Horizontal gene transfer in human pathogens

References

• Alvarez-Martinez CE, Christie PJ. (2009). Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73:775–808
   PubMed Web of Science ®Google Scholar
• Ambur OH, Davidsen T, Frye SA, et al. (2009). Genome dynamics in major bacterial pathogens. FEMS Microbiol Rev 33:453–70
   PubMedGoogle Scholar
• Ambur OH, Frye SA, Tønjum T. (2007). New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators. J Bacteriol 189:2077–85
   PubMed Web of Science ®Google Scholar
• Asadulghani M, Ogura Y, Ooka T, et al. (2009). The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PLoS Pathog 5:e1000408
   PubMed Web of Science ®Google Scholar
• Aslantas O, Türkyilmaz S, Yilmaz MA, et al. (2012). Isolation and molecular characterization of methicillin-resistant staphylococci from horses, personnel and environmental sites at an equine hospital in Turkey. J Vet Med Sci 74:1583–8
   PubMedGoogle Scholar
• Bielaszewska M, Mellmann A, Zhang W, et al. (2011). Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. Lancet Infect Dis 11:671–6
   PubMed Web of Science ®Google Scholar
• Bikard D, Hatoum-Aslan A, Mucida D, Marraffini LA. (2012). CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12:177–86
   PubMed Web of Science ®Google Scholar
• Bloemendaal AL, Brouwer EC, Fluit AC. (2010). Methicillin resistance transfer from Staphylocccus epidermidis to methicillin-susceptible Staphylococcus aureus in a patient during antibiotic therapy. PLoS One 5:e11841
   Google Scholar
• Boundy S, Safo MK, Wang L, et al. (2013). Characterization of the Staphylococcus aureus rRNA methyltransferase encoded by orfX, the gene containing the staphylococcal chromosome Cassette mec (SCCmec) insertion site. J Biol Chem 288:132–40
   PubMed Web of Science ®Google Scholar
• Brouwer MS, Warburton PJ, Roberts AP, et al. (2011). Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile. PLoS One 6:e23014
   Google Scholar
• Burgos Y, Beutin L. (2010). Common origin of plasmid encoded alpha-hemolysin genes in Escherichia coli. BMC Microbiol 10:193
   PubMed Web of Science ®Google Scholar
• Cairns MD, Stabler RA, Shetty N, Wren BW. (2012). The continually evolving Clostridium difficile species. Future Microbiol 7:945–57
   Google Scholar
• Chan CX, Beiko RG, Ragan MA. (2011). Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. J Bacteriol 193:3964–77
   PubMedGoogle Scholar
• Chen J, Novick RP. (2009). Phage-mediated intergeneric transfer of toxin genes. Science 323:139–41
   PubMed Web of Science ®Google Scholar
• Cirl C, Wieser A, Yadav M, et al. (2008). Subversion of toll-like receptor signaling by a unique family of bacterial Toll/interleukin-1 receptor domain-containing proteins. Nat Med 14:399–406
   PubMed Web of Science ®Google Scholar
• Coleman ML, Sullivan MB, Martiny AC, et al. (2006). Genomic islands and the ecology and evolution of Prochlorococcus. Science 311:1768–70
   Google Scholar
• Corvaglia AR, François P, Hernandez D, et al. (2010). A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains. Proc Natl Acad Sci U S A 107:11954–8
   PubMedGoogle Scholar
• Corver J, Bakker D, Brouwer MS, et al. (2012). Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164. BMC Microbiol 12:130
   PubMedGoogle Scholar
• Croxen MA, Finlay BB. (2010). Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 8:26–38
   PubMed Web of Science ®Google Scholar
• Damle PK, Wall EA, Spilman MS, et al. (2012). The roles of SaPI1 proteins gp7 (CpmA) and gp6 (CpmB) in capsid size determination and helper phage interference. Virology 432:277–82
   Google Scholar
• de Niederhäusern S, Bondi M, Messi P, et al. (2011). Vancomycin-resistance transferability from VanA enterococci to Staphylococcus aureus. Curr Microbiol 62:1363–7
   Google Scholar
• Deurenberg RH, Vink C, Kalenic S, et al. (2007). The molecular evolution of methicillin-resistant Staphylococcus aureus. Clin Microbiol Infect 13:222–35
   PubMed Web of Science ®Google Scholar
• Dobrindt U, Chowdary MG, Krumbholz G, Hacker J. (2010). Genome dynamics and its impact on evolution of Escherichia coli. Med Microbiol Immunol 199:145–54
   PubMed Web of Science ®Google Scholar
• Dostál L, Shao S, Schildbach JF. (2011). Tracking F plasmid TraI relaxase processing reactions provides insight into F plasmid transfer. Nucleic Acids Res 39:2658–70
   PubMedGoogle Scholar
• Dubey GP, Ben-Yehuda S. (2011). Intercellular nanotubes mediate bacterial communication. Cell 144:590–600
   PubMed Web of Science ®Google Scholar
• Ficht TA. (2011). Bacterial exchange via nanotubes: lessons learned from the history of molecular biology. Front Microbiol 2:179
   PubMedGoogle Scholar
• Fluit AC, Carpaij N, Majoor EA, et al. (2013). Shared reservoir of ccrB gene sequences between coagulase-negative staphylococci and methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother April 18 (Epub ahead of print), doi: 10.1093/jac/dkt121
   PubMedGoogle Scholar
• Freeman J, Bauer MP, Baines SD, et al. (2010). The changing epidemiology of Clostridium difficile infections. Clin Microbiol Rev 23:529–49
   PubMed Web of Science ®Google Scholar
• Frost LS, Leplae R, Summers AO, Toussaint A. (2005). Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722–32
   PubMed Web of Science ®Google Scholar
• Gardner SP, Olson JW. (2012). Barriers to horizontal gene transfer in Campylobacter jejuni. Adv Appl Microbiol 79:19–42
   PubMed Web of Science ®Google Scholar
• Goldenfeld N, Woese C. (2007). Biology's next revolution. Nature 445:369
   PubMed Web of Science ®Google Scholar
• Grad YH, Godfrey P, Cerquiera GC, et al. (2013). Comparative genomics of recent shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. MBio 4:e00452--12
   Google Scholar
• Guinane CM, Penadés JR, Fitzgerald JR. (2011). The role of horizontal gene transfer in Staphylococcus aureus host adaptation. Virulence 2:241–3
   PubMed Web of Science ®Google Scholar
• He M, Sebaihia M, Lawley TD, et al. (2010). Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci USA 107:7527–32
   PubMed Web of Science ®Google Scholar
• Horvath P, Barrangou R. (2010). CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–70
   PubMed Web of Science ®Google Scholar
• Ito T, Ma XX, Takeuchi F, et al. (2004). Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC. Antimicrob Agents Chemother 48:2637–51
   PubMed Web of Science ®Google Scholar
• Ito T, Okuma K, Ma XX, et al. (2003). Insights on antibiotic resistance of Staphylococcus aureus from its whole genome: genomic island SCC. Drug Resist Updat 6:41–52
   PubMed Web of Science ®Google Scholar
• Jasni AS, Mullany P, Hussain H, Roberts AP. (2010). Demonstration of conjugative transposon (Tn5397)-mediated horizontal gene transfer between Clostridium difficile and Enterococcus faecalis. Antimicrob Agents Chemother 54:4924–6
   PubMedGoogle Scholar
• Juhas M, Crook DW, Dimopoulou ID, et al. (2007a). Novel type IV secretion system involved in propagation of genomic islands. J Bacteriol 189:761–71
   PubMedGoogle Scholar
• Juhas M, Crook DW, Hood DW. (2008). Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence. Cellular Microbiology 10:2377–86
   PubMedGoogle Scholar
• Juhas M, Power PM, Harding RM, et al. (2007b). Sequence and functional analyses of Haemophilus spp. genomic islands. Genome Biol 8:R237
   PubMed Web of Science ®Google Scholar
• Juhas M, van der Meer JR, Gaillard M, et al. (2009). Genomic islands: tools of bacterial horizontal gene transfer and evolution. Fems Microbiology Reviews 33:376–93
   PubMed Web of Science ®Google Scholar
• Kachrimanidou M, Malisiovas N. (2011). Clostridium difficile infection: a comprehensive review. Crit Rev Microbiol 37:178–87
   PubMed Web of Science ®Google Scholar
• Katayama Y, Ito T, Hiramatsu K. (2000). A new class of genetic element, staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 44:1549–55
   PubMed Web of Science ®Google Scholar
• Kinnevey PM, Shore AC, Brennan GI, et al. (2013). Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harboring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals. Antimicrob Agents Chemother 57:524–31
   PubMedGoogle Scholar
• Klockgether J, Wurdemann D, Reva O, et al. (2007). Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol 189:2443–59
   PubMed Web of Science ®Google Scholar
• Kloesges T, Popa O, Martin W, Dagan T. (2011). Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28:1057–74
   PubMedGoogle Scholar
• Konczy P, Ziebell K, Mascarenhas M, et al. (2008). Genomic O island 122, locus for enterocyte effacement, and the evolution of virulent verocytotoxin-producing Escherichia coli. J Bacteriol 190:5832–40
   PubMed Web of Science ®Google Scholar
• Koonin EV, Wolf YI. (2008). Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36:6688–719
   PubMed Web of Science ®Google Scholar
• Krüger NJ, Stingl K. (2011). Two steps away from novelty–principles of bacterial DNA uptake. Mol Microbiol 80:860–7
   PubMedGoogle Scholar
• Larbig KD, Christmann A, Johann A, et al. (2002). Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol 184:6665–80
   PubMedGoogle Scholar
• Li M, Diep BA, Villaruz AE, Braughton KR, et al. (2009). Evolution of virulence in epidemic community-associated methicillin-resistant Staphylococcus aureus. Proc Natl Acad Sci USA 106:5883–8
   PubMed Web of Science ®Google Scholar
• Maiques E, Ubeda C, Tormo MA, et al. (2007). Role of staphylococcal phage and SaPI integrase in intra- and interspecies SaPI transfer. J Bacteriol 189:5608–16
   PubMed Web of Science ®Google Scholar
• Marraffini LA, Sontheimer EJ. (2008). CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843–5
   PubMed Web of Science ®Google Scholar
• Marraffini LA, Sontheimer EJ. (2010). Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463:568–71
   PubMed Web of Science ®Google Scholar
• Mathers AJ, Cox HL, Kitchel B, et al. (2011). Molecular dissection of an outbreak of carbapenem-resistant enterobacteriaceae reveals Intergenus KPC carbapenemase transmission through a promiscuous plasmid. MBio 2:e00204–11
   PubMed Web of Science ®Google Scholar
• Meessen-Pinard M, Sekulovic O, Fortier LC. (2012). Evidence of in vivo prophage induction during Clostridium difficile infection. Appl Environ Microbiol 78:7662–70
   Google Scholar
• Mellmann A, Harmsen D, Cummings CA, et al. (2011). Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6:e22751
   PubMed Web of Science ®Google Scholar
• Millen AM, Horvath P, Boyaval P, Romero DA. (2012). Mobile CRISPR/Cas-mediated bacteriophage resistance in Lactococcus lactis. PLoS One 7:e51663
   PubMed Web of Science ®Google Scholar
• Moskowitz SM, Wiener-Kronish JP. (2010). Mechanisms of bacterial virulence in pulmonary infections. Curr Opin Crit Care 16:8–12
   PubMed Web of Science ®Google Scholar
• Müller D, Greune L, Heusipp G, et al. (2007). Identification of unconventional intestinal pathogenic Escherichia coli isolates expressing intermediate virulence factor profiles by using a novel single-step multiplex PCR. Appl Environ Microbiol 73:3380–90
   PubMed Web of Science ®Google Scholar
• Nishio M, Okada N, Miki T, et al. (2005). Identification of the outer-membrane protein PagC required for the serum resistance phenotype in Salmonella enterica serovar Choleraesuis. Microbiology 151:863–73
   PubMed Web of Science ®Google Scholar
• Novick RP, Christie GE, Penadés JR. (2010). The phage-related chromosomal islands of Gram-positive bacteria. Nat Rev Microbiol 8:541–51
   Google Scholar
• Nozawa T, Furukawa N, Aikawa C, et al. (2011). CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PLoS One 6:e19543
   PubMed Web of Science ®Google Scholar
• Ogura Y, Ooka T, Asadulghani M, et al. (2007). Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes. Genome Biol 8:R138
   Google Scholar
• Pituch H. (2009). Clostridium difficile is no longer just a nosocomial infection or an infection of adults. Int J Antimicrob Agents 33:S42–5
   Web of Science ®Google Scholar
• Pleckaityte M, Zilnyte M, Zvirbliene A. (2012). Insights into the CRISPR/Cas system of Gardnerella vaginalis. BMC Microbiol 12:301
   PubMedGoogle Scholar
• Popa O, Dagan T. (2011). Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol 14:615–23
   Google Scholar
• Popa O, Hazkani-Covo E, Landan G, et al. (2011). Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599–609
   PubMed Web of Science ®Google Scholar
• Queck SY, Khan BA, Wang R, et al. (2009). Mobile genetic element-encoded cytolysin connects virulence to methicillin resistance in MRSA. PLoS Pathog 5:e1000533
   PubMed Web of Science ®Google Scholar
• Ram G, Chen J, Kumar K, et al. (2012). Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism. Proc Natl Acad Sci U S A 109:16300–5
   Web of Science ®Google Scholar
• Rasko DA, Rosovitz MJ, Myers GS, et al. (2008). The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–93
   PubMed Web of Science ®Google Scholar
• Rasko DA, Webster DR, Sahl JW, et al. (2011). Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365:709–17
   PubMed Web of Science ®Google Scholar
• Roberts AP, Chandler M, Courvalin P, et al. (2008). Revised nomenclature for transposable genetic elements. Plasmid 60:167–73
   PubMed Web of Science ®Google Scholar
• Rothberg JM, Hinz W, Rearick TM, et al. (2011). An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–52
   PubMed Web of Science ®Google Scholar
• Rupnik M, Wilcox MH, Gerding DN. (2009). Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol 7:526–36
   PubMed Web of Science ®Google Scholar
• Schertzer JW, Whiteley M. (2011). Microbial communication superhighways. Cell 144:469–70
   PubMedGoogle Scholar
• Schijffelen MJ, Boel CH, van Strijp JA, Fluit AC. (2010). Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis. BMC Genomics 11:376
   PubMed Web of Science ®Google Scholar
• Schmidt MA. (2010). LEEways: tales of EPEC, ATEC and EHEC. Cell Microbiol 12:1544–52
   PubMed Web of Science ®Google Scholar
• Schubert S, Nörenberg D, Clermont O, et al. (2010). Prevalence and phylogenetic history of the TcpC virulence determinant in Escherichia coli. Int J Med Microbiol 300:429–34
   PubMedGoogle Scholar
• Scott J, Thompson-Mayberry P, Lahmamsi S, et al. (2008). Phage-associated mutator phenotype in group A streptococcus. J Bacteriol 190:6290–301
   Google Scholar
• Sebaihia M, Wren BW, Mullany P, et al. (2006). The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 38:779–86
   PubMed Web of Science ®Google Scholar
• Sentchilo V, Czechowska K, Pradervand N, et al. (2009). Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13. Mol Microbiol 72:1293–306
   PubMed Web of Science ®Google Scholar
• Severin A, Tabei K, Tenover F, et al. (2004). High level oxacillin and vancomycin resistance and altered cell wall composition in Staphylococcus aureus carrying the staphylococcal mecA and the enterococcal vanA gene complex. J Biol Chem 279:3398–407
   PubMedGoogle Scholar
• Smyth DS, Wong A, Robinson DA. (2011). Cross-species spread of SCCmec IV subtypes in staphylococci. Infect Genet Evol 11:446–53
   PubMedGoogle Scholar
• Spigaglia P, Barbanti F, Mastrantonio P. (2005). Horizontal transfer of erythromycin resistance from Clostridium difficile to Butyrivibrio fibrisolvens. Antimicrob Agents Chemother 49:5142–5
   PubMedGoogle Scholar
• Stabler RA, Gerding DN, Songer JG, et al. (2006). Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol 188:7297–305
   PubMed Web of Science ®Google Scholar
• Stabler RA, He M, Dawson L, Martin M, et al. (2009). Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol 10:R102
   PubMed Web of Science ®Google Scholar
• Stingl K, Müller S, Scheidgen-Kleyboldt G, et al. (2010). Composite system mediates two-step DNA uptake into Helicobacter pylori. Proc Natl Acad Sci USA 107:1184–9
   PubMedGoogle Scholar
• Sung JM, Lindsay JA. (2007). Staphylococcus aureus strains that are hypersusceptible to resistance gene transfer from enterococci. Antimicrob Agents Chemother 51:2189–91
   Google Scholar
• Tobe T, Beatson SA, Taniguchi H, et al. (2006). An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc Natl Acad Sci USA 103:14941–6
   PubMed Web of Science ®Google Scholar
• Tock MR, Dryden DT. (2005). The biology of restriction and anti-restriction. Curr Opin Microbiol 8:466–72
   PubMed Web of Science ®Google Scholar
• Toleman MA, Walsh TR. (2011). Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 35:912–35
   Google Scholar
• Touchon M, Hoede C, Tenaillon O, et al. (2009). Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344
   PubMed Web of Science ®Google Scholar
• Treangen TJ, Ambur OH, Tonjum T, Rocha EP. (2008). The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 9:R60
   Google Scholar
• Ubeda C, Barry P, Penadés JR, Novick RP. (2007). A pathogenicity island replicon in Staphylococcus aureus replicates as an unstable plasmid. Proc Natl Acad Sci USA 104:14182–8
   PubMedGoogle Scholar
• Ubeda C, Olivarez NP, Barry P, et al. (2009). Specificity of staphylococcal phage and SaPI DNA packaging as revealed by integrase and terminase mutations. Mol Microbiol 72:98–108
   Google Scholar
• Ubeda C, Tormo-Más M, Penadés JR, Novick RP. (2012). Structure-function analysis of the SaPIbov1 replication origin in Staphylococcus aureus. Plasmid 67:183–90
   PubMedGoogle Scholar
• van der Meer JR, Ravatn R, Sentchilo V. (2001). The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases. Arch Microbiol 175:79–85
   PubMedGoogle Scholar
• Wallden K, Rivera-Calzada A, Waksman G. (2010). Type IV secretion systems: versatility and diversity in function. Cell Microbiol 12:1203–12
   PubMed Web of Science ®Google Scholar
• Wang L, Archer GL. (2010). Roles of CcrA and CcrB in excision and integration of staphylococcal cassette chromosome mec, a Staphylococcus aureus genomic island. J Bacteriol 192:3204–12
   PubMedGoogle Scholar
• Wang L, Safo M, Archer GL. (2012). Characterization of DNA sequences required for the CcrAB-mediated integration of staphylococcal cassette chromosome mec, a Staphylococcus aureus genomic island. J Bacteriol 194:486–98
   PubMedGoogle Scholar
• Wang R, Braughton KR, Kretschmer D, et al. (2007). Identification of novel cytolytic peptides as key virulence determinants for community-associated MRSA. Nat Med 13:1510–4
   PubMed Web of Science ®Google Scholar
• Weigel LM, Clewell DB, Gill SR, et al. (2003). Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science 302:1569–71
   PubMed Web of Science ®Google Scholar
• Wong JJ, Lu J, Glover JN. (2012). Relaxosome function and conjugation regulation in F-like plasmids – a structural biology perspective. Mol Microbiol 85:602–17
   PubMedGoogle Scholar
• Wozniak RA, Waldor MK. (2010). Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8:552–63
   PubMed Web of Science ®Google Scholar
• Zhu W, Clark NC, McDougal LK, et al. (2008). Vancomycin-resistant Staphylococcus aureus isolates associated with Inc18-like vanA plasmids in Michigan. Antimicrob Agents Chemother 52:452–7
   PubMedGoogle Scholar
• Zhu W, Murray PR, Huskins WC, et al. (2010). Dissemination of an Enterococcus Inc18-Like vanA plasmid associated with vancomycin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 54:4314–20
   PubMed Web of Science ®Google Scholar