Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis

Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites

BACKGROUND

Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated.

RESULTS

The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms.

CONCLUSIONS

Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.

Staphylococcus borealis - A newly identified pathogen of bovine mammary glands

Twelve Staphylococcus borealis strains, isolated in Canada and Poland from milk of cows with intramammary infections, were characterized phenotypically (biochemical reactions on ID 32 STAPH and Biolog Phenotype MicroArrays™ PM1 and PM2A, ability of biofilm production) and genotypically (random amplified polymorphic DNA). In addition, a genomic comparison was done with S. borealis strains of human and porcine origin using the multilocus sequence typing (MLST) technique. The bovine isolates showed a high degree of phenotypic and genotypic diversity, however, they could be differentiated from human strains by the negative test for urease (found in all but one bovine isolate examined with ID 32 STAPH) and positive reaction for D-galactose (on Biolog phenotype microarray PM1) and D-lactose (on both commercial systems). The MLST method, utilizing six concatenated genes of the total length of ∼2930 bp, revealed that bovine strains (irrespective of the country of origin) show a distinctly greater degree of mutual relationship than to the strains of human and porcine origin, suggesting that S. borealis has evolved independently in these hosts. In conclusion, bovine-specific S. borealis can be involved in intramammary infections in cattle.

Streptococcus sciuri sp. nov., Staphylococcus marylandisciuri sp. nov. and Staphylococcus americanisciuri sp. nov., isolated from faeces of eastern grey squirrel (Sciurus carolinensis)

One novel Streptococcus strain (SQ9-PEAT) and two novel Staphylococcus strains (SQ8-PEAT and GRT3T) were isolated from faeces of a wild eastern grey squirrel. The strains were non-spore-forming, non-motile Gram-positive cocci, facultative anaerobes. The genomes for these strains were sequenced. The 16S rRNA gene and core-genome-based phylogenetic analyses showed that strain SQ9-PEAT was closely related to Streptococcus hyointestinalis, strain SQ8-PEAT to Staphylococcus pettenkoferi and Staphylococcus argensis, and strain GRT3T to Staphylococcus rostri, Staphylococcus muscae and Staphylococcus microti. Average nucleotide identity and pairwise digital DNA-DNA hybridization values calculated for these novel strains compared to type strain genomes of phylogenetically related species within the genera Streptococcus and Staphylococcus clearly revealed that strain SQ9-PEAT represents a novel species of the genus Streptococcus and strains SQ8-PEAT and GRT3T represent two novel species of the genus Staphylococcus. Phenotypical features of these novel type strains differed from the features of the type strains of other phylogenetically related species. MALDI-TOF mass spectrometry supported identification of these novel species. Based on these data, we propose one novel species of the genus Streptococcus, for which the name Streptococcus sciuri sp. nov. with the type strain SQ9-PEAT (=DSM 114656T=CCUG 76426T=NCTC 14727T) is proposed, and two novel species of the genus Staphylococcus, for which the names Staphylococcus marylandisciuri sp. nov. with the type strain SQ8-PEAT (=DSM 114685T=CCUG 76423T=NCTC 14723T) and Staphylococcus americanisciuri sp. nov. with the type strain GRT3T (=DSM 114696T=CCUG 76427T=NCTC 14722T) are proposed. The genome G+C contents are 38.29, 36.49 and 37.26 mol% and complete draft genome sizes are 1 692 266, 2 371 088 and 2 237 001 bp for strains SQ9-PEAT, SQ8-PEAT and GRT3T, respectively.

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.

Molecular Mechanism of Staphylococcus xylosus Resistance Against Tylosin and Florfenicol

Purpose

Drug resistance presents an ever-increasing global public health threat that involves all major microbial pathogens and antimicrobial drugs. Strains that are resistant to multiple drugs pose severe clinical problems and cost lives. However, systematic studies on cross-resistance of Staphylococcus xylosus have been missing.

Methods

Here, we investigated various mutations in the sequence of ribosomal proteins involved in cross-resistance. To understand this effect on a molecular basis and to further elucidate the role of cross-resistance, we computationally constructed the 3D model of the large ribosomal subunit from S. xylosus as well as its complexes with both tylosin and florfenicol. Meanwhile, all-atom molecular dynamics simulations was used. In addition, the regulation of protein networks also played an essential role in the development of cross-resistance in S. xylosus.

Results

We discovered that the minimum inhibitory concentration against both tylosin and florfenicol of the mutant strain containing the insertion L22 97KRTSAIN98 changed dramatically. Further, we found that unique structural changes in the β-hairpin of L22 played a central role in this variant in the development of antibiotic resistance in S. xylosus. The regulation of protein networks also played an essential role in the development of cross-resistance in S. xylosus.

Conclusion

Our work provides insightful views into the mechanism of S. xylosus resistance that could be useful for the development of the next generation of antibiotics.

Safety and Technological Characterization of Staphylococcus xylosus and Staphylococcus pseudoxylosus Isolates from Fermented Soybean Foods of Korea

We evaluated the antibiotic susceptibilities, hemolytic activities, and technological properties of 36 Staphylococcus xylosus strains and 49 S. pseudoxylosus strains predominantly isolated from fermented soybean foods from Korea. Most of the strains were sensitive to chloramphenicol, erythromycin, gentamycin, kanamycin, lincomycin, oxacillin, tetracycline, and trimethoprim. However, 23 strains exhibited potential phenotypic acquired resistance to erythromycin, lincomycin, and tetracycline. Based on breakpoint values for staphylococci from the Clinical and Laboratory Standards Institute, >30% of the isolates were resistant to ampicillin and penicillin G, but the population distributions in minimum inhibitory concentration tests were clearly different from those expected for acquired resistance. None of the strains exhibited clear α- or β-hemolytic activity. S. xylosus and S. pseudoxylosus exhibited salt tolerance on agar medium containing 20% and 22% (w/v) NaCl, respectively. S. xylosus and S. pseudoxylosus strains possessed protease and lipase activities, which were affected by the NaCl concentration. Protease activity of S. pseudoxylosus was strain-specific, but lipase activity might be a characteristic of both species. This study confirms the potential of both species for use in high-salt soybean fermentation, but the safety and technological properties of strains must be determined to select suitable starter candidates.

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.

Evolutionary and Functional Analysis of Coagulase Positivity among the Staphylococci

The bacterial genus Staphylococcus comprises a large group of pathogenic and nonpathogenic species associated with an array of host species. Staphylococci are differentiated into coagulase-positive or coagulase-negative groups based on the capacity to promote clotting of plasma, a phenotype historically associated with the ability to cause disease. However, the genetic basis of this important diagnostic and pathogenic trait across the genus has not been examined to date. Here, we selected 54 representative staphylococcal species and subspecies to examine coagulation of plasma derived from six representative host species. In total, 13 staphylococcal species mediated coagulation of plasma from at least one host species including one previously identified as coagulase negative (Staphylococcus condimenti). Comparative genomic analysis revealed that coagulase activity correlated with the presence of a gene (vwb) encoding the von Willebrand binding protein (vWbp) whereas only the Staphylococcus aureus complex contained a gene encoding staphylocoagulase (Coa), the classical mediator of coagulation. Importantly, S. aureus retained vwb-dependent coagulase activity in an S. aureus strain deleted for coa whereas deletion of vwb in Staphylococcus pseudintermedius resulted in loss of coagulase activity. Whole-genome-based phylogenetic reconstruction of the Staphylococcus genus revealed that the vwb gene has been acquired on at least four different occasions during the evolution of the Staphylococcus genus followed by allelic diversification via mutation and recombination. Allelic variants of vWbp from selected coagulase-positive staphylococci mediated coagulation in a host-dependent manner indicative of host-adaptive evolution. Taken together, we have determined the genetic and evolutionary basis of staphylococcal coagulation, revealing vWbp to be its archetypal determinant. IMPORTANCE The ability of some species of staphylococci to promote coagulation of plasma is a key pathogenic and diagnostic trait. Here, we provide a comprehensive analysis of the coagulase positivity of the staphylococci and its evolutionary genetic basis. We demonstrate that the von Willebrand binding protein rather than staphylocoagulase is the archetypal coagulation factor of the staphylococci and that the vwb gene has been acquired several times independently during the evolution of the staphylococci. Subsequently, vwb has undergone adaptive diversification to facilitate host-specific functionality. Our findings provide important insights into the evolution of pathogenicity among the staphylococci and the genetic basis for a defining diagnostic phenotype.

Staphylococcus caledonicus sp. nov. and Staphylococcus canis sp. nov. isolated from healthy domestic dogs

Two strains, H8/1^T and H16/1A^T, of Gram-stain-positive, coagulase-negative staphylococci were isolated from separate healthy domestic dogs in Scotland. Both strains were genome sequenced and their inferred DNA–DNA hybridisation indicates that H8/1^T and H16/1A^T represent two novel species of the genus Staphylococcus. On the basis of the results of genome sequence analysis (genome blast distance phylogeny and single nucleotide polymorphism analysis) H8/1^T is most closely related to Staphylococcus devriesei and H16/1A^T most closely related to Staphylococcus felis. Also, average nucleotide identity distinguished H8/1^T and H16/1A^T from S. devriesei and S. felis as did minor phenotypic differences. On the basis of these results, it is proposed that H8/1^T and H16/1A^T represent novel species with the respective names Staphylococcus caledonicus and Staphylococcus canis. The type strain of S. caledonicus is H8/1^T (=NCTC 14452^T=CCUG 74789^T). The type strain of S. canis is H16/1A^T (=NCTC 14451^T=CCUG 74790^T)

Update on Coagulase-Negative Staphylococci-What the Clinician Should Know

Coagulase-negative staphylococci (CoNS) are among the most frequently recovered bacteria in routine clinical care. Their incidence has steadily increased over the past decades in parallel to the advancement in medicine, especially in regard to the utilization of foreign body devices. Many new species have been described within the past years, while clinical information to most of those species is still sparse. In addition, interspecies differences that render some species more virulent than others have to be taken into account. The distinct populations in which CoNS infections play a prominent role are preterm neonates, patients with implanted medical devices, immunodeficient patients, and those with other relevant comorbidities. Due to the property of CoNS to colonize the human skin, contamination of blood cultures or other samples occurs frequently. Hence, the main diagnostic hurdle is to correctly identify the cases in which CoNS are causative agents rather than contaminants. However, neither phenotypic nor genetic tools have been able to provide a satisfying solution to this problem. Another dilemma of CoNS in clinical practice pertains to their extensive antimicrobial resistance profile, especially in healthcare settings. Therefore, true infections caused by CoNS most often necessitate the use of second-line antimicrobial drugs.

Evaluation of Surrogate Tests for the Presence of mecA-Mediated Methicillin Resistance in Staphylococcus capitis, Staphylococcus haemolyticus, Staphylococcus hominis, and Staphylococcus warneri

Testing of staphylococci other than Staphylococcus aureus (SOSA) for mecA-mediated resistance is challenging. Isolates of Staphylococcus capitis, Staphylococcus haemolyticus, Staphylococcus hominis, and Staphylococcus warneri were evaluated by cefoxitin and oxacillin broth microdilution (BMD), disk diffusion (DD), and PBP2a immunoassay, and the results were compared to mecA PCR results. No phenotypic susceptibility test correlated well with PCR results across all species, although the PBP2a immunoassay yielded 100% correlation. Oxacillin BMD testing by current Clinical and Laboratory Standards Institute (CLSI) SOSA breakpoints led to 2.1% very major errors (VMEs) and 7.1% major errors (ME). Adjusting this breakpoint up by a dilution (susceptible, ≤0.5 μg/ml; resistant, ≥1.0 μg/ml) led to 2.8% VMEs and 0.3% MEs. Among species evaluated, S. haemolyticus had unacceptable VMEs with this new breakpoint (6.4%), as did S. hominis (4.0%). MEs were acceptable by this new breakpoint, ranging from 0 to 1.2%. Oxacillin DD yielded high ME rates (20.7 to 21.7%) using CLSI or European Committee on Antimicrobial Susceptibility Testing breakpoints. VMEs ranged from 0 to 5.3%. Cefoxitin BMD led to 4.9% VMEs and 1.6% MEs. Cefoxitin DD performed best when interpreted with the CLSI SOSA breakpoint, with 1.0% VMEs and 2.9% MEs. This study led CLSI to adjust the oxacillin MIC breakpoints for SOSA. Laboratories should be aware that no individual phenotypic test correlates well across all species of SOSA with mecA PCR results. Molecular testing for mecA or evaluation for PBP2a is the preferred approach.

Prevalence and characterisation of methicillin-resistant staphylococci from bovine bulk tank milk in England and Wales

OBJECTIVES

To investigate the prevalence and characteristics of methicillin-resistant staphylococci on dairy farms in England and Wales including zoonotic MRSA.

METHODS

Bulk tank milk was sampled from 363 dairy farms in 2015-2016 and methicillin-resistant staphylococci were isolated by salt broth enrichment and plating on MRSA Brilliance selective agar. Isolates were characterised through antimicrobial susceptibility testing and whole-genome sequencing.

RESULTS

Methicillin-resistant staphylococci were isolated from ∼5% of dairy farms and belonged to six different species, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lentus, Staphylococcus saprophyticus, Staphylococcus fleurettii and Staphylococcus sciuri. Whole-genome sequencing revealed a large variety of antimicrobial resistance genes and SCCmec elements were present, including mecA and mecC alleles. Potentially zoonotic methicillin-resistance S. aureus were found at a low prevalence (0.83% of sampled dairy farms). Whole-genome sequencing also provided evidence for the mobility of a primordial mec gene complex, independently of a SCCmec element, which appears to have been acquired by S. saprophyticus from S. fleurettii.

CONCLUSIONS

These data give new insight into the epidemiology of veterinary methicillin-resistant staphylococci to inform future surveillance and zoonotic risk evaluation. Our data indicate that MRSA has likely decreased in prevalence since earlier survey work in England and Wales during 2011-12 and highlights the diversity of methicillin resistance and other resistance determinants among bovine-associated staphylococci with implications for veterinary and human medicine.

Genomic epidemiology of methicillin-resistant Staphylococcus sciuri carrying a SCCmec-mecC hybrid element

The recognition in 2011 of the methicillin resistance determinate mecC among staphylococci has raised many questions over its evolution and epidemiology. While mecC has been best studied in Staphylococcus aureus it has also been described in at least nine other species of staphylococci. In most cases these studies are limited to single isolates. In the widespread animal commensal Staphylococcus sciuri mecC has been described in two isolates and is located within a distinct SCCmec-mecC composite element. In this study, a further 11 mecA/mecC S. sciuri isolated from dairy farms in England and Wales in 2015 and 2016 were genome sequenced and characterised. The results show that two variants of the SCCmec-mecC element are present in S. sciuri, differentiated by different ccr alleles and likely to have arisen by homologous recombination. A phylogeny of sixty genome-sequenced S. sciuri isolates was made using core genome multi-locus sequence typing and reveals a diverse population with the SCCmec-mecC element present in four distinct branches, indicative of four independent acquisitions by S. sciuri. Finally, the study identified the rapid clonal expansion of a mecA/mecC lineage of S. sciuri among dairy farms across a wide geographical area which may contribute to the future dissemination of this methicillin resistance cassette.