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Background. Emerging livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) persist in livestock populations and represent a reservoir for transmission to humans. Understanding the routes of introduction and further transmission is crucial to control this threat to human health. Methods. All reported cases of livestock-associated MRSA (CC398) in humans and pigs in Norway between 2008 and 2014 were included. Data were collected during an extensive outbreak investigation, including contact tracing and stringent surveillance. Whole-genome sequencing of isolates from all human cases and pig farms was performed to support and expand the epidemiological findings. The national strategy furthermore included a \"search-and-destroy\" policy at the pig farm level. Results. Three outbreak clusters were identified, including 26 pig farms, 2 slaughterhouses, and 36 humans. Primary introductions likely occurred by human transmission to 3 sow farms with secondary transmission to other pig farms, mainly through animal trade and to a lesser extent via humans or livestock trucks. All MRSA CC398 isolated from humans without an epidemiological link to the outbreaks were genetically distinct from isolates within the outbreak clusters indicating limited dissemination to the general population. Conclusions. This study identified preventable routes of MRSA CC398 introduction and transmission: human occupational exposure, trade of pigs and livestock transport vehicles. These findings are essential for keeping pig populations MRSA free and, from a \"One Health\" perspective, preventing pig farms from becoming reservoirs for MRSA transmission to humans.

Lawsonia intracellularis (LI) and Mycoplasma hyopneumoniae (Mh) are 2 globally distributed pathogens that cause significant morbidity and mortality in grow-finish pigs. However, mechanisms that reduce growth and feed efficiency during LI and Mh infection are poorly defined. We hypothesized that reductions in performance are partially due to declines in intestinal function and integrity; thus, this study aimed to evaluate intestinal function and integrity of pigs during a 21-d Mh and LI dual challenge (MhLI). Littermate pairs of barrows (48.1 ± 6.7 kg BW) were selected; 1 pig from each pair was assigned to either MhLI challenge or nonchallenge treatments (n = 12). Pigs were individually housed, fed a corn-soybean diet, and allowed to acclimate for 21 d prior to inoculation. On days postinoculation (dpi) 0, MhLI pigs were dual inoculated with LI and Mh. On dpi 21, all pigs were euthanized for ileal and colon tissue collection. Formalin-fixed tissues were clinically scored and morphology analyzed, frozen tissues assayed for digestive enzyme activities, and fresh tissues mounted into modified Ussing Chambers to assess active nutrient transport, barrier integrity, and bacterial translocation. Data were analyzed using the Mixed Procedure of SAS with treatment as a fixed effect, age and start BW as covariates, and litter as a random effect. Compared with controls, MhLI pigs had decreased ADG (38%, P < 0.001), ADFI (25%, P < 0.001), and G:F (19%, P = 0.012). The MhLI dual challenge did not alter ileum morphology or transepithelial resistance (P > 0.10); however, ex vivo mucosal to serosal translocation of S. Typhimurium in the colon was increased (60%, P = 0.003) in MhLI pigs compared with controls. Additionally, MhLI pigs had increased ileal glucose transport (30%, P = 0.05) and decreased sucrase activity (30%, P = 0.049) compared with controls. This MhLI challenge antagonized intestinal function and integrity, and this may be a contributing factor to reduced pig performance.

Mycoplasma hyopneumoniae is the etiologic agent of porcine enzootic pneumonia, responsible for major production losses worldwide. The bacteria have a limited metabolism and need to obtain molecules from the growth environment, which causes multiple difficulties for in vitro culture. These limitations have a negative influence on the ability to carry out research for the development of the rational use of antimicrobials and vaccines. The objective of this investigation was to evaluate the genetic profile and in vitro susceptibility of field isolates of M. hyopneumoniae to different antimicrobials. All 16 isolates obtained from the samples presented 100% of identity in the partial sequence of 16S rRNA gene when compared to M. hyopneumoniae . A dendrogram was created using the PCR results of the genes related to pathogenicity, and the isolates were distributed into four clusters, suggesting genetic variability among four different isolates circulating on the same farm. The minimum inhibitory concentration of the isolates was higher for the antimicrobials tylosin (< 0.001–16 mg/L) and spiramycin (< 0.001–16 mg/L) than for enrofloxacin (< 0.001–0.125 mg/L) and tiamulin (< 0.001–0.125 mg/L). Our results demonstrate the genetic variability among M. hyopneumoniae isolates from pigs of the same farm, with differences in their susceptibility to antimicrobial agents.

Most of the microorganisms living in a symbiotic relationship in different animal body sites (microbiota) reside in the gastrointestinal tract (GIT). Several studies have shown that the microbiota is involved in host susceptibilities to pathogens. The fecal microbiota of domestic and wild suids was analyzed. Bacterial communities were determined from feces obtained from domestic pigs ( Sus scrofa ) raised under different conditions: specific-pathogen-free (SPF) pigs and domestic pigs from the same bred, and indigenous domestic pigs from a backyard farm in Kenya. Secondly, the fecal microbiota composition of the African swine fever (ASF) resistant warthogs ( Phacochoerus africanus ) from Africa and a European zoo was determined. African swine fever (ASF) is a devastating disease for domestic pigs. African animals showed the highest microbial diversity while the SPF pigs the lowest. Analysis of the core microbiota from warthogs (resistant to ASF) and pigs (susceptible to ASF) showed 45 shared OTUs, while 6 OTUs were exclusively present in resistant animals. These six OTUs were members of the Moraxellaceae family, Pseudomonadales order and Paludibacter , Anaeroplasma , Petrimonas , and Moraxella genera. Further characterization of these microbial communities should be performed to determine the potential involvement in ASF resistance.

Over the last decade, an increasing number of infections with livestock-associated methicillin-resistant Staphylococcus aureus of clonal complex 398 (LA-MRSA CC398) in persons without contact to livestock has been registered in Denmark. These infections have been suggested to be the result of repeated spillover of random isolates from livestock into the community. However, other studies also found emerging sub-lineages spreading among humans. Based on genome-wide SNPs and genome-wide association studies (GWAS), we assessed the population structure and genomic content of Danish LA-MRSA CC398 isolates from healthcare-associated infections from 2014 to 2016 ( n =  73) and compared these to isolates from pigs in Denmark from 2014 ( n  = 183). Phylogenetic analyses showed that most human isolates were closely related to and scattered among pig isolates showing that the majority of healthcare-associated infections are the result of repeated spillover from pig farms, even though cases of human-to-human transmission also were identified. GWAS revealed frequent loss of antimicrobial resistance genes and acquisition of human-specific virulence genes in the human isolates showing adaptation in response to changes in selective pressures in different host environments, which over time could lead to the emergence of LA-MRSA CC398 lineages more adapted to human colonization and transmission.

Background Infectious diseases are among the primary constraints to pig production, and the globalization of the pig industry has contributed to the emergence and spread of pathogens. However, there is a lack of comprehensive genomic surveillance on the Eurasian scale, resulting in the prevalence and evolution of pig pathogenic viruses and bacteria are still unknown. Results In this study, we proposed a protocol to identify viral and bacterial sequences and estimate the abundance accurately based on the whole-genome sequencing data of the blood samples. Through whole-genome analysis of 685 Eurasian pigs, we constructed the blood virome and bacteriome landscape. There were a total of 15 pathogenic bacteria, 12 pathogenic viruses, and porcine endogenous retrovirus were identified. We divided 685 Eurasian pigs into three subgroups and discovered significant differences in the viral and bacterial composition, prevalence, and abundance among subgroups. Besides, we performed the quantitative Polymerase Chain Reaction experiment to quantify the copy number of porcine endogenous retrovirus and confirm the reliability of the proposed protocol. Furthermore, we constructed the phylogenetic tree of porcine parvovirus 6 and the results suggested that large-scale transportation across China provides viral connectivity between geographically distinct localities, potentially facilitating the spread of viruses. We also discovered the ADAM28 and ADAMDEC1 genes that may relate to porcine lymphotropic herpesvirus, and the ATF4 gene that may correlate with porcine cytomegalovirus. Conclusions Our study provides new insights into the genomic investigation and epidemiology of viruses and bacteria, in turn helping to prevent viral and bacterial infectious diseases in pigs.

Abstract Secreted nucleases, either cell-attached or released in the environment, play varied roles in bacteria–host interactions during an infection. They help to provide nucleotides essential for bacterial growth by degrading host nucleic acids, are involved in the degradation of extracellular traps and hence in immune evasion, and can have direct cytotoxic activity in host cells. Nuclease expression in bacteria of the Mycoplasma genus has been poorly studied so far. In this study, a standardized set of methods was used to detect the in vitro nuclease activities of major animal mycoplasmas. Nucleases were detected in swine (Mycoplasma (M.) hyopneumoniae, M. hyorhinis, and M. flocculare) as well as avian (M. gallisepticum, M. iowae, and M. synoviae) species, but not in the small ruminant subspecies M. mycoides subsp. capri and M. capricolum subsp. capricolum. In swine species, nuclease activity was detected in both the cell pellet and the supernatant, whereas in poultry species, the results were more variable. We showed that detection of nuclease activity—in terms of presence/absence in our experimental conditions—was strain dependent in M. iowae and M. synoviae. The DNA from macrophage extracellular traps was further demonstrated to be a substrate for mycoplasma-expressed nucleases, suggesting that several Mycoplasma species and/or strains infecting animals could feed on resulting nucleotides and hence escape the traps, two features contributing to persistence of the infection. Overview of the capacity of various Mycoplasma species and strains to degrade DNA molecules, independently from their expected pathogenicity in the corresponding animal hosts.

Vaccination stands as one of the most sustainable and promising strategies to control infectious diseases in animal production. Nevertheless, the causes for antibody response variation among individuals are poorly understood. The animal microbiota has been shown to be involved in the correct development and function of the host immunity, including the antibody response. Here, we studied the nasal and rectal microbiota composition in association with the antibody response against the pathobiont Glaesserella parasuis . The nasal and rectal microbiotas of 24 piglets were sampled in two farms before vaccination and in one unvaccinated farm (naturally exposed to the pathobiont) at similar time. Microbiota composition was inferred by V3V4 16S rRNA gene sequencing and bioinformatics analysis, and the antibody response was quantified using the variation between the levels before and after vaccination (normalized per farm). Piglets with higher antibody responses showed more diverse nasal and rectal microbial communities compared to piglets with lower responses. Moreover, swine nasal core microbiota colonizers were associated with higher antibody levels, such as several members from Bacteroidales and Clostridiales orders and genera including Moraxella , Staphylococcus , Fusobacterium and Neisseria . Regarding taxa found in the rectal microbiota, associations with antibody responses were detected only at order level, pointing towards a positive role for Clostridiales while negative for Enterobacteriales . Altogether, these results suggest that the microbiota is associated with the antibody response to G. parasuis (and probably to other pathogens) and serves as starting point to understand the factors that contribute to immunization in pigs.

Livestock-associated methicillin-resistant Staphylococcus aureus clonal complex CC398 (LA-MRSA CC398) is resistant to nearly all β-lactams and several non-β-lactam antimicrobials. Over the last decade, it has become widespread in pig farms across Europe and is now an important cause of human infections in countries with previously low levels of MRSA, such as the Netherlands and Denmark. The hitherto uncontrolled spread of LA-MRSA CC398 underscores an urgent need to understand its epidemiology in order to develop evidence-based interventions. This study demonstrates that pig movements between farms in combination with increased bacterial resistance to specific antibiotics and heavy metals were important drivers of the rapid spread of LA-MRSA CC398 in the Danish pig production system. These findings should be taken into consideration when researchers and policy makers evaluate and decide on actions and policies to limit the spread of LA-MRSA CC398 and other pathogens in food animals. The spread of livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) within the Danish pig production system has been linked to an increased number of human infections. Yet, the population structure and transmission dynamics of this important pathogen remain poorly understood. In this study, whole-genome sequences from 371 LA-MRSA CC398 isolates collected between 2004 and 2015 were subjected to bioinformatic analyses. The isolates originated from Danish pig farms ( n = 209) and people having livestock contact ( n = 79). In addition, whole-genome sequence data from 82 isolates representing an international reference collection and 83 isolates from Danish patients were included in the analysis. The results demonstrated that the increasing prevalence of LA-MRSA CC398 in Danish pigs and patients was caused by clonal expansion of three dominant lineages. The results also showed that these lineages were enriched for the tetracycline resistance gene tet (K) and other determinants conferring resistance to some of the most frequently used antimicrobials in Danish pigs. The association between pig movements and the spread of LA-MRSA CC398 was assessed in a Poisson regression analysis of 17,009 pig movements into 273 farms with known LA-MRSA CC398 status. The results demonstrated that animal movements have played a critical role in the dissemination of LA-MRSA CC398 within the Danish pig production system, although other transmission routes may also have contributed. Consistent with this scenario, the genetic relatedness of isolates from different farms was positively correlated with the number of animal movements between the farms. IMPORTANCE Livestock-associated methicillin-resistant Staphylococcus aureus clonal complex CC398 (LA-MRSA CC398) is resistant to nearly all β-lactams and several non-β-lactam antimicrobials. Over the last decade, it has become widespread in pig farms across Europe and is now an important cause of human infections in countries with previously low levels of MRSA, such as the Netherlands and Denmark. The hitherto uncontrolled spread of LA-MRSA CC398 underscores an urgent need to understand its epidemiology in order to develop evidence-based interventions. This study demonstrates that pig movements between farms in combination with increased bacterial resistance to specific antibiotics and heavy metals were important drivers of the rapid spread of LA-MRSA CC398 in the Danish pig production system. These findings should be taken into consideration when researchers and policy makers evaluate and decide on actions and policies to limit the spread of LA-MRSA CC398 and other pathogens in food animals.

Livestock is an important agriculture sector in India and exhibits an indispensable part of economy of the country. The rising prevalence of Staphylococcus aureus ( S. aureus ), particularly methicillin-resistant (MRSA) and vancomycin-resistant (VRSA) strains, in livestock has become a significant concern in public health and veterinary medicine. S. aureus is a versatile pathogen capable of colonizing various animal species, leading to potential zoonotic transmission. This study aimed to assess the prevalence, biofilm formation, antimicrobial resistance (AMR), and molecular characterization of S. aureus isolates from cattle, buffalo, and pigs in Bareilly district, Uttar Pradesh, India. A total of 406 samples including 187 milk samples and 200 nasal swabs from apparently healthy animals and 19 wound swabs were collected from cattle, buffalo, and pigs. Isolation was performed using Brain Heart Infusion (BHI) broth enrichment followed by streaking on Mannitol Salt Agar (MSA). Biochemical and molecular tests were conducted to identify S. aureus , and the prevalence rates were calculated. PCR was used to confirm species identity and to detect biofilm-associated genes ( icaA , icaD ), as well as methicillin resistance genes ( mecA , femA ). Antimicrobial susceptibility was determined by the Kirby-Bauer disc diffusion method. The overall prevalence of S. aureus was 17.73%, with cattle exhibiting the highest prevalence (22.77%), followed by buffaloes (15.90%) and pigs (6.94%). Biofilm-associated genes were detected in 40.28% of isolates, and 20.83% and 13.89% of isolates were positive for the mecA and femA genes, respectively, indicating MRSA. Among the 72 S. aureus isolates, 62 (86.11%) were multidrug-resistant (MDR), with high resistance to streptomycin (80.56%) and β-lactams. Four isolates (5.55%) showed resistance to vancomycin, designated as VRSA. The prevalence of MRSA was 26.39% among the S. aureus isolates. The study highlights the significant prevalence of S. aureus and emerging multidrug-resistant strains, including MRSA and VRSA, in livestock in Bareilly district. These findings underscore the need for stringent antimicrobial stewardship and surveillance programs to prevent the spread of resistant strains, which pose both veterinary and public health risks. The presence of biofilm-forming isolates further complicates treatment and emphasizes the necessity for continued research and interventions to combat antimicrobial resistance in the agricultural sector.