democratic Republic of the Congo. We report a case of severe clade Ia mpox in an adult woman with indeterminate HIV status who died 16 days after symptom onset. She self-identified as a sex worker and had spent time in the capital city, Kinshasa.

• 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 highlight 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. View Abstract

  We describe a large urban outbreak of feline sporotrichosis caused by Sporothrix brasiliensis fungi in Argentina. Over a 7-month period in Puerto Iguazú, which borders Brazil, we identified culture-proven sporotrichosis in 9 cases across 7 households. Public health officials should coordinate cross-border One Health actions and institute context-specific interventions.

• 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 Zoonotic and Hybrid Schistosome Egg Excretion Patterns, Malawi, 2024
  A. M. O’Ferrall et al. View Abstract

  Two exemplary cases of mixed urogenital and intestinal schistosomiasis in Malawi show hybridizations of Schistosoma mattheei with S. haematobium and S. mansoni, indicating newly emerging genetic diversity. Complex egg excretion patterns in feces expose current diagnostic gaps and alert to future sampling needs for effective surveillance of zoonotic schistosomiasis.

• 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. View Abstract

  We detected St. Louis encephalitis virus (SLEV) in 0.16% (3/3,375) of Aedes and Sabethes spp. mosquitoes captured during 2016–2018 in São Paulo State, Brazil. We also isolated and confirmed that the SLEV strains belong to genotype III. Continued surveillance is required to clarify the burden of SLEV in Brazil.

• Trichophyton indotineae Infection, São Paulo, Brazil, 2024
  J. de Almeida et al. View Abstract

  We report an extensive, terbinafine-resistant (squalene epoxidase F397L mutation) Trichophyton indotineae infection in a previously healthy businessman from São Paulo, Brazil. The patient had previously traveled to France, Spain, and the United States. Clinician awareness, laboratory testing capacity, and surveillance are essential to prevent T. indotineae spread and inform healthcare practices.

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

About the Cover

• The Oldest Art
  B. Breedlove

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.

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.
• 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.

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.

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.

Research Letter

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

Supplement

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

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