Early Release

Perspective

• Archaea in the Human Microbiome and Potential Effects on Human Infectious Disease
  S. Duller and C. Moissl-Eichinger

Synopses

• Outbreak of Intermediate Species Leptospira venezuelensis Spread by Rodents to Cows and Humans in L. interrogans–Endemic Region, Venezuela
  L. Caraballo et al. View Abstract

  Leptospirosis is a common but underdiagnosed zoonosis. We conducted a 1-year prospective study in La Guaira State, Venezuela, analyzing 71 hospitalized patients who had possible leptospirosis and sampling local rodents and dairy cows. Leptospira rrs gene PCR test results were positive in blood or urine samples from 37/71 patients. Leptospira spp. were isolated from cultured blood or urine samples of 36/71 patients; 29 had L. interrogans, 3 L. noguchii, and 4 L. venezuelensis. Conjunctival suffusion was the most distinguishing clinical sign, many patients had liver involvement, and 8/30 patients with L. interrogans infections died. The Leptospira spp. found in humans were also isolated from local rodents; L. interrogans and L. venezuelensis were isolated from cows on a nearby, rodent-infested farm. Phylogenetic clustering of L. venezuelensis isolates suggested a recently expanded outbreak strain spread by rodents. Increased awareness of leptospirosis prevalence and rapid diagnostic tests are needed to improve patient outcomes.

• Systematic Review of Prevalence of Histoplasma Antigenuria in Persons with HIV in Latin America and Africa
  P. Sekar et al.

Research

• Retrospective Study of Infections by Corynebacteria of diphtheriae Species Complex, French Guiana, 2016–2021
  M. Gaillet et al.
• SARS-CoV-2 Seropositivity in Urban Population of Wild Fallow Deer, Dublin, Ireland, 2020–2022
  K. Purves et al. View Abstract

  SARS-CoV-2 can infect wildlife, and SARS-CoV-2 variants of concern might expand into novel animal reservoirs, potentially by reverse zoonosis. White-tailed deer and mule deer of North America are the only deer species in which SARS-CoV-2 has been documented, raising the question of whether other reservoir species exist. We report cases of SARS-CoV-2 seropositivity in a fallow deer population located in Dublin, Ireland. Sampled deer were seronegative in 2020 when the Alpha variant was circulating in humans, 1 deer was seropositive for the Delta variant in 2021, and 12/21 (57%) sampled deer were seropositive for the Omicron variant in 2022, suggesting host tropism expansion as new variants emerged in humans. Omicron BA.1 was capable of infecting fallow deer lung type-2 pneumocytes and type-1–like pneumocytes or endothelial cells ex vivo. Ongoing surveillance to identify novel SARS-CoV-2 reservoirs is needed to prevent public health risks during human–animal interactions in periurban settings.

• Detection of Nucleocapsid Antibodies Associated with Primary SARS-CoV-2 Infection in Unvaccinated and Vaccinated Blood Donors
  E. Grebe et al. View Abstract

  Nucleocapsid antibody assays can be used to estimate SARS-CoV-2 infection prevalence in regions implementing spike-based COVID-19 vaccines. However, poor sensitivity of nucleocapsid antibody assays in detecting infection after vaccination has been reported. We derived a lower cutoff for identifying previous infections in a large blood donor cohort (N = 142,599) by using the Ortho VITROS Anti-SARS-CoV-2 Total-N Antibody assay, improving sensitivity while maintaining specificity >98%. We validated sensitivity in samples donated after self-reported swab-confirmed infections diagnoses. Sensitivity for first infections in unvaccinated donors was 98.1% (95% CI 98.0–98.2) and for infection after vaccination was 95.6% (95% CI 95.6–95.7) based on the standard cutoff. Regression analysis showed sensitivity was reduced in the Delta compared with Omicron period, in older donors, in asymptomatic infections, <30 days after infection, and for infection after vaccination. The standard Ortho N antibody threshold demonstrated good sensitivity, which was modestly improved with the revised cutoff.

• Emergence of Bluetongue Virus Serotype 3, the Netherlands, September 2023
  M. Holwerda et al. View Abstract

  Since 1998, notifiable bluetongue virus (BTV) serotypes 1–4, 6, 8, 9, 11, and 16 have been reported in Europe. In August 2006, a bluetongue (BT) outbreak caused by BTV serotype 8 began in northwestern Europe. The Netherlands was declared BT-free in February 2012, and annual monitoring continued. On September 3, 2023, typical BT clinical manifestations in sheep were notified to the Netherlands Food and Product Safety Consumer Authority. On September 6, we confirmed BTV infection through laboratory diagnosis; notifications of clinical signs in cattle were also reported. We determined the virus was serotype 3 by whole-genome sequencing. Retrospective analysis did not reveal BTV circulation earlier than September. The virus source and introduction route into the Netherlands remains unknown. Continuous monitoring and molecular diagnostic testing of livestock will be needed to determine virus spread, and new prevention strategies will be required to prevent BTV circulation within the Netherlands and Europe.

• Environmental Hot Spots and Resistance-Associated Application Practices for Azole-Resistant Aspergillus fumigatus, Denmark, 2020–2023
  M. Arendrup et al. View Abstract

  Azole-resistant Aspergillus fumigatus (ARAf) fungi have been found inconsistently in the environment in Denmark since 2010. During 2018–2020, nationwide surveillance of clinical A. fumigatus fungi reported environmental TR₃₄/L98H or TR₄₆/Y121F/T289A resistance mutations in 3.6% of isolates, prompting environmental sampling for ARAf and azole fungicides and investigation of selected ARAf in field and microcosmos experiments. ARAf was ubiquitous (20% of 366 samples; 16% TR₃₄/L98H- and 4% TR₄₆/Y121F/T289A-related mechanisms), constituting 4.2% of 4,538 A. fumigatus isolates. The highest proportions were in flower- and compost-related samples but were not correlated with azole-fungicide application concentrations. Genotyping showed clustering of tandem repeat–related ARAf and overlaps with clinical isolates in Denmark. A. fumigatus fungi grew poorly in the field experiment with no postapplication change in ARAf proportions. However, in microcosmos experiments, a sustained complete (tebuconazole) or partial (prothioconazole) inhibition against wild-type A. fumigatus but not ARAf indicated that, under some conditions, azole fungicides may favor growth of ARAf in soil.

• Fatal SARS-CoV-2 Infection Among Children, Japan, January–September 2022
  S. Mitsushima et al.
• Scrapie versus Chronic Wasting Disease in White-Tailed Deer
  Z. J. Lambert et al.
• Metagenomic Detection of Bacterial Zoonotic Pathogens among Febrile Patients, Tanzania, 2007–2009
  R. J. Rolfe et al. View Abstract

  Bacterial zoonoses are established causes of severe febrile illness in East Africa. Within a fever etiology study, we applied a high-throughput 16S rRNA metagenomic assay validated for detecting bacterial zoonotic pathogens. We enrolled febrile patients admitted to 2 referral hospitals in Moshi, Tanzania, during September 2007–April 2009. Among 788 participants, median age was 20 (interquartile range 2–38) years. We performed PCR amplification of V1–V2 variable region 16S rRNA on cell pellet DNA, then metagenomic deep-sequencing and pathogenic taxonomic identification. We detected bacterial zoonotic pathogens in 10 (1.3%) samples: 3 with Rickettsia typhi, 1 R. conorii, 2 Bartonella quintana, 2 pathogenic Leptospira spp., and 1 Coxiella burnetii. One other sample had reads matching a Neoerhlichia spp. previously identified in a patient from South Africa. Our findings indicate that targeted 16S metagenomics can identify bacterial zoonotic pathogens causing severe febrile illness in humans, including potential novel agents.

• Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan
  P. Tobias Cudahy et al. View Abstract

  Little is known about environmental transmission of Mycobacterium kansasii. We retrospectively investigated potential environmental acquisition, primarily water sources, of M. kansasii among 216 patients with pulmonary disease from an industrial city in Taiwan during 2015–2017. We analyzed sputum mycobacterial cultures using whole-genome sequencing and used hierarchical Bayesian spatial network methods to evaluate risk factors for genetic relatedness of M. kansasii strains. The mean age of participants was 67 years; 24.1% had previously had tuberculosis. We found that persons from districts served by 2 water purification plants were at higher risk of being infected with genetically related M. kansasii isolates. The adjusted odds ratios were 1.81 (1.25–2.60) for the Weng Park plant and 1.39 (1.12–1.71) for the Fongshan plant. Those findings unveiled the association between water purification plants and M. kansasii pulmonary disease, highlighting the need for further environmental investigations to evaluate the risk for M. kansasii transmission.

• Potential of Pan-Tuberculosis Treatment to Drive Emergence of Novel Resistance
  C. McQuaid et al. View Abstract

  New tuberculosis (TB) drugs with little existing antimicrobial resistance enable a pan-TB treatment regimen, intended for universal use without prior drug-susceptibility testing. However, widespread use of such a regimen could contribute to an increasing prevalence of antimicrobial resistance, potentially rendering the pan-TB regimen ineffective or driving clinically problematic patterns of resistance. We developed a model of multiple sequential TB patient cohorts to compare treatment outcomes between continued use of current standards of care (guided by rifampin-susceptibility testing) and a hypothetical pan-TB approach. A pan-TB regimen that met current target profiles was likely to initially outperform the standard of care; however, a rising prevalence of transmitted resistance to component drugs could make underperformance likely among subsequent cohorts. Although the pan-TB approach led to an increased prevalence of resistance to novel drugs, it was unlikely to cause accumulation of concurrent resistance to novel drugs and current first-line drugs.

• Phylogenetic Classification of Human Respiratory Syncytial Virus Below the Subgroup Level
  S. Goya et al.
• Geographic Distribution of Rabies Virus and Genomic Sequence Alignment of Wild and Vaccine Strains, Kenya
  E. N. Wambugu et al.
• Wastewater Surveillance to Confirm Differences in Influenza A Infection between Michigan, USA, and Ontario, Canada, September 2022–March 2023
  R. Corchis-Scott et al. View Abstract

  Wastewater surveillance is an effective way to track the prevalence of infectious agents within a community and, potentially, the spread of pathogens between jurisdictions. We conducted a retrospective wastewater surveillance study of the 2022–23 influenza season in 2 communities, Detroit, Michigan, USA, and Windsor-Essex, Ontario, Canada, that form North America’s largest cross-border conurbation. We observed a positive relationship between influenza-related hospitalizations and the influenza A virus (IAV) wastewater signal in Windsor-Essex (ρ = 0.785; p<0.001) and an association between influenza-related hospitalizations in Michigan and the IAV wastewater signal for Detroit (ρ = 0.769; p<0.001). Time-lagged cross correlation and qualitative examination of wastewater signal in the monitored sewersheds showed the peak of the IAV season in Detroit was delayed behind Windsor-Essex by 3 weeks. Wastewater surveillance for IAV reflects regional differences in infection dynamics which may be influenced by many factors, including the timing of vaccine administration between jurisdictions.

Dispatches

• Detection of Rustrela Virus in Wild Mountain Lion (Puma concolor) with Staggering Disease, Colorado, USA
  K. A. Fox et al.
• Crimean-Congo Hemorrhagic Fever Virus Kinetics in Serum, Saliva, and Urine Specimens, Iran, 2018
  M. Metanat et al.
• Highly Pathogenic Avian Influenza Virus A(H5N1) Clade 2.3.4.4b Infection in Free-Ranging Polar Bear, Alaska, USA
  R. Stimmelmayr et al. View Abstract

  We report a natural infection with a Eurasian highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus in a free-ranging juvenile polar bear (Ursus maritimus) found dead in North Slope Borough, Alaska, USA. Continued community and hunter-based participation in wildlife health surveillance is key to detecting emerging pathogens in the Arctic.

• Macrolide-Resistant Mycoplasma pneumoniae Infections among Children before and during the COVID-19 Pandemic, Taiwan, 2017–2023
  T. Wu et al.
• Spatiotemporal Modeling of Cholera, Uvira, Democratic Republic of the Congo, 2016−2020
  R. Ratnayake et al.
• Hepatitis B Virus Reactivation After Switch to Cabotegravir/Rilpivirine in Patient with Low Hepatitis B Surface Antibody
  E. Adachi et al.
• Recurrent Occupational Hantavirus Infections Linked to Feeder Rodent Breeding Farm, Taiwan, 2022
  K. Wang et al.
• Multiplex Dual-Target Reverse Transcription PCR for Subtyping Avian Influenza A(H5) Virus
  M. K. Sahoo et al. View Abstract

  An increased risk for human infection with avian influenza A(H5N1) viruses is of concern. We developed an internally controlled, dual-target reverse transcription PCR for influenza A(H5) subtyping. This test could be used to detect influenza A(H5) in clinical samples.

• Surge in Ceftriaxone-resistant Neisseria gonorrhoeae FC428-like Strains, Asia-Pacific Region, 2015−2022
  L. Xiu et al.
• Real-Time Enterovirus D68 Outbreak Detection through Hospital Surveillance of Severe Acute Respiratory Infection, Senegal, 2023
  M. Jallow et al.
• Characterization of Influenza D Virus Reassortant Strain in Swine from Mixed Pig and Beef Farm, France
  S. Gorin et al.
• Group B Streptococcus ST103 as Human and Bovine Pathogen, Brazil
  L. A. Oliveira et al.
• ST913-IVa-t991 Methicillin-Resistant Staphylococcus aureus among Pediatric Patients, Israel
  M. Baum et al.

Research Letters

• Emayella augustorita, New Member of Pasteurellaceae, Isolated from Blood Cultures of Septic Patient
  S. Meyer et al. View Abstract

  We report discovery of a new bacterial genus and species of the family Pasteurellaceae by using phylogenetic and metabolic analysis. The bacterium, Emayella augustorita, was isolated from blood cultures of a patient in France diagnosed with an adenocarcinoma of the intestines and who was treated with a biliary prosthesis placement.

• Fecal Microbiota Transplantation for Severe Infant Botulism, China
  C. Fan et al. View Abstract

  Infant botulism in a 4-month-old boy in China who continued to excrete toxins for over a month despite antitoxin therapy was further treated with fecal microbiota transplantation. After treatment, we noted increased gut microbial diversity and altered fecal metabolites, which may help reduce intestinal pH and enhance anti-inflammatory capabilities.

• Persistence of Influenza H5N1 and H1N1 Viruses in Unpasteurized Milk on Milking Unit Surfaces
  V. Le Sage et al. View Abstract

  Examining the persistence of highly pathogenic avian influenza A(H5N1) from cattle and human influenza A(H1N1)pdm09 pandemic viruses in unpasteurized milk revealed that both remain infectious on milking equipment materials for several hours. Those findings highlight the risk for H5N1 virus transmission to humans from contaminated surfaces during the milking process.

• Rare Case of Echinostoma cinetorchis Infection, South Korea
  S. Hong et al.
• Infective SARS-CoV-2 in Skull Sawdust at Autopsy, Finland
  J. N. Kantonen et al. View Abstract

  We assessed the distribution of SARS-CoV-2 at autopsy in 22 deceased persons with confirmed COVID-19. SARS-CoV-2 was found by PCR (2/22, 9.1%) and by culture (1/22, 4.5%) in skull sawdust, suggesting that live virus is present in tissues postmortem, including bone. Occupational exposure risk is low with appropriate personal protective equipment.

• Panton-Valentine Leukocidin–Positive Staphylococcus aureus in Family and Pet Cat
  A. Bethe et al. View Abstract

  Continued detection of Panton-Valentine leukocidin–positive Staphylococcus aureus in samples from a family with severe repeated skin infections and their pet cat suggests transmission between the family and cat. Decolonizing the pet led to successful elimination of the bacteria from the household. Clinicians should consider pet cats as possible reinfection sources.

• Novel Genotypes of Highly Pathogenic Avian Influenza H5N1 Clade 2.3.4.4b Viruses, Germany, November 2023
  A. Ahrens et al. View Abstract

  Several subtypes and many different genotypes of highly pathogenic avian influenza viruses of subtype H5 clade 2.3.4.4b have repeatedly caused outbreaks in Germany. Four new highly pathogenic avian influenza genotypes emerged in November 2023 after reassortment with low pathogenicity precursors, replacing genotype BB, which had dominated in Europe since 2022.

• Vibrio mimicus Lineage Carrying CTX and Vibrio Pathogenicity Island, United States and China
  S. Morgado et al.

Letter

• Transmission and Surveillance of Rat Hepatitis E Virus in Swine
  M. Bezerra et al.

Etymologia

• Microbiota [mī′′-krō-bī′-ō-′tә], microbiome [mī′′-krō-bī′-ōm]
  J. Cabrera and D. Monte

Online Report

• Wastewater Target Pathogens of Public Health Importance for Expanded Sampling, Houston, Texas, USA
  K. Sheth et al.

Synopses

• Morphologic and Molecular Identification of Human Ocular Infection Caused by Pelecitus species, Thailand
  P. Rujkorakarn et al.
• Clinical Significance, Species Distribution, and Temporal Trends of Nontuberculous Mycobacteria, Denmark, 1991–2022
  V. Dahl et al.

Research

• Clinical Aspects and Disease Severity of Streptococcus dysgalactiae Subspecies equisimilis Bacteremia, Finland
  V. Nevanlinna et al.
• Loop-Mediated Isothermal Amplification Assay to Detect Invasive Malaria Vector Anopheles stephensi Mosquitoes
  C. Rafferty et al. View Abstract

  Spread of the Anopheles stephensi mosquito, an invasive malaria vector, threatens to put an additional 126 million persons per year in Africa at risk for malaria. To accelerate the early detection and rapid response to this mosquito species, confirming its presence and geographic extent is critical. However, existing molecular species assays require specialized laboratory equipment, interpretation, and sequencing confirmation. We developed and optimized a colorimetric rapid loop-mediated isothermal amplification assay for molecular An. stephensi species identification. The assay requires only a heat source and reagents and can be used with or without DNA extraction, resulting in positive color change in 30–35 minutes. We validated the assay against existing PCR techniques and found 100% specificity and analytical sensitivity down to 0.0003 nanograms of genomic DNA. The assay can successfully amplify single mosquito legs. Initial testing on samples from Marsabit, Kenya, illustrate its potential as an early vector detection and malaria mitigation tool.

Dispatch

• Co-Circulation of Genetically Distinct High Pathogenicity Avian Influenza A(H5N5) and (H5N1) Viruses in Crows, Hokkaido, Japan
  Y. Hew et al.

Photo Quiz

• Photo Quiz
  A. Cucu et al.

Research Letter

• Molecular Confirmation of Taenia solium Taeniasis in Child, Timor-Leste
  H. Jin et al.