Molecular Typing and Antimicrobial Susceptibility Profiles of Streptococcus uberis Isolated from Sheep Milk

Antimicrobial susceptibility rates in gram-positive catalase-negative cocci from sheep and goat genital microbiota

Gram-positive catalase-negative cocci (GPCNCs) are significant components of the genital microbiota in sheep and goats. However, characterizing them can be difficult due to overlapping culture features and the limited information on their susceptibility to antibiotics. In this study, 97 foreskin and 13 vaginal swabs were investigated using a culturomic approach. Of 110 animals, 76 (69.09 %) hosted GPCNCs, including strains from Streptococcaceae (37, 33.64 %), Aerococcaceae (30, 27.27 %), Enterococcaceae (6, 5.45 %) and other minor species. With increasing antimicrobial resistance rates in livestock, surveillance programs are globally required, so we conducted a pilot study on GPCNCs isolated from the genital mucosa surfaces of sheep and goats using the minimal inhibitory concentration assay (MIC). Due to gaps in interpretative standard breakpoints, normalized resistance interpretation was used for setting epidemiological susceptibility cut-off values (COWTs). Of 57 suitable strains, the majority (80.71 %) showed high COWTs with decrease susceptibility to at least one antimicrobial class, with 22.81 % displaying multiresistant profiles. Of interest, combined resistances to beta-lactams, macrolides, lincosamides, and tetracyclines were detected in strains of Streptococcus plurianimalium. Further combinations, including resistance to beta-lactams, pleuromutilins, aminoglycosides, and lincosamides, were also recorded in both Streptococcus uberis and Enterococcus spp. strains. Being beta-lactams, macrolides, and tetracyclines the most used antibiotics in livestock worldwide, our results highlight the need for their prudent use. Collectively, our findings highlight that small ruminant genital microbiota can serve as reservoirs for opportunistic severe pathogens, often zoonotic, carrying multidrug resistances, thus standing for high risks for both animals and humans.

Antimicrobial resistance patterns of Streptococcus uberis isolates from bovine milk in Chiba prefecture, Japan: association between multidrug resistance and clonal complex 996

Streptococcus uberis is one of major pathogens causing bovine mastitis. However, there is poor information on antimicrobial resistance (AMR) among the Japanese isolates. To provide treatment information for the mastitis caused by S. uberis in Japan, we aimed to clarify AMR patterns of the isolates from bovine milk mainly in Chiba. AMR phenotyping/genotyping [blaZ-erm(A)-erm(B)-mef(A)-linB-lnuD-tet(M)-tet(O)-tet(K)-tet(L)-tet(S)] and multilocus sequence typing were performed to analyze relationships between AMR patterns and clonal complexes (CCs). Resistance to tetracycline-, macrolide-, and lincosamide-classes was mainly associated with possession of tet(O), tet(S), erm(B), linB, and lnuD genes. CC996 was significantly associated with multidrug resistance (P<0.0001). These findings will aid Chiba farm animal clinics in treating bovine mastitis.

A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen

Streptococcus uberis is a globally endemic and poorly controlled cause of bovine mastitis impacting the sustainability of the modern dairy industry. A core genome was derived from 579 newly sequenced S. uberis isolates, along with 305 publicly available genome sequences of S. uberis isolated from 11 countries around the world and used to develop a core genome multi-locus sequence typing (cgMLST) scheme. The S. uberis core genome comprised 1475 genes, and these were used to identify 1447 curated loci that were indexed into the cgMLST scheme. This was able to type 1012 of 1037 (>97  %) isolates used and differentiated the associated sequences into 932 discrete core genome sequence types (cgSTs). Analysis of the phylogenetic relationships of cgSTs revealed no clear clustering of isolates based on metadata such as disease status or year of isolation. Geographical clustering of cgSTs was limited to identification of a UK-centric clade, but cgSTs from UK isolates were also dispersed with those originating from other geographical regions across the entire phylogenetic topology. The cgMLST scheme offers a new tool for the detailed analysis of this globally important pathogen of dairy cattle. Initial analysis has re-emphasized and exemplified the genetically diverse nature of the global population of this opportunistic pathogen.

Seroprevalence and risk factors of Streptococcus ovis infection in Tibet, China

Sheep septicemic streptococcosis is an acute, febrile, and septic zoonotic disease caused by Streptococcus ovis. There are few reports of this disease especailly at high-altitude areas of Tibet, China. A cross-sectional study was conducted at five different counties of Shigatse area (a city in Tibet territory) from 2021 to 2022. Sera from 1458 randomly selected sheep and goats from 50 flocks were tested for antigens of Streptococcus ovis using a commercial ELISA kit. The individual animal level prevalence was 6.93% (95% CI: 5.7-8.4), and the flock prevalence level was 84% (95% CI: 70.9-92.8). At the individual animal level, year and management type were significantly associated with seropositivity by binary logistic regression analysis. Prevalence of Streptococcus in 2021 significantly differed from 2022 (OR = 2.16, 95% CI: 1.39-3.39). The prevalence of Streptococcus varied between management types with herds having higher odds of disease than intensive farms (OR = 2.64, 95% CI: 1.71-4.10). Hence, our study reports for the first time on seroepidemiology and risk factors of Streptococcus ovis infection, laying a theoretical foundation for preventing and controlling streptococcosis in Tibet area.

Evaluation of Streptococcus species isolated from subclinical sheep mastitis by molecular methods and determination of virulence factors and antimicrobial resistance genes

Streptococcus (S.) species are important pathogens that cause mastitis in sheep. The study aimed to examine Streptococcus species in sheep milk with subclinical mastitis, assessing their prevalence, antimicrobial resistance, and virulence genes. A total of 200 milk samples were collected from sheep farms in İzmir's five districts. Out of 32 (28.6%) Streptococcus isolates identified by phenotypic methods, 25 were genotypically identified as S. uberis, 5 as S. agalactiae, and 2 as S. dysgalactiae. Disk diffusion was used to determine the antimicrobial resistance of the isolates. PCR was employed to identify antimicrobial resistance and virulence genes in the isolates. The highest resistance was found for cloxacillin (100%), and the highest sensitivity was found for florfenicol (84%). The most common resistance gene combination was tetM+tetS (3/32) for S. uberis in 9.4%. A total of five virulence genes were detected. GapC+sua (56.2%) constituted the most common gene pattern. The highest virulence gene gapC was detected in 78.1% (25/32) of the isolates. The cylE gene was not detected (0%) in the isolates. Streptococcus species may play a role in mastitis in sheep, emphasising the need for meticulous hygienic milking practices.

Genomic surveillance reveals antibiotic resistance gene transmission via phage recombinases within sheep mastitis-associated Streptococcus uberis

Background

Streptococcus uberis is one of the main causative agents of ovine mastitis, however little is known about this global, environmental pathogen and its genomic mechanisms of disease. In this study, we performed genomic analysis on 46 S. uberis isolates collected from mastitis-infected sheep in Sardinia (Italy).

Results

Genomes were assigned into lineage clusters using PopPUNK, which found 27 distinct isolate clusters, indicating considerable genetic variability consistent with environmental isolates. Geographic trends were identified including regional linkage of several isolate clusters. Multi-locus Sequence Typing (MLST) performed poorly and provided no new insights.

Genomes were then screened for antimicrobial resistance genes, which were compared to phenotypic resistance profiles. Isolates showed consistent phenotypic resistance to aminoglycosides with variable resistance to novobiocin and tetracycline. In general, identification of antimicrobial resistance genes did not correlate with phenotypic resistance profiles, indicating unknown genetic determinants. A multi-antimicrobial resistance cassette (aminoglycoside, lincosamide and streptogramin) was identified in the chromosome of three genomes, flanked by vestigial phage recombinases. This locus appears to have spread horizontally within discrete S. uberis populations within a 40 km radius (Sassari region).

Genomes were screened for putative virulence factors, which identified 16 genes conserved between sheep and cow isolates, with no host-specific genes shared uniformly across all host-specific isolates.

Pangenomic analysis was then performed to identify core genes which were putatively surface-exposed, for identification of potential vaccine targets. As all genomes encoded sortase, core genes were screened for the sortase cleavage motif. Of the 1445 core S. uberis genes, 64 were putative sortase substrates and were predominantly adhesins, permeases and peptidases, consistent with compounds found within ruminant milk such as xanthine, fibronectin and lactoferrin.

Conclusions

This study demonstrated the importance of whole genome sequencing for surveillance of S. uberis and tracking horizontal acquisition of antimicrobial resistance genes, as well as providing insight into genetic determinants of disease, which cannot be inferred from the MLST schemes. Future mastitis surveillance should be informed by genomic analysis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03341-1.