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Antimicrobial and Methicillin Resistance Pattern of Potential Mastitis-Inducing Staphylococcus aureus and Coagulase-Negative Staphylococci Isolates from the Mammary Secretion of Dairy Goats. BIOLOGY 2022; 11:biology11111591. [PMID: 36358292 PMCID: PMC9687969 DOI: 10.3390/biology11111591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 01/24/2023]
Abstract
Staphylococcus spp. is an important mastitis-inducing zoonotic pathogen in goats and is associated with antimicrobial resistance (AMR). The objectives of this study were to determine the prevalence and composition of staphylococci in individual mammary secretion (MS) samples of clinically healthy goats and to evaluate the phenotypic AMR pattern and the presence of methicillin resistance in the Staphylococcus spp. strains. Staphylococcus spp. isolates (n = 101) from the MS samples (n = 220) were identified to species level using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The antimicrobial susceptibility testing included a disk diffusion assay and the determination of the minimum inhibitory concentrations (MIC) of resistant strains (n = 46). Presumptive methicillin-resistant strains (n = 9) were assessed for the presence of mecA, mecC and SCCmec/orfx genes. Staphylococcus spp. isolates were recovered from 45.9% of the MS samples, of which, 72.3% was identified as coagulase-negative staphylococci (CoNS), with the remaining being Staphylococcus aureus. CoNS and S. aureus were most commonly resistant to ampicillin (56.2% and 57.1%, respectively), penicillin (26.0% and 39.3%, respectively), amoxicillin (26 % and 25 %, respectively) and cephalexin (12.3% and 25%, respectively) in the disk diffusion method. CoNS exhibited a broader AMR pattern and a higher percentage of resistant strains than S. aureus in the disk diffusion and MIC methods. Of the nine oxacillin- and cefoxitin-resistant strains, three S. aureus and five CoNS strains carried the mecA gene and, thus, were identified as methicillin-resistant. The mecC gene was not found in any of the studied strains. The presence of AMR and methicillin resistance in caprine S. aureus and CoNS poses a concern for animal and public health.
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2
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Rosa NM, Penati M, Fusar-Poli S, Addis MF, Tola S. Species identification by MALDI-TOF MS and gap PCR-RFLP of non-aureus Staphylococcus, Mammaliicoccus, and Streptococcus spp. associated with sheep and goat mastitis. Vet Res 2022; 53:84. [PMID: 36243811 PMCID: PMC9569034 DOI: 10.1186/s13567-022-01102-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococci and streptococci are common causes of intramammary infection in small ruminants, and reliable species identification is crucial for understanding epidemiology and impact on animal health and welfare. We applied MALDI-TOF MS and gap PCR–RFLP to 204 non-aureus staphylococci (NAS) and mammaliicocci (NASM) and to 57 streptococci isolated from the milk of sheep and goats with mastitis. The top identified NAS was Staphylococcus epidermidis (28.9%) followed by Staph. chromogenes (27.9%), haemolyticus (15.7%), caprae, and simulans (6.4% each), according to both methods (agreement rate, AR, 100%). By MALDI-TOF MS, 13.2% were Staph. microti (2.9%), xylosus (2.0%), equorum, petrasii and warneri (1.5% each), Staph. sciuri (now Mammaliicoccus sciuri, 1.0%), arlettae, capitis, cohnii, lentus (now M. lentus), pseudintermedius, succinus (0.5% each), and 3 isolates (1.5%) were not identified. PCR–RFLP showed 100% AR for Staph. equorum, warneri, arlettae, capitis, and pseudintermedius, 50% for Staph. xylosus, and 0% for the remaining NASM. The top identified streptococcus was Streptococcus uberis (89.5%), followed by Strep. dysgalactiae and parauberis (3.5% each) and by Strep. gallolyticus (1.8%) according to both methods (AR 100%). Only one isolate was identified as a different species by MALDI-TOF MS and PCR–RFLP. In conclusion, MALDI-TOF MS and PCR–RFLP showed a high level of agreement in the identification of the most prevalent NAS and streptococci causing small ruminant mastitis. Therefore, gap PCR–RFLP can represent a good identification alternative when MALDI-TOF MS is not available. Nevertheless, some issues remain for Staph. haemolyticus, minor NAS species including Staph. microti, and species of the novel genus Mammaliicoccus.
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Affiliation(s)
- Nives Maria Rosa
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Via Duca degli Abruzzi 8, 07100, Sassari, Italy
| | - Martina Penati
- Dipartimento di Medicina Veterinaria e Scienze Animali, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.,MILab, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Sara Fusar-Poli
- Dipartimento di Medicina Veterinaria e Scienze Animali, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.,MILab, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria e Scienze Animali, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy. .,MILab, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.
| | - Sebastiana Tola
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Via Duca degli Abruzzi 8, 07100, Sassari, Italy
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Theisinger SM, de Smidt O, Lues JFR. Categorisation of culturable bioaerosols in a fruit juice manufacturing facility. PLoS One 2021; 16:e0242969. [PMID: 33882058 PMCID: PMC8059861 DOI: 10.1371/journal.pone.0242969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/12/2020] [Indexed: 11/18/2022] Open
Abstract
Bioaerosols are defined as aerosols that comprise particles of biological origin or activity that may affect living organisms through infectivity, allergenicity, toxicity, or through pharmacological or other processes. Interest in bioaerosol exposure has increased over the last few decades. Exposure to bioaerosols may cause three major problems in the food industry, namely: (i) contamination of food (spoilage); (ii) allergic reactions in individual consumers; or (iii) infection by means of pathogenic microorganisms present in the aerosol. The aim of this study was to characterise the culturable fraction of bioaerosols in the production environment of a fruit juice manufacturing facility and categorise isolates as harmful, innocuous or potentially beneficial to the industry, personnel and environment. Active sampling was used to collect representative samples of five areas in the facility during peak and off-peak seasons. Areas included the entrance, preparation and mixing area, between production lines, bottle dispersion and filling stations. Microbes were isolated and identified using 16S, 26S or ITS amplicon sequencing. High microbial counts and species diversity were detected in the facility. 239 bacteria, 41 yeasts and 43 moulds were isolated from the air in the production environment. Isolates were categorised into three main groups, namely 27 innocuous, 26 useful and 39 harmful bioaerosols. Harmful bioaerosols belonging to the genera Staphylococcus, Pseudomonas, Penicillium and Candida were present. Although innocuous and useful bioaerosols do not negatively influence human health their presence act as an indicator that an ideal environment exists for possible harmful bioaerosols to emerge.
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Affiliation(s)
- Shirleen M. Theisinger
- Centre for Applied Food Sustainability and Biotechnology (CAFSaB), Faculty of Health and Environmental Sciences, Central University of Technology, Free State, Bloemfontein, South Africa
| | - Olga de Smidt
- Centre for Applied Food Sustainability and Biotechnology (CAFSaB), Faculty of Health and Environmental Sciences, Central University of Technology, Free State, Bloemfontein, South Africa
| | - Jan F. R. Lues
- Centre for Applied Food Sustainability and Biotechnology (CAFSaB), Faculty of Health and Environmental Sciences, Central University of Technology, Free State, Bloemfontein, South Africa
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Michels R, Last K, Becker SL, Papan C. Update on Coagulase-Negative Staphylococci-What the Clinician Should Know. Microorganisms 2021; 9:microorganisms9040830. [PMID: 33919781 PMCID: PMC8070739 DOI: 10.3390/microorganisms9040830] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023] Open
Abstract
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.
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Madhaiyan M, Wirth JS, Saravanan VS. Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae. Int J Syst Evol Microbiol 2020; 70:5926-5936. [DOI: 10.1099/ijsem.0.004498] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analyses based on 16S rRNA gene sequences of members of the family
Staphylococcaceae
showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the
Staphylococcaceae
family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals:
Auricoccus indicus
was reduced in taxonomic rank as a later heterotypic synonym of
Abyssicoccus albus
;
Staphylococcus petrasii
subsp.
jettensis
as a later heterotypic synonym of
Staphylococcus petrasii
subsp.
petrasii
; the unification of
Staphylococcus aureus
subsp.
anaerobius
and
Staphylococcus aureus
subsp.
aureus
as
Staphylococcus aureus
; the unification of
Staphylococcus carnosus
subsp.
utilis
and
Staphylococcus carnosus
subsp.
carnosus
as
Staphylococcus carnosus
; the unification of
Staphylococcus saprophyticus
subsp.
bovis
and
Staphylococcus saprophyticus
subsp.
saprophyticus
as
Staphylococcus saprophyticus
; Staphylococcus succinis subsp. casei as the novel species Staphylococcus casei;
Staphylococcus schleiferi
subsp.
coagulans
as the novel species Staphylococcus coagulans;
Staphylococcus petrasii
subsp.
croceilyticus
as the novel species Staphylococcus croceilyticus;
Staphylococcus petrasii
subsp.
pragensis
as the novel species Staphylococcus pragensis;
Staphylococcus cohnii
subsp.
urealyticus
as the novel species Staphylococcus urealyticus; the reassignment of
Staphylococcus sciuri
,
Staphylococcus fleurettii
,
Staphylococcus lentus
,
Staphylococcus stepanovicii
and
Staphylococcus vitulinus
to the novel genus Mammaliicoccus with Mammaliicoccus sciuri as the type species; and the formal assignment of
Nosocomiicoccus
as a member of the family
Staphylococcaceae
.
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Affiliation(s)
- Munusamy Madhaiyan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Joseph S. Wirth
- Department of Biology, Harvey Mudd College Claremont, CA 91711, USA
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Vrbovská V, Kovařovic V, Mašlaňová I, Indráková A, Petráš P, Šedo O, Švec P, Fišarová L, Šiborová M, Mikulášek K, Sedláček I, Doškař J, Pantůček R. Staphylococcus petrasii diagnostics and its pathogenic potential enhanced by mobile genetic elements. Int J Med Microbiol 2019; 309:151355. [PMID: 31563331 DOI: 10.1016/j.ijmm.2019.151355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus petrasii is recently described coagulase negative staphylococcal species and an opportunistic human pathogen, still often misidentified in clinical specimens. Four subspecies are distinguished in S. petrasii by polyphasic taxonomical analyses, however a comparative study has still not been done on the majority of isolates and their genome properties have not yet been thoroughly analysed. Here, we describe the phenotypic and genotypic characteristics of 65 isolates and the results of de novo sequencing, whole genome assembly and annotation of draft genomes of five strains. The strains were identified by MALDI-TOF mass spectrometry to the species level and the majority of the strains were identified to the subspecies level by fingerprinting methods, (GTG)5 repetitive PCR and ribotyping. Macrorestriction profiling by pulsed-field gel electrophoresis was confirmed to be a suitable strain typing method. Comparative genomics revealed the presence of new mobile genetic elements carrying antimicrobial resistance factors such as staphylococcal cassette chromosome (SCC) mec, transposones, phage-inducible genomic islands, and plasmids. Their mosaic structure and similarity across coagulase-negative staphylococci and Staphylococcus aureus suggest the possible exchange of these elements. Numerous putative virulence factors such as adhesins, autolysins, exoenzymes, capsule formation genes, immunomodulators, the phage-associated sasX gene, and SCC-associated spermidine N-acetyltransferase gene, pseudouridine and sorbitol utilization operons might explain clinical manifestations of S. petrasii isolates. The increasing recovery of S. petrasii isolates from human clinical material, the multi-drug resistance including methicillin resistance of S. petrasii subsp. jettensis strains, and virulence factors homologous to other pathogenic staphylococci demonstrate the importance of the species in human disease.
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Affiliation(s)
- Veronika Vrbovská
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Vojtěch Kovařovic
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Ivana Mašlaňová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Adéla Indráková
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Šrobárova 48, 100 42 Praha 10, Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lenka Fišarová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Marta Šiborová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Doškař
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Roman Pantůček
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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Munson E, Carroll KC. What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015. J Clin Microbiol 2017; 55:24-42. [PMID: 27795334 PMCID: PMC5228236 DOI: 10.1128/jcm.01379-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2013-2014. Diagn Microbiol Infect Dis 2015; 83:82-8. [PMID: 26014276 DOI: 10.1016/j.diagmicrobio.2015.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate and rapid reporting and communications regarding infectious agents of clinical significance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics causes changes in this taxonomy at a rapid rate further complicating this process. This review focuses on the description of new species and classification changes proposed over the past 2 years.
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Švec P, Bel AD, Sedláček I, Petráš P, Gelbíčová T, Černohlávková J, Mašlanˇová I, Cnockaert M, Varbanovová I, Echahidi F, Vandamme P, Pantu Ček R. Staphylococcus petrasii subsp. pragensis subsp. nov., occurring in human clinical material. Int J Syst Evol Microbiol 2015; 65:2071-2077. [PMID: 25829332 DOI: 10.1099/ijs.0.000220] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven coagulase-negative, oxidase-negative and novobiocin-susceptible staphylococci assigned tentatively as Staphylococcus petrasii were investigated in this study in order to elucidate their taxonomic position. All strains were initially shown to form a genetically homogeneous group separated from remaining species of the genus Staphylococcus by using a repetitive sequence-based PCR fingerprinting with the (GTG)5 primer. Phylogenetic analysis based on 16S rRNA gene, hsp60, rpoB, dnaJ, gap and tuf sequences showed that the group is closely related to Staphylococcus petrasii but separated from the three hitherto known subspecies, S. petrasii subsp. petrasii, S. petrasii subsp. croceilyticus and S. petrasii subsp. jettensis. Further investigation using automated ribotyping, MALDI-TOF mass spectrometry, fatty acid methyl ester analysis, DNA-DNA hybridization and extensive biotyping confirmed that the analysed group represents a novel subspecies within S. petrasii, for which the name Staphylococcus petrasii subsp. pragensis subsp. nov. is proposed. The type strain is NRL/St 12/356(T) ( = CCM 8529(T) = LMG 28327(T)).
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Affiliation(s)
- Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Annelies De Bel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Tereza Gelbíčová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Jitka Černohlávková
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Ivana Mašlanˇová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
| | - Margo Cnockaert
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ivana Varbanovová
- Reference Laboratory for Staphylococci, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Fedoua Echahidi
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Roman Pantu Ček
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
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