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Schweizer Archiv Fur Tierheilkunde Feb 2022The prevalence of methicillin-resistant Macrococcus spp. in calves and pigs at slaughterhouses and in retail beef and pork meat was determined using samples taken in...
The prevalence of methicillin-resistant Macrococcus spp. in calves and pigs at slaughterhouses and in retail beef and pork meat was determined using samples taken in 2019 within the framework of the national monitoring of methicillin-resistant Staphylococcus aureus in food producing animals in Switzerland. The isolates were submitted to antimicrobial susceptibility testing of 19 antibiotics and to molecular techniques (e.g. PCR, microarray, WGS) for the identification of resistance genes, elements containing the methicillin resistance genes mec and sequence type (ST). Methicillin-resistant Macrococcus spp. (M. caseolyticus (n=38), M. bohemicus (n=4) and Macrococcus spp. (n=2)) were isolated in 40 of 299 nasal swabs from calves representing a prevalence of 13,38 % (95 % CI, 9,98 % - 17,70 %), and in four of 303 nasal swabs from pigs [1,32 % (95 % CI, 0,36 % - 3,35 %)]. One of 311 samples of Swiss pork meat contained a Macrococcus sp. [0,32 % (95 % CI, 0,01 % - 1,78 %)], and four of 309 beef meat samples (260 domestic and 49 imported) contained M. caseolyticus [1,29 % (95 % CI, 0,35 % - 3,28 %)]. The M. caseolyticus strains belonged to diverse STs, with ST21 being the most common in both pigs and calves. The mecD gene was located on Macrococcus resistance island mecD (McRImecD) in 42 strains and on staphylococcal cassette chromosome mec (SCCmecD) in three strains, while mecB was found on plasmids in four strains. In addition to resistance to β-lactams, the strains also exhibited resistance to tetracycline (n=17; tet(L), tet(K), tet(M)), streptomycin (n=13; str, ant(6)-Ia, rpsL mutation [K56R in ribosomal protein S12]), kanamycin (n=10; aac(6')-Ie - aph(2'')-Ia, aph(2')-Ib, aph(2')-Ic, ant(4')-Ia), clindamycin (n=9; erm(B), erm(45)), erythromycin (n=9; erm(B), msr(G), erm(45)), fusidic acid (n=9; fusC) and gentamicin (n=1; aac(6')-Ie - aph(2'')-Ia). This study represents the first national prevalence study of methicillin-resistant Macrococcus spp. in pigs, calves, pork and beef meat in Switzerland and revealed a reservoir of genetically diverse strains carrying several resistance traits.
Topics: Animals; Cattle; Genes, Bacterial; Meat; Methicillin Resistance; Methicillin-Resistant Staphylococcus aureus; Microbial Sensitivity Tests; Prevalence; Swine; Switzerland
PubMed: 35103598
DOI: 10.17236/sat00343 -
Frontiers in Microbiology 2018The genus is a close relative of the genus . Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical...
Description and Comparative Genomics of subsp. subsp. nov., sp. nov., sp. nov., and sp. nov., Novel Macrococci From Human Clinical Material With Virulence Potential and Suspected Uptake of Foreign DNA by Natural Transformation.
The genus is a close relative of the genus . Whilst staphylococci are widespread as human pathogens, macrococci have not yet been reported from human clinical specimens. Here we investigated Gram-positive and catalase-positive cocci recovered from human clinical material and identified as sp. by a polyphasic taxonomic approach and by comparative genomics. Relevant phenotypic, genotypic and chemotaxonomic methods divided the analyzed strains into two separate clusters within the genus . Comparative genomics of four representative strains revealed enormous genome structural plasticity among the studied isolates. We hypothesize that high genomic variability is due to the presence of a operon, which plays a key role in the natural transformation of bacilli and streptococci. The possible uptake of exogenous DNA by macrococci can contribute to a different mechanism of evolution from staphylococci, where phage-mediated horizontal gene transfer predominates. The described macrococcal genomes harbor novel plasmids, genomic islands and islets, as well as prophages. Capsule gene clusters, intracellular protease, and a fibronectin-binding protein enabling opportunistic pathogenesis were found in all four strains. Furthermore, the presence of a CRISPR-Cas system with 90 spacers in one of the sequenced genomes corresponds with the need to limit the burden of foreign DNA. The highly dynamic genomes could serve as a platform for the exchange of virulence and resistance factors, as was described for the methicillin resistance gene, which was found on the novel composite SCC-like element containing a unique gene complex that is considered to be one of the missing links in SCC evolution. The phenotypic, genotypic, chemotaxonomic and genomic results demonstrated that the analyzed strains represent one novel subspecies and three novel species of the genus , for which the names subsp. subsp. nov. (type strain CCM 7927 = DSM 103682), sp. nov. (type strain CCM 4927 = DSM 103683), sp. nov. (type strain CCM 7099 = DSM 103681), and sp. nov. (type strain CCM 7100 = DSM 103680) are proposed. Moreover, a formal description of subsp. subsp. nov. and an emended description of the genus are provided.
PubMed: 29951040
DOI: 10.3389/fmicb.2018.01178 -
Frontiers in Microbiology 2023species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be...
INTRODUCTION
species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.
METHODS
All high-quality, publicly available genomes ( = 104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).
RESULTS
Overall, the 110 genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across included macrolides, beta-lactams, and aminoglycosides ( = 81, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively). Genes showing homology to exoenzyme aureolysin were detected across multiple species (using 90% coverage, = 40 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). Panton-Valentine leucocidin toxin-associated and homologs were identified in eight genomes (≥40% AA identity, >85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species ( and ) were composed of multiple within-species populations. Notably, was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT < 0.05).
DISCUSSION
Overall, this study leverages all publicly available genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.
PubMed: 37547688
DOI: 10.3389/fmicb.2023.1181376 -
Antibiotics (Basel, Switzerland) Sep 2020A methicillin-resistant isolate from canine otitis, H889678/16/1, was whole-genome sequenced using HiSeq technology to identify the species, antimicrobial resistance...
A methicillin-resistant isolate from canine otitis, H889678/16/1, was whole-genome sequenced using HiSeq technology to identify the species, antimicrobial resistance determinates and their genomic context. H889678/16/1 belonged to the newly described species . It encoded within a novel SCC element most similar to that of KM45013. This SCC element also encoded and , but no other resistance determinates were found in the H889678/16/1 genome. The and recombinase genes within SCC were distinct from those previously described in staphylococci and macrococci and therefore designated here as and . Our study represents, to the best of our knowledge, the first description of being encoded by . and of methicillin resistance in this species. Furthermore, the SCC described here is highly dissimilar to other such elements and encodes novel genes. Our report demonstrates a wider distribution of among species and expands the genomic context in which may be found. The potential for dissemination of genes from to related but more pathogenic species highlights the need to understand the epidemiology of these genes in macrococci.
PubMed: 32927653
DOI: 10.3390/antibiotics9090590 -
Microbiology Resource Announcements May 2019Here, we present the draft genome sequences of 14 strains of 4 species of the genus These strains were isolated from bovine milk and tongue samples obtained during a...
Here, we present the draft genome sequences of 14 strains of 4 species of the genus These strains were isolated from bovine milk and tongue samples obtained during a screening program.
PubMed: 31072881
DOI: 10.1128/MRA.00343-19 -
Infection, Genetics and Evolution :... Dec 2021A hemolytic Macrococcus canis strain (LI021) was isolated for the first time from a human skin infection. The complete genome of LI021 consisting of a 2,216,765-bp...
A hemolytic Macrococcus canis strain (LI021) was isolated for the first time from a human skin infection. The complete genome of LI021 consisting of a 2,216,765-bp circular chromosome was obtained by de novo hybrid assembly of Illumina and Oxford Nanopore technology reads. Strain LI021 belonged to the new sequence type ST75 and was resistant to β-lactam antibiotics due to the presence of a methicillin resistance gene mecB. The mecB gene as well as putative hemolysin genes hlgB and hlgC were located on a novel composite pseudo (Ψ) SCCmec island. These findings show that a methicillin-resistant M. canis may be associated with human infection and indicate that this bacterium should be considered by human diagnostic laboratories.
Topics: Female; Genome, Bacterial; Gram-Positive Bacterial Infections; Humans; Methicillin Resistance; Middle Aged; Skin Diseases, Bacterial; Staphylococcaceae; Whole Genome Sequencing
PubMed: 34715385
DOI: 10.1016/j.meegid.2021.105125 -
Microbiology Resource Announcements May 2019We report here the draft genome sequences of ATCC 51825, ATCC 51828, ATCC 51831, CCM4811, CCM4809, and CCM4815 The availability of the genome sequences of these...
We report here the draft genome sequences of ATCC 51825, ATCC 51828, ATCC 51831, CCM4811, CCM4809, and CCM4815 The availability of the genome sequences of these species will enable cross-species comparison, which could lead to a more comprehensive understanding of organisms of the genus.
PubMed: 31072882
DOI: 10.1128/MRA.00344-19 -
Frontiers in Microbiology 2021In current study, bacterial diversity and community in different tissues of pork bacon were determined using high-throughput sequencing. In total, six phyla and 111...
In current study, bacterial diversity and community in different tissues of pork bacon were determined using high-throughput sequencing. In total, six phyla and 111 bacterial genera were identified. Among them, three dominant genera (, , and ) were shared by all bacon samples. The linear discriminant analysis showed that 24 bacterial taxa significantly differentiated between the tissues. Results of non-metric Multidimensional Scaling and redundancy analysis showed that physicochemical characteristics of the tissue prominently structured the bacterial communities. Network analysis also illustrated that tissue type was an important factor impacting the bacterial interactions in different types of tissue. The results of current study can add valuable insights to the traditional homemade pork bacon.
PubMed: 34925308
DOI: 10.3389/fmicb.2021.799332 -
The Journal of Antimicrobial... Sep 2019To analyse the genetic context of mecB in two Macrococcus canis strains from dogs, compare the mecB-containing elements with those found in other Macrococcus and...
OBJECTIVES
To analyse the genetic context of mecB in two Macrococcus canis strains from dogs, compare the mecB-containing elements with those found in other Macrococcus and Staphylococcus species, and identify possible mobilizable mecB subunits.
METHODS
Whole genomes of the M. canis strains Epi0076A and KM0218 were sequenced using next-generation sequencing technologies. Multiple PCRs and restriction analysis confirmed structures of mecB-containing elements, circularization and recombination of mecB subunits.
RESULTS
Both M. canis strains contained novel composite pseudo (Ψ) staphylococcal cassette chromosome mec (SCCmec) elements. Integration site sequences for SCC flanked and subdivided composite ΨSCCmecEpi0076A (69569 bp) into ΨSCC1Epi0076A-ΨSCCmecEpi0076A-ΨSCC2Epi0076A and composite ΨSCCmecKM0218 (24554 bp) into ΨSCCKM0218-ΨSCCmecKM0218. Putative γ-haemolysin genes (hlgB and hlgC) were found at the 3' end of both composite elements. ΨSCCmecKM0218 contained a complete mecB gene complex (mecIm-mecR1m-mecB-blaZm) downstream of a new IS21-family member (ISMaca1). ΨSCCmecEpi0076A carried a blaZm-deleted mecB gene complex similar to that reported in 'Macrococcus goetzii' CCM4927T. A second mecB gene was found on the 81325 bp MDR plasmid pKM0218 in KM0218. This plasmid contained a complete Tn6045-associated mecB gene complex distinct from that of ΨSCCmecKM0218. pKM0218 was almost identical to the mecB-containing plasmid recently reported in Staphylococcus aureus (overall 99.96% nucleotide identity). Mobilization of mecB within an unconventional circularizable structure was observed in Epi0076A as well as chromosomal plasmid insertion via recombination of mecB operons in KM0218.
CONCLUSIONS
Our findings provide evidence of both the continuing evolution of mecB-containing elements in macrococci and M. canis as a potential source of the mecB-containing plasmid found in staphylococci.
Topics: Animals; Bacterial Proteins; Dog Diseases; Dogs; Methicillin Resistance; Operon; Otitis Externa; Plasmids; Staphylococcaceae; Staphylococcal Infections; Staphylococcus aureus; Whole Genome Sequencing
PubMed: 31243455
DOI: 10.1093/jac/dkz260 -
Antimicrobial Agents and Chemotherapy Apr 2020Chromosomal resistance islands containing the methicillin resistance gene (McRI ) have been reported in Here, we identified novel macrolide resistance genes in on...
Chromosomal resistance islands containing the methicillin resistance gene (McRI ) have been reported in Here, we identified novel macrolide resistance genes in on similar elements, called McRI These elements were also integrated into the 3' end of the 30S ribosomal protein S9 gene (), delimited by characteristic attachment () sites, and carried a related site-specific integrase gene () at the 5' end. They carried novel macrolide resistance genes belonging to the family of ABC subfamily F (ABC-F)-type ribosomal protection protein [(F) and (H)] and the macrolide efflux family [(D)]. Highly related (D)-(F) fragments were found on diverse McRI elements in , and Another McRI -like element identified in an strain lacked the classical site at the 3' end and carried the (H) gene but no neighboring gene. The expression of the novel resistance genes in resulted in a low-to-moderate increase in the MIC of erythromycin but not streptogramin B. In the (D)-(F) operon, the (F) gene was shown to be the crucial determinant for macrolide resistance. The detection of circular forms of McRI and the (D)-(F) fragment suggested mobility of both the island and the resistance gene subunit. The discovery of McRI in different species and indicates that these islands have a potential for dissemination of antibiotic resistance within the family.
Topics: Anti-Bacterial Agents; Base Sequence; Carboxylic Ester Hydrolases; DNA Transposable Elements; Drug Resistance, Bacterial; Macrolides; Membrane Transport Proteins; Methicillin Resistance; Microbial Sensitivity Tests; Staphylococcaceae; Staphylococcus aureus
PubMed: 32122903
DOI: 10.1128/AAC.00160-20