Browsing by Author "Barkema, Herman W"

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    Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation
    (2018-11-12) Derakhshani, Hooman; Plaizier, Jan C; De Buck, Jeroen; Barkema, Herman W; Khafipour, Ehsan
    Abstract Background The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility complex (BoLA) gene has been associated with susceptibility to several infectious diseases, most importantly mastitis. However, mechanisms underlying this association are yet poorly understood. In the present study, we sought to explore the association of BoLA gene polymorphism with the dynamics of mammary microbiota during the first week of lactation. Results Colostrum and milk samples were collected from multiparous Holstein dairy cows at the day of calving and days 1 and 6 after calving. Microbiota profiling was performed using high-throughput sequencing of the V1-V2 regions of the bacterial 16S rRNA genes and ITS2 region of the fungal ribosomal DNA. Polymorphism of BoLA genes was determined using PCR-RFLP of exon 2 of the BoLA-DRB3. In general, transition from colostrum to milk resulted in increased species richness and diversity of both bacterial and fungal communities. The most dominant members of intramammary microbiota included Staphylococcus, Ruminococcaceae, and Clostridiales within the bacterial community and Alternaria, Aspergillus, Candida, and Cryptococcus within the fungal community. Comparing the composition of intramammary microbiota between identified BoLA-DRB3.2 variants (n = 2) revealed distinct clustering pattern on day 0, whereas this effect was not significant on the microbiota of milk samples collected on subsequent days. On day 0, proportions of several non-aureus Staphylococcus (NAS) OTUs, including those aligned to Staphylococcus equorum, Staphylococcus gallinarum, Staphylococcus sciuri, and Staphylococcus haemolyticus, were enriched within the microbiota of one of the BoLA-DRB3.2 variants, whereas lactic acid bacteria (LAB) including Lactobacillus and Enterococcus were enriched within the colostrum microbiota of the other variant. Conclusion Our results suggest a potential role for BoLA-gene polymorphism in modulating the composition of colostrum microbiota in dairy cows. Determining whether BoLA-mediated shifts in the composition of colostrum microbiota are regulated directly by immune system or indirectly by microbiota-derived colonization resistant can have important implications for future development of preventive/therapeutic strategies for controlling mastitis.
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    Composition and co-occurrence patterns of the microbiota of different niches of the bovine mammary gland: potential associations with mastitis susceptibility, udder inflammation, and teat-end hyperkeratosis
    (2020-04-14) Derakhshani, Hooman; Plaizier, Jan C; De Buck, Jeroen; Barkema, Herman W; Khafipour, Ehsan
    Abstract Background Within complex microbial ecosystems, microbe-microbe interrelationships play crucial roles in determining functional properties such as metabolic potential, stability and colonization resistance. In dairy cows, microbes inhabiting different ecological niches of the udder may have the potential to interact with mastitis pathogens and therefore modulate susceptibility to intramammary infection. In the present study, we investigated the co-occurrence patterns of bacterial communities within and between different niches of the bovine mammary gland (teat canal vs. milk) in order to identify key bacterial taxa and evaluate their associations with udder health parameters and mastitis susceptibility. Results Overall, teat canal microbiota was more diverse, phylogenetically less dispersed, and compositionally distinct from milk microbiota. This, coupled with identification of a large number of bacterial taxa that were exclusive to the teat canal microbiota suggested that the intramammary ecosystem, represented by the milk microbiota, acts as a selective medium that disfavors the growth of certain environmental bacterial lineages. We further observed that the diversity of milk microbiota was negatively correlated with udder inflammation. By performing correlation network analysis, we identified two groups of phylogenetically distinct hub species that were either positively (unclassified Bacteroidaceae and Phascolarctobacterium) or negatively (Sphingobacterium) correlated with biodiversity metrics of the mammary gland (MG). The latter group of bacteria also showed positive associations with the future incidence of clinical mastitis. Conclusions Our results provide novel insights into the composition and structure of bacterial communities inhabiting different niches of the bovine MG. In particular, we identified hub species and candidate foundation taxa that were associated with the inflammatory status of the MG and/or future incidences of clinical mastitis. Further in vitro and in vivo interrogations of MG microbiota can shed light on different mechanisms by which commensal microbiota interact with mastitis pathogens and modulate udder homeostasis.
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    Fecal shedding and tissue infections demonstrate transmission of Mycobacterium avium subsp. paratuberculosis in group-housed dairy calves
    (2017-04-28) Corbett, Caroline S; De Buck, Jeroen; Orsel, Karin; Barkema, Herman W
    Abstract Current Johne’s disease control programs primarily focus on decreasing transmission of Mycobacterium avium subsp. paratuberculosis (MAP) from infectious adult cows to susceptible calves. However, potential transmission between calves is largely overlooked. The objective was to determine the extent of MAP infection in calves contact-exposed to infectious penmates. Thirty-two newborn Holstein–Friesian calves were grouped into 7 experimental groups of 4, consisting of 2 inoculated (IN) calves, and 2 contact-exposed (CE) calves, and 1 control pen with 4 non-exposed calves. Calves were group housed for 3 months, with fecal samples were collected 3 times per week, blood and environmental samples weekly, and tissue samples at the end of the trial. The IN calves exited the trial after 3 months of group housing, whereas CE calves were individually housed for an additional 3 months before euthanasia. Control calves were group-housed for the entire trial. All CE and IN calves had MAP-positive fecal samples during the period of group housing; however, fecal shedding had ceased at time of individual housing. All IN calves had MAP-positive tissue samples at necropsy, and 7 (50%) of the CE had positive tissue samples. None of the calves had a humoral immune response, whereas INF-γ responses were detected in all IN calves and 5 (36%) CE calves. In conclusion, new MAP infections occurred due to exposure of infectious penmates to contact calves. Therefore, calf-to-calf transmission is a potential route of uncontrolled transmission on cattle farms.
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    Pathogens at the livestock-wildlife interface in Western Alberta: does transmission route matter?
    (BioMed Central, 2014-02-12) Pruvot, Mathieu; Kutz, Susan J; van der Meer, Frank; Musiani, Marco; Barkema, Herman W; Orsel, Karin
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    Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureusStaphylococci Isolated from Canadian Dairy Herds
    (Frontiers in Microbiology, 2018-01) Nobrega, Diego B; Naushad, Sohail; Naqvi, S Ali; Condas, Larissa A Z; Saini, Vineet; Kastelic, John P; Luby, Christopher; De Buck, Jeroen; Barkema, Herman W
    Emergence and spread of antimicrobial resistance is a major concern for the dairy industry worldwide. Objectives were to determine: (1) phenotypic and genotypic prevalence of drug-specific resistance for 25 species of non-aureus staphylococci, and (2) associations between presence of resistance determinants and antimicrobial resistance. Broth micro-dilution was used to determine resistance profiles for 1,702 isolates from 89 dairy herds. Additionally, 405 isolates were sequenced to screen for resistance determinants. Antimicrobial resistance was clearly species-dependent. Resistance to quinupristin/dalfopristin was common inStaphylococcus gallinarum(prevalence of 98%), whereasS. cohniiandS. arlettaewere frequently resistant to erythromycin (prevalence of 63 and 100%, respectively). Prevalence of resistance was 10% against β-lactams and tetracyclines. In contrast, resistance to antimicrobials critically important for human medicine, namely vancomycin, fluoroquinolones, linezolid and daptomycin, was uncommon (< 1%). Genes encoding multidrug-resistance efflux pumps and resistance-associated residues in deducted amino acid sequences of thefolPgene were the most frequent mechanisms of resistance, regardless of species. The estimated prevalence of themecAgene was 17% forS. epidermidis. Several genes, includingblaZ, mecA, fexA, erm, mphC, msrA, andtetwere associated with drug-specific resistance, whereas other elements were not. There were specific residues ingyrBfor all isolates of species intrinsically resistant to novobiocin. This study provided consensus protein sequences of key elements previously associated with resistance for 25 species of non-aureusstaphylococci from dairy cattle. These results will be important for evaluating effects of interventions in antimicrobial use in Canadian dairy herds.
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    Quantifying transmission of Mycobacterium avium subsp. paratuberculosis among group-housed dairy calves
    (2019-08-20) Corbett, Caroline S; de Jong, Mart C M; Orsel, Karin; De Buck, Jeroen; Barkema, Herman W
    Abstract Johne’s disease (JD) is a chronic enteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP), with control primarily aimed at preventing new infections among calves. The aim of the current study was to quantify calf-to-calf transmission of MAP among penmates in an experimental trial. Newborn Holstein bull calves (n = 32) were allocated into pens of 4, with 2 inoculated (IN) calves and 2 calves that were contact exposed (CE). Calves were group-housed for 3 months, with frequent collection of fecal and blood samples and tissue collection after euthanasia. The basic reproduction ratio (R0) was estimated using a final size (FS) model with a susceptible-infected model, based on INF-γ ELISA and tissue culture followed by qPCR. In addition, the transmission rate parameter (β) for new shedding events was estimated using a general linearized method (GLM) model with a susceptible-infected-susceptible model based on culture, followed by qPCR, of fecal samples collected during group housing. The R0 was derived for IN and CE calves separately, due to a difference in susceptibility, as well as differences in duration of shedding events. Based on the FS model, interferon-γ results from blood samples resulted in a R 0 IG of 0.90 (0.24, 2.59) and tissue culture resulted in a R 0 T of 1.36 (0.45, 3.94). Based on the GLM model, the R0 for CE calves to begin shedding (R 0 CE ) was 3.24 (1.14, 7.41). We concluded that transmission of MAP infection between penmates occurred and that transmission among calves may be an important cause of persistent MAP infection on dairy farms that is currently uncontrolled for in current JD control programs.
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    Virulence gene profiles: alpha-hemolysin and clonal diversity in Staphylococcus aureus isolates from bovine clinical mastitis in China
    (2018-03-02) Zhang, Limei; Gao, Jian; Barkema, Herman W; Ali, Tariq; Liu, Gang; Deng, Youtian; Naushad, Sohail; Kastelic, John P; Han, Bo
    Abstract Background Staphylococcus aureus, a common cause of bovine mastitis, is known for its ability to acquire to antimicrobial resistance and to secrete numerous virulence factors that can exacerbate inflammation. In addition, alpha-hemolysin has an important role in S. aureus infections, diversity of the hla gene (that produces alpha-hmolysin) in S. aureus isolated from bovine mastitis has not been well characterized. The objective was, therefore, to determine diversity of virulence genes, hla gene sequences, and clonal profiles of S. aureus from bovine mastitis in Chinese dairy herds, and to evaluate inter-relationships. Results The antimicrobials resistance varies from as low as 1.9% (2/103) for CTX to as high as 76.7% (79/103) for penicilin in the 103 isolates and 46 (44.7%) S. aureus were determined as multi-resistant isolates with diverse resistance patterns. Thirty-eight virulence gene patterns (with variable frequencies) were identified in the 103 isolates and correlated with MLST types, indicating a great diversity. Although the hla gene also had great diversity (14 genotypes), Hla peptides were relatively more conserved. With 7 clonal complexes identified from 24 spa types and 7 MLST types. Regarding the letter, ST 97 was the dominant type in S. aureus from bovine mastitis in China. Furthermore, based on phylogenetic analysis, there was a distinct evolutionary relationship between the hla gene and MLST. Conclusion Multi-resistant S. aureus occurred in bovine mastitis with diverse resistance patterns. The diversity of virulence gene profiles, especially the hla gene and, their relationship with molecular types were reported for the first time in S. aureus from bovine mastitis, which will be useful for future studies on immunogenicity and vaccine development. In addition, based on the distinct evolutionary relationship between the hla gene and MLST types, we inferred that the hla gene has potential role for molecular typing of S. aureus.