Sam Abraham

Exudative epidermitis (EE) causes substantial morbidity and mortality in piglets. This study investigated the microbial ecology, antimicrobial resistance (AMR), and genomic diversity of Staphylococcus hyicus associated with an EE outbreak in an Australian piggery.

Lesion swabs from 20 affected piglets yielded 160 bacterial isolates (including S. hyicus and cohabiting species). Isolates underwent species identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) of S. hyicus for AMR/virulence gene profiling and core-genome SNP analysis to assess genomic relatedness.

S. hyicus predominated among lesion isolates. Phenotypic testing showed varied AMR, with frequent resistance to erythromycin and tetracycline. WGS of 27 S. hyicus isolates identified five distinct genotypic AMR profiles, including combinations spanning multiple drug classes. All S. hyicus carried the exfoliative toxin gene shetA, and 24 also carried exhD.

Core-genome analysis indicated a highly clonal outbreak: 24/27 genomes differed by 0 core SNPs, with the remaining three closely related. Despite this clonality, resistance gene carriage varied across isolates. Consequently, reliance on a single colony to represent an outbreak could understate resistance and overstate treatability.

These findings support routine multi-isolate sampling to capture within-clone AMR variability, bolster antimicrobial selection during EE management, and inform consideration of autogenous vaccines targeting dominant outbreak clones.

Bovine viral diarrhea virus (BVDV) is globally endemic, with the ability to establish persistent infection (PI) being central to its complex epidemiology. Currently the genetic variability of BVDV in Bangladesh remains poorly understood. This study involved a survey in commercial dairy herds in the south-eastern part of Bangladesh in 2024/2025. A total of 373 blood samples were collected from cattle in 24 dairy herds. Serum and buffy coat samples were analyzed using antibody-ELISA and RT-qPCR targeting the 5′-UTR region, followed by sequencing. The MDBK cell line was used for virus isolation and biotyping. Herd and animal-level seroprevalences were 83.3% and 15.3%, respectively, while the corresponding viremic rates were 79.2% and 11.0%. Analysis of 41 sequences identified nine distinct BVDV-1 subgenotypes (1a, 1b, 1c, 1d, 1e, 1 k, 1p, 1o, and 1v), with BVDV-1b (41.5%) and BVDV-2a (14.6%) predominating. Additionally, five HoBiPeV-a pestiviruses were detected. Among antigen-positive cattle, 38 (92.68%) were identified as transiently infected and 3 (7.3%) were confirmed as PI. Six (14.6%) and 27 (65.9%) were identified as cytopathic and non-cytopathic biotypes, respectively. Risk factors for BVDV seropositivity included: female sex (OR: 3.0), clinical disease in the past three months (OR: 2.4), crowding (OR: 2.9), and lack of dedicated clothing for farm workers (OR: 5.7). Active infection was associated with calves (OR: 6.2), heifers (OR: 2.3), stunted growth (OR: 3.0), technician-performed artificial insemination (OR: 10.4), and frequent neighboring farm visits (OR: 3.1). This study has provided data crucial for formulating prevention and control strategies against BVDV to safeguard the Bangladeshi dairy industry.

Objectives
Enterococci are opportunistic, sometimes life-threatening pathogens with increasing antimicrobial resistance, particularly among clinical human isolates in Australia. While recent studies have ruled out pigs and chickens as major reservoirs of resistant enterococci, the role of cattle remains unclear. This study examines the antimicrobial resistance (AMR) profiles of enterococci from Australian cattle and explores the phylogenetic relationship of bovine E. faecium with isolates from other livestock and human sepsis cases.

Methods
A total of 1001 bovine faecal samples were tested, yielding E. faecium (n=343), E. faecalis (n=92), and E. hirae (n=284). Minimum inhibitory concentration assays were conducted against 15 antimicrobials. A subset of 67 isolates underwent whole genome sequencing (WGS).

Results
Most isolates were wild-type to all tested antimicrobials. Resistance was most common to erythromycin in E. faecium (18.7%), daptomycin in E. faecalis (12.1%), and tetracycline in E. hirae (13.3%). A single E. faecalis isolate was non-wild-type to vancomycin, and nine isolates (E. faecium n=4, E. faecalis n=2, E. hirae n=3) showed linezolid resistance. However, WGS did not detect known resistance genes or mutations for vancomycin or linezolid. Phylogenetic analysis revealed that bovine E. faecium clustered with other livestock isolates and vancomycin-negative human isolates.

Conclusion
Antimicrobial resistance among enterococci from Australian cattle is low. These strains are genetically distinct from vancomycin-resistant E. faecium circulating in hospitals, suggesting that cattle are not a significant source of clinically relevant AMR enterococci in Australia.

Bovine viral diarrhea virus (BVDV) remains a signiicant and highly contagious pathogen that markedly impacts production and reproductive performances of diierent animals worldwide. .is review represents the global epidemiology of BVDV, emphasizing its genetic diversity, prevalence, host range, associated risk factors, diagnostic advancements, and control strategies. A systematic electronic search was performed to retrieve relevant published articles. A total of 248 studies published over the past 26 years (from January 2000 to March 2025) across 69 countries were included. Data showed that BVDV-1 has been detected across all the continents and comprises 25 subgenotypes (1a-1x and Chinese ZM-95), of which the predominant subgenotypes are 1a, 1b, and 1c. Multiple subgenotypes, such as BVDV-1f, 1g, 1h, 1k, 1l, 1r, 1s, 1t, 1u, and 1x, were distinct and circulating in European countries. Additionally, ,ve subgenotypes (2a–2e) of BVDV-2 have been identiied, with BVDV-2a being the most frequently reported in diierent geographical locations. Notably, the emergence of HoBi-like pestivirus subgenotypes (BVDV-3a–3d) has been detected in Russia, Italy, ,ailand, India, and Bangladesh. Overall, the high prevalence of BVDV has been reported in various European (2.9%–87.1%) and Asian countries (0.2%–89.49%). Although cattle are the primary host, BVDV infections have been documented across a wide range of domestic and wild species, including buualo, sheep, goats, deer, bison, yak, camelids (camels, alpacas, and llamas), pigs, and wild boar. While Ag/Ab-ELISA remains a widely used diagnostic method, advanced techniques, such as RT-qPCR, CRISPR-Cas12a, RT-LAMP, and genome sequencing, are utilized for connrmatory identiication and genotyping of BVDV. Introduction of persistently infected (PI) animals into herds, grazing on common pasture, animal movements, mixed farming practices, and unhygienic breeding practices were frequently documented as potential risk factors. Key measures for controlling and eradicating BVDV include culling of PI animals, prophylactic vaccination, and avoiding mixed farming practices.

The bovine viral diarrhea virus (BVDV) infects a wide range of domestic and wild mammals. This review hypothesized that there might be cross-species transmission of BVDV. Therefore, the aim was to explore the BVDV-5′ UTR and N-pro sequence-based evidence to understand host plasticity among different animals. A total of 146 unique BVDV sequences retrieved from GenBank, originating from 12 distinct mammalian species that are submitted from 55 countries, were analyzed. The phylogenetic analysis revealed that all three BVDV species exhibited genetic relatedness infecting diverse animal species. BVDV-1 sequences obtained from cattle, buffalo, and pigs and BVDV-2 and HoBi-like pestivirus sequences from cattle, goats, and sheep showed a genetic resemblance. Surprisingly, cattle and buffalo in China, cattle and yak in Mongolia, cattle and wild boar in Serbia, cattle and deer in Mexico, cattle and alpacas in Canada, goats and pigs in the USA, and sheep and buffalo in Argentina were infected with BVDV-1 within the same county and strongly positioned in the same cluster, indicating potential spillover with host tropism. Moreover, BVDV sequences isolated from various neighboring countries clustered closely, suggesting potential cross-border transmission events. Based on genomic evidence, the BVDV transmission cycle could be depicted, where cattle act as a primary source of infection, while other domestic and wild animals maintain the infection ecology within their habitat due to virus tropism.

Over the decades, cattle have not been considered primary hosts for influenza A viruses (IAV), and their role in influenza epidemiology has been largely unrecognized. While bovines are known reservoirs for influenza D virus, the recent emergence of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in U.S. dairy cattle marks an alarming shift in influenza ecology. Since March 2024, this virus has affected thousands of dairy cows, causing clinical signs such as fever, reduced feed intake, drastic declines in milk production, and abnormal milk appearance. Evidence suggests that the virus may be replicated within mammary tissue, raising urgent concerns about milk safety, foodborne transmission, and occupational exposure. This review highlights the unprecedented expansion of viruses into bovine populations, exploring the potential for host adaptation, and interconnected roles of pets, peridomestic animals, and human exposure within shared environments. The potential impacts on dairy production, food safety, and zoonotic spillover highlight the urgent need for integrated One Health surveillance to stay ahead of this evolving threat.

Escherichia coli recovered from dogs with clinical conditions such as urinary tract infections are often used to assess populations for resistance to critically important antimicrobials (CIAs). Despite the potential importance of such strains, the number of organisms scrutinised is very small and no information is obtained from the preponderance of normal, healthy dogs. Commensal E. coli are a valuable alternative, but little is gained if the number of isolates also remains small. In this work we demonstrate novel technology reliant on laboratory robots to examine the CIA resistance status of millions of commensal E. coli in the faeces of 86 healthy companion dogs. Fluoroquinolone-resistant isolates also underwent phenotypic resistance testing to detect multi-class resistant strains, and multi-locus sequence types and antimicrobial resistance genes identified with whole genome sequencing. Ciprofloxacin resistance was detected in isolates from five (5.8 %) of the healthy dogs, with a high ratio of ciprofloxacin-resistant E. coli to total E. coli being found in three of these animals. Antimicrobial susceptibility testing of the five isolates identified four resistance profiles, with all isolates having multi-class phenotypic resistance to between three and six antimicrobial classes. Genomic analysis confirmed the presence of genes encoding multi-class resistance, with four isolates being resistant to multiple classes. The five isolates belonged to sequence types ST1193 (n = 3) and ST354 (n = 2). All five isolates possessed multiple mutations within the quinolone resistance-determining regions. The predominant sequence type ST1193 is an emerging multidrug resistant E. coli strain harbouring fluoroquinolone resistance, which previously primarily has been detected in clinical samples from dogs. The current study demonstrates the power of robotics for delivering a multi-staged approach based on mass screening to achieve sensitivity and specificity achieved with detailed phenotypic and genotypic characterisation. Based on this experience, future studies can be expanded to yield a much richer understanding of antimicrobial resistance in canines.

The increasing resistance of bacteria to antimicrobials is a major threat to public health. This study investigates the prevalence of antimicrobial resistance, both phenotypic and genotypic, among Campylobacter isolates from Australian meat chickens in 2022, as a follow up to investigate trends since the last national surveillance undertaken in 2016. Isolates (n = 186) were obtained at slaughter from 200 pooled cecal samples taken from 1,000 meat chickens. The majority of C. jejuni (68.7%) and C. coli (88.9%) isolates were susceptible to all the antibiotics that were tested, and no multi-drug resistance was found. Resistance to ciprofloxacin (fluoroquinolone) was detected in 24.4% of the C. jejuni and 3.2% of the C. coli isolates. Whole genome sequencing revealed a diverse range of sequence types (STs). These included 32 previously reported STs for C. jejuni and 13 for C. coli, as well as four and seven previously undescribed STs for each species, respectively. The STs containing fluoroquinolone-resistant isolates were ST2083, ST10130, ST2895, ST7323, ST2398, and ST1078 for C. jejuni, and ST860 and ST894 for C. coli. Although fluoroquinolones are not used in animal production in Australia, resistance amongst C. jejuni isolates was high (24.4%). This finding emphasizes the need for enhanced surveillance and regular sampling along the food chain to understand the source of the isolates and to mitigate risks of antimicrobial resistance to protect public health.

Enterotoxigenic F4 E. coli (F4-ETEC) pose an economic threat to the swine industry through reduced growth, increased mortality and morbidity, and increased costs associated with treatment. Prevention and treatment of F4-ETEC often relies on antimicrobials; however, due to the threat of antimicrobial resistance, antimicrobial use is being minimized, and hence alternative control methods are needed. This study investigated the effects of postbiotics in the form of Lactobacillus acidophilus fermentation products (LFP) and Saccharomyces cerevisiae fermentation products (SFP), on pigs challenged with an F4 ETEC strain. Eighty pigs were selected based on a pre-screening F4-ETEC susceptibility test. The animals were divided into five treatments each with four replicate pens. Pigs were assigned to five different diets: a control diet (CON); CON diet with 3,000 ppm ZnO (ZnO); CON diet with 2,000 ppm LFP (LFP); CON diet with 2,000 ppm SFP (SFP); CON diet with both 2,000 ppm LFP and 2,000 ppm SFP (LAS). Pigs were inoculated per os with F4-ETEC twice, on day 0 and day1 of the experiment.BACKGROUNDEnterotoxigenic F4 E. coli (F4-ETEC) pose an economic threat to the swine industry through reduced growth, increased mortality and morbidity, and increased costs associated with treatment. Prevention and treatment of F4-ETEC often relies on antimicrobials; however, due to the threat of antimicrobial resistance, antimicrobial use is being minimized, and hence alternative control methods are needed. This study investigated the effects of postbiotics in the form of Lactobacillus acidophilus fermentation products (LFP) and Saccharomyces cerevisiae fermentation products (SFP), on pigs challenged with an F4 ETEC strain. Eighty pigs were selected based on a pre-screening F4-ETEC susceptibility test. The animals were divided into five treatments each with four replicate pens. Pigs were assigned to five different diets: a control diet (CON); CON diet with 3,000 ppm ZnO (ZnO); CON diet with 2,000 ppm LFP (LFP); CON diet with 2,000 ppm SFP (SFP); CON diet with both 2,000 ppm LFP and 2,000 ppm SFP (LAS). Pigs were inoculated per os with F4-ETEC twice, on day 0 and day1 of the experiment.No significant differences in fecal consistency scores or fecal F4-ETEC concentration in pigs supplemented with LFP and/or SFP were detected. An increased diversity and abundance of Lactobacillaceae in the fecal microbiome of pigs supplemented with LFP were detected, as well as an increased final liveweight of pigs supplemented with LFP and/or SFP.RESULTSNo significant differences in fecal consistency scores or fecal F4-ETEC concentration in pigs supplemented with LFP and/or SFP were detected. An increased diversity and abundance of Lactobacillaceae in the fecal microbiome of pigs supplemented with LFP were detected, as well as an increased final liveweight of pigs supplemented with LFP and/or SFP.This study demonstrated that the fecal microbiome is modified in F4-ETEC-challenged pigs supplemented with the combination of LFP and SFP, with these modifications previously associated with increased growth performance and health status in young pigs. Pigs receiving this combination of postbiotics also demonstrated an increased final liveweight, indicating that management of ETEC-associated performance loss may not require the complete removal of ETEC from a production system.CONCLUSIONThis study demonstrated that the fecal microbiome is modified in F4-ETEC-challenged pigs supplemented with the combination of LFP and SFP, with these modifications previously associated with increased growth performance and health status in young pigs. Pigs receiving this combination of postbiotics also demonstrated an increased final liveweight, indicating that management of ETEC-associated performance loss may not require the complete removal of ETEC from a production system.

Bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV) are vector-borne orbiviruses that pose an emerging threat to livestock, including cattle and sheep. This review summarizes the global distribution, genetic diversity, and key factors driving their spread along with the existing knowledge gaps and recommendations to mitigate their impact. Both viruses cause hemorrhagic disease in susceptible ruminants and are commonly reported in tropical and subtropical regions including North America, Asia, Africa, Oceania, and some parts of Europe. The geographical distribution of these viruses, encompassing 27 BTV and 7 EHDV serotypes, has shifted, particularly with the recent invasion of BTV-3, 4, and 8 and EHDV-8 serotypes in Europe. Several factors contribute to the recent spread of these viruses such as the distribution of virulent strains by the movement of temperature-dependent Culicoides vectors into new areas due to rapid climate change, the reassortment of viral strains during mixed infections, and unrestricted global trade. These diseases cause significant economic impacts including morbidity, mortality, reduced production, high management costs, and the disruption of international trade. Effective prevention and control strategies are paramount and rely on vaccination, vector control using insecticides, and the destruction of breeding sites, husbandry practices including the isolation and quarantine of infected hosts, restriction of animal movement, prompt diagnosis and identification of circulating strains, and effective surveillance and monitoring plans such as the pre-export and post-import screening of semen used for artificial insemination. However, challenges remain with intercontinental virus spread, live vaccines, and the failure of inactivated vaccines to produce protective immunity against dissimilar strains. Significant knowledge gaps highlight the need for a better scientific understanding and a strategic plan to ensure healthy livestock and global food security.