The roles of inflammation, nutrient availability and the commensal microbiota in enteric pathogen infection

Microbiology Spectrum

Volumn 3, Issue 3, 2015, Pages

  Stecher, Bärbel ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CROHN DISEASE; DYSBIOSIS; ENTEROBACTERIACEAE; ENTEROBACTERIACEAE INFECTION; GASTROINTESTINAL DISEASE; GENETICS; HUMAN; IMMUNOLOGY; INFLAMMATION; INTESTINE; INTESTINE FLORA; INTESTINE MUCOSA; METABOLISM; MICROBIOLOGY; PATHOLOGY; SYMBIOSIS; ULCERATIVE COLITIS;

COLITIS, ULCERATIVE; CROHN DISEASE; DYSBIOSIS; ENTEROBACTERIACEAE; ENTEROBACTERIACEAE INFECTIONS; GASTROINTESTINAL DISEASES; GASTROINTESTINAL MICROBIOME; HUMANS; INFLAMMATION; INTESTINAL MUCOSA; INTESTINES; SYMBIOSIS;

EID: 84957553597     PISSN: None     EISSN: 21650497     Source Type: Journal    
DOI: 10.1128/microbiolspec.MBP-0008-2014     Document Type: Article

References (181)

1. Blumberg R, Powrie F. 2012. Microbiota, disease, and back to health: a metastable journey. Sci Transl Med 4:137rv137.
2. Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. 2012. Host-gut microbiota metabolic interactions. Science 336:1262-1267.
3. Cho I, Blaser MJ. 2012. The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260-270.
4. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220-230.
5. Dethlefsen L, Relman DA. 2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 108(Suppl 1):4554-4561.
6. Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, Kirn TJ, Bushman FD, Artis D. 2010. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol 3:148-158.
7. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105-108.
8. Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A, Louis P, McIntosh F, Johnstone AM, Lobley GE, Parkhill J, Flint HJ. 2011. Dominant and dietresponsive groups of bacteria within the human colonic microbiota. ISME J 5:220-230.
9. Zhang X, Zhao Y, Zhang M, Pang X, Xu J, Kang C, Li M, Zhang C, Zhang Z, Zhang Y, Li X, Ning G, Zhao L. 2012. Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats. PLoS ONE 7:e42529.
10. Stecher B, Berry D, Loy A. 2013. Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. FEMS Microbiol Rev 37:793-829.
11. Stecher B, Maier L, Hardt WD. 2013. 'Blooming' in the gut: how dysbiosis might contribute to pathogen evolution. Nat Rev Microbiol 11:277-284.
12. Hooper LV, Littman DR, Macpherson AJ. 2012. Interactions between the microbiota and the immune system. Science 336:1268-1273.
13. Manichanh C, Borruel N, Casellas F, Guarner F. 2012. The gut microbiota in IBD. Nat Rev Gastroenterol Hepatol 9:599-608.
14. Winter SE, Lopez CA, Baumler AJ. 2013. The dynamics of gutassociated microbial communities during inflammation. EMBO Rep 14:319-327.
15. Strober W, Fuss I, Mannon P. 2007. The fundamental basis of inflammatory bowel disease. Journal Clin Invest 117:514-521.
16. Sartor RB. 2008. Microbial influences in inflammatory bowel diseases. Gastroenterology 134:577-594.
17. Sansonetti PJ. 2008. Host-bacteria homeostasis in the healthy and inflamed gut. Current opinion in gastroenterology 24:435-439.
18. Peach S, Lock MR, Katz D, Todd IP, Tabaqchali S. 1978. Mucosalassociated bacterial flora of the intestine in patients with Crohn's disease and in a control group. Gut 19:1034-1042.
19. Giaffer MH, Holdsworth CD, Duerden BI. 1991. The assessment of faecal flora in patients with inflammatory bowel disease by a simplified bacteriological technique. J Med Microbiol 35:238-243.
20. Wensinck F, Custers-van L, Poppelaars-Kustermans PA, Schroder AM. 1981. The faecal flora of patients with Crohn's disease. J Hyg (Lond) 87:1-12.
21. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. 2007. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104:13780-13785.
22. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Jian M, Zhou Y, Li Y, Zhang X, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65.
23. Fyderek K, Strus M, Kowalska-Duplaga K, Gosiewski T, Wedrychowicz A, Jedynak-Wasowicz U, Sladek M, Pieczarkowski S, Adamski P, Kochan P, Heczko PB. 2009. Mucosal bacterial microflora and mucus layer thickness in adolescents with inflammatory bowel disease. World J Gastroenterol 15:5287-5294.
24. Gosiewski T, Strus M, Fyderek K, Kowalska-Duplaga K, Wedrychowicz A, Jedynak-Wasowicz U, Sladek M, Pieczarkowski S, Adamski P, Heczko PB. 2012. Horizontal distribution of the fecal microbiota in adolescents with inflammatory bowel disease. J Pediatr Gastroenterol Nutr 54:20-27.
25. Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, Orsi RH, Wiedmann M, McDonough P, Kim SG, Berg D, Schukken Y, Scherl E, Simpson KW. 2007. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum. ISME J 1:403-418.
26. Sokol H, Seksik P, Rigottier-Gois L, Lay C, Lepage P, Podglajen I, Marteau P, Dore J. 2006. Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm Bowel Dis 12:106-111.
27. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Dore J. 2009. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 15:1183-1189.
28. Fujimoto T, Imaeda H, Takahashi K, Kasumi E, Bamba S, Fujiyama Y, Andoh A. 2013. Decreased abundance of Faecalibacterium prausnitzii in the gut microbiota of Crohn's disease. J Gastroenterol Hepatol 28: 613-619.
29. Duncan SH, Hold GL, Harmsen HJ, Stewart CS, Flint HJ. 2002. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol 52:2141-2146.
30. Bibiloni R, Mangold M, Madsen KL, Fedorak RN, Tannock GW. 2006. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients. J Med Microbiol 55:1141-1149.
31. Swidsinski A, Weber J, Loening-Baucke V, Hale LP, Lochs H. 2005. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol 43:3380-3389.
32. Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, Barnich N, Bringer MA, Swidsinski A, Beaugerie L, Colombel JF. 2004. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127:412-421.
33. Kotlowski R, Bernstein CN, Sepehri S, Krause DO. 2007. High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease. Gut 56:669-675.
34. Maharshak N, Packey CD, Ellermann M, Manick S, Siddle JP, Huh EY, Plevy S, Sartor RB, Carroll IM. 2013. Altered enteric microbiota ecology in interleukin 10-deficient mice during development and progression of intestinal inflammation. Gut Microbes 4:316-324.
35. Garrett WS, Gallini CA, Yatsunenko T, Michaud M, DuBois A, Delaney ML, Punit S, Karlsson M, Bry L, Glickman JN, Gordon JI, Onderdonk AB, Glimcher LH. 2010. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8:292-300.
36. Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, Finlay BB. 2007. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of enterobacteriaceae. Cell Host Microbe 2:119-129.
37. Berry D, Schwab C, Milinovich G, Reichert J, Ben Mahfoudh K, Decker T, Engel M, Hai B, Hainzl E, Heider S, Kenner L, Muller M, Rauch I, Strobl B, Wagner M, Schleper C, Urich T, Loy A. 2012. Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis. ISME J 6:2091-2096.
38. Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J, Dougan G, von Mering C, Hardt WD. 2007. Salmonella enterica Serovar Typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol 5:e244.
39. Barman M, Unold D, Shifley K, Amir E, Hung K, Bos N, Salzman N. 2008. Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract. Infect Immun 76:907-915.
40. Molloy MJ, Grainger JR, Bouladoux N, Hand TW, Koo LY, Naik S, QuinonesM, Dzutsev AK, Gao JL, Trinchieri G, Murphy PM, Belkaid Y. 2013. Intraluminal containment of commensal outgrowth in the gut during infection-induced dysbiosis. Cell Host Microbe 14:318-328.
41. Ma AT, Mekalanos JJ. In vivo actin cross-linking induced by Vibrio cholerae type VI secretion system is associated with intestinal inflammation. Proc Natl Acad Sci U S A 107:4365-4370.
42. Lawley TD, Clare S, Walker AW, Goulding D, Stabler RA, Croucher N, Mastroeni P, Scott P, Raisen C, Mottram L, Fairweather NF, Wren BW, Parkhill J, Dougan G. 2009. Antibiotic treatment of Clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun 77:3661-3669.
43. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, Gonzalez A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, GriffithsA, Sylvester F, Mack D, KimS, CrandallW, Hyams J, Huttenhower C, Knight R, Xavier RJ. 2014. The treatment-naive microbiome in newonset Crohn's disease. Cell Host Microbe 15:382-392.
44. Adlerberth I. 2008. Factors influencing the establishment of the intestinal microbiota in infancy. Nestle Nutr Workshop Ser Pediatr Program 62:13-29; discussion 29-33.
45. Palmer C, Bik EM, Digiulio DB, Relman DA, Brown PO. 2007. Development of the human infant intestinal microbiota. PLoS Biol 5:e177.
46. Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R. 2011. Development of the human gastrointestinal microbiota and insights from highthroughput sequencing. Gastroenterology 140:1713-1719.
47. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Consortium M, Weissenbach J, Ehrlich SD, Bork P, Antolin M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Merieux A, Melo Minardi R, M'Rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G. 2011. Enterotypes of the human gut microbiome. Nature 473:174-180.
48. Vollaard EJ, Clasener HA. 1994. Colonization resistance. Antimicrob Agents Chemother 38:409-414.
49. Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, Ubeda-Morant C, Xavier J, Pamer EG. 2012. Profound alterations of intestinal microbiota following a single dose of Clindamycin results in sustained susceptibility to C. difficile-induced colitis. Infect Immun 80:62-73.
50. Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, Lee YJ, Dubin KA, Socci ND, Viale A, Perales MA, Jenq RR, van den Brink MR, Pamer EG. 2012. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis 55:905-914.
51. Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. 2009. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37:D464-470.
52. 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.
53. Vieira G, Sabarly V, Bourguignon PY, Durot M, Le Fevre F, Mornico D, Vallenet D, Bouvet O, Denamur E, Schachter V, Medigue C. 2011. Core and panmetabolism in Escherichia coli. J Bacteriol 193:1461-1472.
54. Chang DE, Smalley DJ, Tucker DL, Leatham MP, Norris WE, Stevenson SJ, Anderson AB, Grissom JE, Laux DC, Cohen PS, Conway T. 2004. Carbon nutrition of Escherichia coli in the mouse intestine. Proc Natl Acad Sci U S A 101:7427-7432.
55. Unden G, Bongaerts J. 1997. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim Biophys Acta 1320:217-234.
56. Neidhardt FC CIR, Ingraham JL, Edmund CCL, Brooks Low K, Magasanik B, ReznikoffWS, Riley M, Schaechter M, Umbarger HE. 1995. Escherichia coliand Salmonella. ASM Press, Washington, DC.
57. Qin X, Galloway-Pena JR, Sillanpaa J, Roh JH, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ, Ding Y, Dugan-Rocha S, Liu W, Kovar C, Sodergren E, Highlander S, Petrosino JF, Worley KC, Gibbs RA, Weinstock GM, Murray BE. 2012. Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol 12:135.
58. Ramsey M, Hartke A, Huycke M. 2014. The physiology and metabolism of Enterococci. In Gilmore MS, Clewell DB, Ike Y, Shankar N (ed), Enterococci: From commensals to leading causes of drug resistant infection [Internet]. Boston: Massachusetts Eye and Ear Infirmary; 2014-. 2014 Feb 15.
59. Pritchard GG, Wimpenny JW. 1978. Cytochrome formation, oxygeninduced proton extrusion and respiratory activity in Streptococcus faecalis var. zymogenes grown in the presence of haematin. J Gen Microbiol 104:15-22.
60. Bourgogne A, Garsin DA, Qin X, Singh KV, Sillanpaa J, Yerrapragada S, Ding Y, Dugan-Rocha S, Buhay C, Shen H, Chen G, Williams G, Muzny D, Maadani A, Fox KA, Gioia J, Chen L, Shang Y, Arias CA, Nallapareddy SR, Zhao M, Prakash VP, Chowdhury S, Jiang H, Gibbs RA, Murray BE, Highlander SK, Weinstock GM. 2008. Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol 9:R110.
61. Rigottier-Gois L. 2013. Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J 7:1256-1261.
62. Karhausen J, Furuta GT, Tomaszewski JE, Johnson RS, Colgan SP, Haase VH. 2004. Epithelial hypoxia-inducible factor-1 is protective in murine experimental colitis. Journal Clin Invest 114:1098-1106.
63. He G, Shankar RA, Chzhan M, Samouilov A, Kuppusamy P, Zweier JL. 1999. Noninvasive measurement of anatomic structure and intraluminal oxygenation in the gastrointestinal tract of living mice with spatial and spectral EPR imaging. Proc Natl Acad Sci U S A 96:4586-4591.
64. Handa K, Ohmura M, Nishime C, Hishiki T, Nagahata Y, Kawai K, Suemizu H, Nakamura M, Wakui M, Kitagawa Y, Suematsu M, Tsukada K. 2010. Phosphorescence-assisted microvascular O(2) measurements reveal alterations of oxygen demand in human metastatic colon cancer in the liver of superimmunodeficient NOG mice. Adv Exp Med Biol 662:423-429.
65. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, ZasloffM, Eisen JA. 2009. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A 106:17187-17192.
66. Hensel M, Hinsley AP, Nikolaus T, Sawers G, Berks BC. 1999. The genetic basis of tetrathionate respiration in Salmonella Typhimurium. Molecular Microbiol 32:275-287.
67. Fang FC. 2004. Antimicrobial reactive oxygen and nitrogen species: concepts and controversies. Nat Rev Microbiol 2:820-832.
68. Kuwano Y, Kawahara T, Yamamoto H, Teshima-Kondo S, Tominaga K, Masuda K, Kishi K, Morita K, Rokutan K. 2006. Interferongamma activates transcription of NADPH oxidase 1 gene and upregulates production of superoxide anion by human large intestinal epithelial cells. Am J Physiol Cell Physiol 290:C433-443.
69. Harper RW, Xu C, Eiserich JP, Chen Y, Kao CY, Thai P, Setiadi H, Wu R. 2005. Differential regulation of dual NADPH oxidases/peroxidases, Duox1 and Duox2, by Th1 and Th2 cytokines in respiratory tract epithelium. FEBS Lett 579:4911-4917.
70. Nathan C. 2006. Neutrophils and immunity: challenges and opportunities. Nat Rev Immunol 6:173-182.
71. Zhu H, Li YR. 2012. Oxidative stress and redox signaling mechanisms of inflammatory bowel disease: updated experimental and clinical evidence. Exp Biol Med (Maywood) 237:474-480.
72. Lundberg JO, Hellstrom PM, Lundberg JM, Alving K. 1994. Greatly increased luminal nitric oxide in ulcerative colitis. Lancet 344:1673-1674.
73. Songhet P, Barthel M, Rohn TA, Van Maele L, Cayet D, Sirard JC, Bachmann M, Kopf M, Hardt WD. 2010. IL-17A/F-signaling does not contribute to the initial phase of mucosal inflammation triggered by S. Typhimurium. PLoS ONE 5:e13804.
74. Winter SE, Thiennimitr P, Winter MG, Butler BP, Huseby DL, Crawford RW, Russell JM, Bevins CL, Adams LG, Tsolis RM, Roth JR, Baumler AJ. 2010. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467:426-429.
75. Levitt MD, Furne J, Springfield J, Suarez F, DeMaster E. 1999. Detoxification of hydrogen sulfide and methanethiol in the cecal mucosa. J ClinInvest 104:1107-1114.
76. Szabo C, Ischiropoulos H, Radi R. 2007. Peroxynitrite: biochemistry, pathophysiology and development of therapeutics. Nat Rev Drug Discov 6:662-680.
77. Rajagopalan KV, Johnson JL. 1992. The pterin molybdenum cofactors. J Biol Chem 267:10199-10202.
78. Winter SE, Winter MG, Xavier MN, Thiennimitr P, Poon V, Keestra AM, Laughlin RC, Gomez G, Wu J, Lawhon SD, Popova IE, Parikh SJ, Adams LG, Tsolis RM, Stewart VJ, Baumler AJ. 2013. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 339:708-711.
79. Bertin Y, Girardeau JP, Chaucheyras-Durand F, Lyan B, Pujos-Guillot E, Harel J, Martin C. 2011. Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content. Environ Microbiol 13:365-377.
80. Thiennimitr P, Winter SE, Winter MG, Xavier MN, Tolstikov V, Huseby DL, Sterzenbach T, Tsolis RM, Roth JR, Baumler AJ. 2011. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc Natl Acad Sci U S A 108:17480-17485.
81. Kofoid E, Rappleye C, Stojiljkovic I, Roth J. 1999. The 17-gene ethanolamine (eut) operon of Salmonella Typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181:5317-5329.
82. Price-Carter M, Tingey J, Bobik TA, Roth JR. 2001. The alternative electron acceptor tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar typhimurium on ethanolamine or 1, 2-propanediol. J Bacteriol 183:2463-2475.
83. Roof DM, Roth JR. 1988. Ethanolamine utilization in Salmonella typhimurium. J Bacteriol 170:3855-3863.
84. Tsoy O, Ravcheev D, Mushegian A. 2009. Comparative genomics of ethanolamine utilization. J Bacteriol 191:7157-7164.
85. Garsin DA. 2010. Ethanolamine utilization in bacterial pathogens: roles and regulation. Nat Rev Microbiol 8:290-295.
86. Pitts AC, Tuck LR, Faulds-Pain A, Lewis RJ, Marles-Wright J. 2012. Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment. PLoS ONE 7:e48360.
87. Del Papa MF, Perego M. 2008. Ethanolamine activates a sensor histidine kinase regulating its utilization in Enterococcus faecalis. Journal Bacteriol 190:7147-7156.
88. Bradbeer C. 1965. The clostridial fermentations of choline and ethanolamine. II. Requirement for a cobamide coenzyme by an ethanolamine deaminase. J Biol Chem 240:4675-4681.
89. Johansson ME, Ambort D, Pelaseyed T, Schutte A, Gustafsson JK, Ermund A, Subramani DB, Holmen-Larsson JM, Thomsson KA, Bergstrom JH, van der Post S, Rodriguez-Pineiro AM, Sjovall H, BackstromM, Hansson GC. 2011. Composition and functional role of the mucus layers in the intestine. Cell Mol Life Sci 68:3635-3641.
90. McGuckin MA, Linden SK, Sutton P, Florin TH. 2011. Mucin dynamics and enteric pathogens. Nat Rev Microbiol 9:265-278.
91. Allen A, Cunliffe WJ, Pearson JP, Sellers LA, Ward R. 1984. Studies on gastrointestinal mucus. Scand J Gastroenterol Suppl 93:101-113.
92. Stecher B, Barthel M, Schlumberger MC, Haberli L, Rabsch W, Kremer M, Hardt WD. 2008. Motility allows S. Typhimurium to benefit from the mucosal defence. Cell Microbiol 10:1166-1180.
93. Zarepour M, Bhullar K, Montero M, Ma C, Huang T, Velcich A, Xia L, Vallance BA. 2013. The mucin Muc2 limits pathogen burdens and epithelial barrier dysfunction during Salmonella enterica serovar Typhimurium colitis. Infect Immun 81:3672-3683.
94. Bergstrom KS, Kissoon-Singh V, Gibson DL, Ma C, Montero M, Sham HP, Ryz N, Huang T, Velcich A, Finlay BB, Chadee K, Vallance BA. 2010. Muc2 protects against lethal infectious colitis by disassociating pathogenic and commensal bacteria from the colonic mucosa. PLoS Pathog 6:e1000902.
95. Songhet P, Barthel M, Stecher B, Muller AJ, Kremer M, Hansson GC, Hardt WD. 2011. Stromal IFN-gammaR-signaling modulates goblet cell function during Salmonella Typhimurium infection. PLoS ONE 6: e22459.
96. Png CW, Linden SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, McGuckin MA, Florin TH. 2010. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol 105:2420-2428.
97. Schwab C, Berry D, Rauch I, Rennisch I, Ramesmayer J, Hainzl E, Heider S, Decker T, Kenner L, Muller M, Strobl B, Wagner M, Schleper C, Loy A, Urich T. 2014. Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery. ISME J 8:1101-1114.
98. Derrien M, Vaughan EE, Plugge CM, de Vos WM. 2004. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucindegrading bacterium. Int J Syst Evol Microbiol 54:1469-1476.
99. Robertson BR, O'Rourke JL, Neilan BA, Vandamme P, On SL, Fox JG, Lee A. 2005. Mucispirillum schaedleri gen. nov., sp. nov., a spiralshaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents. Int J Syst Evol Microbiol 55:1199-1204.
100. Berry D, Stecher B, Schintlmeister A, Reichert J, Brugiroux S, Wild B, Wanek W, Richter A, Rauch I, Decker T, Loy A, Wagner M. 2013. Hostcompound foraging by intestinal microbiota revealed by single-cell stable isotope probing. Proc Natl Acad Sci U S A 110:4720-4725.
101. Ruseler-van Embden JG, van Lieshout LM. 1987. Increased faecal glycosidases in patients with Crohn's disease. Digestion 37:43-50.
102. Deatherage Kaiser BL, Li J, Sanford JA, Kim YM, Kronewitter SR, Jones MB, Peterson CT, Peterson SN, Frank BC, Purvine SO, Brown JN, Metz TO, Smith RD, Heffron F, Adkins JN. 2013. A multi-omic view of host-pathogen-commensal interplay in mediated intestinal infection. PLoS ONE 8:e67155.
103. Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, Kashyap PC, Gopinath S, Naidu N, Choudhury B, Weimer BC, Monack DM, Sonnenburg JL. 2013. Microbiota-liberated host sugars facilitate postantibiotic expansion of enteric pathogens. Nature 502:96-99.
104. Rivera-Chavez F, Winter SE, Lopez CA, Xavier MN, Winter MG, Nuccio SP, Russell JM, Laughlin RC, Lawhon SD, Sterzenbach T, Bevins CL, Tsolis RM, Harshey R, Adams LG, Baumler AJ. 2013. Salmonella uses energy taxis to benefit from intestinal inflammation. PLoS Pathog 9: e1003267.
105. Zipfel PF, Hallstrom T, Riesbeck K. 2013. Human complement control and complement evasion by pathogenic microbes-tipping the balance. Mol Immunol 56:152-160.
106. Stecher B, Hardt WD. 2008. The role of microbiota in infectious disease. Trends Microbiol 16:107-114.
107. Andrews NC, Schmidt PJ. 2007. Iron homeostasis. Annu Rev Physiol 69:69-85.
108. Galy B, Ferring-Appel D, Becker C, Gretz N, Grone HJ, Schumann K, Hentze MW. 2013. Iron regulatory proteins control a mucosal block to intestinal iron absorption. Cell Rep 3:844-857.
109. De Domenico I, Ward DM, Kaplan J. 2011. Hepcidin and ferroportin: the new players in iron metabolism. Semin Liver Dis 31:272-279.
110. Neilands JB. 1995. Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270:26723-26726.
111. Muller SI, Valdebenito M, Hantke K. 2009. Salmochelin, the long-overlooked catecholate siderophore of Salmonella. Biometals 22: 691-695.
112. Raffatellu M, George MD, Akiyama Y, Hornsby MJ, Nuccio SP, Paixao TA, Butler BP, Chu H, Santos RL, Berger T, Mak TW, Tsolis RM, Bevins CL, Solnick JV, Dandekar S, Baumler AJ. 2009. Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine. Cell Host Microbe 5:476-486.
113. Loetscher Y, Wieser A, Lengefeld J, Kaiser P, Schubert S, Heikenwalder M, Hardt WD, Stecher B. 2012. Salmonella transiently reside in luminal neutrophils in the inflamed gut. PLoS ONE 7:e34812.
114. 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.
115. Gill N, Ferreira RB, Antunes LC, Willing BP, Sekirov I, Al-Zahrani F, Hartmann M, Finlay BB. 2012. Neutrophil elastase alters the murine gut microbiota resulting in enhanced salmonella colonization. PLoS ONE 7: e49646.
116. Corbin BD, Seeley EH, Raab A, Feldmann J, Miller MR, Torres VJ, Anderson KL, Dattilo BM, Dunman PM, Gerads R, Caprioli RM, Nacken W, Chazin WJ, Skaar EP. 2008. Metal chelation and inhibition of bacterial growth in tissue abscesses. Science 319:962-965.
117. Kehl-Fie TE, Chitayat S, Hood MI, Damo S, Restrepo N, Garcia C, Munro KA, Chazin WJ, Skaar EP. 2011. Nutrient metal sequestration by calprotectin inhibits bacterial superoxide defense, enhancing neutrophil killing of Staphylococcus aureus. Cell Host Microbe 10:158-164.
118. Liu JZ, Jellbauer S, Poe AJ, Ton V, Pesciaroli M, Kehl-Fie TE, Restrepo NA, Hosking MP, Edwards RA, Battistoni A, Pasquali P, Lane TE, Chazin WJ, Vogl T, Roth J, Skaar EP, Raffatellu M. 2012. Zinc sequestration by the neutrophil protein calprotectin enhances Salmonella growth in the inflamed gut. Cell Host Microbe 11:227-239.
119. Wehkamp J, Salzman NH, Porter E, Nuding S, Weichenthal M, Petras RE, Shen B, Schaeffeler E, Schwab M, Linzmeier R, Feathers RW, Chu H, Lima H, Jr., Fellermann K, Ganz T, Stange EF, Bevins CL. 2005. Reduced Paneth cell alpha-defensins in ileal Crohn's disease. Proc Natl Acad Sci U S A 102:18129-18134.
120. Salzman NH, Hung K, Haribhai D, Chu H, Karlsson-Sjoberg J, Amir E, Teggatz P, Barman M, Hayward M, Eastwood D, Stoel M, Zhou Y, Sodergren E, Weinstock GM, Bevins CL, Williams CB, Bos NA. 2010. Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol 11:76-83.
121. Rahman A, Fahlgren A, Sundstedt C, Hammarstrom S, Danielsson A, Hammarstrom ML. 2011. Chronic colitis induces expression of betadefensins in murine intestinal epithelial cells. Clin Exp Immunol 163:123-130.
122. Ho S, Pothoulakis C, Koon HW. 2013. Antimicrobial peptides and colitis. Curr Pharm Des 19:40-47.
123. Joly S, Maze C, McCray PB, Jr., Guthmiller JM. 2004. Human betadefensins 2 and 3 demonstrate strain-selective activity against oral microorganisms. J Clin Microbiol 42:1024-1029.
124. Salzman NH, Ghosh D, Huttner KM, Paterson Y, Bevins CL. 2003. Protection against enteric salmonellosis in transgenic mice expressing a human intestinal defensin. Nature 422:522-526.
125. Sperandio B, Regnault B, Guo J, Zhang Z, Stanley SL, Jr., Sansonetti PJ, Pedron T. 2008. Virulent Shigella flexneri subverts the host innate immune response through manipulation of antimicrobial peptide gene expression. Journal Exp Med 205:1121-1132.
126. Pazgier M, Hoover DM, Yang D, Lu W, Lubkowski J. 2006. Human beta-defensins. Cell Mol Life Sci 63:1294-1313.
127. Cash HL, Whitham CV, Behrendt CL, Hooper LV. 2006. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313:1126-1130.
128. Stelter C, Kappeli R, Konig C, Krah A, Hardt WD, Stecher B, Bumann D. 2011. Salmonella-induced mucosal lectin regIIIbeta kills competing gut microbiota. PLoS ONE 6:e20749.
129. Miki T, Holst O, Hardt WD. 2012. The bactericidal activity of the C-type lectin RegIIIbeta against Gram-negative bacteria involves binding to lipid A. J Biol Chem 287:34844-34855.
130. Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley R, Wakeland EK, Hooper LV. 2011. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334:255-258.
131. Craven M, Egan CE, Dowd SE, McDonough SP, Dogan B, Denkers EY, Bowman D, Scherl EJ, Simpson KW. 2012. Inflammation drives dysbiosis and bacterial invasion in murine models of ileal Crohn's disease. PLoS ONE 7:e41594.
132. Chow J, Mazmanian SK. 2010. A pathobiont of the microbiota balances host colonization and intestinal inflammation. Cell Host Microbe 7:265-276.
133. Ayres JS, Trinidad NJ, Vance RE. 2012. Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota. Nat Med 18:799-806.
134. Barnich N, Darfeuille-Michaud A. 2007. Adherent-invasive Escherichia coli and Crohn's disease. Curr Opin Gastroenterol 23:16-20.
135. Darfeuille-Michaud A. 2002. Adherent-invasive Escherichia coli: a putative new E. coli pathotype associated with Crohn's disease. Int J Med Microbiol 292:185-193.
136. Tabaqchali S, O'Donoghue DP, Bettelheim KA. 1978. Escherichia coli antibodies in patients with inflammatory bowel disease. Gut 19:108-113.
137. Wehkamp J, Stange EF. 2006. A new look at Crohn's disease: breakdown of the mucosal antibacterial defense. Ann N Y Acad Sci 1072:321-331.
138. Barnich N, Carvalho FA, Glasser AL, Darcha C, JantscheffP, Allez M, Peeters H, Bommelaer G, Desreumaux P, Colombel JF, Darfeuille-Michaud A. 2007. CEACAM6 acts as a receptor for adherentinvasive E. coli, supporting ileal mucosa colonization in Crohn disease. Journal Clin Invest 117:1566-1574.
139. Carvalho FA, Barnich N, Sivignon A, Darcha C, Chan CH, Stanners CP, Darfeuille-Michaud A. 2009. Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM. J Exp Med 206:2179-2189.
140. Vijay-Kumar M, Sanders CJ, Taylor RT, Kumar A, Aitken JD, Sitaraman SV, Neish AS, Uematsu S, Akira S, Williams IR, Gewirtz AT. 2007. Deletion of TLR5 results in spontaneous colitis in mice. J Clinical Invest 117:3909-3921.
141. Carvalho FA, Koren O, Goodrich JK, Johansson ME, Nalbantoglu I, Aitken JD, Su Y, Chassaing B, Walters WA, Gonzalez A, Clemente JC, Cullender TC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, Gewirtz AT. 2012. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe 12:139-152.
142. Kuhn R, Lohler J, Rennick D, Rajewsky K, Muller W. 1993. Interleukin-10-deficient mice develop chronic enterocolitis. Cell 75:263-274.
143. Kim SC, Tonkonogy SL, Albright CA, Tsang J, Balish EJ, Braun J, Huycke MM, Sartor RB. 2005. Variable phenotypes of enterocolitis in interleukin 10-deficient mice monoassociated with two different commensal bacteria. Gastroenterology 128:891-906.
144. Kim SC, Tonkonogy SL, Karrasch T, Jobin C, Sartor RB. 2007. Dual-association of gnotobiotic IL-10-/-mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis. Inflamm Bowel Dis 13:1457-1466.
145. Steck N, Hoffmann M, Sava IG, Kim SC, Hahne H, Tonkonogy SL, Mair K, Krueger D, Pruteanu M, Shanahan F, Vogelmann R, Schemann M, Kuster B, Sartor RB, Haller D. 2011. Enterococcus faecalis metalloprotease compromises epithelial barrier and contributes to intestinal inflammation. Gastroenterology 141:959-971.
146. Cahill RJ, Foltz CJ, Fox JG, Dangler CA, Powrie F, Schauer DB. 1997. Inflammatory bowel disease: an immunity-mediated condition triggered by bacterial infection with Helicobacter hepaticus. Infect Immun 65:3126-3131.
147. Dieleman LA, Arends A, Tonkonogy SL, Goerres MS, Craft DW, Grenther W, Sellon RK, Balish E, Sartor RB. 2000. Helicobacter hepaticus does not induce or potentiate colitis in interleukin-10-deficient mice. Infect Immun 68:5107-5113.
148. Yang I, Eibach D, Kops F, Brenneke B, Woltemate S, Schulze J, Bleich A, Gruber AD, Muthupalani S, Fox JG, Josenhans C, Suerbaum S. 2013. Intestinal microbiota composition of interleukin-10 deficient C57BL/6J mice and susceptibility to Helicobacter hepaticus-induced colitis. PLoS ONE 8:e70783.
149. Deriu E, Liu JZ, Pezeshki M, Edwards RA, Ochoa RJ, Contreras H, Libby SJ, Fang FC, Raffatellu M. 2013. Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron. Cell Host Microbe 14:26-37.
150. Valdebenito M, Crumbliss AL, Winkelmann G, Hantke K. 2006. Environmental factors influence the production of enterobactin, salmochelin, aerobactin, and yersiniabactin in Escherichia coli strain Nissle 1917. Int J Med Microbiol 296:513-520.
151. Hibbing ME, Fuqua C, Parsek MR, Peterson SB. 2010. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8:15-25.
152. 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.
153. Riley MA, Gordon DM. 1999. The ecological role of bacteriocins in bacterial competition. Trends Microbiol 7:129-133.
154. Riley MA, Gordon DM. 1992. A survey of Col plasmids in natural isolates of Escherichia coli and an investigation into the stability of Colplasmid lineages. J Gen Microbiol 138:1345-1352.
155. Nedialkova LP, Denzler R, Koeppel MB, Diehl M, Ring D, Wille T, Gerlach RG, Stecher B. 2014. Inflammation fuels colicin Ib-dependent competition of Salmonella serovar Typhimurium and E. coli in Enterobacterial blooms. PLoS Pathog 10:e1003844.
156. Rakin A, Saken E, Harmsen D, Heesemann J. 1994. The pesticin receptor of Yersinia enterocolitica: a novel virulence factor with dual function. Mol Microbiol 13:253-263.
157. Braun V, Hantke K, Koster W. 1998. Bacterial iron transport: mechanisms, genetics, and regulation. Met Ions Biol Syst 35:67-145.
158. Butala M, Zgur-Bertok D, Busby SJ. 2009. The bacterial LexA transcriptional repressor. Cell Mol Life Sci 66:82-93.
159. Kamensek S, Podlesek Z, Gillor O, Zgur-Bertok D. 2010. Genes regulated by the Escherichia coli SOS repressor LexA exhibit heterogeneous expression. BMC Microbiol 10:283.
160. Mrak P, Podlesek Z, van Putten JP, Zgur-Bertok D. 2007. Heterogeneity in expression of the Escherichia coli colicin K activity gene cka is controlled by the SOS system and stochastic factors. Mol Genet Genomics 277:391-401.
161. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241-244.
162. Kelly BG, Vespermann A, Bolton DJ. 2009. Gene transfer events and their occurrence in selected environments. Food Chem Toxicol 47:978-983.
163. Brown Kav A, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I. 2012. Insights into the bovine rumen plasmidome. Proc Natl Acad Sci U S A 109:5452-5457.
164. Stecher B, Denzler R, Maier L, Bernet F, Sanders MJ, Pickard DJ, Barthel M, Westendorf AM, Krogfelt KA, Walker AW, Ackermann M, Dobrindt U, Thomson NR, Hardt WD. 2012. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc Natl Acad Sci U S A 109:1269-1274.
165. Hoiseth SK, Stocker BA. 1981. Aromatic-dependent Salmonella typhimurium are non-virulent and effective as live vaccines. Nature 291:238-239.
166. Stecher B, Chaffron S, Kappeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, von Mering C, Macpherson AJ, Hardt WD. 2010. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog 6:e1000711.
167. Christenson JK, Gordon DM. 2009. Evolution of colicin BM plasmids: the loss of the colicin B activity gene. Microbiology 155:1645-1655.
168. Reid SD, Herbelin CJ, Bumbaugh AC, Selander RK, Whittam TS. 2000. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406:64-67.
169. Welch RA, Burland V, Plunkett G, 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 99:17020-17024.
170. Brzuszkiewicz E, Bruggemann H, Liesegang H, Emmerth M, Olschlager T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L, Gottschalk G, Hacker J, Dobrindt U. 2006. How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci U S A 103:12879-12884.
171. McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-856.
172. McClelland M, Florea L, Sanderson K, Clifton SW, Parkhill J, Churcher C, Dougan G, Wilson RK, Miller W. 2000. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res 28:4974-4986.
173. Baumler AJ. 1997. The record of horizontal gene transfer in Salmonella. Trends Microbiol 5:318-322.
174. Poppe C, Smart N, Khakhria R, Johnson W, Spika J, Prescott J. 1998. Salmonella typhimurium DT104: a virulent and drug-resistant pathogen. Can Vet J 39:559-565.
175. Threlfall EJ. 2000. Epidemic salmonella typhimurium DT 104-a truly international multiresistant clone. J Antimicrob Chemother 46:7-10.
176. Poppe C, Ziebell K, Martin L, Allen K. 2002. Diversity in antimicrobial resistance and other characteristics among Salmonella typhimurium DT104 isolates. Microb Drug Resist 8:107-122.
177. Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor TR, Suchard MA, Lemey P, Mellor DJ, Haydon DT, Thomson NR. 2013. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science 341:1514-1517.
178. Gordon MA, Graham SM, Walsh AL, Wilson L, Phiri A, Molyneux E, Zijlstra EE, Heyderman RS, Hart CA, Molyneux ME. 2008. Epidemics of invasive Salmonella enterica serovar enteritidis and S. enterica Serovar typhimurium infection associated with multidrug resistance among adults and children in Malawi. Clin Infect Dis 46:963-969.
179. Kruger T, Szabo D, Keddy KH, Deeley K, Marsh JW, Hujer AM, Bonomo RA, Paterson DL. 2004. Infections with nontyphoidal Salmonella species producing TEM-63 or a novel TEM enzyme, TEM-131, in South Africa. Antimicrob Agents Chemother 48:4263-4270.
180. Kim EB, Marco ML. 2014. Nonclinical and clinical Enterococcus faecium strains, but not Enterococcus faecalis strains, have distinct structural and functional genomic features. Appl Environ Microbiol 80:154-165.
181. Clewell DB, Weaver KE, Dunny GM, Coque TM, Francia MV, Hayes F. 2014. Extrachromosomal and mobile elements in enterococci: Transmission, maintenance, and epidemiology. In Gilmore MS, Clewell DB, Ike Y, Shankar N (ed), Enterococci: From commensals to leading causes of drug resistant infection [Internet]. Boston: Massachusetts Eye and Ear Infirmary; 2014-. 2014 Feb 9.