Identification of staphylococcal cassette chromosome mec in Staphylococcus aureus and non-aureus staphylococci from dairy cattle in Belgium: Comparison of multiplex PCR and whole genome sequencing
[en] The present study compared multiplex PCR (mPCR) and Whole Genome Sequencing (WGS) using the SCCmecFinder database to identify the Staphylococcal Cassette Chromosome (SCC) mec in five Staphylococcus aureus (SA)
and nine non-aureus staphylococci (NAS) isolated from dairy cattle. mPCR identified an SCCmecIV in four SA and
one NAS, but could not differentiate between SCCmecII and IV in the fifth SA, that all harbored the mecA gene
and were phenotypically resistant to cefoxitin. SCCmecFinder confirmed the presence of an SCCmecIVc(2B) in
four SA and of the SCCmecIVa(2B) in the fifth SA and the one NAS. Both methods also detected one untypeable
SCCmec in another cefoxitin-resistant NAS harboring the mecA gene and a pseudo SCCmec in one cefoxitinsensitive NAS harboring one mecC-related gene. No SCCmec elements were identified either in one cefoxitinsensitive NAS harboring the mecA2 gene, or in five NAS (one resistant and four sensitive to cefoxitin)
harboring the mecA1 gene. SCCmecFinder could even not identify the presence of any mecA1 gene in these five
NAS, whose presence was nevertheless confirmed by ResFinder. The conclusions of this study are: (i) mPCR and
WGS sequencing using SCCmecFinder are complementary methodologies to identify SCCmec; (ii) SCCmecFinder
and ResFinder to a lesser extent cannot identify all mec gene allotypes; (iii) a specific classification of the SCCmec
in NAS would be epidemiologically helpful; (iv) presence of a mecA gene and a complete SCCmec is linked to
cefoxitin resistance, whereas presence of other mec genes and of pseudo or no SCCmec is not.
Disciplines :
Veterinary medicine & animal health
Author, co-author :
Ngassam Tchamba, Cyrille
Touzain, Fabrice
Fergestad, Marte
De Visscher, Anneleen
L'Abee-Lund, Trine
De Vliegher, Sarne
Wasteson, Yngvild
Blanchard, Yannick
Argudín, Maria A.
Mainil, Jacques ✱; Université de Liège - ULiège > Département des maladies infectieuses et parasitaires (DMI)
Thiry, Damien ✱; Université de Liège - ULiège > Département des maladies infectieuses et parasitaires (DMI) > Bactériologie vétérinaire et maladies bactériennes animales
✱ These authors have contributed equally to this work.
Language :
English
Title :
Identification of staphylococcal cassette chromosome mec in Staphylococcus aureus and non-aureus staphylococci from dairy cattle in Belgium: Comparison of multiplex PCR and whole genome sequencing
Argudín, M.A., Dodémont, M., Vandendriessche, S., Rottiers, S., Tribes, C., Roisin, S., de Mendonça, R., Nonhoff, C., Deplano, A., Denis, O., Low occurrence of the new species Staphylococcus argenteus in a Staphylococcus aureus collection of human isolates from Belgium. Eur. J. Clin. Microbiol. Infect. Dis. 35 (2016), 1017–1022.
Bardiau, M., Yamazaki, K., Duprez, J.N., Taminiau, B., Mainil, J.G., Ote, I., Genotypic and phenotypic characterization of methicillin-resistant Staphylococcus aureus (MRSA) isolated from milk of bovine mastitis. Lett. Appl. Microbiol. 57 (2013), 181–186.
Becker, K., van Alen, S., Idelevich, E.A., Schleimer, N., Seggewiß, J., Mellmann, A., Kaspar, U., Peters, G., Plasmid-encoded transferable mecB-mediated methicillin resistance in Staphylococcus aureus. Emerg. Infect. Dis. 24 (2018), 242–248.
Clausen, P.T.L.C., Aarestrup, F.M., Lund, O., Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinforma. 19 (2018), 1–8.
De Visscher, A., Piepers, S., Haesebrouck, F., Supré, K., De Vliegher, S., Coagulase-negative Staphylococcus species in bulk milk: prevalence, distribution, and associated subgroup- and species-specific risk factors. J. Dairy Sci. 100 (2017), 629–642.
Devriese, L.A., Van Damme, L.R., Fameree, L., Methicillin (cloxacillin)-resistant Staphylococcus aureus strains isolated from bovine mastitis cases. Zentralbl. Veterinarmed. B 19 (1972), 598–605.
Fergestad, M.E., Stamsås, G.A., Morales Angeles, D., Salehian, Z., Wasteson, Y., Kjos, M., Penicillin-binding protein PBP2a provides variable levels of protection toward different β-lactams in Staphylococcus aureus RN4220. Microbiologyopen, 9, 2020, e1057.
Fergestad, M.E., De Visscher, A., L'Abee-Lund, T., Ngassam Tchamba, C., Mainil, J.G., Thiry, D., De Vliegher, S., Wasteson, Y., Antimicrobial resistance and virulence characteristics in 3 collections of staphylococci from bovine milk samples. J. Dairy Sci. 104 (2021), 10250–10267.
Fergestad, M.E., Touzain, F., De Vliegher, S., De Visscher, A., Thiry, D., Ngassam Tchamba, C., Mainil, J.G., L'Abee-Lund, T., Blanchard, Y., Wasteson, Y., Whole genome sequencing of staphylococci isolated from bovine milk samples. Front. Microbiol., 12, 2021 Article 715851.
Frey, Y., Rodriguez, J.P., Thomann, A., Schwendener, S., Perreten, V., Genetic characterization of antimicrobial resistance in coagulase-negative staphylococci from bovine mastitis milk. J. Dairy Sci. 96 (2013), 2247–2257.
Garza-González, E., Morfín-Otero, R., Llaca-Díaz, J.M., Rodriguez-Noriega, E., Staphylococcal cassette chromosome mec (SCCmec) in methicillin-resistant coagulase-negative staphylococci. A review and the experience in a tertiary-care setting. Epidemiol. Infect. 138 (2010), 645–654.
Hajia, M., Limitations of different PCR protocols used in diagnostic laboratories: a short review. Mod. Med. Lab. J. 1 (2017), 01–06.
Hanssen, A.-E., Sollid, J.U., Multiple staphylococcal cassette chromosomes and allelic variants of cassette chromosome recombinases in Staphylococcus aureus and coagulase-negative staphylococci from Norway. Antimicrob. Agents Chemother. 51 (2007), 1671–1677.
Harrison, E.M., Paterson, G.K., Holden, M.T.G., Morgan, F.J., Larsen, A.R., Petersen, A., Leroy, S., De Vliegher, S., Perreten, V., Fox, L.K., Lam, T.J., Sampimon, O.C., Zadoks, R.N., Peacock, S.J., Parkhill, J., Holmes, M.A., A Staphylococcus xylosus isolate with a new mecC allotype. Antimicrob. Agents Chemother. 57 (2013), 1524–1528.
Ito, T., Hiramatsu, K., Oliveira, D.C., De Lencastre, H., Zhang, K., Westh, H., O'Brien, F., Giffard, P.M., Coleman, D., Tenover, F.C., Boyle-Vavra, S., Skov, R.L., Enright, M.C., Kreiswirth, B., Kwan, S.K., Grundmann, H., Laurent, F., Sollid, J.E., Kearns, A.M., Goering, R., John, J.F., Daum, R., Soderquist, B., Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements. Antimicrob. Agents Chemother. 53 (2009), 4961–4967.
Kaya, H., Hasman, H., Larsen, J., Stegger, M., Johannesen, B., Allesøe, L., SCCmecFinder, a web-based tool for typing of cassette chromosome mec in Staphylococcus aureus using whole-genome sequence data. mSphere 3 (2018), e00612–e00617.
Lakhundi, S., Zhang, K., Methicillin-resistant Staphylococcus aureus: molecular characterization, evolution, and epidemiology. Clin. Microbiol. Rev. 31 (2018), 1–103.
Liu, J., Chen, D., Peters, B.M., Li, L., Li, B., Xu, Z., Shirliff, M.E., Staphylococcal chromosomal cassettes mec (SCCmec): a mobile genetic element in methicillin-resistant Staphylococcus aureus. Microb. Pathog. 101 (2016), 56–67.
Loncaric, I., Kübber-Heiss, A., Posautz, A., Ruppitsch, W., Lepuschitz, S., Schauer, B., Feßler, A.T., Krametter-Frötscher, R., Harrison, E.M., Holmes, M.A., Künzel, F., Szostak, M.P., Hauschild, T., Desvars-Larrive, A., Misic, D., Rosengarten, R., Walzer, C., Slickers, P., Moneckem, S., Ehricht, R., Schwarz, S., Spergser, J., Characterization of mecC gene-carrying coagulase-negative Staphylococcus spp. isolated from various animals. Vet. Microbiol. 230 (2019), 138–144.
MacFadyen, A.C., Harrison, E.M., Drigo, I., Parkhill, J., Holmes, M.A., Paterson, G.K., A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC. J. Antimicrob. Chemother. 74 (2019), 547–552.
Madhaiyan, M., Wirth, J.S., Saravanan, V.S., 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. 70 (2020), 5926–5936.
Martins, A., de Lourdes Cunha, A.R.S., Methicillin resistance in Staphylococcus aureus and coagulase-negative staphylococci: epidemiology and molecular aspects. Microbiol. Immunol. 51 (2007), 787–795.
McClure, J.-A., Conly, J.M., Zhang, K., Characterizing a novel staphylococcal cassette chromosome mec with a composite structure from a clinical strain of Staphylococcus hominis, C34847. Antimicrob. Agents Chemother., 65, 2021 e00777–21.
Miragaia, M., Factors contributing to the evolution of mecA-mediated β-lactam resistance in staphylococci: update and new insights from whole genome sequencing (WGS). Front. Mcrobiol., 9, 2018 Article 2723.
Ngassam Tchamba, C., Rao, A.S., Boyen, F., Haesebrouck, F., Duprez, J.N., Théron, L., Thiry, D., Mainil, J.G., Comparison of quantitative PCR and MALDI-TOF mass spectrometry assays for identification of bacteria in milk samples from cows with subclinical mastitis. J. Appl. Microbiol. 127 (2019), 683–692.
Ngassam Tchamba, C., Duprez, J.-N., Lucas, P., Blanchard, Y., Boyen, F., Haesebrouck, F., Argudín, M.A., Mainil, J., Thiry, D., Comparison of the staphylococcal chromosome cassette (SCC) mec in methicillin-resistant Staphylococcus aureus (MRSA) and non-aureus staphylococci (MRNAS) from animals and humans. Antibiotics, 10, 2021, 256.
Oliveira, D.C., de Lencastre, H., Methicillin-resistance in Staphylococcus aureus is not affected by the overexpression in trans of the mecA gene repressor: a surprising observation. PLoS One, 6, 2011, e23287.
Pantosti, A., Sanchini, A., Monaco, M., Mechanisms of antibiotic resistance in Staphylococcus aureus. Future Microbiol. 2 (2007), 323–334.
Schnitt, A., Tenhagen, B.-A., Risk factors for the occurrence of methicillin-resistant Staphylococcus aureus in dairy herds: an update. Foodborne Pathog. Dis. 17 (2020), 585–596.
Shore, A.C., Coleman, D.C., Staphylococcal cassette chromosome mec: recent advances and new insights. Int. J. Med. Microbiol. 303 (2013), 350–359.
Song, M.D., Wachi, M., Doi, M., Ishino, F., Matsuhashi, M., Evolution of an inducible penicillin-target protein in methicillin-resistant Staphylococcus aureus by gene fusion. FEBS Lett. 221 (1987), 167–171.
Uehara, Y., Current status of staphylococcal cassette chromosome mec (SCCmec). Antibiotics, 11, 2022, 86.
Urushibara, N., Paul, S.K., Hossain, M.A., Kawaguchiya, M., Kobayashi, N., Analysis of staphylococcal cassette chromosome mec in Staphylococcus haemolyticus and Staphylococcus sciuri: identification of a novel ccr gene complex with a newly identified ccrA allotype (ccrA7). Microb. Drug Resist. 17 (2011), 291–297.
Vanderhaeghen, W., Cerpentier, T., Adriaensen, C., Vicca, J., Hermans, K., Butaye, P., Methicillin-resistant Staphylococcus aureus (MRSA) ST398 associated with clinical and subclinical mastitis in Belgian cows. Vet. Microbiol. 144 (2010), 166–171.
Vanderhaeghen, W., Vandendriessche, S., Crombé, F., Nemeghaire, S., Dispas, M., Denis, O., Hermans, K., Haesebrouck, F., Butaye, P., Characterization of methicillin-resistant non-Staphylococcus aureus staphylococci carriage isolates from different bovine populations. J. Antimicrob. Chemother. 68 (2013), 300–307.
Xue, H., Wu, Z., Li, L., Li, F., Wang, Y., Zhao, X., Coexistence of heavy metal and antibiotic resistance within a novel composite staphylococcal cassette chromosome in a Staphylococcus haemolyticus isolate from bovine mastitis milk. Antimicrob. Agents Chemother. 59 (2015), 5788–5792.
Yamada, K., Namikawa, H., Fujimoto, H., Nakaie, K., Takizawa, E., Okada, Y., Fujita, A., Kawaguchi, H., Nakamura, Y., Abe, J., Kaneko, Y., Kakeya, H., Clinical characteristics of methicillin-resistant coagulase-negative staphylococcal bacteremia in a tertiary hospital. Intern. Med. 56 (2017), 781–785.
Yu, D., Pi, B., Chen, Y., Wang, Y., Ruan, Z., Otto, M., Yu, Y., Characterization of the staphylococcal composite island of Staphylococcus haemolyticus SH32, a methicillin-resistant clinical isolate from China. PLoS One, 9, 2014, e87346.
Zong, Z., Lü, X., Characterization of a new SSCmec element in Staphylococcus cohnii. PLoS One, 5, 2010, e14016.
