1. Toft C, Andersson SG. 2010. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet 11:465–475.[PubMed] [CrossRef]
2. Dawkins R, Krebs JR. 1979. Arms races between and within species. Proc R Soc London B Biol Sci 205:489–511.[PubMed] [CrossRef]
3. Woolhouse ME, Webster JP, Domingo E, Charlesworth B, Levin BR. 2002. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat Genet 32:569–577.[PubMed] [CrossRef]
4. Taubenberger JK, Kash JC. 2010. Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 7:440–551.[PubMed] [CrossRef]
5. Mideo N. 2009. Parasite adaptations to within-host competition. Trends Parasitol 25:261–268.[PubMed] [CrossRef]
6. Cooney NM, Klein BS. 2008. Fungal adaptation to the mammalian host: it is a new world, after all. Curr Opin Microbiol 11:511–516.[PubMed] [CrossRef]
7. Williams GC. 1957. Pleiotropy, natural selection, and the evolution of senescence. Evolution 11:398–411.[CrossRef]
8. Salazar-Gonzalez RM, Srinivasan A, Griffin A, Muralimohan G, Ertelt JM, Ravindran R, Vella AT, McSorley SJ. 2007. Salmonella flagellin induces bystander activation of splenic dendritic cells and hinders bacterial replication in vivo. J Immunol 179:6169–6175.[PubMed] [CrossRef]
9. Wu W, Badrane H, Arora S, Baker HV, Jin S. 2004. MucA-mediated coordination of type III secretion and alginate synthesis in Pseudomonas aeruginosa. J Bacteriol 186:7575–7585.[PubMed] [CrossRef]
10. Boucher JC, Yu H, Mudd MH, Deretic V. 1997. Mucoid Pseudomonas aeruginosa in cystic fibrosis: characterization of muc mutations in clinical isolates and analysis of clearance in a mouse model of respiratory infection. Infect Immun 65:3838–3846.[PubMed]
11. Hauser AR. 2009. The type III secretion system of Pseudomonas aeruginosa: infection by injection. Nat Rev Microbiol 7:654–665.[PubMed] [CrossRef]
12. Schulz zur Wiesch P, Engelstadter J, Bonhoeffer S. 2010. Compensation of fitness costs and reversibility of antibiotic resistance mutations. Antimicrob Agents Chemother 54:2085–2095.[PubMed] [CrossRef]
13. Morgan AD, Koskella B. 2011. Coevolution of host and pathogen, p 147–171. In Tibayreng M (ed), Genetics and Evolution of Infectious Diseases. Elsevier, Burlington, MA. [CrossRef]
14. Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HM, Barquist L, Stedman A, Humphrey T, Wigley P, Peters SE, Maskell DJ, Corander J, Chabalgoity JA, Barrow P, Parkhill J, Dougan G, Thomson NR. 2015. Patterns of genome evolution that have accompanied host adaptation in Salmonella. Proc Natl Acad Sci USA 112:863–868.[PubMed] [CrossRef]
15. Kemen AC, Agler MT, Kemen E. 2015. Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism. New Phytol 206:1207–1228.[PubMed] [CrossRef]
16. Price CT, Richards AM, Von Dwingelo JE, Samara HA, Abu Kwaik Y. 2014. Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution. Environ Microbiol 16:350–358.[PubMed] [CrossRef]
17. Davies J, Davies D. 2010. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–433.[PubMed] [CrossRef]
18. Wiedenbeck J, Cohan FM. 2011. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35:957–976.[PubMed] [CrossRef]
19. Houchhut B, Dobrindt U, Hacker J. 2006. The contribution of pathogenicity islands to the evolution of bacterial pathogens, p 83–107. In Seifert HS, DiRita V (ed), The Evolution of Microbial Pathogens. ASM Press, Washington, DC. [CrossRef]
20. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583.[PubMed] [CrossRef]
21. Doran KS, Banerjee A, Disson O, Lecuit M. 2013. Concepts and mechanisms: crossing host barriers. Cold Spring Harbor Perspect Med 3:a010090. doi:10.1101/cshperspect.a010090 [PubMed] [CrossRef]
22. Tsukita S, Yamazaki Y, Katsuno T, Tamura A, Tsukita S. 2008. Tight junction-based epithelial microenvironment and cell proliferation. Oncogene 27:6930–6938.[PubMed] [CrossRef]
23. McGuckin MA, Linden SK, Sutton P, Florin TH. 2011. Mucin dynamics and enteric pathogens. Nat Rev Microbiol 9:265–278.[PubMed] [CrossRef]
24. Linden SK, Sutton P, Karlsson NG, Korolik V, McGuckin MA. 2008. Mucins in the mucosal barrier to infection. Mucosal Immunol 1:183–197.[PubMed] [CrossRef]
25. Gutierrez-Jimenez J, Arciniega I, Navarro-Garcia F. 2008. The serine protease motif of Pic mediates a dose-dependent mucolytic activity after binding to sugar constituents of the mucin substrate. Microb Pathog 45:115–123.[PubMed] [CrossRef]
26. Henderson IR, Czeczulin J, Eslava C, Noriega F, Nataro JP. 1999. Characterization of pic, a secreted protease of Shigella flexneri and enteroaggregative Escherichia coli. Infect Immun 67:5587–5596.[PubMed]
27. Sonnenburg JL, Xu J, Leip DD, Chen CH, Westover BP, Weatherford J, Buhler JD, Gordon JI. 2005. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307:1955–1959.[PubMed] [CrossRef]
28. Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J. 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190:6881–6893.[PubMed] [CrossRef]
29. Jones B, Pascopella L, Falkow S. 1995. Entry of microbes into the host: using M cells to break the mucosal barrier. Curr Opin Immunol 7:474–478.[PubMed] [CrossRef]
30. Wu S, Lim KC, Huang J, Saidi RF, Sears CL. 1998. Bacteroides fragilis enterotoxin cleaves the zonula adherens protein, E-cadherin. Proc Natl Acad Sci USA 95:14979–14984.[PubMed] [CrossRef]
31. Hanakawa Y, Schechter NM, Lin C, Garza L, Li H, Yamaguchi T, Fudaba Y, Nishifuji K, Sugai M, Amagai M, Stanley JR. 2002. Molecular mechanisms of blister formation in bullous impetigo and staphylococcal scalded skin syndrome. J Clin Invest 110:53–60.[PubMed] [CrossRef]
32. Franco AA, Cheng RK, Chung GT, Wu S, Oh HB, Sears CL. 1999. Molecular evolution of the pathogenicity island of enterotoxigenic Bacteroides fragilis strains. J Bacteriol 181:6623–6633.[PubMed]
33. Yamaguchi T, Nishifuji K, Sasaki M, Fudaba Y, Aepfelbacher M, Takata T, Ohara M, Komatsuzawa H, Amagai M, Sugai M. 2002. Identification of the Staphylococcus aureus etd pathogenicity island which encodes a novel exfoliative toxin, ETD, and EDIN-B. Infect Immun 70:5835–5845.[PubMed] [CrossRef]
34. Jackson MP, Iandolo JJ. 1986. Cloning and expression of the exfoliative toxin B gene from Staphylococcus aureus. J Bacteriol 166:574–580.[PubMed]
35. Jensen VB, Harty JT, Jones BD. Interactions of the invasive pathogens Salmonella typhimurium, Listeria monocytogenes, and Shigella flexneri with M cells and murine Peyer’s patches. Infect Immun 66:3758–3766.[PubMed]
36. McGuckin MA, Every AL, Skene CD, Linden SK, Chionh YT, Swierczak A, McAuley J, Harbour S, Kaparakis M, Ferrero R, Sutton P. 2007. Muc1 mucin limits both Helicobacter pylori colonization of the murine gastric mucosa and associated gastritis. Gastroenterology 133:1210–1218.[PubMed] [CrossRef]
37. Vinall LE, King M, Novelli M, Green CA, Daniels G, Hilkens J, Sarner M, Swallow DM. 2002. Altered expression and allelic association of the hypervariable membrane mucin MUC1 in Helicobacter pylori gastritis. Gastroenterology 123:41–49.[PubMed] [CrossRef]
38. Costa NR, Mendes N, Marcos NT, Reis CA, Caffrey T, Hollingsworth MA, Santos-Silva F. 2008. Relevance of MUC1 mucin variable number of tandem repeats polymorphism in H pylori adhesion to gastric epithelial cells. World J Gastroenterol 14:1411–1414.[PubMed] [CrossRef]
39. Vos HL, de Vries Y, Hilkens J. 1991. The mouse episialin (Muc1) gene and its promoter: rapid evolution of the repetitive domain in the protein. Biochem Biophys Res Commun 181:121–130.[PubMed] [CrossRef]
40. Lambris JD, Ricklin D, Geisbrecht BV. 2008. Complement evasion by human pathogens. Nat Rev Microbiol 6:132–142.[PubMed] [CrossRef]
41. Rooijakkers SH, Ruyken M, Roos A, Daha MR, Presanis JS, Sim RB, van Wamel WJ, van Kessel KP, van Strijp JA. 2005. Immune evasion by a staphylococcal complement inhibitor that acts on C3 convertases. Nature Immunol 6:920–927.[PubMed] [CrossRef]
42. Rooijakkers SH, van Wamel WJ, Ruyken M, van Kessel KP, van Strijp JA. 2005. Anti-opsonic properties of staphylokinase. Microbes Infect 7:476–484.[PubMed] [CrossRef]
43. Del Tordello E, Vacca I, Ram S, Rappuoli R, Serruto D. 2014. Neisseria meningitidis NalP cleaves human complement C3, facilitating degradation of C3b and survival in human serum. Proc Natl Acad Sci USA 111:427–432.[PubMed] [CrossRef]
44. Skaar EP. 2010. The battle for iron between bacterial pathogens and their vertebrate hosts. PLoS Pathog 6:e1000949. [PubMed] [CrossRef]
45. Rogers HJ. 1973. Iron-binding catechols and virulence in Escherichia coli. Infect Immun 7:445–456.[PubMed]
46. Goetz DH, Holmes MA, Borregaard N, Bluhm ME, Raymond KN, Strong RK. 2002. The neutrophil lipocalin NGAL is a bacteriostatic agent that interferes with siderophore-mediated iron acquisition. Mol Cell 10:1033–1043.[PubMed] [CrossRef]
47. Fischbach MA, Lin H, Zhou L, Yu Y, Abergel RJ, Liu DR, Raymond KN, Wanner BL, Strong RK, Walsh CT, Aderem A, Smith KD. 2006. The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2. Proc Natl Acad Sci USA 103:16502–16507.[PubMed] [CrossRef]
48. Hornef MW, Wick MJ, Rhen M, Normark S. 2002. Bacterial strategies for overcoming host innate and adaptive immune responses. Nat Immunol. 3:1033–1040.[PubMed] [CrossRef]
49. Gebert B, Fischer W, Weiss E, Hoffmann R, Haas R. 2003. Helicobacter pylori vacuolating cytotoxin inhibits T lymphocyte activation. Science 301:1099–1102.[PubMed] [CrossRef]
50. Nothelfer K, Arena ET, Pinaud L, Neunlist M, Mozeleski B, Belotserkovsky I, Parsot C, Dinadayala P, Burger-Kentischer A, Raqib R, Sansonetti PJ, Phalipon A. 2014. B lymphocytes undergo TLR2-dependent apoptosis upon Shigella infection. J Exp Med 211:1215–1229.[PubMed] [CrossRef]
51. Blair JM, Webber MA, Baylay AJ, Ogbolu DO, Piddock LJ. 2015. Molecular mechanisms of antibiotic resistance. Nat Rev Microbiol 13:42–51.[PubMed] [CrossRef]
52. Andersen JL, He GX, Kakarla P, K CR, Kumar S, Lakra WS, Mukherjee MM, Ranaweera I, Shrestha U, Tran T, Varela MF. 2015. Multidrug efflux pumps from Enterobacteriaceae, Vibrio cholerae and Staphylococcus aureus bacterial food pathogens. Int J Environ Res Public Health 12:1487–1547.[PubMed] [CrossRef]
53. Wilson DN, Schluenzen F, Harms JM, Starosta AL, Connell SR, Fucini P. 2008. The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning. Proc Natl Acad Sci USA 105:13339–13344.[PubMed] [CrossRef]
54. Feng J, Lupien A, Gingras H, Wasserscheid J, Dewar K, Legare D, Ouellette M. 2009. Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance. Genome Res 19:1214–1223.[PubMed] [CrossRef]
55. Meka VG, Gold HS. 2004. Antimicrobial resistance to linezolid. Clin Infect Dis 39:1010–1015.[PubMed] [CrossRef]
56. Frere JM. 1995. Beta-lactamases and bacterial resistance to antibiotics. Mol Microbiol 16:385–395.[PubMed] [CrossRef]
57. Wright GD. 2005. Bacterial resistance to antibiotics: enzymatic degradation and modification. Adv Drug Deliv Rev 57:1451–1470.[PubMed] [CrossRef]
58. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304.[PubMed] [CrossRef]
59. Andersson DI, Hughes D. 2010. Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 8:260–271.[PubMed] [CrossRef]
60. Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D, Nelson WC, Heidelberg JF, Mekalanos JJ. 2006. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc Natl Acad Sci USA 103:1528–1533.[PubMed] [CrossRef]
61. Cascales E, Buchanan SK, Duche D, Kleanthous C, Lloubes R, Postle K, Riley M, Slatin S, Cavard D. 2007. Colicin biology. Microbiol Mol Biol Rev 71:158–229.[PubMed] [CrossRef]
62. Gagliano VJ, Hinsdill RD. 1970. Characterization of a Staphylococcus aureus bacteriocin. J Bacteriol 104:117–125.[PubMed]
63. Duche D, Parker MW, Gonzalez-Manas JM, Pattus F, Baty D. 1994. Uncoupled steps of the colicin A pore formation demonstrated by disulfide bond engineering. J Biol Chem 269:6332–6339.[PubMed]
64. Vankemmelbeke M, Healy B, Moore GR, Kleanthous C, Penfold CN, James R. 2005. Rapid detection of colicin E9-induced DNA damage using Escherichia coli cells carrying SOS promoter-lux fusions. J Bacteriol 187:4900–4907.[PubMed] [CrossRef]
65. Boon T. 1972. Inactivation of ribosomes in vitro by colicin E3 and its mechanism of action. Proc Natl Acad Sci USA 69:549–552.[PubMed] [CrossRef]
66. Harkness RE, Braun V. 1989. Colicin M inhibits peptidoglycan biosynthesis by interfering with lipid carrier recycling. J Biol Chem 264:6177–6182.[PubMed]
67. El Ghachi M, Bouhss A, Barreteau H, Touze T, Auger G, Blanot D, Mengin-Lecreulx D. 2006. Colicin M exerts its bacteriolytic effect via enzymatic degradation of undecaprenyl phosphate-linked peptidoglycan precursors. J Biol Chem 281:22761–22772.[PubMed] [CrossRef]
68. Olschlager T, Turba A, Braun V. 1991. Binding of the immunity protein inactivates colicin M. Mol Microbiol 5:1105–1111.[PubMed] [CrossRef]
69. Moss JE, Cardozo TJ, Zychlinsky A, Groisman EA. 1999. The selC-associated SHI-2 pathogenicity island of Shigella flexneri. Mol Microbiol 33:74–83.[PubMed] [CrossRef]
70. Gerard F, Pradel N, Wu LF. 2005. Bactericidal activity of colicin V is mediated by an inner membrane protein, SdaC, of Escherichia coli. J Bacteriol 187:1945–1950.[PubMed] [CrossRef]
71. Russell AB, Peterson SB, Mougous JD. 2014. Type VI secretion system effectors: poisons with a purpose. Nat Rev Microbiol 12:137–148.[PubMed] [CrossRef]
72. Suarez G, Sierra JC, Erova TE, Sha J, Horneman AJ, Chopra AK. 2010. A type VI secretion system effector protein, VgrG1, from Aeromonas hydrophila that induces host cell toxicity by ADP ribosylation of actin. J Bacteriol 192:155–168.[PubMed] [CrossRef]
73. Russell AB, Hood RD, Bui NK, LeRoux M, Vollmer W, Mougous JD. 2011. Type VI secretion delivers bacteriolytic effectors to target cells. Nature 475:343–347.[PubMed] [CrossRef]
74. Russell AB, LeRoux M, Hathazi K, Agnello DM, Ishikawa T, Wiggins PA, Wai SN, Mougous JD. 2013. Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature 496:508–512.[PubMed] [CrossRef]
75. Koskiniemi S, Lamoureux JG, Nikolakakis KC, t’Kint de Roodenbeke C, Kaplan MD, Low DA, Hayes CS. 2013. Rhs proteins from diverse bacteria mediate intercellular competition. Proc Natl Acad Sci USA 110:7032–7037.[PubMed] [CrossRef]
76. Fritsch MJ, Trunk K, Diniz JA, Guo M, Trost M, Coulthurst SJ. 2013. Proteomic identification of novel secreted antibacterial toxins of the Serratia marcescens type VI secretion system. Mol Cell Proteomics 12:2735–2749.[PubMed] [CrossRef]
77. Borgeaud S, Metzger LC, Scrignari T, Blokesch M. 2015. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science 347:63–67.[PubMed] [CrossRef]