Free-ranging white-tailed deer (WTD) are highly susceptible to the SARS-CoV-2 virus. Through an opportunistic sampling of WTD in northeast Ohio, USA, during January–March 2023, we identified 6 SARS-CoV-2 lineages from 36 sequences using the pangolin lineages tool, including the B.1.1.7 lineage (Alpha variant) and BQ.1.1, BQ.1.1.63, BQ.1.1.67, BQ.1.23, and XBB.1.5.35 lineages (Omicron variant). The

Norovirus GII.17 outbreaks in the United States increased from <10% during the 2022–23 season to 75% during the 2024–25 season, surpassing the number of GII.4 outbreaks. The norovirus season also started earlier in 2024–25 than in previous seasons. Continued norovirus surveillance is needed to detect and monitor emerging strains.

Spiroplasma ixodetis has been reported to cause the rare combination of cataract and uveitis in infants. Through a retrospective analysis of available literature and additional unpublished cases, we identified 28 eyes from 18 infants from 8 countries in Europe with cataracts and intraocular inflammation. The cataracts were bilateral in 55.6%, unilateral in 44.4%, and progressive in 46.4% of patients

We confirmed influenza A virus (IAV) by PCR in serum from 18 cows on 3 affected dairy farms in California, USA. Our findings indicate the presence of viremia and might help explain IAV transmission dynamics and shedding patterns in cows. An understanding of those dynamics could enable development of IAV mitigation strategies.

Streptococcus suis, a swine pathogen that causes zoonotic infections in Europe and Asia, has increasingly been observed in South America. We reviewed all available reports from the continent and identified S. suis cases in Argentina, Brazil, Chile, French Guiana, and Uruguay. We also identified 8 novel infections from Argentina, bringing the total documented human cases in South America to 47. We reclassified

We polled infectious disease specialists about cryptococcal antigen screening for patients initiating HIV antiretroviral therapy. Of 215 respondents, 33% reported typically obtaining screening for patients with CD4 counts <200 cells/mm3 and 63% for counts <100 CD4 cells/mm3. Uncertainty about cryptococcal antigen screening benefits and recommendations suggests opportunities for education and increased

During 2007–2020, we conducted a cross-sectional prevalence study among patients with acute undifferentiated febrile illness to describe the burden and long-term epidemiology of rickettsioses in Cambodia. Serum samples were collected from 10,243 participants, along with epidemiologic data, information on clinical symptoms, demographic characteristics, and risk factors. A total of 802 (7.8%) participants

Plasmodium falciparum strains lacking P. falciparum histidine-rich protein 2 (PfHRP2) and PfHRP3 threaten malaria rapid test reliability. We show that pfhrp2/pfhrp3–deleted parasites circulated in Ethiopia as early as 2009, before widespread PfHRP2-based rapid test use, and had high pfhrp3 deletion prevalence. Monitoring of pfhrp2 and of pfhrp3 deletions is needed.

Positive laboratory results are increasingly used for Lyme disease surveillance in the United States. We found 6%–15% of persons with a positive test each year tested positive in a prior year; repeat testing frequency increased with patient age. Repeat testing of persons with previous seropositivity could affect surveillance data interpretation.

We report on a patient in China with no underlying illnesses who died of Burkholderia thailandensis infection despite timely treatment. This case challenges the perception that B. thailandensis is nonlethal or has low virulence. Increased clinical awareness and prompt diagnosis are essential for managing B. thailandensis infections and preventing fatal outcomes.

We explored the role of black flying foxes (Pteropus alecto) in Australia as reservoirs of Borrelia bacteria. We found bats infected with 2 Borrelia haplotypes phylogenetically distinct from Lyme or relapsing fever clades. Efforts to sample black flying foxes and their ectoparasites are needed to evaluate zoonotic potential of those Borrelia lineages.

Informed by passive tick surveillance, we collected questing Haemaphysalis longicornis ticks from southwestern Connecticut, USA. Of 445 ticks tested by PCR, 3 nymphs were positive: 1 for Ehrlichia chaffeensis and 2 for Borrelia burgdorferi. This finding highlights the enduring public health challenges of invasive ticks and associated pathogens.

We characterized highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b genotype D1.1 in wild birds and a human in British Columbia, Canada, during 2024. D1.1, the predominant genotype circulating in fall 2024, is a reassortment between Eurasian A3 lineage viruses, introduced to North America in 2022, and North American lineage viruses.

We describe a pediatric case of recurrent skin infections caused by a Panton-Valentine leukocidin and exfoliative toxin E double-positive methicillin-susceptible Staphylococcus aureus clonal complex 188 clone. Most of the patient’s family members were infected with the same strain, and intrafamilial transmission was strongly suspected. Decolonization procedures were not effective.

We report 3 cases of dual-genotype Orientia tsutsugamushi infection in Hainan Island, China. Patients exhibited diverse clinical manifestations, including afebrile illness and multiorgan involvement, highlighting the complexity associated with genetic diversity in scrub typhus. Clinicians should maintain heightened suspicion for atypical scrub typhus manifestations in endemic regions.

Cache Valley virus (CVV), a mosquitoborne virus, can cause neuroinvasive disease in humans and adverse reproductive outcomes in sheep and goats. In 2023, CVV RNA was detected in an aborted lamb from a flock in Arkansas, USA. We conducted a One Health investigation to explore the potential effects of CVV in Arkansas.

Oropouche virus (OROV), historically endemic to the Amazon, had spread to nearly all Brazil states by 2024; Espírito Santo emerged as a transmission hotspot in the Atlantic Forest biome. We characterized the epidemiologic factors driving OROV spread in nonendemic southeast Brazil, analyzing environmental and agricultural conditions contributing to viral transmission. We tested samples from 29,080 suspected

We monitored mosquitoes in 3 bus stations in Bogota, Colombia, located at 2,625 m above sea level. During December 2023–January 2024, we collected 27 larvae and 1 adult female Aedes aegypti mosquitoes at 1 station. Detection of Ae. aegypti mosquitoes in Bogota is a call to continue monitoring mosquitoes at stations.

Etymologia

We report a Dirofilaria repens nematode infection in a woman in Italy who sought care for a fast-creeping lesion within her subcutaneous facial tissue. Dirofilariosis should be included in differential diagnosis of subcutaneous nodules or creeping lesions. This case highlights the need for controlling canine dirofilarioses to mitigate zoonotic risk.

We found the zoonotic nematode, Baylisascaris procyonis, in a common raccoon (Procyon lotor) in Mexico. Expansion of raccoons into human-dominated regions might increase the risk of B. procyonis infections in humans. Increased surveillance and healthcare provider awareness of baylisascariasis in Mexico will be needed to prevent those infections in humans.

We conducted a hospital-based cross-sectional study of Plasmodium falciparum in 2017 in southeastern Sudan. Among 257 P. falciparum samples, we found 22% harbored the pfkelch13 R622I mutation and 10.7% showed hrp2/3 gene deletions. Our findings highlight the urgent need for enhanced surveillance of drug- and diagnostic-resistant parasites in the Horn of Africa.

We report 3 cases of babesiosis in Italy caused by Babesia species that are rarely reported in humans. The circulation of Babesia spp. among vectors, animals, and humans might be more common than previously thought, and babesiosis might be an underdiagnosed and emerging disease in Italy and Europe.

Histoplasmosis is one of the most common pulmonary mycosis diseases in the world. Genome sequencing has revealed that Histoplasma, the cause of histoplasmosis, is composed of several phylogenetic species. The genetic diversity of the pathogen remains largely unknown, especially in the tropics. We sequenced the genomes of 91 Histoplasma isolates from the Amazon basin of South America and used phylogenomics

Dengue is a major cause of illness among local populations and travelers in dengue-endemic areas, particularly those who stay for an extended period. However, little is known about dengue risk among expatriates and other long-term travelers. We used catalytic models of force of infection to estimate time to 60% dengue virus (DENV) seropositivity for a cross-section of expatriates living in Bangkok

We conducted a multicenter, observational, 12-month follow-up study to identify the extended health burden of severe COVID-19 pneumonia by characterizing long-term sequelae of acute infection in participants previously enrolled in clinical trials for severe COVID-19 pneumonia requiring hospitalization. Overall, 134 (77.5%) of 173 participants completed the study. At 12 months, 51 (29.5%) participants

In the aftermath of 2 extreme weather events in 2022, Malawi experienced a severe cholera outbreak; 59,325 cases and 1,774 deaths were reported by March 31, 2024. We generated 49 Vibrio cholerae full genomes from isolates collected during December 2022–March 2023. Phylogenetic and phylogeographic methods confirmed that the Malawi outbreak strains originated from Pakistan’s 2022 cholera outbreak. That

A Pictorial Human Case of “Furious Rabies”

We used PCR, Sanger sequencing, and phylogenetic analysis to identify Wesselsbron virus (WSLV) clade 1 in sick camels from Borana Zone, Ethiopia. Although WSLV primarily infects sheep and cattle, its pathogenicity in camels remains unclear. Camel farmers in the region should be aware of WSLV and its health effects in camels.

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Treatment-refractory giardiasis is an emerging clinical problem. Of 4,285 giardiasis cases identified during 2008–2020 in Stockholm, Sweden, 102 (2.4%) were nitroimidazole-refractory. Among cases acquired in India, the percentage was high (64/545 [12%]) and increased over time. The region of acquisition needs to be taken into consideration when managing patients.

We report fatal tularemia in stranded beluga whales in Cook Inlet, Alaska, USA. Francisella tularensis was detected by nanopore metagenomics, confirmed by quantitative PCR and immunohistochemistry, and characterized as F. tularensis subspecies holarctica by multilocus sequence typing. Our findings should be considered when assessing biosecurity and marine mammal health in the North Pacific.

Usutu virus is a zoonotic arbovirus that causes massive mortality in blackbirds. Using a unique longitudinal dataset on the kinetics of virus-specific antibodies in naturally infected wild blackbirds (Turdus merula), we found that individual birds may remain seropositive for >1 year and that reinfection can occur despite low-level virus neutralizing antibodies.

We report a case of iatrogenic Creutzfeldt-Jakob disease (iCJD) after a 48.3-year incubation period in a patient treated with cadaveric human growth hormone. iCJD was pathologically confirmed; genetic analysis was negative for pathogenic mutations. Clinicians should consider iCJD in patients with progressive neurologic signs who had received cadaveric human growth hormone treatment.

We tested cross-neutralization against highly pathogenic avian influenza A(H5N1) virus in adults vaccinated with 2021–2023 seasonal quadrivalent influenza vaccine in the United Kingdom. Seasonal quadrivalent influenza vaccines are unlikely to protect vulnerable persons against severe H5N1 disease during widespread transmission. Enhanced measures are needed to protect vulnerable people from H5N1 virus

We report an OXA-204–producing Pseudomonas guariconensis clinical isolate in, Tunisia, proving the spread of OXA-48 variants beyond Enterobacterales. The blaOXA-204 gene was carried on a 119-kb chromosomally integrated plasmid fragment, along with multiple additional resistance genes. Surveillance, diagnostic tools, and antimicrobial drug access are needed to mitigate spread of carbapenem-resistant

Mycoplasma arginini is a bacterium primarily found in animals and is seldom reported in human infections. We identified M. arginini infection in a severely immunocompromised kidney transplant recipient in Slovenia. Clinicians should be aware of M. arginini’s potential as a pathogen in immunocompromised persons with animal contact.

Murine typhus, a fleaborne bacterial disease caused by Rickettsia typhi, has reemerged and spread in the United States. We tested spinosad, an oral flea preventive, in opossum flea reservoirs. Spinosad killed 98% of fleas infesting opossums. Oral preventives could control fleas in host species and curb murine typhus spread to humans.

To evaluate non–H. pylori Helicobacter (NHPH) infections in Japan, we enrolled 673 consecutive patients who underwent gastric endoscopy during annual medical checkups at 4 hospitals during May–August 2022. We collected intragastric fluid and serum samples to detect NHPH infection by PCR and serologic tests. The prevalence of NHPH was 3% (20/673); 70% (14/20) of patients were infected with H. suis and

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We investigated epidemiologic and molecular characteristics of healthcare-associated (HA) and community-associated (CA) Clostridioides difficile infection (CDI) among adult and pediatric patients in Canadian Nosocomial Infection Surveillance Program hospitals during 2015–2022. Of 30,824 reported CDI cases, 94.9% (29,250/30,824) were among adult (73.2% HA; 26.8% CA) and 5.1% (1,574/30,824) pediatric

Gene PCR and sequencing using 16S ribosomal RNA (rRNA) can help diagnose challenging bacterial infections. Data on the optimal clinical settings for this type of testing are limited. We performed a retrospective study at Mayo Clinic, Rochester, Minnesota, USA, with typically sterile specimens from children that underwent 16S rRNA PCR testing during September 2020–December 2023. Of 162 tests performed

In the United States, Shiga toxin–producing Escherichia coli (STEC) outbreaks cause >265,000 infections and cost $280 million annually. We investigated REPEXH01, a persistent strain of STEC O157:H7 associated with multiple sources, including romaine lettuce and recreational water, that has caused multiple outbreaks since emerging in late 2015. By comparing the genomes of 729 REPEXH01 isolates with

We report the detection of a Shigella sonnei outbreak from a small investigation in the San Francisco Bay area, California, USA, in 2024. By combining outbreak investigation with genomic sequencing, we show the utility of phylodynamics to aid outbreak investigations of bacterial pathogens by state or local public health departments.

We assessed turnaround times in the national Listeria monocytogenes genomic surveillance system in Australia before and after decentralized sequencing. Using 1,204 samples collected during 2016–2023, we observed statistically significant reductions in median time from sample collection to issuance of national genomic surveillance report to 26 days, despite sample numbers doubling in 2022 and 2023.

Detecting and responding to clusters of rapid HIV transmission is a core HIV prevention strategy in the United States, guiding public health interventions and identifying gaps in prevention and care services. In 2016, the Centers for Disease Control and Prevention (CDC) initiated molecular cluster detection using data from 27 jurisdictions. During 2016–2023, CDC expanded sequence reporting nationwide

We report nosocomial Plasmodium falciparum malaria in Spain, which was confirmed microbiologically and genomically. Transmission occurred through insufficiently disinfected reusable syringe lead shielding during thyroid scintigraphy. Genomic analysis showed high similarity between isolates from index and source cases. Strict biosafety measures are needed in healthcare settings to prevent malaria transmission

Whole-genome sequencing (WGS) is routine for surveillance of Shiga toxin–producing Escherichia coli human isolates in France. Protocols use EnteroBase hierarchical clustering at <5 allelic differences (HC5) as screening for cluster detection. We assessed current implementation after 5 years for 1,002 sequenced isolates. From genomic distances of serotypes O26:H11, O157:H7, O80:H2, and O103:H2, we determined

In Europe, highly pathogenic avian influenza (HPAI) virus circulates in avian wildlife, undergoing frequent reassortment, sporadic introductions in domestic birds, and spillover to mammals. An H5N1 clade 2.3.4.4b reassortant, EA-2023-DG, affecting wild and domestic birds was detected in western Europe in November 2023. Six of its RNA segments came from the EA-2021-AB genotype, but the polymerase basic

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

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.

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

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

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

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.

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

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

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

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

Partnerships and Progress in Pathogen Genomics