Antimicrobial resistance and genomic insights into bovine mastitis-associated Staphylococcus aureus in Australia

Comparative genomic analysis and multilocus sequence typing of Staphylococcus aureus reveals candidate genes for low-temperature tolerance

Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types. The ST352 strains exhibited the greatest tolerance to low temperature, with a mean reduction in survival rate of 10.34 % (p < 0.05). Comparative genomics revealed a total of 1941 core genes in the three S. aureus strains, and BB-1 had 468 specific genes, which were enriched mainly in translation, DNA recombination, DNA repair, metabolic pathways, two-component systems, and quorum sensing. Molecular docking analysis revealed that the binding of the RsbW protein to the SigB protein of BB-1 decreased due to base mutations in rsbW, while the binding to the RsbV protein was enhanced. In addition, the results of real-time quantitative PCR showed that the RsbV-RsbW/SigB system of BB-1 may play a role in the low-temperature survival of S. aureus and the formation of SCVs. These results suggest that genes specific to BB-1 may contribute to the mechanism of adaptation to low temperature and the formation of SCVs. This study helps elucidate the causes of SCV formation by S. aureus at low temperature at the molecular level and provides a basis for exploring the safety control of cold chain food environments.

Evaluation of close up antimicrobial therapies for treatment and prevention of subclinical mastitis in the herds with high prevalence of Staphylococcus aureus

This field trial was conducted to evaluate two antibiotics at a close-up period in curing the existing IMI and to prevent new clinical and subclinical Intramammary infection (IMI). Two hundred and twelve Holstein cows were assigned to one of three treatment groups: TYLO, MARB and CONT. Cows in TYLO group received 10 mg/kg Tylosin for three days at the close-up period (21 days before calving), cows in MARB group received single SC injection of 8 mg/kg SC marbofloxacin at the close-up period and cows in CONT group remained untreated. Milk samples were collected for somatic cell count, microbial culture and Total oxidant/antioxidant capacity before drying-off, and 3 and 7days post calving. Antimicrobial susceptibility test and RAPT-PCR were performed on S.aureus isolates. No significant differences were detected in total cure rate within the groups, but S. aureus cure rates in TYLO and MARB were significantly higher than in CONT (74 and 73.5 % Vs 58.1 %). No significant differences in total new IMI were observed. Furthermore, the rate of new S. aureus IMI was higher in both treatment groups than in CONT group. Clinical mastitis rate in TYLO (3.8 %) and MARB (5.8 %) was significantly lower than CONT (11.3 %). Paired S. aureus isolates from dry-off and post-calving have been clustered into 9 different RAPD types (A-I). 8 paired strains collected at dry-off were identical to those at post-calving,and 35 strains had more than 60 % dissimilarity. Administration of Tylosin or Marbofloxacin is not useful in all cases;however, they have the potential to reduce the incidence of post-calving clinical mastitis and improve S.aureus cure rate if used selectively.

Bacterial culture and antimicrobial susceptibility results from bovine milk samples submitted to four veterinary diagnostic laboratories in Australia from 2015 to 2019

A 5-year retrospective study was conducted to describe the mastitis-causing organisms isolated from bovine milk samples submitted to four veterinary diagnostic laboratories in Australia. The aim of this study was to identify temporal, geographical, and seasonal patterns of occurrence for the organisms and report the in vitro susceptibility of the most common mastitis-causing pathogens. In total, 22,102 milk samples were submitted between 2015 and 2019. The results were reported as positive growth for at least one significant organism (n = 11,407; 51.6%), no growth (n = 5,782; 26.2%), and mixed/contaminated growth (n = 4,913; 22.2%). Culture results for no growth, gram-negative bacteria, and eukaryotic organisms were combined for each region, and they were accounted for between 23 and 46% of submissions. These results represent a subset of mastitis cases for which the antibiotic treatment may not be warranted. A total of 11,907 isolates were cultured from 11,407 milk samples. The most common isolated organisms were Streptococcus uberis [41.3%; 95% confidence interval (CI): 40.4-42.1%] and Staphylococcus aureus (23.6%; 95% CI: 22.8-24.3%). For S. uberis and S. aureus, there was an association between a positive culture result and the dairy region. All regions except for the Sub-tropical Dairy region were more likely to culture S. uberis compared to the reference, Dairy NSW (P < 0.001). Similarly, for S. aureus, a positive culture result was more likely in all other dairy regions compared to Dairy NSW (P < 0.001). The LISA cluster analysis identified differences between High-High (hotspot) postcodes for S. aureus and S. uberis throughout all the analyzed dairy regions. These results highlight the need for further investigations into specific risk factors, such as environmental factors and herd-level predictors, which may have influenced the observed regional variations. Common mastitis-causing pathogens showed overall good susceptibility to a range of antimicrobials used in the treatment of mastitis. On-going surveillance of mastitis-causing pathogens and their antimicrobial susceptibilities will facilitate targeted mastitis control and treatment programs.

Genomic epidemiology of bovine mastitis-causing Staphylococcus aureus in New Zealand

We analysed the genomes of 188 bovine-mastitis-causing S. aureus isolates obtained over a 17-year period from more than 65 dairy farms across New Zealand. The analysis revealed a unique pattern of dominance over the entire period of study, of clonal complex 1, sequence type 1 (CC1/ST1), which accounted for ∼75% of the isolates. CC1/ST1 was also the commonest lineage infecting humans in New Zealand in the same period, but most bovine CC1/ST1 analysed in this study carried the genes coding for the bovine-adaptive bicomponent leucocidin lukF and lukM and lacked the corresponding human-adaptive lukF-PV and lukS-PV genes. Typical ruminant-associated lineages, such as ST97, ST151 and CC133 were also observed. Cluster analyses of the core and accessory genomes revealed genomic segregations according to the CCs, but lack of segregation based on the geographical location or collection year, suggesting a stable population in space and time. To our knowledge, this is the first identification of genomic markers of host adaptation to cattle in S. aureus CC1/ST1, a lineage commonly associated with humans, worldwide. The temporal clonal stability observed would enable the development of a S. aureus vaccine for New Zealand cattle, which is unlikely to undergo substantial reduction of efficacy due to clonal drifts or shifts.

Resistance Profile of Bovine Mastitis Isolates, Presence of the mecA Gene and Identification of ESBL Producing Strains from Small Rural Dairy Properties

Bovine mastitis is an inflammation of the mammary gland in response to invasion by opportunistic agents. Due to the high economic importance of dairy production and the complexity related to animal health, the objective of this work was to identify and evaluate the antibacterial resistance profile of samples of mastitis milk, milking hand and milking equipment from small rural dairy farms belonging to the northwest region of the state of Paraná, Brazil. Five small, non-technical dairy farms in the municipalities of Boa Esperança, Juranda and Tapejara, all belonging to the northwest region of the state of Paraná, Brazil, were selected. The properties had Holstein and/or crossbred herds, carried out a bucket-by-foot milking system and all had the presence of animals with subclinical mastitis confirmed by the California Mastitis Test. Samples of sterile swabs from the milking insufflators, the milking hand and milk samples were collected-and later, isolation tests and phenotypic characterization of the samples, sensitivity tests to antimicrobials and phenotypic tests for the detection of beta-producing strains were performed with extended-spectrum beta-lactamase (ESBL), molecular identification of Staphylococcus aureus isolates and mecA gene research. Of the 199 samples collected from the 15 selected properties in the municipalities of Boa Esperança, Tapejara and Juranda, 72 (36.20%) were classified as multiresistant. Isolated from milkers' hands and milking machines, which phenotypically produce extended-spectrum beta-lactamase (ESBL), the presence of the mecA gene was also observed in 11 isolates of Staphylococcus spp. of milk samples, machines and milking hands. Mastitis can be spread to the herd through the milking process by the milkers' instruments and hands, and adequate management measures can prevent its transmission and the conscious use of antibiotics decreases the prevalence of multidrug-resistant pathogens. In this work, different pathogenic bacteria were detected in mastitic milk, milking equipment and milking hand with a high percentage (36.20%) of isolates classified as multidrug resistant. In addition, the presence phenotypically (ESBL) and molecularly (mecA gene) of isolates carrying resistance genes was also verified. These results directly reflect on the health of the animals, the health of the workers and the health of the respective environment, which can enable the continuity of the propagation of the etiological agents involved in the mastitis infection. The awareness of producers and workers on these properties about the disease, transmission, sanitary aspects and adequate management and treatment are essential for improving milk production and production efficiency.

Divergent Analyses of Genetic Relatedness and Evidence-Based Assessment of Therapeutics of Staphylococcus aureus from Semi-intensive Dairy Systems

Use of antibiotics without following standard guidelines is routine practice in developing countries which is giving rise to genetic divergence and increased drug resistance. The current study analyzed genetic divergence and drug resistance by S. aureus and therapeutic efficacy of novel antibiotic combinations. The study revealed that 42.30% (minimum 20%-maximum 70%) of milk samples are positive for S. aureus. Study also revealed seven SNPs in the S. aureus nuc gene (c.53A>G, c.61A>G, c.73T>C, c.93C>A, c.217C>T, c.280T>C, and c.331T>A). Local isolates Staph-2 and Staph-3 were closely related to Bos taurus nuc gene (bovine S. aureus), while Staph-1 was closely related to Homo sapiens (human S. aureus) indicating shifting of host. Change of two amino acids and staphylococcal nuclease conserved domain was observed in all local isolates of S. aureus. The isoelectric points predicted by protParam of Staph-1, Staph-2, and Staph-3 proteins were 9.30, 9.20, and 9.20, respectively. The antibiotic susceptibility profile of S. aureus presented highest resistance against penicillin (46.67%) and glycopeptide (43.33%). When a single antibiotic regimen was adopted in a field trial, the highest efficacy was reported in the case of oxytetracycline (80%) while lowest was presented by azithromycin. Among antibiotics' combined regimen, the highest efficacy (80%) was presented by gentamicin with oxytetracycline: cefotaxime with vancomycin; and ciprofloxacin with vancomycin. The current study concluded rising percentages of S. aureus from dairy milk, proofs of genetic host shifts, and altered responses of in on field therapeutics.

Bacterial pathogens associated with clinical and subclinical mastitis in a Mediterranean pasture-based dairy production system of Australia

Mastitis is an economically important production disease in the dairy industry worldwide. There is limited information on the aetiology of clinical mastitis (CM) and subclinical mastitis (SCM) in Australia's Mediterranean pasture-based production system. A prospective study was conducted in the south-west region of Western Australia to characterise the bacterial pathogens associated with CM and SCM cases and their associated antimicrobial susceptibility profiles. A total of 102 CM and 132 SCM milk samples were collected in twelve dairy farms between April 2020 and September 2020 recovering a total of 310 bacterial isolates. The isolates were evaluated for their antimicrobial susceptibility to twelve antibiotics using the agar disk diffusion (ADD) method. The most common pathogens associated with CM was Bacillus spp. (35.29%), followed by coagulase-negative staphylococci (CNS) (22.55%), Pseudomonas spp. (19.61%), Staphylococcus aureus (10.78%), Escherichia coli (5.88%) and Streptococcus uberis (2.94%). The most common pathogens associated with SCM was CNS (44.70%), followed by Bacillus spp. (30.30%), S. aureus (20.45%), Strep. uberis (15.91%), coliforms (Citrobacter spp., Cronobacter spp., Enterobacter spp., Klebsiella spp., Kosakonia spp., Morganella spp., Serratia spp.) (9.86%), environmental Streptococci (6.06%) and E. coli (6.06%). Beta-lactams resistance was the most common resistance observed in the Staphylococcal isolates and a high proportion of Streptococcal isolates exhibited resistance to enrofloxacin. Overall, the proportion of bacterial pathogens isolated in this study was comparable to the figures reported in other studies in Australia. Future research should focus on risk factors and the determination of resistant genetic components among the common isolates.