Staphylococcus chromogenes and Staphylococcus simulans are commonly found in intramammary infections (IMI) associated with bovine subclinical mastitis, but little is known about genotypic variation and relatedness within species. This includes knowledge about genes encoding antimicrobial resistance (AMR) and potential virulence factors (pVF). The aim of this study was therefore to investigate these aspects by whole-genome sequencing of milk isolates from Swedish dairy cows with subclinical mastitis in an observational study. We also wanted to study if specific genotypes were associated with persistent IMI and the inflammatory response at udder quarter level. In total, 105 and 118 isolates of S. chromogenes and S. simulans, respectively, were included. Isolates were characterized using a 7-locus multilocus sequence typing (7-MLST), core genome analysis and in-silico analysis of AMR and pVF genes. Forty-seven sequence types (ST) and 7 core genome clusters of S. chromogenes were identified, and the most common ST were ST-6 and ST-109, both belonging to cluster VII. A 7-locus MLST scheme for S. simulans was not available, but 3 core genome clusters and 5 subclusters were described. Overall, substantial variation in ST and clusters among cows and herds were found in both species. Some ST of S. chromogenes were found in several herds, indicating spread between herds. Moreover, within-herd spread of the same genotype was observed for both species. Only a few AMR genes (blaZ, str_pS194, vga(A)) were detected in a limited number of isolates, with the exception of blaZ coding for β-lactamase, which was identified in 22% of the isolates of S. chromogenes with ST-19, ST-102, and ST-103 more commonly carrying this gene compared with other STs. However, the blaZ gene was not identified in S. simulans. The average total number of pVF detected per isolate was similar in S. chromogenes (n = 30) and S. simulans (n = 33), but some variation in total numbers and presence of specific pVF or functional groups of pVF, was shown between ST/clusters within species. Differences in inflammatory response and potentially in persistent IMI at udder quarter level were found between S. chromogenes subtypes but not between S. simulans subtypes. In conclusion, the results from the present study generates new insight into the epidemiology of bovine S. chromogenes and S. simulans IMI, which can have implications for future prevention and antimicrobial treatment of infections related to these species.

Background/Objectives: Staphylococcus pseudintermedius is part of the normal microbiota in dogs. Since 2006, an increase in multidrug-resistant clones of methicillin-resistant S. pseudintermedius has been reported, as well as zoonotic transmission. Longitudinal investigations into clonal population structures, antibiotic resistance patterns, and the presence of resistance and virulence genes are important tools for gaining knowledge of the mechanisms behind the emergence of such clones. Methods: We investigated 87% of all non-repetitive MRSP isolates from dogs and cats in Sweden over a ten-year period (n = 356). All isolates were subjected to staphylococcal chromosomal cassette mec identification, whole-genome sequencing, multi-locus sequence typing, and analyses of genomic relatedness, as well as investigation of phenotypical resistance patterns and the presence of antibiotic resistance genes and virulence genes. Results: A considerable increase over time in the number of clonal lineages present was observed, indicating genomic diversification, and four clones became dominant: ST71, ST258, ST265, and ST551. In total, 96% of the isolates were multidrug-resistant. Statistically significant differences in resistance to several antibiotic classes between the four dominant clones were present. All isolates carried several virulence genes encoding factors associated with attachment, colonization, toxin synthesis, quorum sensing, antibiotic resistance, and immune evasion.

This study aimed to investigate the diversity of milk isolates of Streptococcus uberis from Swedish dairy cows with mastitis, focusing on antibiotic resistance and virulence genes. We analyzed 115 S. uberis isolates using whole genome sequencing revealing a high level of diversity. Within the same farms, we identified both indistinguishable strains with identical sequence types (ST), and distinct isolates belonging to different ST types. This suggests both clonal and non-clonal spread of the bacterium, although primarily non-clonal. We found small clusters of two to eight closely related isolates both within and between farms. Differences in penicillin susceptibility were observed, probably linked to specific variants of penicillin-binding proteins. Few isolates were resistant to antibiotics, and few resistance genes were detected. In most cases, only one or two resistance genes were present, and only one isolate was multi-drug resistant. Two isolates had resistance genes against tetracyclines, a tet(M) and a tet(O) gene, two had a resistance gene against lincosamides, an lnu(C) and an lnu(D) gene, while a single isolate had an erm(B) gene conferring resistance to both macrolides and lincosamides. A single isolate carried a mef(A) gene, which confers resistance to macrolides via an efflux pump mechanism. However, we found aminoglycoside genes in 10 isolates, all 10 had the ant(6)-Ia gene, and one in addition aph(3')-IIIa, and a spectinomycin resistance gene, spw, in eight isolates. Finally, one isolate carried a streptothricin resistance gene, sat4. The genes sat4 and spw have apparently not previously been reported in S. uberis. Interestingly, isolates with elevated MIC to penicillin also significantly more often carried other resistance factors. Most isolates carried several virulence genes, including genes for capsule formation, adhesion to host cells or extracellular matrix proteins, and acquisition of essential nutritional factors, such as amino acids, iron and manganese.

This short communication addresses the hypothesis that the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) is low in dairy goats in Sweden. Methicillin-resistant S. aureus is a widespread zoonotic bacterium of clinical importance in both animals and humans. In Sweden, MRSA is rare among both animals and humans. However, MRSA has been detected in a few goat herds in Sweden with a high within-herd occurrence of mecC-MRSA, but only a limited number of herds were investigated and most of them were not producing milk for human consumption. The prevalence of MRSA among dairy goat herds in Sweden is not known and a cross-sectional prevalence study was therefore conducted. A total of 22 bulk milk samples from the same number of herds, and pooled swabs from nose, mouth, and perineum from 113 goats, were collected during August and September 2019 for bacteriological investigation. After culturing on selective media, suspected isolates were confirmed as S. aureus using MALDI-TOF and subjected to PCR targeting the mecA and mecC genes to confirm MRSA status. No samples were found to be positive for MRSA, and there are therefore no indications of a spread of MRSA in Swedish dairy goat herds.

This manuscript presents the phylogeny and conservation of IncK2 plasmids in Europe. It also provides insights into genetic traits responsible for IncK2 plasmids and its Escherichia coli host adaptation to the chicken gut. Fifty-eight E. coli isolates from nine European countries were sequenced using Illumina and Nanopore technology. Genetic analyses were performed to determine the relatedness of IncK2 plasmids and their E. coli hosts from poultry (80% of the total) and other sources. To analyse genetic traits associated with E. coli and IncK2 plasmid from chicken origin, a genome-wide association study (GWAS) was performed. The phylogenetic analysis of IncK2 plasmids revealed conservation across sources and countries of isolation. GWAS revealed multiple genes associated with IncK2 plasmids or its E. coli host from chicken origin. The predicted functions of these genes can indicate a selective advantage in the chicken gut, and that IncK2 plasmids are adapted to the physiological environment of the chicken gut.