Prevalence of non-aureus staphylococci species causing intramammary infections in Canadian dairy herds

The occurrence of Aerococcus urinaeequi and non-aureus staphylococci in raw milk negatively correlates with Escherichia coli clinical mastitis

Escherichia coli is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to E. coli CM; however, the details of which members of the healthy udder microbiome may play a role in antagonizing E. coli are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed E. coli CM during lactation, including milk from both healthy and diseased quarters (n = 1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and metagenomic sequencing was used generate data sets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing E. coli CM, indicating that E. coli displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera, Staphylococcus and Aerococcus, and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera, Staphylococcus auricularis, Staphylococcus haemolyticus, and Aerocussus urinaeequi, were identified by metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage E. coli colonization without triggering inflammation.IMPORTANCEIn this study, we show that E. coli outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by S. auricularis, S. haemolyticus, A. urinaeequi, and S. marcescens without increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species might have potential as prophylactic probiotics which could contribute to colonization resistance and prevent future instances of E. coli CM.

Distribution of Bovine Mastitis Pathogens in Quarter Milk Samples from Bavaria, Southern Germany, between 2014 and 2023-A Retrospective Study

The objective of this study was to investigate the distribution of mastitis pathogens in quarter milk samples (QMSs) submitted to the laboratory of the Bavarian Animal Health Service (TGD) between 2014 and 2023 in general, in relation to the clinical status of the quarters, and to analyze seasonal differences in the detection risk. Each QMS sent to the TGD during this period was analyzed and tested using the California Mastitis Test (CMT). Depending on the result, QMSs were classified as CMT-negative, subclinical, or clinical if the milk character showed abnormalities. Mastitis pathogens were detected in 19% of the QMSs. Non-aureus staphylococci (NAS) were the most common species isolated from the culture positive samples (30%), followed by Staphylococcus (S.) aureus (19%), Streptococcus (Sc.) uberis (19%), and Sc. dysgalactiae (9%). In culture-positive QMSs from CMT-negative and subclinically affected quarters, the most frequently isolated pathogens were NAS (44% and 27%, respectively), followed by S. aureus (25% and 17%, respectively) and Sc. uberis (8% and 22%, respectively). In QMSs from clinically affected quarters, the most frequently isolated pathogens were Sc. uberis (32%), S. aureus (13%), Sc. dysgalactiae (11%), and Escherichia (E.) coli (11%). The distribution of NAS and Sc. uberis increased throughout the study period, while that of S. aureus decreased. From June to October, QMSs from subclinically affected quarters increased and environmental pathogens, such as Sc. uberis, were detected more frequently. In conclusion, this study highlights the dynamic nature of the distribution of mastitis pathogens, influenced by mastitis status and seasonal factors. Environmental pathogens still play an important role, especially in clinical mastitis and seasonal dependency, with the number of positive samples continuing to increase. It is therefore essential to continue mastitis control measures and to regularly monitor the spread of mastitis pathogens in order to track trends and adapt targeted prevention measures.

An update on non-aureus staphylococci and mammaliicocci in cow milk: unveiling the presence of Staphylococcus borealis and Staphylococcus rostri by MALDI-TOF MS

Non-aureus staphylococci and mammaliicocci (NASM) are the microorganisms most frequently isolated from milk. Given their numerosity and complexity, MALDI-TOF MS is one of the preferred species identification approaches. Nevertheless, reference mass spectra for the novel species Staphylococcus borealis were included only recently in the Bruker Biotyper System (MBT) library, and other species of veterinary interest such as S. rostri are still absent. This work provides an updated picture of the NASM species found in milk, gained by retrospectively analyzing the data relating to 21,864 milk samples, of which 6,278 from clinical mastitis (CM), 4,039 from subclinical mastitis (SCM), and 11,547 from herd survey (HS), with a spectrum library including both species. As a result, S. borealis was the second most frequently isolated NASM (17.07%) after S. chromogenes (39.38%) in all sample types, with a slightly higher percentage in CM (21.84%), followed by SCM (17.65%), and HS (14.38%). S. rostri was also present in all sample types (3.34%), reaching 8.43% of all NASM in SCM and showing a significant association (p < 0.01) with this condition. Based on our findings, the presence of S. borealis and S. rostri in milk and their potential association with mastitis might have been overlooked, possibly due to the difficulties in differentiating these species from other closely related NASM. Our results indicate that S. borealis could be a more frequent contributor to bovine udder infections than previously thought and that S. rostri should also not be underestimated considering its significant association with SCM.

Prevalence and spatial distribution of infectious diseases of dairy cattle in Ontario, Canada

We investigated the prevalence and spatial distribution of selected pathogens associated with infectious diseases of dairy cattle in Ontario, Canada. The cross-sectional study surveyed bulk tank milk for antibodies against bovine leukemia virus (BLV), Mycobacterium avium ssp. paratuberculosis (MAP), and Salmonella Dublin, and for the presence of mastitis pathogens (Staphylococcus aureus, Streptococcus agalactiae, Mycoplasma bovis). Between October 2021 and June 2022, bulk tank milk samples were obtained from every commercial dairy farm in Ontario (n = 3,286). Samples underwent ELISA testing for the presence of BLV, MAP, and S. Dublin antibodies, and quantitative PCR testing for the detection of specific antigens of pathogens associated with mastitis. Bayesian models were used to estimate prevalence, and spatial analysis was carried out to identify regional clusters of high pathogen prevalence. Prevalence varied for different pathogens, and BLV was widespread across dairy farms in Ontario, with an estimated prevalence of 88.3%. The prevalence of MAP, Staph. aureus and S. Dublin in Ontario dairy herds was 39.8%, 31.5%, and 5.1%, respectively. The vast majority of dairy herds in Ontario were free of intramammary infections caused by Strep. agalactiae and M. bovis. Clusters of increased positive test rates were detected for S. Dublin, MAP, and Staph. aureus, indicating potential geographic risk factors for pathogen transmission. For S. Dublin, an area of increased test positivity rates was detected in southwestern Ontario, close to the Canada-United States border where most of the dairy herds in Ontario are located. Conversely, a localized cluster of positive test outcomes involving 14 subdivisions located in the southeastern region of Ontario was detected for Staph. aureus. Findings from our survey highlight the importance of the testing of aggregated samples and conducting spatial analysis as part of disease surveillance programs, and for implementing risk-based trading approaches among dairy producers.

Relationship Between Facility Type and Bulk Tank Milk Bacteriology, Udder Health, Udder Hygiene, and Milk Production on Vermont Organic Dairy Farms

The primary objective of this cross-sectional observational study was to determine whether bulk tank milk quality, udder health, udder hygiene and milk production outcomes were associated with facility type on organic dairies. A secondary objective was to identify other management-related risk factors associated with bulk tank milk quality, udder health, udder hygiene, and milk production on organic dairy herds in Vermont. We aimed to enroll 40 farms, to compare herds using the 2 most common systems (freestalls, tiestalls) for housing organic dairy cattle in the state with those using a bedded pack during the non-grazing season (typically November-May). Two general styles of bedded packs were observed: cultivated bedded packs and untilled deep bedded packs. Due to the limited number of herds using bedded packs to house lactating dairy cattle in Vermont, we combined untilled and cultivated bedded packs to describe udder hygiene, milk quality, and udder health on these loose-housing systems deeply-bedded with organic material. The study was completed on 21 farms (5 bedded packs, 6 freestalls, 10 tiestalls) before interruption due to the COVID-19 pandemic. Data captured from Dairy Herd Improvement Association records from the test closest to the date of the farm visit included average somatic cell score (SCS), standardized 150-d milk (pounds), % cows with current high SCS (SCS ≥ 4.0), % cows with newly elevated SCS (previous SCS < 4.0 to current ≥ 4.0), and % cows with chronically elevated SCS (SCS ≥ 4.0 last 2 tests). Multivariable linear regression models were used to describe outcomes by facility type, but suffered from limited statistical power due to small group sample sizes. Unconditional comparisons failed to find statistically significant differences between farms grouped by facility type in metrics captured from Dairy Herd Improvement Association test data, bulk tank milk somatic cell count (BTSCC) and aerobic culture data, or udder hygiene scores. A secondary analysis was conducted using univariate linear regression to identify associations between herd management factors and outcomes for all 21 farms combined. Although not all differences found were statistically significant in this secondary analysis combining all farms, numeric differences that may be biologically important are reported showing farms with deeper bedding had a lower BTSCC, lower newly elevated SCS, lower chronically elevated SCS, lower elevated current SCS, lower average SCS, and better udder hygiene metrics. Farms with lower mean udder hygiene scores had numerically lower chronically elevated SCS, lower elevated current SCS, and lower average SCS. We could not reject the null hypothesis that milk quality and udder health outcomes did not differ by facility type, and this does not preclude the existence of biological differences in these outcomes between facility types. The current study provides insight on factors affecting bulk tank milk quality, udder health and hygiene measures on organic dairy farms in Vermont. Bedded packs may be a viable option for confinement housing during the winter non-grazing season for pasture-based herds interested in a loose-housing system in the Northeastern US, but more research such as longitudinal studies with a larger sample size is needed to test this hypothesis.

Discriminating bovine mastitis pathogens by combining loop-mediated isothermal amplification and amplicon-binding split trehalase assay

Bovine mastitis is predominantly caused by intramammary infections with various Gram-positive and Gram-negative bacteria, requiring accurate pathogen identification for effective treatment and antimicrobial resistance prevention. Here, a novel diagnostic method was developed to detect mastitis pathogens in milk samples by combining loop-mediated isothermal amplification with a split enzyme biosensor whereby trehalase fragments were fused with a DNA-binding protein, SpoIIID. Three primer sets, LAMPstaph, LAMPstrep, and LAMPneg, harboring SpoIIID recognition sequences targeted Staphylococcus, Streptococcus, and Gram-negative pathogens, respectively. Limits of detection were determined for DNA extracted from bacterial culture and bacteria-spiked milk. The combined method detected as low as 2, 24, and 10 copies of genomic DNA of staphylococci, streptococci and Escherichia coli and 11 CFU/ml for milk spiked with Escherichia coli. Higher detection limits were observed for Gram-positive bacteria in spiked milk. When testing genomic DNA of 10 mastitis isolates at concentrations of 106 and 103 copies per reaction, no cross-reactivity was detected for LAMPstaph nor LAMPstrep, whereas the LAMPneg assay cross-reacted only with Corynebacterium sp. at the highest concentration. This combined method demonstrated the potential to distinguish mastitis pathogenic Gram types for a rapid decision of antimicrobial treatment without culturing.

Frequency of non-aureus staphylococci and mammaliicocci species isolated from quarter clinical mastitis: A 6-year retrospective study

Non-aureus staphylococci and mammaliicocci (NASM) are the most frequently isolated bacterial group from bovine milk samples. Most studies focus on subclinical mastitis caused by NASM; however, NASM can cause clinical mastitis (CM) as well. We evaluated retrospective data from 6 years (2017-2022) to determine the species and frequency of NASM isolated from quarter bovine CM. The data was comprised of microbiological results from quarter CM samples routinely submitted to Quality Milk Production Services at Cornell University for microbial identification by MALDI-TOF mass spectrometry. A total of 9,909 microbiological results from 410 dairy herds were evaluated. Our results showed that 29 distinct NASM species were identified, with the 8 most prevalent NASM species being Staphylococcus chromogenes, Staphylococcus haemolyticus, Staphylococcus simulans, Staphylococcus epidermidis, Staphylococcus sciuri (now Mammaliicoccus sciuri), Staphylococcus agnetis/Staphylococcus hyicus, Staphylococcus borealis, and Staphylococcus xylosus. The NASM distribution remained similar among seasons, but the frequency of NASM CM cases was higher during the summer. Our results showed different patterns of variations in the isolation frequency over time, depending on the bacterial species: increasing or decreasing trends, cyclic fluctuations, and, except for Staphylococcus borealis, a significant seasonality effect for our study's most prevalent NASM. This study showed that Staphylococcus chromogenes remains the most frequent (43%) NASM species identified from bovine CM, followed by Staphylococcus haemolyticus (18%), and Staphylococcus simulans (12%).

Staphylococcal mastitis in dairy cows

Bovine mastitis is one of the most common diseases of dairy cattle. Even though different infectious microorganisms and mechanical injury can cause mastitis, bacteria are the most common cause of mastitis in dairy cows. Staphylococci, streptococci, and coliforms are the most frequently diagnosed etiological agents of mastitis in dairy cows. Staphylococci that cause mastitis are broadly divided into Staphylococcus aureus and non-aureus staphylococci (NAS). NAS is mainly comprised of coagulase-negative Staphylococcus species (CNS) and some coagulase-positive and coagulase-variable staphylococci. Current staphylococcal mastitis control measures are ineffective, and dependence on antimicrobial drugs is not sustainable because of the low cure rate with antimicrobial treatment and the development of resistance. Non-antimicrobial effective and sustainable control tools are critically needed. This review describes the current status of S. aureus and NAS mastitis in dairy cows and flags areas of knowledge gaps.

Efficacy of novel staphylococcal surface associated protein vaccines against Staphylococcus aureus and non-aureus staphylococcal mastitis in dairy cows

Mastitis is an inflammation of the mammary gland commonly caused by bacteria or fungi. Staphylococcus aureus is a major bacterium that causes mastitis in dairy cows. Non-aureus staphylococci are also increasingly reported, with Staphylococcus chromogenes being the most common species. Current staphylococcal mastitis control programs are not fully effective, and treatment with antibiotics is not sustainable. Non-antibiotic sustainable control tools, such as effective vaccines, are critically needed. We previously developed S. aureus surface-associated proteins (SASP) and S. chromogenes surface-associated proteins (SCSP) vaccines that conferred partial protective effects. We hypothesized that vaccination with SASP or SCSP would reduce the incidence of S. aureus mastitis throughout the lactation period. The objective of this study was to evaluate the efficacy of SASP and SCSP vaccines against S. aureus and non-aureus staphylococcal mastitis under natural exposure over 300 days of lactation. Pregnant Holstein dairy cows (n = 45) were enrolled and assigned to receive SASP (n = 15) or SCSP (n = 16) vaccines or unvaccinated control (n = 14). Cows were vaccinated with 1.2 mg of SASP or SCSP with Emulsigen-D adjuvant. Control cows were injected with phosphate-buffered saline with Emulsigen-D adjuvant. Three vaccine injections were given subcutaneously at 60, 40, and 20 days before the expected calving. Booster vaccinations were given at 120 and 240 days in milk. Cows were monitored for mastitis at quarter and cow levels, staphylococcal mastitis incidence, changes in serum and milk anti-SASP and anti-SCSP antibody titers, bacterial counts in milk, adverse reactions, milk yield and milk somatic cells count over 300 days of lactation. The SCSP vaccine conferred a significant reduction in the incidence of staphylococcal mastitis. Milk and serum anti-SASP and anti-SCSP antibody titers were increased in the vaccinated cows compared to unvaccinated control cows. Anti-SASP and anti-SCSP antibody titers decreased at about 120 days in milk, indicating the duration of immunity of about four months. In conclusion, the SASP and SCSP vaccines conferred partial protection from natural infection.

Non-aureus staphylococci and mammaliicocci isolated from bovine milk in Italian dairy farms: a retrospective investigation

Non-aureus staphylococci and mammaliicocci (NASM) are associated with bovine mastitis and increased milk somatic cell count (SCC) but their relationships with mammary gland health at the species level are not clearly defined. Regional differences have also been reported in their specific prevalence. The implementation of MALDI-TOF MS in milk microbiology is generating large and dependable datasets with the potential of providing useful epidemiological information. We present the retrospective analysis of 17,213 milk samples sent to our laboratory in 2021-2022, including 13,146 quarter samples from cows with subclinical (SCM) or clinical mastitis (CM) from 104 farms, and 4,067 composite herd survey (HS) samples from 21 farms. NASM were isolated from 21.12% of SCM, 11.49% of CM, and 15.59% of HS milk samples. The three most frequently identified NASM in SCM milk were Staphylococcus chromogenes (33.33%), S. haemolyticus (26.07%), and S. epidermidis (10.65%); together with S. microti and S. hyicus, these species were significantly more prevalent in quarters with SCM (p < 0.05). The three most frequently identified NASM in CM milk were S. chromogenes (31.69%), S. haemolyticus (21.42%), and Mammaliicoccus sciuri (18.38%), although no significant associations were found between these NASM species and CM. The three most frequently identified NASM in HS milk were S. chromogenes (44.49%), S. epidermidis (17.84%), and S. haemolyticus (17.23%), with S. chromogenes being isolated in all the farms sending HS milk (100%). In conclusion, this retrospective study provides the first information on the NASM species isolated from cow milk in Italy, expanding our knowledge on the epidemiology of NASM at the species level and providing further insights into their relationships with mammary gland health in modern dairy farms.

Comparison of non-aureus staphylococcal and mammaliicoccal species found in both composite milk and bulk-tank milk samples of dairy cows collected in tandem

Non-aureus staphylococci and the closely related mammaliicoccal species (NASM) are the most common causes of bovine subclinical mastitis on modern dairy farms and are highly prevalent in bulk-tank milk. The purpose of this study was to determine the distribution of NASM in both composite cow milk (CCM) and bulk-tank milk (BTM) samples collected in tandem in commercial Flemish dairy herds and to estimate the origin of the different (subgroups of) NASM species present in BTM by applying strain typing (random amplification of polymorphic DNA or random amplified DNA [RAPD]). A single cross-sectional sampling was performed over 5 herds that volunteered to participate in the study. Composite cow milk samples (n = 356) were collected from all lactating cows (except those with clinical mastitis) during a milking in tandem with 6 BTM samples per herd sequentially collected immediately post that milking (n = 30). In total, 421 and 80 NASM isolates were recovered and identified by MALDI-TOF mass spectrometry from the CCM and BTM samples, respectively and a total of 21 and 12 different NASM species were identified from CCM and BTM samples, respectively. Staphylococcus cohnii was the most prevalent NASM species found in BTM followed by Staphylococcus haemolyticus, Staphylococcus epidermidis, Mammaliicoccus lentus, and Staphylococcus equorum, whereas from CCM samples the most common species were S. hemolyticus, S. cohnii, S. equorum, S. epidermidis, and Staphylococcus chromogenes. The prevalent NASM species in both CCM and BTM samples was distinct for each herd, corroborating other studies observing a herd-specific NASM microbiota. Random amplified DNA analysis was performed on 9 NASM species (S. chromogenes, S. epidermidis, S. haemolyticus, S. equorum, Mammaliicoccus sciuri, Staphylococcus xylosus, S. cohnii, Staphylococcus debuckii, and M. lentus) because these species were isolated from both sample types in a herd. The same RAPD types were found in both sample types for all NASM species selected for strain typing in varying degrees. When assessing the distribution of NASM species, differences within NASM species should be examined meaning a closer look should be taken at the strain level rather than at the species level only.

Apparent prevalence and selected risk factors of methicillin-resistant Staphylococcus aureus and non-aureus staphylococci and mammaliicocci in bulk tank milk of dairy herds in Indiana, Ohio, and Michigan

The purpose of this study was to determine the apparent prevalence and risk factors of methicillin-resistant Staphylococcus aureus and non-aureus staphylococci and mammaliicocci (NASM) in bulk tank milk (BTM) obtained from 300 dairy farms that belong to a cooperative collecting milk from Indiana, Michigan, and Ohio. Dairy field personnel recorded information about selected farm level risk factors and collected and froze BTM samples (n = 300) that were sent to Michigan State University researchers. Milk samples were thawed at room temperature and pre-enriched by adding 1 to 4 mL of Mueller-Hinton broth supplemented with 6.5% NaCl and incubated at 37°C for 24 h. Subsequently, 10 µL was plated on mannitol salt agar and Mueller-Hinton agar supplemented with 2.5% NaCl containing 2 mg/L oxacillin and 20 mg/L aztreonam. Colonies that grew on the selective media were subcultured on blood agar and identified using MALDI-TOF mass spectrometry. Phenotypic methicillin resistance was tested using cefoxitin disk diffusion. Conventional PCR was used to detect mecA and mecC in phenotypically resistant isolates. Of 550 isolates that were obtained from mannitol salt agar plates and 10 isolates from Mueller-Hinton agar plates, 16 species of NASM accounted for 84% of staphylococci, while S. aureus accounted for the remaining 16%. Among S. aureus, 4 isolates from 4 farms (1.3%) demonstrated phenotypic resistance to methicillin resistance but none carried mecA or mecC genes. Among NASM, 45 isolates from 40 farms (13.3%) demonstrated phenotypic resistance to methicillin. However, only 13 NASM isolates (7 Mammaliicoccus sciuri, 2 Staphylococcus haemolyticus, 1 Mammaliicoccus fleuretti, 1 Staphylococcus epidermidis, 1 Staphylococcus saprophyticus, and 1 Staphylococcus hyicus) from 13 farms were positive for mecA, whereas all were negative for mecC. Thus, the prevalence of mecA-positive NASM in BTM was 4.3%. Based on molecular results, this study demonstrated a low prevalence of methicillin resistance NASM from BTM samples collected from farms in the Upper Midwest. Dairy farms that contained ≤200 lactating cows and had swine located on the farm had a higher prevalence of methicillin-resistant NASM than smaller farms that did not contain swine.

Genomic analysis and assessment of pathogenic (toxicogenic) potential of Staphylococcus haemolyticus and Bacillus paranthracis consortia isolated from bovine mastitis in Russia

Three stable microbial consortia, each composed of Bacillus paranthracis and Staphylococcus haemolyticus strains, were isolated from milk of cows diagnosed with mastitis in three geographically remote regions of Russia. The composition of these consortia remained stable following multiple passages on culture media. Apparently, this stability is due to the structure of the microbial biofilms formed by the communities. The virulence of the consortia depended on the B. paranthracis strains. It seems plausible that the ability of the consortia to cause mastitis in cattle was affected by mutations of the cytK gene of B. paranthracis.

Antimicrobial Resistance Profiles of Staphylococcus Isolated from Cows with Subclinical Mastitis: Do Strains from the Environment and from Humans Contribute to the Dissemination of Resistance among Bacteria on Dairy Farms in Colombia?

Staphylococcus is a very prevalent etiologic agent of bovine mastitis, and antibiotic resistance contributes to the successful colonization and dissemination of these bacteria in different environments and hosts on dairy farms. This study aimed to identify the antimicrobial resistance (AMR) genotypes and phenotypes of Staphylococcus spp. isolates from different sources on dairy farms and their relationship with the use of antibiotics. An antimicrobial susceptibility test was performed on 349 Staphylococcus strains (S. aureus, n = 152; non-aureus staphylococci (NAS), n = 197) isolated from quarter milk samples (QMSs) from cows with subclinical mastitis (176), the teats of cows (116), the milking parlor environment (32), and the nasal cavities of milk workers (25). Resistance and multidrug resistance percentages found for S. aureus and NAS were (S. aureus = 63.2%, NAS = 55.8%) and (S. aureus = 4.6%, NAS = 11.7%), respectively. S. aureus and NAS isolates showed resistance mainly to penicillin (10 IU) (54.1% and 32.4%) and ampicillin (10 mg) (50.3% and 27.0%) drugs. The prevalence of AMR Staphylococcus was higher in environmental samples (81.3%) compared to other sources (52.6-76.0%). In S. aureus isolates, the identification of the blaZ (83.9%), aacAaphD (48.6%), ermC (23.5%), tetK (12.9%), and mecA (12.1%) genes did not entirely agree with the AMR phenotype. We conclude that the use of β-lactam antibiotics influences the expression of AMR in Staphylococcus circulating on dairy farms and that S. aureus isolates from the environment and humans may be reservoirs of AMR for other bacteria on dairy farms.

Investigation of milk microbiota of healthy and mastitic Sahiwal cattle

BACKGROUND

Sahiwal cattle is an indigenous cattle breed of Pakistan and mastitis is one of the major problems faced by Sahiwal cattle which hinders its production potential. The study was designed to investigate the milk microbiota of healthy and mastitic Sahiwal cattle as part of a multistep project to develop probiotics for the mitigation and control of mastitis. Milk samples of Sahiwal cattle (healthy clinical mastitis and subclinical mastitis) reared under similar husbandry and management practices were processed for 16S rRNA gene base metagenomics analysis.

RESULTS

Results revealed that Proteobacteria were dominant in the healthy group and subclinical mastitis group (56.48% and 48.77%, respectively) as compared to the clinical mastitis group (2.68%). In contrast, Firmicutes were abundant in the clinical mastitis group (64%) as compared to the healthy and subclinical mastitis groups (15.87% and 38.98%, respectively). Dominant species assigned in the healthy group were Ignavibacterium album, Novosphingobium capsulatum, Akkermansia muciniphila and Lactobacillus fermentum.The clinical mastitis group was dominated by Streptococcus dysgalactiae and Corynebacterium bovis, while subclinical mastitis group included Lactobacillus fermentum and uncultured acidobacteriales and Akkermansia muciniphila as dominant species. Alpha diversity indices showed higher microbial diversity in the healthy group compared to the clinical and sub-clinical mastitis groups.

CONCLUSION

It is concluded that the milk microbiota of healthy sahiwal cattle has higher diversity and dominant taxa in the different groups may be used as signature microbes for mastitis susceptibility. Akkermansia muciniphila is one of candidate specie that was identified and may be used for development of probiotics.

Virulence Mechanisms of Staphylococcal Animal Pathogens

Staphylococci are major causes of infections in mammals. Mammals are colonized by diverse staphylococcal species, often with moderate to strong host specificity, and colonization is a common source of infection. Staphylococcal infections of animals not only are of major importance for animal well-being but have considerable economic consequences, such as in the case of staphylococcal mastitis, which costs billions of dollars annually. Furthermore, pet animals can be temporary carriers of strains infectious to humans. Moreover, antimicrobial resistance is a great concern in livestock infections, as there is considerable antibiotic overuse, and resistant strains can be transferred to humans. With the number of working antibiotics continuously becoming smaller due to the concomitant spread of resistant strains, alternative approaches, such as anti-virulence, are increasingly being investigated to treat staphylococcal infections. For this, understanding the virulence mechanisms of animal staphylococcal pathogens is crucial. While many virulence factors have similar functions in humans as animals, there are increasingly frequent reports of host-specific virulence factors and mechanisms. Furthermore, we are only beginning to understand virulence mechanisms in animal-specific staphylococcal pathogens. This review gives an overview of animal infections caused by staphylococci and our knowledge about the virulence mechanisms involved.

Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin

Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.

Genome-Wide DNA Methylation and Transcriptome Integration Associates DNA Methylation Changes with Bovine Subclinical Mastitis Caused by Staphylococcus chromogenes

Staphylococcus chromogenes (SC) is a common coagulase-negative staphylococcus described as an emerging mastitis pathogen and commonly found in dairy farms. This study investigated the potential involvement of DNA methylation in subclinical mastitis caused by SC. The whole-genome DNA methylation patterns and transcriptome profiles of milk somatic cells from four cows with naturally occurring SC subclinical mastitis (SCM) and four healthy cows were characterized by next-generation sequencing, bioinformatics, and integration analyses. Comparisons revealed abundant DNA methylation changes related to SCM, including differentially methylated cytosine sites (DMCs, n = 2,163,976), regions (DMRs, n = 58,965), and methylation haplotype blocks (dMHBs, n = 53,098). Integration of methylome and transcriptome data indicated a negative global association between DNA methylation at regulatory regions (promoters, first exons, and first introns) and gene expression. A total of 1486 genes with significant changes in the methylation levels of their regulatory regions and corresponding gene expression showed significant enrichment in biological processes and pathways related to immune functions. Sixteen dMHBs were identified as candidate discriminant signatures, and validation of two signatures in more samples further revealed the association of dMHBs with mammary gland health and production. This study demonstrated abundant DNA methylation changes with possible involvement in regulating host responses and potential as biomarkers for SCM.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021

Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.

Staphylococcus microti Strains Isolated from an Italian Mediterranean Buffalo Herd

S. microti is a new species among non-aureus staphylococci (NAS) frequently found in bovine milk samples and associated with subclinical mastitis (SCM). The aim of this study was to analyze the presence of S. microti in 200 composite milk samples and 104 milking parlor surface swabs collected at a buffalo farm in Southern Italy to define its presence in milk and a milking parlor environment. The samples were inoculated onto different agar plates, and the isolates were identified by MALDI-TOF MS. The strains identified as S. microti (54/304 samples, 17.8%) were collected, and their purified genomic DNA was subjected to PCR amplification and whole 16S rRNA gene sequencing. Furthermore, their phenotypic resistance profiles were evaluated by a disk diffusion method, and the genotypic characterization of the tetracycline resistance was performed for the tetM and tetK genes by multiplex PCR. Four and forty-seven S. microti isolates from milk samples of lactating animals with subclinical mastitis (SCM) and intramammary infection (IMI), respectively, and three isolates from milking parlor surfaces were recovered. The genomic DNA was purified from the bacterial isolates, and the amplification and sequencing of the 16S gene further supported the proteomic identification as S. microti. No clinical mastitis was detected in the herd during the study period. The antimicrobial susceptibility testing revealed a worrisome 100% resistance to tetracyclines, genotypically mediated by the tetM gene for all strains. This study highlights that S. microti may be commonly isolated from dairy buffalo milk and milking parlor equipment. Its association with SCM or IMI remains to be established.

Chitosan can improve antimicrobial treatment independently of bacterial lifestyle, biofilm biomass intensity and antibiotic resistance pattern in non-aureus staphylococci (NAS) isolated from bovine clinical mastitis

Bovine mastitis is the most frequent and costly disease that affects dairy cattle. Non-aureus staphylococci (NAS) are currently one of the main pathogens associated with difficult-to-treat intramammary infections. Biofilm is an important virulence factor that can protect bacteria against antimicrobial treatment and prevent their recognition by the host's immune system. Previously, we found that chronic mastitis isolates which were refractory to antibiotic therapy developed strong biofilm biomass. Now, we evaluated the influence of biofilm biomass intensity on the antibiotic resistance pattern in strong and weak biofilm-forming NAS isolates from clinical mastitis. We also assessed the effect of cloxacillin (Clx) and chitosan (Ch), either alone or in combination, on NAS isolates with different lifestyles and abilities to form biofilm. The antibiotic resistance pattern was not the same in strong and weak biofilm producers, and there was a significant association (p ≤ 0.01) between biofilm biomass intensity and antibiotic resistance. Bacterial viability assays showed that a similar antibiotic concentration was effective at killing both groups when they grew planktonically. In contrast, within biofilm the concentrations needed to eliminate strong producers were 16 to 128 times those needed for weak producers, and more than 1,000 times those required for planktonic cultures. Moreover, Ch alone or combined with Clx had significant antimicrobial activity, and represented an improvement over the activity of the antibiotic on its own, independently of the bacterial lifestyle, the biofilm biomass intensity or the antibiotic resistance pattern. In conclusion, the degree of protection conferred by biofilm against antibiotics appears to be associated with the intensity of its biomass, but treatment with Ch might be able to help counteract it. These findings suggest that bacterial biomass should be considered when designing new antimicrobial therapies aimed at reducing antibiotic concentrations while improving cure rates.

Genetic diversity and iron metabolism of Staphylococcus hominis isolates originating from bovine quarter milk, rectal feces, and teat apices

Staphylococcus hominis, a member of the non-aureus staphylococci (NAS) group, is part of the human and animal microbiota. Although it has been isolated from multiple bovine-associated habitats, its relevance as a cause of bovine mastitis is currently not well described. To successfully colonize and proliferate in the bovine mammary gland, a bacterial species must be able to acquire iron from host iron-binding proteins. The aims of this study were (1) to assess the genetic diversity of S. hominis isolated from bovine quarter milk, rectal feces, and teat apices, and (2) to investigate the capacity of bovine S. hominis isolates belonging to these different habitats to utilize ferritin and lactoferrin as iron sources. To expand on an available collection of bovine S. hominis isolates (2 from quarter milk, 8 from rectal feces, and 19 from teat apices) from one commercial dairy herd, a subsequent single cross-sectional quarter milk sampling (n = 360) was performed on all lactating cows (n = 90) of the same herd. In total, 514 NAS isolates were recovered and identified by MALDI-TOF mass spectrometry; the 6 most prevalent NAS species were S. cohnii (33.9%), S. sciuri (16.7%), S. haemolyticus (16.3%), S. xylosus (9.6%), S. equorum (9.4%), and S. hominis (3.5%). A random amplified polymorphic DNA (RAPD) analysis was performed on 46 S. hominis isolates (19 from quarter milk, 8 from rectal feces, and 19 from teat apices). Eighteen distinct RAPD fingerprint groups were distinguished although we were unable to detect the presence of the same RAPD type in all 3 habitats. One S. hominis isolate of a distinct RAPD type unique to a specific habitat (8 from quarter milk, 3 from rectal feces, and 4 from teat apices) along with the quality control strain Staphylococcus aureus ATCC 25923 and 2 well-studied Staphylococcus chromogenes isolates ("IM" and "TA") were included in the phenotypical iron test. All isolates were grown in 4 types of media: iron-rich tryptic soy broth, iron-rich tryptic soy broth deferrated by 2,2'-bipyridyl, and deferrated tryptic soy broth supplemented with human recombinant lactoferrin or equine spleen-derived ferritin. The growth of the different strains was modified by the medium in which they were grown. Staphylococcus chromogenes TA showed significantly lower growth under iron-deprived conditions, and adding an iron supplement (lactoferrin or ferritin) resulted in no improvement in growth; in contrast, growth of S. chromogenes IM was significantly recovered with iron supplementation. Staphylococcus hominis strains from all 3 habitats were able to significantly utilize ferritin but not lactoferrin as an iron source to reverse the growth inhibition, in varying degrees, caused by the chelating agent 2,2'-bipyridyl.

The Impact of Selective Dry Cow Therapy Adopted in a Brazilian Farm on Bacterial Diversity and the Abundance of Quarter Milk

Simple Summary

The current study sought to assess the impact of selective dry cow therapy (SDCT) (protocol 1: antibiotics combined with internal teat sealant (ITS); vs. protocol 2: ITS alone) on bacterial diversity and the abundance of quarter milk. Based on the results of bacteriological culturing, the quarters (n = 313) were categorized as healthy, cured, persistent, and new intramammary infection. The bacterial diversity was similar when comparing both healthy and cured quarters submitted to both drying-off protocols. Although healthy cows that were treated at drying-off using only teat sealant showed no alteration in the alpha and beta diversity of bacteria, they showed a higher abundance of bacterial groups that may be beneficial to or commensals of the mammary gland, which implies that antibiotic therapy should be reserved for mammary quarters with a history of mastitis.

Abstract

We aimed to evaluate the impact of selective dry cow therapy (SDCT) (protocol 1: antimicrobial combined with internal teat sealant (ITS); vs. protocol 2: ITS alone) on bacterial diversity and the abundance of quarter milk. Eighty high production cows (parity ≤ 3 and an average milk yield of 36.5 kg/cow/day) from the largest Brazilian dairy herd available were randomly selected; milk quarter samples were collected for microbiological culture (MC) on the day of drying-off (n = 313) and on day 7 post-calving (n = 313). Based on the results of the MC before and after calving, 240 quarters out of 313 were considered healthy, 38 were cured, 29 showed new infections and 6 had persistent infections. Mammary quarters were randomly selected based on intramammary information status and SDCT protocols for bacterial diversity analyses. The bacterial diversity was similar when comparing both healthy and cured quarters submitted to both drying-off protocols. Despite healthy cows that were treated at dry-off using only teat sealant showing no alteration in the alpha and beta bacterial diversity, they did show a higher abundance of bacterial groups that may be beneficial to or commensals of the mammary gland, which implies that antibiotic therapy should be reserved for mammary quarters with a history of mastitis.

Comparison of Dynamics of Udder Skin Microbiota From Grazing Yak and Cattle During the Perinatal Period on the Qinghai–Tibetan Plateau

The perinatal period has an important impact on the health of ruminants, and the imbalance of udder skin microbiota might be an important inducement of bovine mastitis. However, it is not clear how the perinatal period affects the microbial structure and stability of the udder skin of yak and cattle. Here, we used 16S rRNA gene high-throughput sequencing to analyze the udder skin microbiota of yak and cattle during the perinatal period. We found that the diversity and richness of microbiota of bovine udder skin during 1–2 weeks postpartum were significantly lower than those in the 1–2 weeks prenatal and 1-month postpartum period (Wilcoxon, p < 0.05). Besides, we found sharing of 2,533 OTUs in the udder skin microbiota of yak and cattle during the perinatal period, among which the core microbiota at the genera level was mainly composed of Staphylococcus, Moraxella, and Acinetobacter. However, the genus Acinetobacter was significantly abundant in the udder skin of cattle during 1–2 weeks postpartum. The NMDS and LEfSe results showed that the perinatal period had more effects on the composition and stability of microbial community in the udder skin of cattle compared to yak, particularly during 1–2 weeks postpartum. In addition, the average content of total whey proteins and immunoglobulin G of whey protein were significantly higher in the yak colostrum when compared to those found in the cattle (p < 0.05). In conclusion, the structure of udder skin microbiota of yak during the perinatal period is more stable than that of cattle in the same habitat, and 1–2 weeks postpartum may be a potential window period to prevent cattle mastitis.

Values and Risk Perception Shape Canadian Dairy Farmers' Attitudes toward Prudent Use of Antimicrobials

Antimicrobial resistance (AMR) is an important challenge in public health. Ensuring rational antimicrobial use (AMU) on farms is one of the key components of antimicrobial stewardship. We aimed to describe a sample of Canadian dairy farmers' personal factors for AMUand their AMR risk perception, and to associate these factors with their attitude toward promotion of prudent AMU. We distributed an online survey among dairy farmers in Ontario and Atlantic Canada (New Brunswick, Nova Scotia, and Prince Edward Island). The questionnaire was designed to solicit information on dairy farmers' AMU decision-making process, attitudes toward AMU reduction, awareness of AMR, and individual values. We performed a factor analysis on 15 statements related to AMR awareness and AMU reduction and used a logistic regression model to identify variables associated with the probability of disagreeing with the need to increase promotion of responsible AMU in the dairy industry. Respondents' (n = 193) previous experience was the main reason to select an antimicrobial treatment for their cattle. We identified four groups of factors related to knowledge, risk perception, and emotional states among respondents. To the question "Should there be more initiatives to promote responsible use of antibiotics in the dairy industry?" 23% of respondents answered no, which was associated in a logistic regression model with being a farm owner, having a tie-stall barn, and considering their own experience as the most important factor in selecting antimicrobial treatments. The score for the conservation value dimension and score for a factor described as sense of responsibility when using antimicrobials were also retained in the final model. Our results indicate that tailored strategies to promote prudent AMU on dairy farms may be preferable to a generic strategy because there are individual differences in attitudes, values, and AMR awareness that shape AMR risk perception and willingness to modify current AMU practices.

Microbiological Diagnoses on Clinical Mastitis—Comparison between Diagnoses Made in Veterinary Clinics versus in Laboratory Applying MALDI-TOF MS

The present study compares the diagnoses on clinical bovine mastitis made in veterinary clinics using conventional diagnostic methods with diagnoses on the same samples made by a veterinary reference laboratory using MALDI-TOF MS as diagnostics. The study enables targeted and evidence-based consulting on prudent mastitis diagnostics and related antibiotic usage. In total, 492 samples from clinical mastitis were included. When applying MALDI-TOF MS as gold standard, only 90 out of 492 diagnoses made in veterinary clinics, equal to 18%, were correct. Four main findings were important: (1) the veterinary clinics overlooked contamination in mastitis samples; (2) the veterinary clinics only assigned 2 fully correct diagnoses out of 119 samples with mixed growth cultures; (3) the veterinary clinics made close to half of their diagnoses on pure culture erroneously; (4) the veterinary clinics applied a limited number of the relevant pathogen identifications on pure culture samples. Altogether, the present study shows that a large part of Danish clinical mastitis cases are misdiagnosed. Lack of correct diagnoses and diagnostic quality control may lead to the choice of wrong treatment and thus hamper prudent use of antibiotics. Hence, the present study warns a risk of overuse of antibiotics in Denmark. Consequently, the present study calls for training of veterinary clinics in diagnostics of mastitis pathogens and national guidelines on quality assurance of mastitis diagnostics.

Novel Quantitative Assay to Describe In Vitro Bovine Mastitis Bacterial Pathogen Inhibition by Non-aureus Staphylococci

In this paper, we describe a new quantitative method to evaluate and quantify in vitro growth inhibition of mastitis-related bacteria. Colony-forming units of Staphylococcus (S.) aureus (n = 10), Escherichia (E.) coli (n = 10), and Streptococcus (S.) uberis (n = 10) were quantified after their growth on top of layers of trypticase soy agar (TSA) containing six different concentrations (varying from 10² to 10⁷ CFU/mL) of bovine non-aureus staphylococci (NAS), i.e., S. chromogenes (n = 3) and S. simulans (n = 3) isolates. Growth inhibition of the mastitis-related major bacterial pathogens, including E. coli, was confirmed by all NAS, an effect that varied highly among NAS isolates and was not evident from the semiquantitative method with which the new method was compared. By subsequent application of the new method on a larger set of 14 bovine NAS isolates, we observed that S. simulans and NAS originating from teat apices (especially S. epidermidis) required lower concentrations to inhibit both methicillin-sensitive (MSSA) (n = 5) and methicillin-resistant S. aureus (MRSA) isolates (n = 5) originating from milk. Therefore, the new assay is a promising tool to precisely quantify the intra- and inter-species differences in growth inhibition between NAS.

Microscopic differential cell count and specific mastitis pathogens in cow milk from compost-bedded pack barns and cubicle barns

Compost bedded pack barns (compost) as a new free walk housing system favorably influence udder health due to improved animal welfare and lying comfort. On the other hand, unfavorable effects on udder health are possible, due to the open bedded pack and the associated larger bacterial content in moisture. For in-depth farming system comparisons, the present study aimed to evaluate the specific cell fractions and mastitis pathogens in milk from cows kept in compost and in conventional cubical barns (cubicle). For milk sample collection we used a repeated measurement data structure of 2,198 udder quarters from 537 Holstein cows kept in six herds (3 in compost and 3 in cubicle). Differential cell counting was conducted including lymphocytes, macrophages and polymorphonuclear leukocytes (PMN). Specific mastitis pathogens comprised major and minor pathogens. Mixed models were applied to infer environmental and cow associated effects on cell fractions and on prevalences for pathogen infections, with specific focus on system × lactation stage, system × milk yield and system × somatic cell count effects. The interaction between system and lactation stage showed significant differences (P < 0.01) between the systems. A significantly smaller number of bacteriologically positive quarters and lower prevalences for minor pathogens were detected in compost compared to cubicle. Least squares means for pathogen prevalences indicated a quite constant proportion of bacteriologically negative udder quarters across milk yield levels in compost, but a slight increase with increasing milk yield in cubicle. Cell fraction responses in both systems differed in relation to the overall bacteriological infection status and farming system particularities. In conclusion, different cell fractions and specific mastitis pathogens should be considered as an indicator for udder health in different production systems, taking into account cow associated factors (lactation stage, milk yield).

Etiology of Mastitis and Antimicrobial Resistance in Dairy Cattle Farms in the Western Part of Romania

The present study aimed to determine the bacteria isolated from bovine mastitis and their antimicrobial resistance in the western part of Romania. Clinical mastitis was diagnosed based on local inflammation in the udder, changes in milk, and when present, generalized symptoms. Subclinical mastitis was assessed using a rapid test—the California Mastitis Test. The identification of bacterial strains was performed based on biochemical profiles using API system tests (API 20 E, API Staph, API 20 Strep, API Coryne, API 20 NE (bioMerieux, Marcy l’Etoile, France), and MALDI-TOF mass spectrometry (MS). The prevalent isolated bacteria were Staphylococcus spp. (50/116; 43.19%), followed by Streptococcus spp. (26/116; 22.41%), E. coli (16/116; 13.79%), Corynebacterium spp. (9/116; 7.75%), Enterococcus spp. (10/116; 8.62%), and Enterobacter spp. (5/116; 4.31%). Phenotype antimicrobial resistance profiling was performed used the disc diffusion method. Generally, Gram-positive bacteria showed low susceptibility to most of the antimicrobials tested, except cephalothin. Susceptibilities to penicillins and quinolones were fairly high in Gram-negative bacteria, whereas resistance was observed to macrolides, aminoglycosides, and tetracyclines. The highest number of isolates were multidrug resistant (MDR), the resistance pathotypes identified including the most frequently antimicrobials used in cow mastitis treatment in Romania.

Whole Genome Sequencing of Staphylococci Isolated From Bovine Milk Samples

Staphylococci are among the commonly isolated bacteria from intramammary infections in bovines, where Staphylococcus aureus is the most studied species. This species carries a variety of virulence genes, contributing to bacterial survival and spread. Less is known about non-aureus staphylococci (NAS) and their range of virulence genes and mechanisms, but they are the most frequently isolated bacteria from bovine milk. Staphylococci can also carry a range of antimicrobial resistance genes, complicating treatment of the infections they cause. We used Illumina sequencing to whole genome sequence 93 staphylococcal isolates selected from a collection of staphylococcal isolates; 45 S. aureus isolates and 48 NAS isolates from 16 different species, determining their content of antimicrobial resistance genes and virulence genes. Antimicrobial resistance genes were frequently observed in the NAS species as a group compared to S. aureus. However, the lincosamide resistance gene lnuA and penicillin resistance gene blaZ were frequently identified in NAS, as well as a small number of S. aureus. The erm genes conferring macrolide resistance were also identified in several NAS isolates and in a small number of S. aureus isolates. In most S. aureus isolates, no antimicrobial resistance genes were detected, but in five S. aureus isolates three to six resistance genes were identified and all five of these carried the mecA gene. Virulence genes were more frequently identified in S. aureus, which contained on average five times more virulence genes compared to NAS. Among the NAS species there were also differences in content of virulence genes, such as S. chromogenes with a higher average number of virulence genes. By determining the content of a large selection of virulence genes and antimicrobial resistance genes in S. aureus and 16 different NAS species our results contribute with knowledge regarding the genetic basis for virulence and antimicrobial resistance in bovine staphylococci, especially the less studied NAS. The results can create a broader basis for further research into the virulence mechanisms of this important group of bacteria in bovine intramammary infections.

Spatio-Temporal Variation in the Prevalence of Major Mastitis Pathogens Isolated From Bovine Milk Samples Between 2008 and 2017 in Ontario, Canada

An understanding of the spatio-temporal distribution of several groups of mastitis pathogens can help to inform programs for the successful control and management of mastitis. However, in the absence of an active surveillance program such information is not readily available. In this retrospective study we analyzed passive surveillance data from a diagnostic laboratory with an aim to describe the spatio-temporal trend of major mastitis pathogens between 2008 and 2017 in Ontario dairy cattle. Data for all milk culture samples submitted to the Animal Health Laboratory (AHL) at the University of Guelph between 2008 and 2017 was accessed. Descriptive analyses were conducted to identify the major pathogens and Chi-square goodness-of-fit tests were used to compare between multiple proportions. Likewise, univariable logistic regression analysis was performed to determine if there was a change in the probability of isolating the major mastitis pathogens depending on geography or time. Seasonality was assessed by calculating the seasonal relative risk (RR). Of a total of 85,979 milk samples examined, more than half of the samples (61.07%) showed no growth and the proportion of samples that showed no growth almost halved during the study period. Of the samples (36.21%, n = 31,133) that showed any growth, the major bacterial pathogens were Staphylococcus aureus (15.60%), Non-aureus Staphylococci (NAS) (5.04%), Corynebacterium spp. (2.96%), and Escherichia coli (2.00%). Of the NAS, the major species reported were Staphylococcus chromogenes (69.02%), Staphylococcus simulans (14.45%), Staphylococcus epidermidis (12.99%), and Staphylococcus hyicus (2.13%). A temporal change in the prevalence of contagious pathogens like S. aureus and Corynebacterium spp. was observed with an increasing odds of 1.06 and 1.62, respectively. Likewise, except for Trueperella pyogenes, the prevalence of all the major environmental mastitis pathogens increased during the study period. The isolation of most of the pathogens peaked in summer, except for S. aureus, T. pyogenes, and Streptococcus dysgalactiae which peaked in spring months. Interestingly, a regional pattern of isolation of some bacterial pathogens within Ontario was also observed. This study showed a marked spatio-temporal change in the prevalence of major mastitis pathogens and suggests that a regional and seasonal approach to mastitis control could be of value.

Secondary Staphylococcus aureus intramammary colonization is reduced by non-aureus staphylococci exoproducts

Non-aureus staphylococci (NAS) and Staphylococcus aureus are pathogens that cause bovine mastitis, a costly disease for dairy farmers, however; many NAS are considered part of the normal udder microbiota. It has been suggested that through a mechanism that remains to be elucidated, NAS intramammary colonization can prevent subsequent infection with other bacterial pathogens. This study shows that in a murine mastitis model, secondary Staph. aureus intramammary colonization is reduced by exoproducts from Staph. chromogenes and Staph. simulans, both NAS, while Streptococcus spp. exoproducts have much less ability to affect the course of the infection caused by S. aureus.

Identification of bovine mastitis pathogens using MALDI-TOF mass spectrometry in Brazil

In this Research Communication we evaluate the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify 380 bacteria isolated from cases of bovine mastitis in Brazil. MALDI-TOF MS identifications were compared to previous identifications by biochemical tests and 16S rRNA sequencing. MALDI-TOF MS achieved a typeability of 95.5%. The accuracy of MALDI-TOF MS for the identification of Staphylococcus isolates was 93.2%. The agreement between MALDI-TOF MS and biochemical identification of Streptococcus agalactiae was 96%, however, the agreement between these techniques for identifying other catalase-negative, Gram-positive cocci was lower. Agreement in identifying Gram-negative bacteria at the genus level was 90.5%. Our findings corroborate that MALDI-TOF MS is an accurate, rapid and simple technique for identifying bovine mastitis pathogens. The availability of this methodology in some research institutions would represent a significant step toward increasing the diagnosis and epidemiological studies of bovine mastitis and other animal infectious diseases in Brazil.

Invited review: The welfare of dairy cattle housed in tiestalls compared to less-restrictive housing types: A systematic review

Many dairy cattle worldwide are housed in tiestalls, meaning that they are tethered by the neck to individual stalls. On some farms, tied cattle are permitted seasonal access to pasture, but otherwise their movements are restricted compared with cows housed in freestall barns or other loose housing systems. The aim of this systematic review is to summarize the scientific literature pertaining the welfare of tied dairy cattle through comparison with less-restrictive housing systems. Articles identified by PubMed and Web of Science underwent a 5-phase screening process, resulting in the inclusion of 102 papers. These papers addressed measures of welfare related to affective state, natural behavior, and health (with the lattermost category subdivided into hoof and leg disorders, lameness, mastitis, transition disease, and other diseases or conditions). Health was the most researched topic (discussed in 86% of articles); only 19% and 14% of studies addressed natural behavior and affective state, respectively. Our review highlights different health benefits for tethered and loose cattle. For example, tied cattle experience reduced prevalence of white line disease and digital dermatitis, whereas loose cattle experience fewer leg lesions and injuries. The prevalence of mastitis, transition diseases, and other conditions did not differ consistently across housing types. We found that the expression of certain natural behaviors, particularly those associated with lying down (e.g., time spent kneeling, unfulfilled intentions to lie down), were impaired in tiestalls. Articles addressing affective state found benefits to loose housing, but these studies focused almost exclusively on (1) physiological measurements and (2) cow comfort, a concept that lacks a consistent operational definition across studies. We call for future research into the affective state of tied cattle that extends beyond these explorations and employs more sophisticated methodologies.

Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems

Simple Summary

New free walk housing systems such as compost-bedded pack barns might positively influence animal welfare. However, udder health can be negatively affected due to the microbial environment in the pack. Udder health depends on many factors, such as the environment, the feed, the pathogen species, and the genetic mechanisms of the cow’s immune system. For a more precise evaluation of udder health, we examined novel traits including specific mastitis pathogens and differential somatic cell fractions in milk. In order to identify possible candidate genes for udder health, a genome-wide association study, including single-nucleotide polymorphisms (SNP) by housing system interactions (compost-bedded pack barn and conventional cubicle barn), was performed. We identified two potential candidate genes for the interaction effect in relation to udder health. The identified potential candidate gene HEMK1 (HemK methyltransferase family member 1) is involved in immune system development, and CHL1 (cell adhesion molecule L1 like) has an immunosuppressive effect during stress conditions. The results suggest housing system-specific breeding strategies in order to improve udder health in compost-bedded pack and conventional cubicle barns.

Abstract

The aim of the present study was to detect significant SNP (single-nucleotide polymorphism) effects and to annotate potential candidate genes for novel udder health traits in two different farming systems. We focused on specific mastitis pathogens and differential somatic cell fractions from 2198 udder quarters of 537 genotyped Holstein Friesian cows. The farming systems comprised compost-bedded pack and conventional cubicle barns. We developed a computer algorithm for genome-wide association studies allowing the estimation of main SNP effects plus consideration of SNPs by farming system interactions. With regard to the main effect, 35 significant SNPs were detected on 14 different chromosomes for the cell fractions and the pathogens. Six SNPs were significant for the interaction effect with the farming system for most of the udder health traits. We inferred two possible candidate genes based on significant SNP interactions. HEMK1 plays a role in the development of the immune system, depending on environmental stressors. CHL1 is regulated in relation to stress level and influences immune system mechanisms. The significant interactions indicate that gene activity can fluctuate depending on environmental stressors. Phenotypically, the prevalence of mastitis indicators differed between systems, with a notably lower prevalence of minor bacterial indicators in compost systems.

Metabolites of bovine-associated non-aureus staphylococci influence expression of Staphylococcus aureus agr-related genes in vitro

Communications via quorum sensing (QS) between non-aureus staphylococci (NAS) and Staphylococcus (S.) aureus in the bovine mammary gland remains largely unexplored. We determined whether 34 S. chromogenes, 11 S. epidermidis, and 14 S. simulans isolates originating from bovine milk samples and teat apices were able to regulate the QS of S. aureus, and if so, how in vitro growth inhibition of S. aureus by NAS, or NAS metabolites, or NAS cells themselves play a role in this process. In co-culture with S. aureus we observed that these 3 NAS species in general downregulated the expression of rnaIII, the effector molecule of the QS system, but this effect was more pronounced in S. chromogenes and S. simulans isolates than in S. epidermidis isolates. In vitro growth inhibition of S. aureus by NAS resulted in a small underestimation of the downregulating effect of NAS on rnaIII expression of S. aureus. Additionally, the culture supernatant of these NAS isolates and supernatant treated with proteinase K expressed greater regulatory activity over S. aureus virulence genes rnaIII, hla, and spa than washed NAS cells suspended in sterile water. These microbial interactions may influence S. aureus virulence and pathogenesis within the host. Isolation and identification of NAS metabolites affecting the QS system of S. aureus might help to develop alternative strategies for treatment and control of S. aureus mastitis.

Changes in the Microbiome of Milk in Cows with Mastitis

Analysis of milk micrbiomes from healthy cows and cows with different (clinical and subclinical) forms of mastitis was performed at two farms of the Central Russia. An increase in the operational taxonomic units (OTUs) of bacteria of the phylum Proteоbacteria belonging primarily to Pseudomonadales, Burkholderiales, as well as Streptococcaceae, Staphylococcaceae, and Bacillaceae in the animals with mastitis was detected. The Planococcaceae OTU percentage decreased. The ratio of rarely presented OTUs also changed in the milk of animals with mastitis.

Non-aureus Staphylococci and Bovine Udder Health: Current Understanding and Knowledge Gaps

Despite considerable efforts to control bovine mastitis and explain its causes, it remains the most costly and common disease of dairy cattle worldwide. The role and impact of non-aureus staphylococci (NAS) in udder health are not entirely understood. These Gram-positive bacteria have become the most frequently isolated group of bacteria in milk samples of dairy cows and are associated with (mild) clinical and subclinical mastitis. Different species and strains of NAS differ in their epidemiology, pathogenicity, virulence, ecology and host adaptation, and antimicrobial resistance profiles. They have distinct relationships with the microbiome composition of the udder and may also have protective effects against other mastitis pathogens. Some appear to persist on the skin and in the teat canal and udder, while others seem to be transient residents of the udder from the environment. Analyzing genotypic and phenotypic differences in individual species may also hold clues to why some appear more successful than others in colonizing the udder. Understanding species-level interactions within the microbiome and its interactions with host genetics will clarify the role of NAS in bovine mastitis and udder health.

The occurrence of methicillin-resistant non-aureus staphylococci in samples from cows, young stock, and the environment on German dairy farms

This study aimed to determine the occurrence of methicillin-resistant (MR) non-aureus staphylococci (NAS) on 20 preselected German dairy farms. Farms were selected based on the detection of methicillin-resistant Staphylococcus aureus (MRSA) during previous diagnostic investigations. Bacterial culture of presumptive MR-NAS was based on a 2-step enrichment method that has been recommended for MRSA detection. Quarter milk samples (QMS), bulk tank milk, swab samples from young stock, and environmental samples were collected for bacterial culture. Methicillin-resistant NAS were detected on all study farms. The MR-NAS positive test rate was 3.3% (77/2,347) in QMS, 42.1% (8/19) in bulk tank milk, 29.1% (59/203) in nasal swabs from milk-fed calves, 18.3% (35/191) in postweaning calves, and 7.3% (14/191) in nasal swabs from prefresh heifers. In the environment, MR-NAS were detected in dust samples on 25% (5/20) of the dairy farms as well as in teat liners and suckers from automatic calf feeders. The geometric mean somatic cell count in QMS affected by MR-NAS (183,000 cells/mL) was slightly higher compared with all QMS (114,000 cells/mL). Nine MR-NAS species were identified; Staph. sciuri, Staph. lentus, Staph. fleurettii, Staph. epidermidis, and Staph. haemolyticus were the most common species. In addition, 170 NAS isolates were identified that showed reduced cefoxitin susceptibility (4 mg/L) but did not harbor the mecA or mecC genes. On some farms, similar mobile genetic elements were detected in MR-NAS and MRSA. It was suggested that resistance genes may be transferred between NAS and Staph. aureus on the respective farms.

A comparative study of antimicrobial activity of differently-synthesized chitosan nanoparticles against bovine mastitis pathogens

The greatest concern in dairy farming nowadays is bovine mastitis (BM), which results mainly from bacterial colonization of the mammary gland. Antibiotics are the most widely used strategy for its prevention and treatment, but overuse has led to growing antimicrobial resistance. Pathogens have also developed other mechanisms to persist in the udder, such as biofilm formation and internalization into bovine epithelial cells. New therapies are therefore needed to reduce or replace antibiotic therapies. In a previous study, we found that chitosan nanoparticles (Ch-NPs) have considerable potential for the treatment of BM. The aim of the present study was to evaluate the antimicrobial activity of differently-synthesized Ch-NPs against BM pathogens and their toxicity in bovine cells in vitro, to further explore the attributes of Ch-NPs for the prevention and treatment of intramammary infections. We also looked into their ability to inhibit biofilm formation and prevent the internalization of S. aureus into mammary epithelial cells. Finally, since an interesting approach for BM prevention is to enhance the host's immune response, we studied whether Ch-NPs could promote the release of pro-inflammatory cytokines in mammary epithelial cells. The results reveal that the bactericidal effect of Ch-NPs on BM pathogens and their ability to inhibit biofilm formation are size-dependent, with smaller particles being more efficient. In contrast, their effect on the viability of the cell lines is not size-dependent and all samples tested were non-toxic. The smallest Ch-NPs successfully prevented the internalization of S. aureus into the cells, but did not promote the production of pro-inflammatory cytokines. These findings make it possible to conclude that Ch-NPs are a great bactericidal agent which can prevent the main mechanisms developed by BM pathogens to persist in the udder.

Genetic analysis of pathogen-specific intramammary infections in dairy cows

Mastitis is one of the most common diseases in dairy cattle, causing severe economic losses to dairy farmers. Mastitis usually occurs due to intramammary infection (IMI) caused by a variety of pathogenic bacteria. Although good progress has been made in understanding genetics of pathogen-specific clinical mastitis, studies involving genetic analysis of pathogen-specific IMI are scarce. The overall objective of this study was, therefore, to assess genetic variation of overall and pathogen-specific IMI in nonclinical primiparous and multiparous cows using bacterial culture. Data and milk samples were collected over a 2-yr interval as part of the Canadian Bovine Mastitis Research Network. The final data set contained records of 46,900 quarter milk samples from 3,382 clinically healthy primiparous and multiparous Holstein cows from 84 dairy herds. For the genetic analysis, we considered the following 7 traits: overall IMI, non-aureus staphylococci (NAS) IMI, contagious pathogen IMI, environmental pathogen IMI, major pathogen IMI, minor pathogen IMI and somatic cell score (SCS). Data were analyzed at the quarter level using a threshold-probit model via Gibbs sampling in BLUPF90. Prevalence of IMI traits at the quarter level in multiparous cow from 0 to 400 DIM ranged from 6.8 to 45.5%. Posterior mean of quarter heritability estimates (on the underlying scale, posterior SD in brackets) of overall IMI and pathogen-specific IMI traits ranged from 0.017 to 0.073 (±0.009 to 0.030). Weak to strong genetic correlations [ranging from 0.18 to 0.97 (±0.01 to 0.29)] among pathogen-specific IMI traits and with overall IMI indicated that not all of these traits were genetically similar. Weak to moderate Spearman rank correlations between estimated breeding values for overall IMI and pathogen-specific IMI traits (from 0.31 to 0.87) indicated possible substantial reranking of sires. The percentage of daughters with IMI caused by various pathogen groups ranged from 13 to 80% and from 38 to 94% for the best (10% decile) and worst sires (90% decile) according to their IMI trait-specific estimated breeding values, respectively. Pathogen-specific IMI traits and overall IMI had weak to moderate positive genetic correlations [ranging from 0.11 to 0.81 (±0.11 to 0.22)] with SCS. Therefore, selection for lower SCS will improve resistance to IMI. However, based on the observed weak to moderate rank correlations (0.04 to 0.47) between pathogen-specific IMI traits and SCS, selection for lower SCC will not improve resistance to IMI from every pathogen-specific IMI group in the same manner. Therefore, despite low heritability estimates, there was sizeable genetic variation for pathogen-specific IMI traits, indicating that long-term direct genetic selection for pathogen-specific IMI can improve pathogen-specific IMI resistance.

Distribution of non-aureus staphylococci from quarter milk, teat apices, and rectal feces of dairy cows, and their virulence potential

Non-aureus staphylococci (NAS) are predominantly isolated from bovine milk samples of quarters suffering from subclinical mastitis. They are also abundantly present on dairy cows' teat apices and can be recovered from bovine fecal samples, as recently described. Differences in ecology, epidemiology, effect on udder health, and virulence or protective traits have been reported among the species within this group. The objectives of this study were (1) to describe the species-specific distribution of NAS in 3 bovine-associated habitats, namely quarter milk, teat apices, and rectal feces, and (2) to evaluate the virulence potential of NAS by comparing their distribution in contrasting milk sample strata and the presence of selected virulence genes. A cross-sectional, systematic sampling procedure was followed in 8 dairy herds that participated in the local Dairy Herd Improvement program in Flanders, Belgium. Quarter milk samples (n = 573) were collected from 144 lactating cows in 8 herds. In 5 of the 8 herds, teat apex swabs (n = 192) were taken from 15 lactating cows, before and after milking, and from 18 dry cows. In the same 5 herds, rectal feces were sampled from 80 lactating cows (n = 80), taking into account that a cow could only serve as the source of one type of sample. In addition, milk samples of all clinical mastitis cases were continuously collected during the 1-yr study period from March 2017 to March 2018 in the 8 herds. In total, 1,676 Staphylococcus isolates were phenotypically identified and subjected to MALDI-TOF mass spectrometry. Thirty-three, 98, and 28% of all quarter milk, teat apex, and rectal fecal samples were NAS-positive, respectively, reaffirming the presence of NAS in rectal feces. The overall predominant species in the 3 habitats combined were Staphylococcus haemolyticus, Staphylococcus chromogenes, and Staphylococcus hominis. Four, 16, and 12% of the healthy quarters (quarter milk somatic cell count ≤50,000 cells/mL of milk), quarters with subclinical mastitis (quarter milk somatic cell count >50,000 cells/mL of milk), and quarters with clinical mastitis, respectively, were NAS-positive, suggesting that the potential to cause (mild) clinical mastitis is present among NAS. This was substantiated by comparing the presence of virulence genes of NAS isolates originating from contrasting milk sample strata (healthy quarters and quarters with clinical mastitis).

Heat load increases the risk of clinical mastitis in dairy cattle

The study was aimed at assessing heat load-related risk of clinical mastitis (CM) in dairy cows. Records of CM for the years 2014 and 2015 were obtained from a large conventional dairy farm milking about 1,200 Holstein cows in central Italy. A case of CM was defined by the presence of clinical signs and veterinary confirmation. Quarter milk samples were collected and bacteriological investigated for each CM. Etiological agents were identified and classified as environmental or contagious pathogens. Hourly weather data from the nearest weather station were used to calculate heat load index (HLI). Upper and lower thresholds of HLI, at which the animal accumulates or dissipates heat, were settled and used to measure heat load balance through the accumulated heat load (AHL) model. Zero and positive values of AHL indicate periods of thermo-neutral and heat accumulation, respectively. Each case of CM was associated with HLI-AHL values recorded 5 d before the event. The risk of CM was evaluated using a case-crossover design. A conditional logistic regression model was used to calculate the odds ratio and 95% confidence intervals of CM recorded in thermo-neutral (AHL = 0) or heat load (AHL > 0) days, pooled or stratified for pathogen type (environmental or contagious). Classes of AHL as low (<6.5), medium (6.6-34.9), and high (>35) were included in the model. Other variables included in the model were milk yield as liters (<20, 20-30, and >30), days in milk (<60, 60-150, and >150), and parity (1, 2-3, and >3). A total of 1,086 CM cases were identified from 677 cows. Escherichia coli, Streptococcus spp., and Streptococcus uberis were the environmental pathogens isolated with the highest frequency; Staphylococcus aureus prevailed within contagious species. The analysis of pooled data indicated a significant effect of heat load on the occurrence of CM in the contagious pathogen stratum. Higher milk yield, middle and late stage of lactation, and older parity increased the risk of CM under heat load conditions. However, the association between pathogen type and these factors was not clear because the model provided significant odds ratios within all pathogen categories. The present study provided the first evidence of an association between HLI and CM in dairy cattle and suggested the ability of the AHL model to assess the risk of mastitis associated with heat load.

Evaluation of 4 different teat disinfection methods prior to collection of milk samples for bacterial culture in dairy cattle

The first objective of this study was to determine whether differences would occur among teat end preparation techniques with regard to potential contamination of milk samples collected for bacterial culture. The second objective was to determine whether differences would be detected in genus or species of bacteria isolated from samples collected using the various methods as well as from contaminated or uncontaminated samples. Mammary quarter foremilk samples were collected from lactating dairy cattle at the University of Missouri Foremost Research Dairy Farm (Columbia). Four different teat end preparation methods were used to compare contamination rates in milk samples. Sampling techniques used before milk collection included (1) no preparation, (2) pre-milking disinfection and single-use towel drying of teats only, (3) scrubbing of the teat end with alcohol only, and (4) pre-milking disinfection, single-use towel drying, and scrubbing of the teat end with alcohol. Milk was plated on Columbia blood agar. Cultures were read at 48 h, with the number of morphologically different bacterial colony types quantified and isolated. Isolates were identified using MALDI-TOF mass spectrometry. Median numbers of colony types were compared among groups using Kruskal-Wallis ANOVA with post-hoc pairwise comparisons, and proportional data were compared using the chi-squared test. A total of 168 cows, including 665 quarters, were sampled, and 1,614 isolates resulted. Analysis with MALDI-TOF identified 29 unique genera and 81 unique species among the samples. More contaminated samples occurred in groups 1 and 2 compared with groups 3 and 4. Group 3 had more contaminated samples than group 4. The majority of Pseudomonas spp. isolates were identified within group 2. When applying previously described niches to Staphylococcus spp., environmental species were more likely to be identified among contaminated samples, whereas host-adapted species were more likely to be identified among uncontaminated samples. These data confirm that scrubbing the teat end with alcohol after pre-milking disinfection with an iodine-based teat disinfectant and drying of the teat minimizes contamination of the milk sample.

Fecal non-aureus Staphylococci are a potential cause of bovine intramammary infection

The presence of non-aureus staphylococci (NAS) in bovine rectal feces has recently been described. Similar to other mastitis causing pathogens, shedding of NAS in the environment could result in intramammary infection. The objective of this study was to investigate whether NAS strains present in feces can cause intramammary infection, likely via teat apex colonization. During a cross-sectional study in 5 dairy herds, samples were collected from the habitats quarter milk, teat apices, and rectal feces from 25%, 10%, and 25% of the lactating cows, respectively, with a cow serving as the source of one type of sample only. Samples from clinical mastitis cases were continuously collected during the 1-year study period as well. The 6 most prevalent NAS species, Staphylococcus (S.) chromogenes, S. cohnii, S. devriesei, S. equorum, S. haemolyticus, and S. hominis, were further subtyped by random amplification of polymorphic deoxyribonucleic acid polymerase chain reaction (RAPD-PCR), when the same NAS species was present in the same herd in the three habitats. For S. chromogenes, S. cohnii, S. devriesei, and S. haemolyticus, the same RAPD type was found in rectal feces, teat apices, and quarter milk, indicating that fecal NAS can infect the mammary gland. For S. hominis and S. equorum, we were unable to confirm the presence of the same RAPD types in the three habitats.

The effect of intramammary infection in early lactation with non-aureus staphylococci in general and Staphylococcus chromogenes specifically on quarter milk somatic cell count and quarter milk yield

This longitudinal study aimed to evaluate the impact of subclinical intramammary infection (IMI) with non-aureus staphylococcal (NAS) species in the first 18 d in milk (DIM) on the quarter milk somatic cell count (qSCC) and quarter milk yield (qMY) during the first 4 mo of lactation in Holstein Friesian heifers. Quarter milk samples were collected from 82 heifers from 1 to 4 DIM until 130 DIM on a biweekly (14 d) basis for determination of the qSCC; qMY data were available through the automatic milking systems. The quarter samples collected on the first (1-4 DIM) and second (15-18 DIM) sampling days were used for bacteriological culturing to determine the IMI status. In this study, 324 quarters from 82 heifers were enrolled, of which 68 were NAS-infected at the first sampling day. Only 16 (23.5%) of these quarters were still NAS-infected at the second sampling day, demonstrating the high spontaneous cure rate of these infections shortly after calving; 9 of these 16 cases were infected with the same NAS species. Interestingly, none of the NAS-infected quarters at the first sampling day acquired a new infection with a major pathogen at the second sampling day, whereas 2.3% of the noninfected quarters did. All 102 isolates phenotypically identified as NAS were further identified to the species level. Staphylococcus chromogenes was the most prevalent species on the first (29.4% of all NAS) and second (52.9%) sampling days. Quarters infected with Staph. chromogenes at the first sampling day had a significantly higher qSCC in later lactation than noninfected quarters, whereas this was not true for quarters infected with all other NAS species (i.e., as a group of species). The average daily qMY in the first 4 mo of lactation did not differ between noninfected quarters and quarters infected with Staph. chromogenes or all other NAS species at the first sampling day. Persistently NAS species-infected quarters in the first 18 DIM (i.e., infected with the same NAS species on the first and second sampling days) had the highest qSCC later in lactation, followed by quarters with a new NAS IMI (i.e., noninfected at the first sampling day and infected with NAS at the second sampling day). The qSCC from transiently NAS species-infected quarters (i.e., not infected with the same NAS species at the second sampling day) was not significantly higher in later lactation compared with that in noninfected quarters. The IMI status of quarters in the first 18 DIM, combining culture results at 1 to 4 and 15 to 18 DIM (new, persistent, and transient IMI), was not significantly associated with daily qMY in the first 4 mo after calving. In general, NAS should be considered minor pathogens with no adverse effect on daily qMY in quarters of heifers infected in the first 18 DIM and with a high spontaneous cure rate. Staphylococcus chromogenes was the most prevalent species, causing an increase in qSCC comparable to the level of quarters infected with a major pathogen; Staph. chromogenes caused most infections that persisted through at least the first 18 DIM.

Bayesian estimation of qPCR and bacterial culture accuracy for detection of bovine coagulase-negative staphylococci from milk and teat apex at different test cut-off points

AIM

To primarily estimate the sensitivity (Se) and specificity (Sp) of the commercially available Mastit4 quantitative PCR (qPCR) assay and bacterial culture (BC) for diagnosis of intramammary infections (IMI) and teat apex colonization (TAC) with coagulase-negative staphylococci (CNS) at different cut-offs for qPCR cycle threshold values using Bayesian latent class analysis. A secondary objective was to evaluate two cut-offs of BC for diagnosis of IMI and TAC with CNS.

METHODS AND RESULTS

We randomly selected 13-20 cows with subclinical mastitis from eight dairy herds. Teat skin samples and aseptically collected foremilk samples were collected from the right hindquarters (n = 149) for BC and qPCR analysis. The Se of qPCR was always higher than BC_Se in diagnosis of IMI, however; the Sp of BC was higher than qPCR_Sp . BC_Se and BC_Sp showed no substantial difference between the tested BC cut-offs. In contrast to IMI, estimates of BC and qPCR in diagnosing TAC were different. BC_Se was higher than qPCR_Se at all tested cut-offs, however; qPCR_Sp was higher than BC_Sp .

CONCLUSION

The overall performance of qPCR is higher than BC in the diagnosis of IMI; however, the performance of BC is better than qPCR in diagnosis of TAC. The qPCR and BC are valid diagnostics for bovine IMI with CNS. However, for TAC, both techniques require further investigation to reduce the uncertainty of the true status of the quarter and teat skin.

SIGNIFICANCE AND IMPACT OF THE STUDY

We reported, for the first time, the diagnostic performance of new mastitis technology (Mastit4 PCR) and culture for detection of CNS in milk and nonmilk samples in dairy herds with automatic milking systems. Our findings will improve the interpretation of the test results of culture and qPCR assay and subsequently, will strengthen the control of IMI with CNS in dairy cows.

Staphylococcus debuckii sp. nov., a coagulase-negative species from bovine milk

A novel type strain, designated SDB 2975^T (=CECT 9737^T=DSM 105892^T), of the novel species Staphylococcus debuckii sp. nov. isolated from bovine milk is described. The novel species belongs to the genus Staphylococcus and showed resistance to tetracycline and was oxidase- and coagulase-negative, catalase-positive, and Gram-stain-positive. Phylogenetic relationships of Staphylococcus debuckii SDB 2975^T to other staphylococcal species were inferred from 16S rRNA gene and whole-genome-based phylogenetic reconstruction. The 16S rRNA gene comparisons showed that the strain is closely related to Staphylococcus condimenti (99.73 %), Staphylococcus piscifermentans (99.66 %), Staphylococcus carnosus (99.59 %) and Staphylococcus simulans (98.03 %). Average nucleotide identity (ANI) values between S.taphylococcus debuckii SDB 2975^T and its closely related Staphylococcus species were 83.96, 94.5, 84.03 and 78.09 %, respectively, and digital DNA-DNA hybridization (dDDH) values were 27.70, 58.02, 27.70 and 22.00 %, respectively. The genome of Staphylococcus debuckii SDB 2975^T was sequenced with PacBio and Illumina technologies and is 2 691 850 bp long, has a G+C content of 36.6 mol% and contains 2678 genes and 80 RNAs, including six copies of each5S rRNA, 16S rRNA and 23S rRNA genes. Biochemical profiling and a newly developed PCR assay enabled differentiation of Staphylococcus debuckii SDB 2975^T and three other SDB strains from its closest staphylococcal species. Differentiation was also achieved by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Genes unique to Staphylococcus debuckii were identified and a PCR-based assay was developed to differentiate Staphylococcus debuckii from other staphylococcal species. In conclusion, the results of phylogenetic analysis along with the ANI values <95 %, and dDDH values <70 % from closely related species along with the phenotypic and biochemical characteristics and specific MALDI-TOF profiles demonstrated that Staphylococcus debuckii SDB 2975^T represents a novel species within the genus Staphylococcus, named Staphylococcus debuckii sp. nov. (SDB 2975^T=CECT 9737^T=DSM 105892^T).

Characterization of Staphylococcus Species Isolated from Bovine Quarter Milk Samples

Staphylococcus (S.) aureus is considered as a major mastitis pathogen, with considerable epidemiological information on such infections while the epidemiology of coagulase-negative staphylococci (CNS) is more controversial. The aim of this study was to use matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology for identification of staphylococci isolated from bovine milk at species level and to characterize them in reference to presentation, somatic cell count (SCC), bacterial shedding (cfu) and antimicrobial resistance patterns. A total of 200 staphylococcal isolates (S. aureus n = 100; CNS n = 100) originating from aseptically collected quarter milk samples from different quarters of dairy cows were included in the study. They originated from cases of clinical (CM) and subclinical mastitis (SCM) or were isolated from milk with SCC ≤ 100,000 cells/mL in pure culture. We found staphylococci predominantly in cases of SCM (n = 120). In low-SCC cows, 12 S. aureus and 32 CNS isolates were detected. Eighteen percent of each were associated with CM. Eleven CNS species were identified, S. chromogenes (n = 26) and S. xylosus (n = 40) predominated. CNS, particularly those in low-SCC cows, showed higher MIC90 (minimal inhibitory concentration) values for penicillin, ampicillin, cefoperazone, pirlimycin and marbofloxacin. Based on the present results, a careful interpretation of laboratory results is recommended to avoid antimicrobial therapy of staphylococci without clinical relevance and to ensure prudent use of antimicrobials.

Efficacy of MALDI-TOF mass spectrometry as well as genotypic and phenotypic methods in identification of staphylococci other than Staphylococcus aureus isolated from intramammary infections in dairy cows in Poland

We compared the effectiveness of various methods for the identification of Staphylococcus spp. other than S. aureus isolated from intramammary infections of cows on 3 dairy farms in Lower Silesia, Poland. A total of 131 isolates belonging to 18 Staphylococcus species were identified by sequence analysis of the 16S rRNA and dnaJ genes, as well using a commercial identification system (ID 32 STAPH; bioMérieux) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; Bruker Daltonics). Sequencing of the 16S rRNA gene was found to have low discriminatory value because only 43% of isolates were recognized unequivocally. Much better results were obtained with the dnaJ gene (all isolates were correctly identified at the species level). However, some of these isolates achieved a low similarity level (<97%) and required a confirmatory test (sequencing of the rpoB gene). The performance of ID 32 STAPH was poor. Regardless of the probability level used (80% or 90%), the commercial system obtained identification rates <40%. Using MALDI-TOF MS and the commercial Bruker database, 67% of isolates were identified correctly with scores ≥2.0 (acceptable species-level identification) but this number increased to 97% after the database was expanded. The definitive identification of Staphylococcus spp. other than S. aureus causing intramammary infections in cattle often requires a combination of different procedures, and the existing databases should be updated.