Bacteria Isolated From Milk of Dairy Cows With and Without Clinical Mastitis in Different Regions of Australia and Their AMR Profiles.

Mastitis is the most common disease in dairy cattle worldwide. The objectives of this study were to estimate the prevalence of different bacterial species associated with mastitis from dairy herds located in geographically and climatically distinct zones in Australia, and to evaluate the antimicrobial susceptibility of the isolated bacteria. Quarter-level milk samples (n = 419) were collected from 151 mastitis cases and 268 healthy controls originating from 18 dairy herds located in tropical (Northern Queensland), subtropical (Southeast Queensland) and temperate zones (Victoria) between March and June 2019. Milk samples were cultured, and the isolated bacteria were grouped into six groups: Enterobacteriaceae spp.; Streptococcus spp.; Staphylococcus aureus, non-aureus staphylococci (NAS); Bacillus spp.; and Others. Mixed effects conditional logistic regression models were applied to quantify the association between the prevalence of each bacterial group and the herd zone and bulk milk tank somatic cell counts (BMTSCC). Of the 205 isolates, 102 (50%) originated from mastitis cases, and 103 (50%) from controls. Staphylococci were the most prevalent (NAS 32% and S. aureus 11%). Contagious mastitis bacteria were more prevalent in Victoria compared to Queensland dairy herds. NAS species (P < 0.001) were less prevalent in herds with BMTSCC >300,000 cells/mL compared with herds with low BMTSCC ≤150,000 cells/mL. Enterobacteriaceae and Streptococcus spp. groups showed high resistance rates to 1 (51 and 47%, respectively), and 2 (11 and 23%, respectively), antimicrobials. More than one third of the Enterobacteriaceae (48%) and Others (43%) groups spp. were resistant to at least three antimicrobials. This study provided a unique opportunity to investigate the prevalence of mastitis-associated bacteria in clinical cases and in apparently healthy controls. The findings of this study help inform mastitis control and antimicrobial stewardship programs aimed to reduce the prevalence of mastitis and antimicrobial resistance in dairy herds.

Sequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds.

Streptococcus uberis is one of the most frequent mastitis-causing pathogens isolated from dairy cows. Further understanding of S. uberis genetics may help elucidate the disease pathogenesis. We compared the genomes of S. uberis isolates cultured from dairy cows located in distinctly different geographic regions of Australia. All isolates had novel multi locus sequence types (MLST) indicating a highly diverse population of S. uberis. Global clonal complexes (GCC) were more conserved. GCC ST86 and GCC ST143 represented 30% of the total isolates (n = 27) and were clustered within different geographic regions. Core genome phylogeny revealed low phylogenetic clustering by region, isolation source, and MLST. Identification of putative sortase (srtA) substrates and generation of a custom putative virulence factor database revealed genes which may explain the affinity of S. uberis for mammary tissue, evasion of antimicrobial efforts and disease pathogenesis. Of 27 isolates, four contained antibiotic resistance genes including an antimicrobial resistance cluster containing mel/mef(A), mrsE, vatD, lnuD, and transposon-mediated lnuC was also identified. These are novel genes for S. uberis, which suggests interspecies lateral gene transfer. The presence of resistance genes across the two geographic regions tested within one country supports the need for a careful, tailored, implementation and monitoring of antimicrobial stewardship.

Survey and Sequence Characterization of Bovine Mastitis-Associated Escherichia coli in Dairy Herds.

Escherichia coli is frequently associated with mastitis in cattle. "Pathogenic" and "commensal" isolates appear to be genetically similar. With a few exceptions, no notable genotypic differences have been found between commensal and mastitis-associated E. coli. In this study, 24 E. coli strains were isolated from dairy cows with clinical mastitis in three geographic regions of Australia (North Queensland, South Queensland, and Victoria), sequenced, then genomically surveyed. There was no observed relationship between sequence type (ST) and region (p = 0.51). The most common Multi Locus Sequence Type was ST10 (38%), then ST4429 (13%). Pangenomic analysis revealed a soft-core genome of 3,463 genes, including genes associated with antibiotic resistance, chemotaxis, motility, adhesion, biofilm formation, and pili. A total of 36 different plasmids were identified and generally found to have local distributions (p = 0.02). Only 2 plasmids contained antibiotic resistance genes, a p1303_5-like plasmid encoding multidrug-resistance (trimethoprim, quaternary ammonium, beta-lactam, streptomycin, sulfonamide, and kanamycin) from two North Queensland isolates on the same farm, while three Victorian isolates from the same farm contained a pCFSAN004177P_01-like plasmid encoding tetracycline-resistance. This pattern is consistent with a local spread of antibiotic resistance through plasmids of bovine mastitis cases. Notably, co-occurrence of plasmids containing virulence factors/antibiotic resistance with putative mobilization was rare, though the multidrug resistant p1303_5-like plasmid was predicted to be conjugative and is of some concern. This survey has provided greater understanding of antibiotic resistance within E. coli-associated bovine mastitis which will allow greater prediction and improved decision making in disease management.

Systematic review of an intervention: the use of probiotics to improve health and productivity of calves.

The aims of this study were to undertake a systematic review and meta-analysis of the types of probiotic formulations that are commercially available and to critically appraise the available evidence for the effectiveness of probiotics in improving the health and productivity of calves. Relevant papers were identified to answer the question: 'In calves aged between birth to one year, is the use of probiotics associated with changes in haematological or biochemical parameters, faecal bacteria counts, average daily live weight gain, dry matter intake, or feed conversion ratio?' The search of the literature yielded 67 studies that fit the primary screening criteria. Included studies were assessed for bias and confounding using a predefined risk assessment tool adapted from the Cochrane Collaboration's tool for assessing risk of bias in randomised trials and GRADE guidelines. Meta-analysis was performed using Review Manager and R. Random sequence generation was low in more than 59 % of studies. Risk of allocation concealment and performance bias were largely unclear in over 68 % of studies. Calves fed probiotics had increased average daily live weight gains (ADG) from birth to weaning (mean difference [MD] = 83.14 g/d 95 % CI = 58.36-107.91, P < 0.001) compared with calves on a control diet. Calf age reduced the level of heterogeneity of the effect of probiotics on ADG for calves between one to three weeks of age (τ2 = 73.15; I2 = 4%; P = 0.40) but not for calves older than three weeks of age (τ2 = 2892.91; I2 = 73 %; P < 0.001). Feed conversion ratio (FCR) was lower for calves on probiotics (MD = -0.13 kg of dry matter intake (DMI) to kg of live weight (LW) gain, 95 % CI = -0.17 to -0.09, P < 0.001), and the heterogeneity of effect was large in younger aged calves (τ2 = 0.05; I2 = 78 %; P = 0.03). The risk of bias regarding the methodology in the included studies was high. The quality of evidence for each outcome was categorised as moderate. There is sufficient data to support the effectiveness of probiotic use in some applications such as for the improvement of performance and productivity parameters of calves. However, the evidence is weak for other potential probiotic uses in calves such as improved health and reduced risk of disease. Therefore, the existing data are inconclusive and do not support the use of probiotics as an alternative to antimicrobials to improve calf health and productivity.