Cui, B., Smooker, P. M., Rouch, D. A., Daley, A. J. & Deighton, M. A. Differences between two clinical Staphylococcus capitis subspecies as revealed by biofilm, antibiotic resistance, and pulsed-field gel electrophoresis profiling. J. Clin. Microbiol. 51, 9–14 (2013).
Google Scholar
Tevell, S., Hellmark, B., Nilsdotter-Augustinsson, Å. & Söderquist, B. Staphylococcus capitis isolated from prosthetic joint infections. Eur. J. Clin. Microbiol. Infect. Dis. 36, 115–122 (2017).
Google Scholar
Van Der Zwet, W. C. et al. Nosocomial spread of a Staphylococcus capitis strain with heteroresistance to vancomycin in a neonatal intensive care unit. J. Clin. Microbiol. 40, 2520–2525 (2002).
Google Scholar
Rasigade, J.-P. et al. Methicillin-resistant Staphylococcus capitis with reduced vancomycin susceptibility causes late-onset sepsis in intensive care neonates. PLoS One 7, e31548 (2012).
Google Scholar
Brodie, S. B. et al. Occurrence of nosocomial bloodstream infections in six neonatal intensive care units. Pediatr. Infect. Dis. J. 19, 56–65 (2000).
Google Scholar
Stoll, B. J. et al. Late-onset sepsis in very low birth weight neonates: The experience of the NICHD Neonatal Research Network. Pediatrics 110, 285–291 (2002).
Google Scholar
Wirth, T. et al. Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis. Nat. Microbiol. 5, 735–745 (2020).
Google Scholar
Laurent, F. & Butin, M. Staphylococcus capitis and NRCS-A clone: The story of an unrecognized pathogen in neonatal intensive care units. Clin. Microbiol. Infect. 25, 1081–1085 (2019).
Google Scholar
Tevell, S. et al. Presence of the neonatal Staphylococcus capitis outbreak clone (NRCS-A) in prosthetic joint infections. Sci. Rep. 10, 1–8 (2020).
Google Scholar
Leopold, S. R., Goering, R. V., Witten, A., Harmsen, D. & Mellmann, A. Bacterial whole-genome sequencing revisited: Portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes. J. Clin. Microbiol. 52, 2365–2370 (2014).
Google Scholar
Jamet, A. et al. High-resolution typing of Staphylococcus epidermidis based on core genome multilocus sequence typing to investigate the hospital spread of multidrug-resistant clones. J. Clin. Microbiol. 59, e02454–02420 (2021).
Google Scholar
Liu, S. et al. A core genome multilocus sequence typing scheme for Streptococcus mutans. Msphere 5, e00348–00320 (2020).
Google Scholar
Zhou, H., Liu, W., Qin, T., Liu, C. & Ren, H. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Klebsiella pneumoniae. Front. Microbiol. 8, 371 (2017).
Google Scholar
Moura, A. et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat. Microbiol. 2, 1–10 (2016).
Ruppitsch, W. et al. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Listeria monocytogenes. J. Clin. Microbiol. 53, 2869–2876 (2015).
Google Scholar
Stenmark, B., Hellmark, B. & Söderquist, B. Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden. Eur. J. Clin. Microbiol. Infect. Dis. 38, 2069–2075 (2019).
Google Scholar
Ding, L., Li, P., Yang, Y., Lin, D. & Xu, X. The epidemiology and molecular characteristics of linezolid-resistant Staphylococcus capitis in Huashan Hospital, Shanghai. J. Med. Microbiol. 69, 1079–1088 (2020).
Google Scholar
Li, X. et al. Whole genome sequence and comparative genomic analysis of multidrug-resistant Staphylococcus capitis subsp. urealyticus strain LNZR-1. Gut Pathog. 6, 1–8 (2014).
Google Scholar
Butin, M. et al. Emergence and dissemination of a linezolid-resistant Staphylococcus capitis clone in Europe. J. Antimicrobial Chemother. 72, 1014–1020 (2017).
Google Scholar
Gu, B., Kelesidis, T., Tsiodras, S., Hindler, J. & Humphries, R. M. The emerging problem of linezolid-resistant Staphylococcus. J. Antimicrobial Chemother. 68, 4–11 (2013).
Google Scholar
Meka, V. G. et al. Linezolid resistance in sequential Staphylococcus aureus isolates associated with a T2500A mutation in the 23S rRNA gene and loss of a single copy of rRNA. J. Infect. Dis. 190, 311–317 (2004).
Google Scholar
Long, K. S., Poehlsgaard, J., Kehrenberg, C., Schwarz, S. & Vester, B. The Cfr rRNA methyltransferase confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A antibiotics. Antimicrobial Agents Chemother. 50, 2500–2505 (2006).
Google Scholar
Tonkin-Hill, G. et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol. 21, 1–21 (2020).
Google Scholar
Liu, Y. et al. Molecular evidence for spread of two major methicillin-resistant Staphylococcus aureus clones with a unique geographic distribution in Chinese hospitals. Antimicrobial Agents Chemother. 53, 512–518 (2009).
Google Scholar
Sun, L. et al. Characterization of vanM carrying clinical Enterococcus isolates and diversity of the suppressed vanM gene cluster. Infect., Genet. Evolution 68, 145–152 (2019).
Google Scholar
Li, W. et al. Large outbreak of herpangina in children caused by enterovirus in summer of 2015 in Hangzhou, China. Sci. Rep. 6, 1–5 (2016).
Google Scholar
Schwarz, S. et al. Lincosamides, streptogramins, phenicols, and pleuromutilins: Mode of action and mechanisms of resistance. Cold Spring Harb. Perspect. Med. 6, a027037 (2016).
Google Scholar
Cai, J. C., Hu, Y. Y., Zhou, H. W., Chen, G.-X. & Zhang, R. Dissemination of the same cfr-carrying plasmid among methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates in China. Antimicrobial Agents Chemother. 59, 3669–3671 (2015).
Google Scholar
Matyi, S. et al. Isolation and characterization of Staphylococcus aureus strains from a Paso del Norte dairy. J. Dairy Sci. 96, 3535–3542 (2013).
Google Scholar
Wu, D. et al. Characterization of an ST5-SCCmec II-t311 methicillin-resistant Staphylococcus aureus strain with a widespread cfr-positive plasmid. J. Infect. Chemother. 26, 699–705 (2020).
Google Scholar
Yang, X.-J. et al. Emergence of cfr-harbouring coagulase-negative staphylococci among patients receiving linezolid therapy in two hospitals in China. J. Med. Microbiol. 62, 845–850 (2013).
Google Scholar
Friedman, N. D., Temkin, E. & Carmeli, Y. The negative impact of antibiotic resistance. Clin. Microbiol. Infect. 22, 416–422 (2016).
Google Scholar
San Millan, A. & Maclean, R. C. Fitness costs of plasmids: A limit to plasmid transmission. Microbiol. Spectrum 5, 5.5. 02 (2017).
Shariati, A. et al. The global prevalence of Daptomycin, Tigecycline, Quinupristin/Dalfopristin, and Linezolid-resistant Staphylococcus aureus and coagulase–negative staphylococci strains: A systematic review and meta-analysis. Antimicrobial Resistance Infect. Control 9, 1–20 (2020).
Google Scholar
Pritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G. & Toth, I. K. Genomics and taxonomy in diagnostics for food security: Soft-rotting enterobacterial plant pathogens. Anal. Methods 8, 12–24 (2016).
Google Scholar
Seemann, T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
Johnson, M. et al. NCBI BLAST: A better web interface. Nucleic Acids Res. 36, W5–W9 (2008).
Google Scholar
Jünemann, S. et al. Updating benchtop sequencing performance comparison. Nat. Biotechnol. 31, 294–296 (2013).
Google Scholar
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Google Scholar
Neumann, B. et al. A core genome multilocus sequence typing scheme for Enterococcus faecalis. J. Clin. Microbiol. 57, e01686–01618 (2019).
Google Scholar
Earls, M. R. et al. Intra-hospital, inter-hospital, and intercontinental spread of ST78 MRSA from two neonatal intensive care unit outbreaks established using whole-genome sequencing. Front. Microbiol. 9, 1485 (2018).
Google Scholar
Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Google Scholar
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: Recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
Google Scholar
Clinical and Laboratory Standards Institute. M100: Performance Standards for Antimicrobial Susceptibility Testing 30th edn, 1–320 (CLSI, 2020).
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).
Google Scholar
Andrews, S. FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2012).
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).
Google Scholar
Deatherage, D. E. & Barrick, J. E. Engineering and Analyzing Multicellular Systems (Springer, 2014).
Cafini, F. et al. Methodology for the study of horizontal gene transfer in Staphylococcus aureus. JoVE (J. Vis. Exp.) 121, e55087 (2017).
Ruiz‐Ripa, L. et al. Linezolid‐resistant MRSA‐CC398 carrying the cfr gene, and MRSA‐CC9 isolates from pigs with signs of infection in Spain. J. Appl. Microbiol. 131, 615–622 (2021).
Google Scholar
Kehrenberg, C. & Schwarz, S. Distribution of florfenicol resistance genes fexA and cfr among chloramphenicol-resistant Staphylococcus isolates. Antimicrobial Agents Chemother. 50, 1156–1163 (2006).
Google Scholar
More Stories
How to gain resilience through mindful meditation
Personalized nutrition | RAPS
Proteotoxicity caused by perturbed protein complexes