Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H. Prophage genomics. Microbiol Mol Biol Rev. 2003;67:238–76.
Lu MJ, Henning U. Superinfection exclusion by T-even-type coliphages. Trends Microbiol. 1994;2:137–9.
Susskind MA, Wright A, Botstein D. Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. IV. genetics and physiology of sieB exclusion. Virology. 1974;62:367–84.
Asadulghani M, Ogura Y, Ooka T, Itoh T, Sawaguchi A, Iguchi A, et al. The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PLoS Pathog. 2009;5:e1000408.
Matos RC, Lapaque N, Rigottier-Gois L, Debarbieux L, Meylheuc T, Gonzalez-Zorn B, et al. Enterococcus faecalis prophage dynamics and contributions to pathogenic traits. PLoS Genet. 2013;9:e1003539.
Touchon M, Bobay LM, Rocha EP. The chromosomal accommodation and domestication of mobile genetic elements. Curr Opin Microbiol. 2014a;22:22–9.
Nakayama K, Takashima K, Ishihara H, Shinomiya T, Kageyama M, Kanaya S, et al. The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol Microbiol. 2000;38:213–31.
Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C, Sanschagrin F, et al. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res. 2009;19:12–23.
Bossi L, Fuentes JA, Mora G, Figueroa-Bossi N. Prophage contribution to bacterial population dynamics. J Bacteriol. 2003;185:6467–71.
Fortier LC, Sekulovic O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence. 2013;4:354–65.
Nanda AM, Thormann K, Frunzke J. Impact of spontaneous prophage induction on the fitness of bacterial populations and host-microbe interactions. J Bacteriol. 2015;197:410–9.
Brown SP, Le Chat L, De Paepe M, Taddei F. Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare. Curr Biol. 2006;16:2048–52.
Sousa JAM, Rocha EPC. Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation. Sci Rep. 2019;9:3149.
Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife. 2015;4:e08490.
Touchon M, Bernheim A, Rocha EP. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 2016;10:2744–54.
Bobay LM, Rocha EP, Touchon M. The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol. 2013;30:737–51.
Wagner PL, Waldor MK. Bacteriophage control of bacterial virulence. Infect Immun. 2002;70:3985–93.
Chen J, Quiles-Puchalt N, Chiang YN, Bacigalupe R, Fillol-Salom A, Chee MSJ, et al. Genome hypermobility by lateral transduction. Science. 2018;362:207–12.
Touchon M, Moura de Sousa JA, Rocha EP. Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Curr Opin Microbiol. 2017;38:66–73.
Haaber J, Leisner JJ, Cohn MT, Catalan-Moreno A, Nielsen JB, Westh H, et al. Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells. Nat Commun. 2016;7:13333.
Brisse S, Grimont F, Grimont PAD. The genus Klebsiella. The Prokaryotes. New York, USA: Springer; 2006. p. 159–96.
Lee CR, Lee JH, Park KS, Jeon JH, Kim YB, Cha CJ, et al. Antimicrobial resistance of hypervirulent Klebsiella pneumoniae: epidemiology, hypervirulence-associated determinants, and resistance mechanisms. Front Cell Infect Microbiol. 2017;7:483.
Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev. 2017;41:252–75.
Blin C, Passet V, Touchon M, Rocha EPC, Brisse S. Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol. 2017;19:1881–98.
Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, et al. Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. PLoS Genet. 2019;15:e1008114.
Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci USA. 2015;112:E3574–81.
Mori M, Ohta M, Agata N, Kido N, Arakawa Y, Ito H, et al. Identification of species and capsular types of Klebsiella clinical isolates, with special reference to Klebsiella planticola. Microbiol Immunol. 1989;33:887–95.
Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, et al. Identification of Klebsiella capsule synthesis loci from whole genome data. Micro Genom. 2016;2:e000102.
Pan YJ, Lin TL, Chen CT, Chen YY, Hsieh PF, Hsu CR, et al. Genetic analysis of capsular polysaccharide synthesis gene clusters in 79 capsular types of Klebsiella spp. Sci Rep. 2015;5:15573.
Favre-Bonte S, Licht TR, Forestier C, Krogfelt KA. Klebsiella pneumoniae capsule expression is necessary for colonization of large intestines of streptomycin-treated mice. Infect Immun. 1999;67:6152–6.
Alvarez D, Merino S, Tomas JM, Benedi VJ, Alberti S. Capsular polysaccharide is a major complement resistance factor in lipopolysaccharide O side chain-deficient Klebsiella pneumoniae clinical isolates. Infect Immun. 2000;68:953–5.
Campos MA, Vargas MA, Regueiro V, Llompart CM, Alberti S, Bengoechea JA. Capsule polysaccharide mediates bacterial resistance to antimicrobial peptides. Infect Immun. 2004;72:7107–14.
Doorduijn DJ, Rooijakkers SHM, van Schaik W, Bardoel BW. Complement resistance mechanisms of Klebsiella pneumoniae. Immunobiology. 2016;221:1102–9.
Rendueles O, Garcia-Garcera M, Neron B, Touchon M, Rocha EPC. Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens. PLoS Pathog. 2017;13:e1006525.
Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC. Genetic exchanges are more frequent in bacteria encoding capsules. PLoS Genet. 2018;14:e1007862.
Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014;46:305–9.
Moller AG, Lindsay JA, Read TD. Determinants of phage host range in Staphylococcus species. Appl Environ Microbiol. 2019;85:e00209–19.
Negus D, Burton J, Sweed A, Gryko R, Taylor PW. Poly-gamma-(D)-glutamic acid capsule interferes with lytic infection of Bacillus anthracis by B. anthracis-specific bacteriophages. Appl Environ Microbiol. 2013;79:714–7.
Scholl D, Adhya S, Merril C. Escherichia coli K1’s capsule is a barrier to bacteriophage T7. Appl Environ Microbiol. 2005;71:4872–4.
Niemann H, Frank N, Stirm S. Klebsiella serotype-13 capsular polysaccharide: primary structure and depolymerization by a bacteriophage-borne glycanase. Carbohydr Res. 1977a;59:165–77.
Niemann H, Kwiatkowski B, Westphal U, Stirm S. Klebsiella serotype 25 capsular polysaccharide: primary structure and depolymerization by a bacteriophage-borne glycanase. J Bacteriol. 1977b;130:366–74.
Pan YJ, Lin TL, Chen CC, Tsai YT, Cheng YH, Chen YY, et al. Klebsiella phage PhiK64-1 encodes multiple depolymerases for multiple host capsular types. J Virol. 2017;91:e02457–02416.
Bessler W, Freund-Molbert E, Knufermann H, Rduolph C, Thurow H, Stirm S. A bacteriophage-induced depolymerase active on Klebsiella K11 capsular polysaccharide. Virology. 1973;56:134–51.
Thurow H, Niemann H, Rudolph C, Stirm S. Host capsule depolymerase activity of bacteriophage particles active on Klebsiella K20 and K24 strains. Virology. 1974;58:306–9.
Latka A, Maciejewska B, Majkowska-Skrobek G, Briers Y, Drulis-Kawa Z. Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process. Appl Microbiol Biotechnol. 2017;101:3103–19.
Scholl D, Rogers S, Adhya S, Merril CR. Bacteriophage K1-5 encodes two different tail fiber proteins, allowing it to infect and replicate on both K1 and K5 strains of Escherichia coli. J Virol. 2001;75:2509–15.
Lin TL, Hsieh PF, Huang YT, Lee WC, Tsai YT, Su PA, et al. Isolation of a bacteriophage and its depolymerase specific for K1 capsule of Klebsiella pneumoniae: implication in typing and treatment. J Infect Dis. 2014;210:1734–44.
Pan YJ, Lin TL, Chen YY, Lai PH, Tsai YT, Hsu CR, et al. Identification of three podoviruses infecting Klebsiella encoding capsule depolymerases that digest specific capsular types. Micro Biotechnol. 2019;12:472–86.
Bertozzi Silva J, Storms Z, Sauvageau D. Host receptors for bacteriophage adsorption. FEMS Microbiol Lett. 2016;363:fnw002.
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16–21.
Daubin V, Lerat E, Perriere G. The source of laterally transferred genes in bacterial genomes. Genome Biol. 2003;4:R57.
Rocha EP, Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet. 2002;18:291–4.
Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci USA. 2014;111:12127–32.
Casjens SR, Gilcrease EB, Huang WM, Bunny KL, Pedulla ML, Ford ME, et al. The pKO2 linear plasmid prophage of Klebsiella oxytoca. J Bacteriol. 2004;186:1818–32.
Leclercq S, Cordaux R. Do phages efficiently shuttle transposable elements among prokaryotes? Evolution. 2011;65:3327–31.
Ghazaryan L, Tonoyan L, Ashhab AA, Soares MI, Gillor O. The role of stress in colicin regulation. Arch Microbiol. 2014;196:753–64.
Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol. 2010;8:317–27.
Samson JE, Magadan AH, Sabri M, Moineau S. Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol. 2013;11:675–87.
Wyres KL, Gorrie C, Edwards DJ, Wertheim HF, Hsu LY, Van Kinh N, et al. Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal group 258. Genome Biol Evol. 2015;7:1267–79.
Tan D, Zhang Y, Qin J, Le S, Gu J, Chen LK et al. A frameshift mutation in wcaJ associated with phage resistance in Klebsiella pneumoniae. Microorganisms. 2020;8:378.
Buffet A, Rocha EPC, Rendueles O. Selection for the bacterial capsule in the absence of biotic and abiotic aggressions depends on growth conditions. BioRxiv. 2020. https://doi.org/10.1101/2020.04.27.059774.
Julianelle LA. Bacterial variation in cultures of Friedlander’s Bacillus. J Exp Med. 1928;47:889–902.
Randall WA. Colony and antigenic variation in Klebsiella pneumoniae types A, B and C. J Bacteriol. 1939;38:461–77.
Flores CO, Meyer JR, Valverde S, Farr L, Weitz JS. Statistical structure of host-phage interactions. Proc Natl Acad Sci USA. 2011;108:E288–97.
Mathieu A, Dion M, Deng L, Tremblay D, Moncaut E, Shah SA, et al. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages. Nat Commun. 2020;11:385.
Weitz JS, Poisot T, Meyer JR, Flores CO, Valverde S, Sullivan MB, et al. Phage-bacteria infection networks. Trends Microbiol. 2013;21:82–91.
Brueggemann AB, Harrold CL, Rezaei Javan R, van Tonder AJ, McDonnell AJ, Edwards BA. Pneumococcal prophages are diverse, but not without structure or history. Sci Rep. 2017;7:42976.
Castillo D, Kauffman K, Hussain F, Kalatzis P, Rorbo N, Polz MF, et al. Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities. Sci Rep. 2018;8:9973.
Allen HK, Looft T, Bayles DO, Humphrey S, Levine UY, Alt D, et al. Antibiotics in feed induce prophages in swine fecal microbiomes. mBio. 2011;2:e00260–11.
Otsuji N, Sekiguchi M, Iijima T, Takagi Y. Induction of phage formation in the lysogenic Escherichia coli K-12 by mitomycin C. Nature. 1959;184:1079–80.
Comeau AM, Tetart F, Trojet SN, Prere MF, Krisch HM. Phage-antibiotic synergy (PAS): beta-lactam and quinolone antibiotics stimulate virulent phage growth. PLoS One. 2007;2:e799.
Kim M, Jo Y, Hwang YJ, Hong HW, Hong SS, Park K et al. Phage-antibiotic synergy via delayed lysis. Appl Environ Microbiol. 2018;84:e02085–18.
De Paepe M, Tournier L, Moncaut E, Son O, Langella P, Petit MA. Carriage of lambda latent virus is costly for its bacterial host due to frequent reactivation in monoxenic mouse intestine. PLoS Genet. 2016;12:e1005861.
Phanphak S, Georgiades P, Li R, King J, Roberts IS, Waigh TA. Super-resolution fluorescence microscopy study of the production of K1 capsules by Escherichia coli: evidence for the differential distribution of the capsule at the poles and the equator of the cell. Langmuir. 2019;35:5635–46.
Krinos CM, Coyne MJ, Weinacht KG, Tzianabos AO, Kasper DL, Comstock LE. Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature. 2001;414:555–8.
Tzeng YL, Thomas J, Stephens DS. Regulation of capsule in Neisseria meningitidis. Crit Rev Microbiol. 2016;42:759–72.
Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 2016;10:2854–66.
Zhang YF, LeJeune JT. Transduction of bla(CMY-2), tet(A), and tet(B) from Salmonella enterica subspecies enterica serovar Heidelberg to S-Typhimurium. Vet Microbiol. 2008;129:418–25.
Brussow H, Kutter E. Phage ecology. Bacteriophages: biology and application. Boca Raton, Florida: CRC Press; 2005. p. 129–64.
Calef E, Marchelli C, Guerrini F. The formation of superinfection-double lysogens of phage lambda in Escherichia coli K-12. Virology. 1965;27:1–10.
Scott JR, West BW, Laping JL. Superinfection immunity and prophage repression in phage P1. IV. The c1 repressor bypass function and the role of c4 repressor in immunity. Virology. 1978;85:587–600.
Bakk A, Metzler R. Nonspecific binding of the OR repressors CI and Cro of bacteriophage lambda. J Theor Biol. 2004;231:525–33.
Casjens S. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol. 2003;49:277–300.
Hendrix RW, Smith MCM, Burns RN, Ford ME, Hatfull GF. Evolutionary relationships among diverse bacteriophages and prophages: All the world’s a phage. Proc Natl Acad Sci USA. 1999;96:2192–7.
Ramisetty BCM, Sudhakari PA. Bacterial ‘Grounded’ Prophages: hotspots for genetic renovation and innovation. Front Genet. 2019;10:65.
Venturini C, Ben Zakour N, Bowring B, Morales S, Cole R, Kovach Z et al. K. pneumoniae ST258 genomic variability and bacteriophage susceptibility. bioRxiv. 2019. https://doi.org/10.1101/628339.
Hsieh PF, Lin HH, Lin TL, Chen YY, Wang JT. Two T7-like bacteriophages, K5-2 and K5-4, each encodes two capsule depolymerases: isolation and functional characterization. Sci Rep. 2017;7:4624.
Majkowska-Skrobek G, Latka A, Berisio R, Squeglia F, Maciejewska B, Briers Y, et al. Phage-borne depolymerases decrease Klebsiella pneumoniae resistance to innate defense mechanisms. Front Microbiol. 2018;9:00209–19.
Paczosa MK, Mecsas J. Klebsiella pneumoniae: going on the offense with a strong defense. Microbiol Mol Biol Rev. 2016;80:629–61.
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 2017;45:D491–D498.
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7:e1002195.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinforma. 2009;10:421.
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34:D32–6.
Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC, Murphy C, et al. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol. 2014b;6:2866–82.
Steinegger M, Soding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35:1026–8.
van Heel AJ, de Jong A, Song C, Viel JH, Kok J, Kuipers OP. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 2018;46:W278–81.
Pires DP, Oliveira H, Melo LD, Sillankorva S, Azeredo J. Bacteriophage-encoded depolymerases: their diversity and biotechnological applications. Appl Microbiol Biotechnol. 2016;100:2141–51.
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Neron B, et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018;46:W246–51.
Oliveira PH, Touchon M, Rocha EP. Regulation of genetic flux between bacteria by restriction-modification systems. Proc Natl Acad Sci USA. 2016;113:5658–63.
Mucke M, Kruger DH, Reuter M. Diversity of Type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res. 2003;31:6079–84.
Ferrieres L, Hemery G, Nham T, Guerout AM, Mazel D, Beloin C, et al. Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery. J Bacteriol. 2010;192:6418–27.
Guy L, Kultima JR, Andersson SG. genoPlotR: comparative gene and genome visualization in R. Bioinformatics. 2010;26:2334–5.
Source: Ecology - nature.com