Tong SYC, Davis JS, Eichenberger E, Holland TL, Fowler VG Jr. Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management. Clin Microbiol Rev. 2015;28:603–61 Available from: https://doi.org/10.1128/CMR.00134-14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Senn L, Clerc O, Zanetti G, Basset P, Prod’hom G, Gordon NC, 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:e02039–15 Available from: https://doi.org/10.1128/mBio.02039-15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wertheim HFL, Melles DC, Vos MC, van Leeuwen W, van Belkum A, Verbrugh HA, et al. The role of nasal carriage in Staphylococcus aureus infections. Lancet Infect Dis. 2005;5:751–62 Available from: https://doi.org/10.1016/S1473-3099(05)70295-4.
Article
PubMed
Google Scholar
Chambers HF, Deleo FR. Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat Rev Microbiol. 2009;7:629–41 Available from: https://doi.org/10.1038/nrmicro2200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Monecke S, Coombs G, Shore AC, Coleman DC, Akpaka P, Borg M, et al. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One. 2011;6:e17936 Available from: https://doi.org/10.1371/journal.pone.0017936.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu J, Chen D, Peters BM, Li L, Li B, Xu Z, et al. Staphylococcal chromosomal cassettes mec (SCCmec): a mobile genetic element in methicillin-resistant Staphylococcus aureus. Microb Pathog. 2016;101:56–67 Available from: https://doi.org/10.1016/j.micpath.2016.10.028.
Article
CAS
PubMed
Google Scholar
Jevons MP. “Celbenin” - resistant staphylococci. Br Med J BMJ Group; 1961 [cited 2017 2];1:124. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952888/
Harkins CP, Pichon B, Doumith M, Parkhill J, Westh H, Tomasz A, et al. Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice. Genome Biol. 2017;18:130 Available from: https://doi.org/10.1186/s13059-017-1252-9.
Article
PubMed
PubMed Central
Google Scholar
Fowler VG Jr, Nelson CL, McIntyre LM, Kreiswirth BN, Monk A, Archer GL, et al. Potential associations between hematogenous complications and bacterial genotype in Staphylococcus aureus infection. J infect dis. 2007;196:738–47 NIH Public Access Available from: https://doi.org/10.1086/520088.
Article
PubMed
Google Scholar
Sharma-Kuinkel BK, Mongodin EF, Myers JR, Vore KL, Canfield GS, Fraser CM, et al. Potential influence of Staphylococcus aureus clonal complex 30 genotype and transcriptome on Hematogenous infections. Open Forum Infect Dis. 2015;2:ofv093. Available from: http://dx.doi.org/10.1093/ofid/ofv093
Article
PubMed
PubMed Central
Google Scholar
Li M, Diep BA, Villaruz AE, Braughton KR, Jiang X, DeLeo FR, et al. Evolution of virulence in epidemic community-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci. 2009;106:5883–8 Available from: https://doi.org/10.1073/pnas.0900743106.
Article
CAS
PubMed
Google Scholar
Talan DA, Krishnadasan A, Gorwitz RJ, Fosheim GE, Limbago B, Albrecht V, et al. Comparison of Staphylococcus aureus from skin and soft-tissue infections in US emergency department patients, 2004 and 2008. Clin Infect Dis. 2011;53:144–9 Available from: https://doi.org/10.1093/cid/cir308.
Article
PubMed
Google Scholar
Glaser P, Martins-Simões P, Villain A, Barbier M, Tristan A, Bouchier C, et al. Demography and intercontinental spread of the USA300 community-acquired methicillin-resistant Staphylococcus aureus lineage. MBio. 2016;7(1):e02183–15 Available from: http://mbio.asm.org/content/7/1/e02183-15.abstract.
Article
CAS
PubMed
PubMed Central
Google Scholar
Strauß L, Stegger M, Akpaka PE, Alabi A, Breurec S, Coombs G, et al. Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8. Proc Natl Acad Sci U S A. 2017;114(49):E10596–604 Available from: https://doi.org/10.1073/pnas.1702472114.
Article
PubMed
PubMed Central
Google Scholar
David MZ, Daum RS. Community-associated methicillin-resistant Staphylococcus aureus: epidemiology and clinical consequences of an emerging epidemic. Clin Microbiol Rev. 2010;23:616–87 Available from: https://doi.org/10.1128/CMR.00081-09.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bowers JR, Driebe EM, Albrecht V, McDougal LK, Granade M, Roe CC, et al. Improved subtyping of Staphylococcus aureus clonal complex 8 strains based on whole-genome phylogenetic analysis. mSphere. 2018;3(3). pii: e00464-e00417. Available from: https://doi.org/10.1128/mSphere.00464-17
Diep BA, Stone GG, Basuino L, Graber CJ, Miller A, des Etages S-A, et al. The arginine catabolic mobile element and staphylococcal chromosomal cassette mec linkage: convergence of virulence and resistance in the USA300 clone of methicillin-resistant Staphylococcus aureus. J Infect Dis. 2008;197:1523–1530. Available from: http://dx.doi.org/10.1086/587907
Article
CAS
PubMed
Google Scholar
Millar EV, Chen W-J, Schlett CD, Cui T, Crawford KB, Lanier JB, et al. Frequent use of chlorhexidine-based body wash associated with a reduction in methicillin-resistant Staphylococcus aureus nasal colonization among military trainees. Antimicrob Agents Chemother. 2015;59:943–9 Available from: https://doi.org/10.1128/AAC.03993-14.
Article
PubMed
PubMed Central
Google Scholar
Azarian T, Daum RS, Petty LA, Steinbeck JL, Yin Z, Nolan D, et al. Intrahost evolution of methicillin-resistant Staphylococcus aureus USA300 among individuals with reoccurring skin and soft-tissue infections. J Infect Dis [Internet]. 2016;214:895–905 Available from: https://doi.org/10.1093/infdis/jiw242.
Article
CAS
Google Scholar
Millar EV, Rice GK, Elassal EM, Schlett CD, Bennett JW, Redden CL, et al. Genomic characterization of USA300 MRSA to evaluate Intraclass transmission and recurrence of SSTI among high risk military trainees. Clin Infect Dis. 2017;65(3):461–8 Available from: https://doi.org/10.1093/cid/cix327.
Article
PubMed
PubMed Central
Google Scholar
Planet PJ, Diaz L, Kolokotronis S-O, Narechania A, Reyes J, Xing G, et al. Parallel epidemics of community-associated methicillin-resistant Staphylococcus aureus USA300 infection in north and South America. J Infect Dis. 2015;212:1874–82 Available from: https://doi.org/10.1093/infdis/jiv320.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jamrozy DM, Harris SR, Mohamed N, Peacock SJ, Tan CY, Parkhill J, et al. Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic. Microb Genom Microbiology Society; 2016 [cited 2016 Apr 7];2:e000058. Available from: https://doi.org/10.1099/mgen.0.000058
Von Dach E, Diene SM, Fankhauser C, Schrenzel J, Harbarth S, François P. Comparative genomics of community-associated methicillin-resistant Staphylococcus aureus shows the emergence of clone ST8-USA300 in Geneva, Switzerland. J Infect Dis. 2016;213:1370–9 Available from: https://doi.org/10.1093/infdis/jiv489.
Article
CAS
PubMed
Google Scholar
Price JR, Cole K, Bexley A, Kostiou V, Eyre DW, Golubchik T, et al. Transmission of Staphylococcus aureus between healthcare workers, the environment and patients in an intensive care unit: a whole-genome sequencing based longitudinal cohort study. Lancet Infect Dis Elsevier; 2016;17:207-14. [cited 2016 Nov 16]; Available from: http://discovery.ucl.ac.uk/1519622/
Sabat AJ, Hermelijn SM, Akkerboom V, Juliana A, Degener JE, Grundmann H, et al. Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname. Sci Rep. 2017;7:41050 Available from: https://doi.org/10.1038/srep41050.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alam MT, Read TD, Petit RA, Boyle-Vavra S, Miller LG, Eells SJ, et al. Transmission and microevolution of USA300 MRSA in U.S. households: evidence from whole-genome sequencing. MBio American Society for Microbiology. 2015;6:e00054–15 Available from: https://doi.org/10.1128/mBio.00054-15.
Google Scholar
Uhlemann A-C, Dordel J, Knox JR, Raven KE, Parkhill J, Holden MTG, et al. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci U S A. 2014;111:6738-43. Available from: https://doi.org/10.1073/pnas.1401006111.
Article
CAS
Google Scholar
Toleman MS, Reuter S, Coll F, Harrison EM, Blane B, Brown NM, et al. Systematic surveillance detects multiple silent introductions and household transmission of methicillin-resistant Staphylococcus aureus USA300 in the east of England. J Infect Dis. 2016;214:447–53. Available from: http://jid.oxfordjournals.org/content/early/2016/04/26/infdis.jiw166.abstract.
Article
PubMed
Google Scholar
Harmsen D, Claus H, Witte W, Rothgänger J, Claus H, Turnwald D, et al. Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol. 2003;41:5442–5448. Available from: https://www.ncbi.nlm.nih.gov/pubmed/14662923
Article
CAS
PubMed
PubMed Central
Google Scholar
Horan TC, Andrus M, Dudeck MA. CDC/NHSN surveillance definition of health care-associated infection and criteria for specific types of infections in the acute care setting. Am J Infect Control. 2008;36:309–32 Available from: https://doi.org/10.1016/j.ajic.2008.03.002.
Article
PubMed
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77 Available from: https://doi.org/10.1089/cmb.2012.0021.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9 Available from: https://doi.org/10.1093/bioinformatics/btu153.
Article
CAS
PubMed
Google Scholar
Gordon NC, Price JR, Cole K, Everitt R, Morgan M, Finney J, et al. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol. 2014;52:1182–91 Available from: https://doi.org/10.1128/JCM.03117-13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6:80–92 Available from: https://doi.org/10.4161/fly.19695.
Article
CAS
PubMed
PubMed Central
Google Scholar
Highlander SK, Hultén KG, Qin X, Jiang H, Yerrapragada S, Mason EO Jr, et al. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol. 2007;7:99 Available from: https://doi.org/10.1186/1471-2180-7-99.
Article
PubMed
PubMed Central
Google Scholar
Pages H, Gentleman R, Aboyoun P, DebRoy S. Biostrings: string objects representing biological sequences, and matching algorithms, 2008. R package version. 2:160.
Baba T, Takeuchi F, Kuroda M, Yuzawa H, Aoki K-I, Oguchi A, et al. Genome and virulence determinants of high virulence community-acquired MRSA. Lancet. 2002;359:1819–1827. Available from: https://www.ncbi.nlm.nih.gov/pubmed/12044378
Article
CAS
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421 Available from: https://doi.org/10.1186/1471-2105-10-421.
Article
PubMed
PubMed Central
Google Scholar
Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD. PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 2016;44:D336–42 Available from: https://doi.org/10.1093/nar/gkv1194.
Article
CAS
PubMed
Google Scholar
Treangen TJ, Ondov BD, Koren S, Phillippy AM. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15:524 Available from:https://doi.org/10.1186/PREACCEPT-2573980311437212.
Article
PubMed
PubMed Central
Google Scholar
Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol. 2015;11:e1004041 Available from: https://doi.org/10.1371/journal.pcbi.1004041.
Article
PubMed
PubMed Central
Google Scholar
Liu K, Linder CR, Warnow T. RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation. PLoS One. 2011;6:e27731 Available from: https://doi.org/10.1371/journal.pone.0027731.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dress AWM, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, et al. Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol. 2008;3:7 Available from: https://doi.org/10.1186/1748-7188-3-7.
Article
PubMed
PubMed Central
Google Scholar
Pupko T, Pe’er I, Shamir R, Graur D. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol. 2000;17:890–896. Available from: https://www.ncbi.nlm.nih.gov/pubmed/10833195
Article
CAS
PubMed
Google Scholar
Paradis E, Claude J, Strimmer K. APE: analyses of Phylogenetics and evolution in R language. Bioinformatics. 2004;20:289–90.
Article
CAS
PubMed
Google Scholar
Goerke C, Pantucek R, Holtfreter S, Schulte B, Zink M, Grumann D, et al. Diversity of prophages in dominant Staphylococcus aureus clonal lineages. J Bacteriol. 2009;191:3462–8 Available from: https://doi.org/10.1128/JB.01804-08.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lozano C, Garcia-Migura L, Aspiroz C, Zarazaga M, Torres C, Aarestrup FM. Expansion of a plasmid classification system for gram-positive bacteria and determination of the diversity of plasmids in Staphylococcus aureus strains of human, animal, and food origins. Appl Environ Microbiol. 2012;78:5948–55 Available from: http://aem.asm.org/cgi/doi/10.1128/AEM.00870-12.
Article
CAS
PubMed
PubMed Central
Google Scholar
David MZ, Acree ME, Sieth JJ, Boxrud DJ, Dobbins G, Lynfield R, et al. Pediatric S. aureus isolate genotypes and infections from the Dawn of the CA-MRSA epidemic era in Chicago, 1995-1997. J Clin Microbiol. 2015;53:2486-91. Available from: https://jcm.asm.org/content/53/8/2486.
Arredondo-Alonso S, van Schaik W, Willems RJ, Schurch AC. On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data. bioRxiv. 2016 [cited 2016 Nov 14]. p. 086744. Available from: http://biorxiv.org/content/early/2016/11/14/086744
Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, et al. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet. 2001;357:1225–1240. Available from: http://www.ncbi.nlm.nih.gov/pubmed/11418146
Article
CAS
Google Scholar
Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, et al. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet. 2006;367:731–9 Available from: https://doi.org/10.1016/S0140-6736(06)68231-7.
Article
CAS
PubMed
Google Scholar
Jensen LB, Garcia-Migura L, Valenzuela AJS, Løhr M, Hasman H, Aarestrup FM. A classification system for plasmids from enterococci and other gram-positive bacteria. J Microbiol Methods [Internet]. 2010;80:25–43 Available from: https://doi.org/10.1016/j.mimet.2009.10.012.
Article
CAS
Google Scholar
Keggins KM, Lovett PS, Duvall EJ. Molecular cloning of genetically active fragments of bacillus DNA in Bacillus subtilis and properties of the vector plasmid pUB110. Proc Natl Acad Sci U S A. 1978;75:1423–1427. Available from: https://www.ncbi.nlm.nih.gov/pubmed/418411
Article
CAS
Google Scholar
Ramsay JP, Kwong SM, Murphy RJT, Yui Eto K, Price KJ, Nguyen QT, et al. An updated view of plasmid conjugation and mobilization in staphylococcus. Mob Genet Elements. 2016;6:e1208317 Available from: https://doi.org/10.1080/2159256x2016.1208317.
Article
PubMed
PubMed Central
Google Scholar
Khan SA, Novick RP. Complete nucleotide sequence of pT181, a tetracycline-resistance plasmid from Staphylococcus aureus. Plasmid. 1983;10:251–259. Available from: https://www.ncbi.nlm.nih.gov/pubmed/6657777
Article
CAS
PubMed
Google Scholar
Rocha EPC, Smith JM, Hurst LD, Holden MTG, Cooper JE, Smith NH, et al. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol. 2006;239:226–35 Available from: https://doi.org/10.1016/j.jtbi.2005.08.037.
Article
CAS
PubMed
Google Scholar
Planet PJ, Larussa SJ, Dana A, Smith H, Xu A, Ryan C, et al. Emergence of the epidemic methicillin-resistant Staphylococcus aureus strain USA300 coincides with horizontal transfer of the arginine catabolic Mobile element and speG-mediated adaptations for survival on skin. MBio. 2013;4(6):e00889–13 Available from: https://doi.org/10.1128/mBio.00889-13.
Article
PubMed
PubMed Central
Google Scholar
Otto M. Community-associated MRSA: what makes them special? Int J Med Microbiol. 2013;303:324–30 Available from: https://doi.org/10.1016/j.ijmm.2013.02.007.
Article
PubMed
PubMed Central
Google Scholar
Shopsin B, Drlica-Wagner A, Mathema B, Adhikari RP, Kreiswirth BN, Novick RP. Prevalence of agr dysfunction among colonizing Staphylococcus aureus strains. J Infect Dis. 2008;198:1171–4 Available from: https://doi.org/10.1086/592051.
Article
PubMed
Google Scholar
Traber KE, Lee E, Benson S, Corrigan R, Cantera M, Shopsin B, et al. Agr function in clinical Staphylococcus aureus isolates. Microbiology. 2008;154:2265–74 Available from: https://doi.org/10.1099/mic.0.2007/011874-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Young BC, Golubchik T, Batty EM, Fung R, Larner-Svensson H, Votintseva AA, et al. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci. 2012;109:4550–5 Available from: https://doi.org/10.1073/pnas.1113219109.
Article
CAS
PubMed
Google Scholar
Oh J, Byrd AL, Park M, Kong HH, Segre JA. Temporal stability of the human skin microbiome. Cell.;2016 [cited 2016 May 5];165:854–866. Available from: http://www.cell.com/cell/fulltext/S0092-8674(16)30399-3
Harris SR, Feil EJ, Holden MTG, Quail MA, Nickerson EK, Chantratita N, et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science. 2010;327:469–74 Available from: https://doi.org/10.1126/science.1182395.
Article
CAS
PubMed
PubMed Central
Google Scholar
Holden MTG, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res. 2013;23:653–64 Available from: https://doi.org/10.1101/gr.147710.112.
Article
CAS
PubMed
PubMed Central
Google Scholar
McAdam PR, Templeton KE, Edwards GF, Holden MTG, Feil EJ, Aanensen DM, et al. Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci. 2012;109(23):9107–12 Available from: https://doi.org/10.1073/pnas.1202869109.
Article
CAS
PubMed
Google Scholar
Spoor LE, Mcadam PR, Weinert LA, Rambaut A, Hasman H, Aarestrup FM, et al. Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus. MBio. 2013;4:e00356–13 Available from: https://doi.org/10.1128/mBio.00356-13.
Article
PubMed
PubMed Central
Google Scholar
Kluytmans J, van Belkum A, Verbrugh H. Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks. Clin Microbiol Rev. 1997;10:505–520. Available from: http://www.ncbi.nlm.nih.gov/pubmed/9227864
Article
CAS
PubMed
PubMed Central
Google Scholar
Williamson DA, Ritchie S, Keren B, Harrington M, Thomas MG, Upton A, et al. Persistence, discordance and diversity of Staphylococcus aureus nasal and oropharyngeal colonization in school-aged children. Pediatr Infect Dis J. 2016;35:744–8 Available from: https://doi.org/10.1097/INF.0000000000001173.
Article
PubMed
Google Scholar
Ledda A, Price JR, Cole K, Llewelyn MJ, Kearns AM, Crook DW, et al. Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus. J Antimicrob Chemother. 2017;72(5):1285–8 Available from: https://doi.org/10.1093/jac/dkw570.
CAS
PubMed
PubMed Central
Google Scholar
Smyth DS, Kafer JM, Wasserman GA, Velickovic L, Mathema B, Holzman RS, et al. Nasal carriage as a source of agr-defective Staphylococcus aureus bacteremia. J Infect Dis. 2012;206:1168–77 Available from: https://doi.org/10.1093/infdis/jis483.
Article
PubMed
PubMed Central
Google Scholar
Golubchik T, Batty EM, Miller RR, Farr H, Young BC, Larner-Svensson H, et al. Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS One. Public Library of Science; 2013;8:e61319. Available from: https://doi.org/10.1371/journal.pone.0061319
Article
CAS
PubMed
PubMed Central
Google Scholar
Worby CJ, Lipsitch M, Hanage WP. Shared genomic variants: identification of transmission routes using pathogen deep sequence data. bioRxiv. 2015 [cited 2015 Nov 30]. p. 032458. Available from: http://biorxiv.org/content/early/2015/11/20/032458
Worby CJ, Lipsitch M, Hanage WP. Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput Biol. 2014;10:e1003549 Available from: https://doi.org/10.1371/journal.pcbi.1003549.
Article
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5 Available from: https://doi.org/10.1093/nar/gkw290.
Article
CAS
PubMed
PubMed Central
Google Scholar