Microdiversity of Enterococcus faecalis isolates in cases of infective endocarditis: selection of non-synonymous mutations and large deletions is associated with phenotypic modifications

References

• Fernandez-Hidalgo N, Escola-Verge L, Pericas JM. Enterococcus faecalis endocarditis: what’s next? Future Microbiol. 2020;15:349–364.
   Web of Science ®Google Scholar
• Benes J, Dzupova O, Setina M, et al. Relapsing endocarditis caused by Enterococcus faecalis forming small colony variants. Scand J Infect Dis. 2013;45:800–803.
   PubMed Web of Science ®Google Scholar
• Egido SH, Ruiz MS, Ines Revuelta S, et al. Enterococcus faecium small colony variant endocarditis in an immunocompetent patient. New Microbes New Infect. 2016;9:47–49.
   Google Scholar
• Wellinghausen N, Chatterjee I, Berger A, et al. Characterization of clinical Enterococcus faecalis small-colony variants. J Clin Microbiol. 2009;47:2802–2811.
   PubMed Web of Science ®Google Scholar
• Royer G, Melloul E, Roisin L, et al. Complete genome sequencing of Enterococcus faecalis strains suggests role of Ebp deletion in infective endocarditis relapse. Clin Microbiol Infect. 2019;25:1565–1567.
   Web of Science ®Google Scholar
• Kahl BC, Becker K, Loffler B. Clinical significance and pathogenesis of staphylococcal small colony variants in persistent infections. Clin Microbiol Rev. 2016;29:401–427.
   PubMed Web of Science ®Google Scholar
• Farfour E, Leto J, Barritault M, et al. Evaluation of the Andromas matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of aerobically growing gram-positive bacilli. J Clin Microbiol. 2012;50:2702–2707.
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–477.
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120.
   PubMed Web of Science ®Google Scholar
• Walker BJ, Abeel T, Shea T, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9:e112963.
   PubMed Web of Science ®Google Scholar
• Parks DH, Imelfort M, Skennerton CT, et al. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–1055.
   PubMed Web of Science ®Google Scholar
• Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67:2640–2644.
   PubMed Web of Science ®Google Scholar
• Chen L, Yang J, Yu J, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33:D325–D328.
   PubMed Web of Science ®Google Scholar
• Carattoli A, Zankari E, Garcia-Fernandez A, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58:3895–3903.
   PubMed Web of Science ®Google Scholar
• Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–2069.
   PubMed Web of Science ®Google Scholar
• Barrick JE, Colburn G, Deatherage DE, et al. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics. 2014;15:1039.
   PubMed Web of Science ®Google Scholar
• Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16–W21.
   PubMed Web of Science ®Google Scholar
• Gilchrist CLM, Chooi YH. Clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics. 2021, btab007. doi: https://doi.org/10.1093/bioinformatics/btab007. Online ahead of print.
   Google Scholar
• Huerta-Cepas J, Szklarczyk D, Forslund K, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44:D286–D293.
   PubMed Web of Science ®Google Scholar
• Ribeiro-Goncalves B, Francisco AP, Vaz C, et al. PHYLOViz online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. Nucleic Acids Res. 2016;44:W246–W251.
   Web of Science ®Google Scholar
• Jacquier H, Birgy A, Le Nagard H, et al. Capturing the mutational landscape of the beta-lactamase TEM-1. Proc Natl Acad Sci USA. 2013;110:13067–13072.
   Web of Science ®Google Scholar
• Melloul E, Luiggi S, Anais L, et al. Characteristics of Aspergillus fumigatus in association with Stenotrophomonas maltophilia in an in vitro model of mixed biofilm. PLoS One. 2016;11:e0166325.
   PubMed Web of Science ®Google Scholar
• Matos RC, Lapaque N, Rigottier-Gois L, et al. Enterococcus faecalis prophage dynamics and contributions to pathogenic traits. PLoS Genet. 2013;9:e1003539.
   PubMed Web of Science ®Google Scholar
• Brinster S, Furlan S, Serror P. C-terminal WxL domain mediates cell wall binding in Enterococcus faecalis and other gram-positive bacteria. J Bacteriol. 2007;189:1244–1253.
   PubMed Web of Science ®Google Scholar
• Galloway-Pena JR, Liang X, Singh KV, et al. The identification and functional characterization of WxL proteins from Enterococcus faecium reveal surface proteins involved in extracellular matrix interactions. J Bacteriol. 2015;197:882–892.
   Web of Science ®Google Scholar
• Sillanpaa J, Xu Y, Nallapareddy SR, et al. A family of putative MSCRAMMs from Enterococcus faecalis. Microbiology. 2004;150:2069–2078.
   Web of Science ®Google Scholar