Using an adaptive modeling framework to identify avian influenza spillover risk at the wild-domestic interface.

The wild to domestic bird interface is an important nexus for emergence and transmission of highly pathogenic avian influenza (HPAI) viruses. Although the recent incursion of HPAI H5N1 Clade 2.3.4.4b into North America calls for emergency response and planning given the unprecedented scale, readily available data-driven models are lacking. Here, we provide high resolution spatial and temporal transmission risk models for the contiguous United States. Considering virus host ecology, we included weekly species-level wild waterfowl (Anatidae) abundance and endemic low pathogenic avian influenza virus prevalence metrics in combination with number of poultry farms per commodity type and relative biosecurity risks at two spatial scales: 3 km and county-level. Spillover risk varied across the annual cycle of waterfowl migration and some locations exhibited persistent risk throughout the year given higher poultry production. Validation using wild bird introduction events identified by phylogenetic analysis from 2022 to 2023 HPAI poultry outbreaks indicate strong model performance. The modular nature of our approach lends itself to building upon updated datasets under evolving conditions, testing hypothetical scenarios, or customizing results with proprietary data. This research demonstrates an adaptive approach for developing models to inform preparedness and response as novel outbreaks occur, viruses evolve, and additional data become available.

vSNP: a SNP pipeline for the generation of transparent SNP matrices and phylogenetic trees from whole genome sequencing data sets.

BACKGROUND: Several single nucleotide polymorphism (SNP) pipelines exist, each offering its own advantages. Among them and described here is vSNP that has been developed over the past decade and is specifically tailored to meet the needs of diagnostic laboratories. Laboratories that aim to provide rapid whole genome sequencing results during outbreak investigations face unique challenges. vSNP addresses these challenges by enabling users to verify and validate sequence accuracy with ease- having utility across various pathogens, being fully auditable, and presenting results that are easy to interpret and can be comprehended by individuals with diverse backgrounds. RESULTS: vSNP has proven effective for real-time phylogenetic analysis of disease outbreaks and eradication efforts, including bovine tuberculosis, brucellosis, virulent Newcastle disease, SARS-CoV-2, African swine fever, and highly pathogenic avian influenza. The pipeline produces easy-to-read SNP matrices, sorted for convenience, as well as corresponding phylogenetic trees, making the output easily understandable. Essential data for verifying SNPs is included in the output, and the process has been divided into two steps for ease of use and faster processing times. vSNP requires minimal computational resources to run and can be run in a wide range of environments. Several utilities have been developed to make analysis more accessible for subject matter experts who may not have computational expertise. CONCLUSION: The vSNP pipeline integrates seamlessly into a diagnostic workflow and meets the criteria for quality control accreditation programs, such as 17025 by the International Organization for Standardization. Its versatility and robustness make it suitable for use with a diverse range of organisms, providing detailed, reproducible, and transparent results, making it a valuable tool in various applications, including phylogenetic analysis performed in real time.

Highly pathogenic avian influenza A(H5N1) virus in a common bottlenose dolphin (Tursiops truncatus) in Florida.

Since late 2021, highly pathogenic avian influenza (HPAI) viruses of A/goose/Guangdong/1/1996 (H5N1) lineage have caused widespread mortality in wild birds and poultry in the United States. Concomitant with the spread of HPAI viruses in birds are increasing numbers of mammalian infections, including wild and captive mesocarnivores and carnivores with central nervous system involvement. Here we report HPAI, A(H5N1) of clade 2.3.4.4b, in a common bottlenose dolphin (Tursiops truncatus) from Florida, United States. Pathological findings include neuronal necrosis and inflammation of the brain and meninges, and quantitative real time RT-PCR reveal the brain carried the highest viral load. Virus isolated from the brain contains a S246N neuraminidase substitution which leads to reduced inhibition by neuraminidase inhibitor oseltamivir. The increased prevalence of A(H5N1) viruses in atypical avian hosts and its cross-species transmission into mammalian species highlights the public health importance of continued disease surveillance and biosecurity protocols.

Surveillance for highly pathogenic avian influenza A (H5N1) in a raptor rehabilitation center-2022.

An ongoing, severe outbreak of highly pathogenic avian influenza virus (HPAI) A H5N1 clade 2.3.4.4b has been circulating in wild and domestic bird populations throughout the world, reaching North America in 2021. This HPAI outbreak has exhibited unique characteristics when compared to previous outbreaks. The global distribution of disease, prolonged duration, extensive number of species and individual wild birds affected, and the large impact on the global poultry industry have all exceeded historical impacts of previous outbreaks in North America. In this study, we describe the results of HPAI surveillance conducted at The Raptor Center, a wildlife rehabilitation hospital at University of Minnesota (Saint Paul, MN, U.S.A.), from March 28th-December 31, 2022. All wild raptors admitted to the facility were tested for avian influenza viruses using polymerase chain reaction (PCR) testing. All non-negative samples were submitted to the United States Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) National Veterinary Services Laboratories for confirmatory HPAI testing and genetic sequencing. During the study period, 996 individual birds representing 20 different species were tested for avian influenza, and 213 birds were confirmed HPAI positive. Highly pathogenic avian influenza surveillance conducted at The Raptor Center contributed 75% of the HPAI positive raptor detections within the state of Minnesota, located within the Mississippi flyway, significantly augmenting state wildlife surveillance efforts. The viral genotypes observed in birds sampled at The Raptor Center were representative of what was seen in wild bird surveillance within the Mississippi flyway during the same time frame. Wildlife rehabilitation centers provide an opportune situation to augment disease surveillance at the human, wildlife and domestic animal interface during ongoing infectious disease outbreaks.

Divergent Pathogenesis and Transmission of Highly Pathogenic Avian Influenza A(H5N1) in Swine.

Highly pathogenic avian influenza (HPAI) viruses have potential to cross species barriers and cause pandemics. Since 2022, HPAI A(H5N1) belonging to the goose/Guangdong 2.3.4.4b hemagglutinin phylogenetic clade have infected poultry, wild birds, and mammals across North America. Continued circulation in birds and infection of multiple mammalian species with strains possessing adaptation mutations increase the risk for infection and subsequent reassortment with influenza A viruses endemic in swine. We assessed the susceptibility of swine to avian and mammalian HPAI H5N1 clade 2.3.4.4b strains using a pathogenesis and transmission model. All strains replicated in the lung of pigs and caused lesions consistent with influenza A infection. However, viral replication in the nasal cavity and transmission was only observed with mammalian isolates. Mammalian adaptation and reassortment may increase the risk for incursion and transmission of HPAI viruses in feral, backyard, or commercial swine.

Highly Pathogenic Avian Influenza A(H5N1) Virus Clade 2.3.4.4b Infections in Wild Terrestrial Mammals, United States, 2022.

We describe the pathology of natural infection with highly pathogenic avian influenza A(H5N1) virus of Eurasian lineage Goose/Guangdong clade 2.3.4.4b in 67 wild terrestrial mammals throughout the United States during April 1‒July 21, 2022. Affected mammals include 50 red foxes (Vulpes vulpes), 6 striped skunks (Mephitis mephitis), 4 raccoons (Procyon lotor), 2 bobcats (Lynx rufus), 2 Virginia opossums (Didelphis virginiana), 1 coyote (Canis latrans), 1 fisher (Pekania pennanti), and 1 gray fox (Urocyon cinereoargenteus). Infected mammals showed primarily neurologic signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.

SARS-CoV-2 Infection Dynamics in the Pittsburgh Zoo Wild Felids with Two Viral Variants (Delta and Alpha) during the 2021-2022 Pandemic in the United States.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported in multiple animal species besides humans. The goal of this study was to report clinical signs, infection progression, virus detection and antibody response in a group of wild felids housed in adjacent but neighboring areas at the Pittsburgh Zoo. Initially, five African lions (Panthera leo krugeri) housed together exhibited respiratory clinical signs with viral shedding in their feces in March of 2021 coinciding with infection of an animal keeper. During the second infection wave in December 2021, four Amur tigers (Panthera tigris altaica) and a Canadian lynx (Lynx canadensis) showed clinical signs and tested positive for viral RNA in feces. In infected animals, viral shedding in feces was variable lasting up to 5 weeks and clinical signs were observed for up to 4 weeks. Despite mounting an antibody response to initial exposure, lions exhibited respiratory clinical signs during the second infection wave, but none shed the virus in their feces. The lions were positive for alpha variant (B.1.1.7 lineage) during the first wave and the tiger and lynx were positive for delta variant (AY.25.1. lineage) during the second wave. The viruses recovered from felids were closely related to variants circulating in human populations at the time of the infection. Cheetahs (Acinonyx jubatus) in the park did not show either the clinical signs or the antibody response.

Investigation of risk factors for introduction of highly pathogenic avian influenza H5N1 infection among commercial turkey operations in the United States, 2022: a case-control study.

Introduction: The 2022-2023 highly pathogenic avian influenza (HPAI) H5N1 outbreak in the United States (U.S.) is the largest and most costly animal health event in U.S. history. Approximately 70% of commercial farms affected during this outbreak have been turkey farms. Methods: We conducted a case-control study to identify potential risk factors for introduction of HPAI virus onto commercial meat turkey operations. Data were collected from 66 case farms and 59 control farms in 12 states. Univariate and multivariable analyses were conducted to compare management and biosecurity factors on case and control farms. Results: Factors associated with increased risk of infection included being in an existing control zone, having both brooders and growers, having toms, seeing wild waterfowl or shorebirds in the closest field, and using rendering for dead bird disposal. Protective factors included having a restroom facility, including portable, available to crews that visit the farm and workers having access and using a shower at least some of the time when entering a specified barn. Discussion: Study results provide a better understanding of risk factors for HPAI infection and can be used to inform prevention and control measures for HPAI on U.S. turkey farms.

Investigation of risk factors for introduction of highly pathogenic avian influenza H5N1 virus onto table egg farms in the United States, 2022: a case-control study.

Introduction: The 2022-2023 highly pathogenic avian influenza (HPAI) H5N1 outbreak in the United States (U.S.) is the most geographically extensive and costly animal health event in U.S. history. In 2022 alone, over 57 million commercial and backyard poultry in 47 U.S. states were affected. Over 75% of affected poultry were part of the commercial table egg production sector. Methods: We conducted a case-control study to identify potential risk factors for introduction of HPAI virus onto commercial table egg operations. Univariate and multivariable analyses were conducted to compare farm characteristics, management, and biosecurity factors on case and control farms. Results: Factors associated with increased risk of infection included being in an existing control zone, sightings of wild waterfowl, mowing or bush hogging vegetation less than 4 times a month, having an off-site method of daily mortality disposal (off-site composting or burial, rendering, or landfill), and wild bird access to feed/feed ingredients at least some of the time. Protective factors included a high level of vehicle washing for trucks and trailers entering the farm (a composite variable that included having a permanent wash station), having designated personnel assigned to specific barns, having a farm entrance gate, and requiring a change of clothing for workers entering poultry barns. Discussion: Study results improve our understanding of risk factors for HPAI infection and control measures for preventing HPAI on commercial U.S. table egg farms.

H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States and reassortments, December 2021-April 2022.

Highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b continue to have a devastating effect on domestic and wild birds. Full genome sequence analyses using 1369 H5N1 HPAIVs detected in the United States (U.S.) in wild birds, commercial poultry, and backyard flocks from December 2021 to April 2022, showed three phylogenetically distinct H5N1 virus introductions in the U.S. by wild birds. Unreassorted Eurasian genotypes A1 and A2 entered the Northeast Atlantic states, whereas a genetically distinct A3 genotype was detected in Alaska. The A1 genotype spread westward via wild bird migration and reassorted with North American wild bird avian influenza viruses. Reassortments of up to five internal genes generated a total of 21 distinct clusters; of these, six genotypes represented 92% of the HPAIVs examined. By phylodynamic analyses, most detections in domestic birds were shown to be point-source transmissions from wild birds, with limited farm-to-farm spread.

Transmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States.

SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variants may persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated from at least 109 independent spillovers from humans, which resulted in 39 cases of subsequent local deer-to-deer transmission and three cases of potential spillover from white-tailed deer back to humans. Viruses repeatedly adapted to white-tailed deer with recurring amino acid substitutions across spike and other proteins. Overall, our findings suggest that multiple SARS-CoV-2 lineages were introduced, became enzootic, and co-circulated in white-tailed deer.

Antiviral susceptibility of clade 2.3.4.4b highly pathogenic avian influenza A(H5N1) viruses isolated from birds and mammals in the United States, 2022.

Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) A(H5N1) viruses that are responsible for devastating outbreaks in birds and mammals pose a potential threat to public health. Here, we evaluated their susceptibility to influenza antivirals. Of 1,015 sequences of HPAI A(H5N1) viruses collected in the United States during 2022, eight viruses (∼0.8%) had a molecular marker of drug resistance to an FDA-approved antiviral: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T). Additionally, 31 viruses contained mutations that may reduce susceptibility to inhibitors of neuraminidase (NA) (n = 20) or cap-dependent endonuclease (CEN) (n = 11). A panel of 22 representative viruses was tested phenotypically. Overall, clade 2.3.4.4b A(H5N1) viruses lacking recognized resistance mutations were susceptible to FDA-approved antivirals. Oseltamivir was least potent at inhibiting NA activity, while the investigational NA inhibitor AV5080 was most potent, including against NA mutants. A novel NA substitution T438N conferred 12-fold reduced inhibition by zanamivir, and in combination with the known marker N295S, synergistically affected susceptibility to all five NA inhibitors. In cell culture-based assays HINT and IRINA, the PA-I38T virus displayed 75- to 108-fold and 37- to 78-fold reduced susceptibility to CEN inhibitors, baloxavir and the investigational AV5116, respectively. Viruses with PA-I38M or PA-A37T showed 5- to 10-fold reduced susceptibilities. As HPAI A(H5N1) viruses continue to circulate and evolve, close monitoring of drug susceptibility is needed for risk assessment and to inform decisions regarding antiviral stockpiling.

Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in New England Seals, United States.

We report the spillover of highly pathogenic avian influenza A(H5N1) into marine mammals in the northeastern United States, coincident with H5N1 in sympatric wild birds. Our data indicate monitoring both wild coastal birds and marine mammals will be critical to determine pandemic potential of influenza A viruses.

Antimicrobial susceptibility of Salmonella and Escherichia coli from equids sampled in the NAHMS 2015-16 equine study and association of management factors with resistance.

Several studies have investigated antimicrobial resistance (AMR) in Salmonella spp. and Escherichia coli isolated from hospitalized horses, but studies conducted on community-based populations of equids are limited. The factors associated with AMR in these bacteria in the general horse population are not well understood. The primary objective of our study was to estimate the prevalence of Salmonella and describe antimicrobial susceptibility of Salmonella and E. coli from equids across the United States. The second objective was to identify associations between health management and biosecurity practices and AMR. Fecal samples submitted from 1357 equids on 199 operations were tested for Salmonella, identifying 27 positive samples with 29 isolates belonging to 18 serotypes. Fecal sample and operation-level prevalence of Salmonella was 2.0% (27/1357) and 7.0% (14/199), respectively. Most (25/29) isolates were pan-susceptible while four isolates exhibited resistance, three of which were multidrug resistant. Of the 721 samples cultured for E. coli, 85% (613/721) were positive. Eighty-six percent of the E. coli isolates recovered were pan-susceptible (529/612). Ten isolates were intermediate to one antimicrobial drug and susceptible to all others. Seventy-three E. coli isolates (11.9%, SE=1.3) were resistant to one or more antimicrobials, corresponding to a 33.0% (64/194) operation-level prevalence. Resistance to sulfonamide drugs was most common with 63 isolates (10.3%) resistant to sulfisoxazole, 57 of which (9.3%) were resistant to trimethoprim-sulfamethoxazole. MDR in E. coli was rare (1.8%, SE=0.5). Univariate and multivariable regression were used to evaluate associations between health management and biosecurity questionnaire items and AMR in E. coli. The outcome modeled was resistance to any of the 14 tested antimicrobials. Depending on the operation type, operations with greater than 20 resident equids were significantly associated with resistance. In addition, performance operations were significantly associated with resistance when compared to farm/ranch operations. Operations with feed containers that prevent fecal contamination and those that had treated any equids for illness or injury were associated with a lower AMR. The study results suggest that equids in the general population appear to pose low risk of shedding antimicrobial resistant strains of Salmonella and E. coli, and therefore low transmission potential to other equids, animals, humans, or the environment. However, it is prudent to practice good hand hygiene to prevent spread of Salmonella as well as AMR, and to protect both animal and human health. Despite study limitations, potential management factors that may influence prevalence and prevent spread of AMR shed by equids were identified.

Detection and molecular characterization of Salmonella species on U.S. goat operations.

Salmonella species are an important cause of gastrointestinal disease in animals, including goats. Additionally, Salmonella species are among the top five U.S. foodborne pathogens causing illness to humans. The goat industry is rapidly expanding in the U.S. yet estimates of Salmonella prevalence within these populations is lacking. The aim of this study was to investigate the fecal prevalence, antimicrobial resistance (AMR), biofilm potential, and virulence profile of Salmonella species isolated from goat feces as part of the United States Department of Agriculture (USDA) National Animal Health Monitoring System (NAHMS) Goat 2019 study, enteric microbe component. A total of 4917 fecal samples were collected from 332 operations, from September 2019-March 2020. Salmonella were isolated using standard enrichment and culture methods; antimicrobial susceptibility was determined by broth microdilution. Biofilm production was assessed using a crystal violet assay and normalized to a positive control strain, and PCR was used to detect virulence genes. Overall, we detected a low prevalence (0.7%, n = 35/4917) of Salmonella in goat feces and identified a broad range of serotypes including S. Bareilly (35%) and a single rare S. Sharon. All isolates were pansusceptible to 14 antimicrobials except one, which was resistant to only tetracycline (MIC ≥ 32 µg/mL). All strains were found to possess the majority of virulence determinants screened, and 40% (14 of 35) formed weak, moderate, or strong biofilm. We found a low prevalence of Salmonella, and characteristics of Salmonella in the U.S. goat population informs ongoing public health efforts to manage risk of animal food products and animal interactions.

Replication of Streptococcus equi subspecies zooepidemicus infection in swine.

Streptococcus equi subspecies zooepidemicus (SEZ) is a commensal bacterium of horses and causes infections in mammalian species, including humans. Historically, virulent strains of SEZ caused high mortality in pigs in China and Indonesia, while disease in the U.S. was infrequent. More recently, high mortality events in sows were attributed to SEZ in North America. The SEZ isolates from these mortality events have high genetic similarity to an isolate from an outbreak in China. Taken together, this may indicate SEZ is an emerging threat to swine health. To generate a disease model and evaluate the susceptibility of healthy, conventionally raised pigs to SEZ, we challenged sows and five-month-old pigs with an isolate from a 2019 mortality event. Pigs were challenged with a genetically similar guinea pig isolate or genetically distinct horse isolate to evaluate comparative virulence. The swine isolate caused severe systemic disease in challenged pigs with 100 % mortality. Disease manifestation in sows was similar to field reports: lethargy/depression, fever, reluctance to rise, and high mortality. The guinea pig isolate also caused severe systemic disease; however, most five-month-old pigs recovered. In contrast, the horse isolate did not cause disease and was readily cleared from the respiratory tract. In conclusion, we were able to replicate disease reported in the field. The results indicate differences in virulence between isolates, with the highest virulence associated with the swine isolate. Additionally, we generated a challenge model that can be used in future research to evaluate virulence factors and disease prevention strategies.

SARS-CoV-2 infection in free-ranging white-tailed deer.

Humans have infected a wide range of animals with SARS-CoV-21-5, but the establishment of a new natural animal reservoir has not been observed. Here we document that free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2, are exposed to multiple SARS-CoV-2 variants from humans and are capable of sustaining transmission in nature. Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021. Deer in six locations were infected with three SARS-CoV-2 lineages (B.1.2, B.1.582 and B.1.596). The B.1.2 viruses, dominant in humans in Ohio at the time, infected deer in four locations. We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses, enabling the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are observed infrequently in humans. No spillback to humans was observed, but these findings demonstrate that SARS-CoV-2 viruses have been transmitted in wildlife in the USA, potentially opening new pathways for evolution. There is an urgent need to establish comprehensive 'One Health' programmes to monitor the environment, deer and other wildlife hosts globally.

SARS-CoV-2 infection in free-ranging white-tailed deer ( Odocoileus virginianus ).

Human-to-animal spillover of SARS-CoV-2 virus has occurred in a wide range of animals, but thus far, the establishment of a new natural animal reservoir has not been detected. Here, we detected SARS-CoV-2 virus using rRT-PCR in 129 out of 360 (35.8%) free-ranging white-tailed deer ( Odocoileus virginianus ) from northeast Ohio (USA) sampled between January-March 2021. Deer in 6 locations were infected with at least 3 lineages of SARS-CoV-2 (B.1.2, B.1.596, B.1.582). The B.1.2 viruses, dominant in Ohio at the time, spilled over multiple times into deer populations in different locations. Deer-to-deer transmission may have occurred in three locations. The establishment of a natural reservoir of SARS-CoV-2 in white-tailed deer could facilitate divergent evolutionary trajectories and future spillback to humans, further complicating long-term COVID-19 control strategies. ONE-SENTENCE SUMMARY: A significant proportion of SARS-CoV-2 infection in free-ranging US white-tailed deer reveals a potential new reservoir.

Antimicrobial resistance and genomic characterization of Salmonella Dublin isolates in cattle from the United States.

Salmonella enterica subspecies enterica serotype Dublin is a host-adapted serotype in cattle, associated with enteritis and systemic disease. The primary clinical manifestation of Salmonella Dublin infection in cattle, especially calves, is respiratory disease. While rare in humans, it can cause severe illness, including bacteremia, with hospitalization and death. In the United States, S. Dublin has become one of the most multidrug-resistant serotypes. The objective of this study was to characterize S. Dublin isolates from sick cattle by analyzing phenotypic and genotypic antimicrobial resistance (AMR) profiles, the presence of plasmids, and phylogenetic relationships. S. Dublin isolates (n = 140) were selected from submissions to the NVSL for Salmonella serotyping (2014-2017) from 21 states. Isolates were tested for susceptibility against 14 class-representative antimicrobial drugs. Resistance profiles were determined using the ABRicate with Resfinder and NCBI databases, AMRFinder and PointFinder. Plasmids were detected using ABRicate with PlasmidFinder. Phylogeny was determined using vSNP. We found 98% of the isolates were resistant to more than 4 antimicrobials. Only 1 isolate was pan-susceptible and had no predicted AMR genes. All S. Dublin isolates were susceptible to azithromycin and meropenem. They showed 96% resistance to sulfonamides, 97% to tetracyclines, 95% to aminoglycosides and 85% to beta-lactams. The most common AMR genes were: sulf2 and tetA (98.6%), aph(6)-Id (97.9%), aph(3'')-Ib, (97.1%), floR (94.3%), and blaCMY-2 (85.7%). All quinolone resistant isolates presented mutations in gyrA. Ten plasmid types were identified among all isolates with IncA/C2, IncX1, and IncFII(S) being the most frequent. The S. Dublin isolates show low genomic genetic diversity. This study provided antimicrobial susceptibility and genomic insight into S. Dublin clinical isolates from cattle in the U.S. Further sequence analysis integrating food and human origin S. Dublin isolates may provide valuable insight on increased virulence observed in humans.

Genetic characterization of Streptococcus equi subspecies zooepidemicus associated with high swine mortality in the United States.

High mortality events due to Streptococcus equi subspecies zooepidemicus (Streptococcus zooepidemicus) in swine have not previously been reported in the United States. In September and October 2019, outbreaks with swine mortality up to 50% due to S. zooepidemicus septicaemia were reported in Ohio and Tennessee. Genomic epidemiological analysis revealed that the eight outbreak isolates were clustered together with ATCC 35246, a Chinese strain caused outbreaks with high mortality, also closely related to three isolates from human cases from Virginia, but significantly different from an outbreak-unrelated swine isolate from Arizona and most isolates from other animal species. Comparative genomic analysis on two outbreak isolates and another outbreak-unrelated isolate identified several genomic islands and virulence genes specifically in the outbreak isolates only, which are likely associated with the high mortality observed in the swine population. These findings have implications for understanding, tracking and possibly preventing diseases caused by S. zooepidemicus in swine.