A multilocus sequence typing method of Staphylococcus aureus DNAs in a sample from human skin.
Staphylococcus aureus
clinical samples
culture-free approach
multilocus sequence typing
multiplex PCR
pressure injury
Journal
Microbiology and immunology
ISSN: 1348-0421
Titre abrégé: Microbiol Immunol
Pays: Australia
ID NLM: 7703966
Informations de publication
Date de publication:
Oct 2023
Oct 2023
Historique:
revised:
03
07
2023
received:
07
04
2023
accepted:
21
07
2023
medline:
6
10
2023
pubmed:
14
8
2023
entrez:
14
8
2023
Statut:
ppublish
Résumé
The skin and mucous membranes are the primary sites of Staphylococcus aureus colonization, particularly those of health care personnel and patients in long-term care centers. We found that S. aureus colonized with a higher abundance ratio on skins which had recovered from pressure injury (PI) than on normal skins in our earlier research on the skin microbiota of bedridden patients. Multilocus sequence typing (MLST) is a useful tool for typing S. aureus isolated from clinical specimens. However, the MLST approach cannot be used in microbiota DNA owing to the contamination from other bacteria species. In this study, we developed a multiplex-nested PCR method to determine S. aureus MLST in samples collected from human skins. The seven pairs of forward and reverse primers were designed in the upstream and downstream regions, which were conserved specifically in S. aureus. The first amplifications of the seven pairs were conducted in a multiplex assay. The samples were diluted and applied to conventional PCR for MLST. We confirmed that the method amplified the seven allele sequences of S. aureus specifically in the presence of untargeted DNAs from human and other skin commensal bacteria. Using this assay, we succeeded in typing sequence types (STs) of S. aureus in the DNA samples derived from the skins healed from PI. Peaks obtained by Sanger sequencing showed that each sample contained one ST, which were mainly categorized into clonal complex 1 (CC1) or CC5. We propose that this culture-free approach may be used in detecting S. aureus in clinical specimens without isolation.
Identifiants
pubmed: 37574717
doi: 10.1111/1348-0421.13094
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
438-446Subventions
Organisme : Japan Society for the Promotion of Science
ID : 21K07002
Informations de copyright
© 2023 The Societies and John Wiley & Sons Australia, Ltd.
Références
Foster T. Staphylococcus. 4th edition. University of Texas Medical Branch at Galveston; 1996.
Taylor TA, Unakal CG. Staphylococcus Aureus. StatPearls; 2022. https://doi.org/10.1128/9781555819972.ch21
Grace, D, Fetsch, A. Staphylococcus aureus-A foodborne pathogen. In: Staphylococcus aureus. Elsevier; 2018. p. 3-10.
Krismer B, Weidenmaier C, Zipperer A, Peschel A. The commensal lifestyle of Staphylococcus aureus and its interactions with the nasal microbiota. Nat Rev Microbiol. 2017;15:675-687.
Lowy FD. Staphylococcus aureus infections. N Engl J Med. 1998;339:520-532.
Rasigade JP, Vandenesch F. Staphylococcus aureus: A pathogen with still unresolved issues. Infect Genet Evol. 2014;21:510-514.
Chambers HF. Community-associated MRSA-Resistance and virulence converge. N Engl J Med. 2005;352:1485-1487.
Baldwin NS, Gilpin DF, Hughes CM, et al. Prevalence of methicillin-resistant Staphylococcus aureus colonization in residents and staff in nursing homes in Northern Ireland. J Am Geriatr Soc. 2009;57:620-626.
Cox RA, Bowie PES. Methicillin-resistant Staphylococcus aureus colonization in nursing home residents: A prevalence study in Northamptonshire. J Hosp Infect. 1999;43:115-122.
Stark L, Olofsson M, Löfgren S, Mölstad S, Lindgren PE, Matussek A. Prevalence and molecular epidemiology of Staphylococcus aureus in Swedish nursing homes - as revealed in the SHADES study. Epidemiol Infect. 2014;142:1310-1316.
Lee BY, Bartsch SM, Wong KF, et al. The importance of nursing homes in the spread of methicillin-resistant Staphylococcus aureus (MRSA) among hospitals. Med Care. 2013;51:205-215.
Zhang J, Gu FF, Zhao SY, et al. Prevalence and molecular epidemiology of staphylococcus aureus among residents of seven nursing homes in Shanghai. PLoS One. 2015;10(9):e0137593. https://doi.org/10.1371/journal.pone.0137593
Hudson LO, Reynolds C, Spratt BG, et al. Diversity of methicillin-resistant Staphylococcus aureus strains isolated from residents of 26 nursing homes in Orange County, California. J Clin Microbiol. 2013;51:3788-3795.
Senn L, Clerc O, Zanetti G, et al. The stealthy superbug: The role of asymptomatic enteric carriage in maintaining a long-term hospital outbreak of ST228 methicillin-resistant Staphylococcus aureus. mBio. 2016;7(1):e02039-25. https://doi.org/10.1128/MBIO.02039-15
Oh J, Byrd AL, Park M, Kong HH, Segre JA. Temporal stability of the human skin microbiome. Cell. 2016;165:854-866.
Parlet CP, Brown MM, Horswill AR. Commensal Staphylococci influence Staphylococcus aureus skin colonization and disease. TIM. 2019;27:497-507.
Moran GJ, Krishnadasan A, Gorwitz RJ, et al. Methicillin-resistant S. aureus infections among patients in the emergency department. N Engl J Med. 2006;355:666-674.
Sollid JUE, Furberg AS, Hanssen AM, Johannessen M. Staphylococcus aureus: Determinants of human carriage. Infect Genet Evol. 2014;21:531-541.
Shopsin B, Mathema B, Alcabes P, et al. Prevalence of agr specificity groups among Staphylococcus aureus strains colonizing children and their guardians. J Clin Microbiol. 2003;41:456-459.
Goh SH, Byrne SK, Zhang JL, Chow AW. Molecular typing of Staphylococcus aureus on the basis of coagulase gene polymorphisms. J Clin Microbiol. 1992;30:1642-1645.
Sakai F, Takemoto A, Watanabe S, et al. Multiplex PCRs for assignment of Staphylocoagulase types and subtypes of type VI Staphylocoagulase. J Microbiol Meth. 2008;75:312-317.
Koreen L, Ramaswamy SV, Graviss EA, Naidich S, Musser JM, Kreiswirth BN. spa Typing method for discriminating among Staphylococcus aureus isolates: Implications for use of a single marker to detect genetic micro- and macrovariation. J Clin Microbiol. 2004;42:792-799.
Takahashi H, Seki M, Yamamoto N, et al Validation of a phage-open reading frame typing kit for rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) transmission in a tertiary hospital. Infect Drug Resist. 2015;8:107-111.
Suzuki M, Tawada Y, Kato M, et al. Development of a rapid strain differentiation method for methicillin-resistant Staphylococcus aureus isolated in Japan by detecting phage-derived open-reading frames. J Appl Microbiol. 2006;101:938-947.
Enright MC, Day NPJ, Davies CE, Peacock SJ, Spratt BG. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol. 2000;38:1008-1015.
Liu N, Liu D, Li K, Hu S, He Z. Pan-genome analysis of staphylococcus aureus reveals key factors influencing genomic plasticity. Microbiol Spectr. 2022;10(6):e0311722. https://doi.org/10.1128/SPECTRUM.03117-22
Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. https://doi.org/10.12688/WELLCOMEOPENRES.14826.1
Ogura K, Furuya H, Takahashi N, et al. Interspecies regulation between Staphylococcus caprae and Staphylococcus aureus colonized on healed skin after injury. Front Microbiol. 2022;13:818398. https://doi.org/10.3389/fmicb.2022.818398
Shibata K, Ogai K, Ogura K, et al. Skin physiology and its microbiome as factors associated with the recurrence of pressure injuries. Biol Res Nurs. 2021;23:75-81.
Kuroda M, Ohta T, Uchiyama I, et al. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet. 2001;357:1225-1240.
Watanabe S, Aiba Y, Tan XE, et al. Complete genome sequencing of three human clinical isolates of Staphylococcus caprae reveals virulence factors similar to those of S. epidermidis and S. capitis. BMC Genomics. 2018;19:810.
Arisandi D, Ogai K, Urai T, et al. Development of recurrent pressure ulcers, risk factors in older patients: A prospective observational study. J Wound Care. 2020;29:S14-S24.
NCBI. (2008). BLAST® Command Line Applications User Manual. National Center for Biotechnology Information.
Shen W, Le S, Li Y, Hu F. SeqKit: A cross-platform and ultrafast toolkit for fasta/q file manipulation. PLoS One. 2016;11(10):e0163962. https://doi.org/10.1371/JOURNAL.PONE.0163962
Enright MC, Robinson DA, Randle G, Feil EJ, Grundmann H, Spratt BG. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc Natl Acad Sci. 2002;99:7687-7692.
Jolley KA, Feil EJ, Chan MS, Maiden MCJ. Sequence type analysis and recombinational tests (START). Bioinformatics. 2001;17:1230-1231.
Igarashi A, Yamamoto-Mitani N, Gushiken Y, Takai Y, Tanaka M, Okamoto Y. Prevalence and incidence of pressure ulcers in Japanese long-term-care hospitals. Arch Gerontol Geriat. 2013;56:220-226.
Ederveen THA, Smits JPH, Hajo K, et al. A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota. Sci Rep. 2019;9:19834.
Hsu TK, Chen JS, Tsai HC, et al. Efficient nested-PCR-based method development for detection and genotype identification of Acanthamoeba from a small volume of aquatic environmental sample. Sci Rep. 2021;11:21740. https://doi.org/10.1038/S41598-021-00968-2
Sun Y, Chen J, Li J, et al. Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis. PLoS One. 2017;12:e0186985. https://doi.org/10.1371/JOURNAL.PONE.0186985
van der Veer C, Himschoot M, Bruisten SM. Multilocus sequence typing of Trichomonas vaginalis clinical samples from Amsterdam, the Netherlands. BMJ Open. 2016;6:e013997.
Poritz MA, Blaschke AJ, Byington CL, et al. FilmArray, an automated nested multiplex pcr system for multi-pathogen detection: development and application to respiratory tract infection. PLoS One. 2011;6:e26047.
Hiramatsu K, Ito T, Tsubakishita S, et al. Genomic basis for methicillin resistance in Staphylococcus aureus. Infect Chemother. 2013;45:117-136.
Mitsuboshi S, Yamaguchi T, Seino H, Fukuhara M, Hosokawa Y, Tsugita M. Regional outbreak of methicillin-resistant Staphylococcus aureus ST2725-t1784 in rural Japan. Infect Control Hosp Epidemiol. 2021;42:1294-1296.
Ogura K, Kaji D, Sasaki M, et al. Predominance of ST8 and CC1/spa-t1784 methicillin-resistant Staphylococcus aureus isolates in Japan and their genomic characteristics. J Glob Antimicrob Resist. 2022;28:195-202. https://doi.org/10.1016/J.JGAR.2022.01.011
Coombs GW, Van Gessel H, Pearson JC, Godsell M-R, O'Brien FG, Christiansen KJ. Controlling a multicenter outbreak involving the New York/Japan methicillin-resistant Staphylococcus aureus clone. Infect Control Hosp Epidemiol. 2007;28:845-852.
Takano T, Hung W-C, Shibuya M, et al. A new local variant (ST764) of the globally disseminated ST5 lineage of hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) carrying the virulence determinants of community-associated MRSA. Antimicrob Agents Chemother. 2013;57:1589-1595. https://doi.org/10.1128/AAC.01147-12
Kondo S, Phokhaphan P, Tongsima S, et al. Molecular characterization of methicillin-resistant Staphylococcus aureus genotype ST764-SCCmec type II in Thailand. Sci Rep. 2022;12(1):2085.
Aung MS, Kawaguchiya M, Urushibara N, et al. Molecular characterization of methicillin-resistant Staphylococcus aureus from outpatients in Northern Japan: Increasing tendency of ST5/ST764 MRSA-IIa with arginine catabolic mobile element. Microb Drug Resist. 2017;23:616-625.
Lakhundi S, Zhang K. Methicillin-resistant Staphylococcus aureus: Molecular characterization, evolution, and epidemiology. Clin Microbiol Rev. 2018;31:e00020-18. https://doi.org/10.1128/CMR.00020-18