Phylogenetic, virulence and antibiotic resistance characteristics of commensal strain populations of escherichia coli from community subjects in the paris area in 2010 and evolution over 30 years

Microbiology (United Kingdom)

Volumn 162, Issue 4, 2016, Pages 642-650

  Massot, Méril ^a,b   Daubié, Anne Sophie ^a,c,d   Clermont, Olivier ^a,b   Jauréguy, Françoise ^a,c,d   Couffignal, Camille ^a,b   Dahbi, Ghizlane ^e   Mora, Azucena ^e   Blanco, Jorge ^e   Branger, Catherine ^a,b   Mentré, France ^a,b   Eddi, Alain ^b,f   Picard, Bertrand ^a,c,d   Denamur, Erick ^a,b   Allouche, Monique ^f   Aubert, Jean Pierre ^f   Aubin, Isabelle ^f   Audran, Ghislaine ^f   Baruch, Dan ^f   Birembaux, Philippe ^f   Budowski, Max ^f   Chemla, Emilie ^f   Frarier, Marc ^f   Galam, Eric ^f   Gelly, Julien ^f   Joly, Serge ^f   Millet, Jean François ^f   Nougairede, Michel ^f   Pillon, Nadja ^f   Septavaux, Guy ^f   Szwebel, Catherine ^f   Vellard, Philippe ^f   Wakim, Raymond ^f   Watelet, Xavier ^f   Zerr, Philippe ^f   more..

^a UNIVERSITÉ PARIS DIDEROT   (France)

^b UNIVERSITÉ PARIS DESCARTES   (France)

^c ASSISTANCE PUBLIQUE HÔPITAUX DE PARIS   (France)

^d UNIVERSITÉ PARIS 13   (France)

^e UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^f NONE

Author keywords

[No Author keywords available]

Indexed keywords

AMIKACIN; AMINOGLYCOSIDE; AMOXICILLIN; AMOXICILLIN PLUS CLAVULANIC ACID; CARBAPENEM DERIVATIVE; CEFOTAXIME; CEFOXITIN; CEPHALOSPORIN DERIVATIVE; CHLORAMPHENICOL; COTRIMOXAZOLE; ERTAPENEM; FOSFOMYCIN; FURAN DERIVATIVE; GENTAMICIN; IMIPENEM; NALIDIXIC ACID; NETILMICIN; NITROFURANTOIN; OFLOXACIN; PENICILLIN DERIVATIVE; PHOSPHONIC ACID DERIVATIVE; QUINOLONE DERIVATIVE; STREPTOMYCIN; SULFONAMIDE; TETRACYCLINE; TETRACYCLINE DERIVATIVE; TOBRAMYCIN; O ANTIGEN; VIRULENCE FACTOR;

ANTIBIOTIC RESISTANCE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM ISOLATE; COMMENSAL ESCHERICHIA COLI; EDITORIAL; FRANCE; HUMAN; NONHUMAN; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRULENCE GENE; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; DRUG EFFECTS; ESCHERICHIA COLI; FECES; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR TYPING; SEROTYPE; TIME FACTOR;

DRUG RESISTANCE, BACTERIAL; ESCHERICHIA COLI; FECES; GENOTYPE; HUMANS; MOLECULAR TYPING; O ANTIGENS; PARIS; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SEROGROUP; TIME FACTORS; VIRULENCE FACTORS;

EID: 84963815808     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.000242     Document Type: Editorial

References (48)

1. Alhashash, F., Weston, V., Diggle, M. & McNally, A. (2013). Multidrugresistant Escherichia coli bacteremia. Emerg Infect Dis 19, 1699–1701.
2. Bailey, J. K., Pinyon, J. L., Anantham, S. & Hall, R. M. (2010a). Commensal Escherichia coli of healthy humans: a reservoir for antibiotic-resistance determinants. J Med Microbiol 59, 1331–1339.
3. Bailey, J. K., Pinyon, J. L., Anantham, S. & Hall, R. M. (2010b). Distribution of human commensal Escherichia coli phylogenetic groups. J Clin Microbiol 48, 3455–3456.
4. Bengtsson, S., Naseer, U., Sundsfjord, A., Kahlmeter, G. & Sundqvist, M. (2012). Sequence types and plasmid carriage of uropathogenic Escherichia coli devoid of phenotypically detectable resistance. J Antimicrob Chemother 67, 69–73.
5. Benjamini, Y. & Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57, 289–300.
6. Berg, R. D. (1996). The indigenous gastrointestinal microflora. Trends Microbiol 4, 430–435.
7. Bert, F., Johnson, J. R., Ouattara, B., Leflon-Guibout, V., Johnston, B., Marcon, E., Valla, D., Moreau, R. & Nicolas-Chanoine, M. H. (2010). Genetic diversity and virulence profiles of Escherichia coli isolates causing spontaneous bacterial peritonitis and bacteremia in patients with cirrhosis. J Clin Microbiol 48, 2709–2714.
8. Bidet, P., Mahjoub-Messai, F., Blanco, J., Blanco, J., Dehem, M., Aujard, Y., Bingen, E. & Bonacorsi, S. (2007). Combined multilocus sequence typing and O serogrouping distinguishes Escherichia coli subtypes associated with infant urosepsis and/or meningitis. J Infect Dis 196, 297–303.
9. Carlet, J. (2012). The gut is the epicentre of antibiotic resistance. Antimicrob Resist Infect Control 1, 39.
10. Chiew, Y. F., Yeo, S. F., Hall, L. M. & Livermore, D. M. (1998). Can susceptibility to an antimicrobial be restored by halting its use? The case of streptomycinversus Enterobacteriaceae.J Antimicrob Chemother 41, 247–251.
11. Clermont, O., Lescat, M., O’Brien, C. L., Gordon, D. M., Tenaillon, O. & Denamur, E. (2008). Evidence for a human-specific Escherichia coli clone. Environ Microbiol 10, 1000–1006.
12. Clermont, O., Gordon, D. M., Brisse, S., Walk, S. T. & Denamur, E. (2011a). Characterization of the cryptic Escherichia lineages: rapid identification and prevalence. Environ Microbiol 13, 2468–2477.
13. Clermont, O., Olier, M., Hoede, C., Diancourt, L., Brisse, S., Keroudean, M., Glodt, J., Picard, B., Oswald, E. & Denamur, E. (2011b). Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Infect Genet Evol 11, 654–662.
14. Clermont, O., Christenson, J. K., Denamur, E. & Gordon, D. M. (2013). The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylogroups. Environ Microbiol Rep 5, 58–65.
15. Clermont, O., Christenson, J. K., Daubié, A. S., Gordon, D. M. & Denamur, E. (2014). Development of an allele-specific PCR for Escherichia coli B2 sub-typing, a rapid and easy to perform substitute of multilocus sequence typing. J Microbiol Methods 101, 24–27.
16. Clermont, O., Gordon, D. & Denamur, E. (2015). Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes. Microbiology 161, 980–988.
17. Desjardins, P., Picard, B., Kaltenböck, B., Elion, J. & Denamur, E. (1995). Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism. J Mol Evol 41, 440–448.
18. Diard, M., Garry, L., Selva, M., Mosser, T., Denamur, E. & Matic, I. (2010). Pathogenicity-associated islands in extraintestinal pathogenic Escherichia coli are fitness elements involved in intestinal colonization. J Bacteriol 192, 4885–4893.
19. Duriez, P., Clermont, O., Bonacorsi, S., Bingen, E., Chaventré, A., Elion, J., Picard, B. & Denamur, E. (2001). Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiology 147, 1671–1676.
20. Escobar-Páramo, P., Clermont, O., Blanc-Potard, A. B., Bui, H., Le Bouguénec, C. & Denamur, E. (2004a). A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol Biol Evol 21, 1085–1094.
21. Escobar-Páramo, P., Grenet, K., Le Menac’h, A., Rode, L., Salgado, E., Amorin, C., Gouriou, S., Picard, B., Rahimy, M. C. & other authors (2004b). Large-scale population structure of human commensal Escherichia coli isolates. Appl Environ Microbiol 70, 5698–5700.
22. Gibreel, T. M., Dodgson, A. R., Cheesbrough, J., Fox, A. J., Bolton, F. J. & Upton, M. (2012). Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from Northwest England. J Antimicrob Chemother 67, 346–356.
23. Gordon, D. M., Stern, S. E. & Collignon, P. J. (2005). Influence of the age and sex of human hosts on the distribution of Escherichia coli ECOR groups and virulence traits. Microbiology 151, 15–23.
24. Guinée, P. A. M. & Jansen, W. H. (1981). Escherichia coli associated with neonatal diarrhoea in piglets and calves. In Laboratory Diagnosis in Neonatal Calf and Pig Diarrhoea, Current Topics in Veterinary and Animal Science, pp. 126–162. Edited by P. M. Leeww & P. A. M. Guinée. The Hague: Martinus-Nijhoff.
25. Johnson, J. R., Owens, K., Manges, A. R. & Riley, L. W. (2004). Rapid and specific detection of Escherichia coli clonal group A by genespecific PCR. J Clin Microbiol 42, 2618–2622.
26. Johnson, J.R., Johnston, B., Kuskowski, M.A., Nougayrede, J. P. & Oswald, E. (2008). Molecular epidemiology and phylogenetic distribution of the Escherichia coli pks genomic island. J Clin Microbiol 46, 3906–3911.
27. Johnson, J. R., Clermont, O., Johnston, B., Clabots, C., Tchesnokova, V., Sokurenko, E., Junka, A. F., Maczynska, B. & Denamur, E. (2014). Rapid and specific detection, molecular epidemiology, and experimental virulence of the O16 subgroup within Escherichia coli sequence type 131. J Clin Microbiol 52, 1358–1365.
28. Kaper, J. B., Nataro, J. P. & Mobley, H. L. (2004). Pathogenic Escherichia coli. Nat Rev Microbiol 2, 123–140.
29. Le Gall, T., Clermont, O., Gouriou, S., Picard, B., Nassif, X., Denamur, E. & Tenaillon, O. (2007). Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol 24, 2373–2384.
30. Lefort, A., Panhard, X., Clermont, O., Woerther, P. L., Branger, C., Mentré, F., Fantin, B., Wolff, M., Denamur, E. & COLIBAFI Group (2011). Host factors and portal of entry outweigh bacterial determinants to predict the severity of Escherichia coli bacteremia. J Clin Microbiol 49, 777–783.
31. Lescat, M., Clermont, O., Woerther, P. L., Glodt, J., Dion, S., Skurnik, D., Djossou, F., Dupont, C., Perroz, G. & other authors (2013). Commensal Escherichia coli strains inGuiana reveal a high genetic diversity with hostdependant population structure. Environ Microbiol Rep 5, 49–57.
32. Li, B., Sun, J. Y., Han, L. Z., Huang, X. H., Fu, Q. & Ni, Y. X. (2010). Phylogenetic groups and pathogenicity island markers in fecal Escherichia coli isolates from asymptomatic humans in China. Appl Environ Microbiol 76, 6698–6700.
33. Mahjoub-Messai, F., Bidet, P., Caro, V., Diancourt, L., Biran, V., Aujard, Y., Bingen, E. & Bonacorsi, S. (2011). Escherichia coli isolates causing bacteremia via gut translocation and urinary tract infection in young infants exhibit different virulence genotypes. J Infect Dis 203, 1844–1849.
34. Manges, A. R., Johnson, J. R., Foxman, B., O’Bryan, T. T., Fullerton, K. E. & Riley, L. W. (2001). Widespread distribution of urinary tract infections caused by a multidrug-resistant Escherichia coli clonal group. N Engl J Med 345, 1007–1013.
35. Messika, J., Magdoud, F., Clermont, O., Margetis, D., Gaudry, S., Roux, D., Branger, C., Dreyfuss, D., Denamur, E. & Ricard, J. D. (2012). Pathophysiology of Escherichia coli ventilator-associated pneumonia: implication of highly virulent extraintestinal pathogenic strains. Intensive Care Med 38, 2007–2016.
36. Moissenet, D., Salauze, B., Clermont, O., Bingen, E., Arlet, G., Denamur, E., Mérens, A., Mitanchez, D. & Vu-Thien, H. (2010). Meningitis caused by Escherichia coli producing TEM-52 extendedspectrum beta-lactamase within an extensive outbreak in a neonatal ward: epidemiological investigation and characterization of the strain. J Clin Microbiol 48, 2459–2463.
37. Nicolas-Chanoine, M. H., Gruson, C., Bialek-Davenet, S., Bertrand, X., Thomas-Jean, F., Bert, F., Moyat, M., Meiller, E., Marcon, E. & other authors (2013). 10-Fold increase (2006-11) in the rate of healthy subjects with extended-spectrum b-lactamase-producing Escherichia coli faecal carriage in a Parisian check-up centre. J Antimicrob Chemother 68, 562–568.
38. Nicolas-Chanoine, M. H., Bertrand, X. & Madec, J. Y. (2014). Escherichia coli ST131, an intriguing clonal group. Clin Microbiol Rev 27, 543–574.
39. Nowrouzian, F. L., Wold, A. E. & Adlerberth, I. (2005). Escherichia coli strains belonging to phylogenetic group B2 have superior capacity to persist in the intestinal microflora of infants. J InfectDis 191, 1078–1083.
40. Partridge, S. R., Tsafnat, G., Coiera, E. & Iredell, J. R. (2009). Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 33, 757–784.
41. Russo, T. A. & Johnson, J. R. (2003). Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem. Microbes Infect 5, 449–456.
42. Schubert, S., Darlu, P., Clermont, O., Wieser, A., Magistro, G., Hoffmann, C., Weinert, K., Tenaillon, O., Matic, I. & Denamur, E. (2009). Role of intraspecies recombination in the spread of pathogenicity islands within the Escherichia coli species. PLoS Pathog 5, e1000257.
43. Smati, M., Clermont, O., Le Gal, F., Schichmanoff, O., Jauréguy, F., Eddi, A., Denamur, E., Picard, B. & Coliville Group (2013). Realtime PCR for quantitative analysis of human commensal Escherichia coli populations reveals a high frequency of subdominant phylogroups. Appl Environ Microbiol 79, 5005–5012.
44. Tapader, R., Chatterjee, S., Singh, A. K., Dayma, P., Haldar, S., Pal, A. & Basu, S. (2014). The high prevalence of serine protease autotransporters of Enterobacteriaceae (SPATEs) in Escherichia coli causing neonatal septicemia. Eur J Clin Microbiol Infect Dis 33, 2015–2024.
45. Tenaillon, O., Skurnik, D., Picard, B. & Denamur, E. (2010).The population genetics of commensal Escherichia coli. Nat Rev Microbiol 8, 207–217.
46. Unno, T., Han, D., Jang, J., Lee, S. N., Ko, G., Choi, H. Y., Kim, J. H., Sadowsky, M. J. & Hur, H. G. (2009). Absence of Escherichia coli phylogenetic group B2 strains in humans and domesticated animals from Jeonnam Province, Republic of Korea. Appl Environ Microbiol 75, 5659–5666.
47. Walk, S. T., Alm, E. W., Gordon, D. M., Ram, J. L., Toranzos, G. A., Tiedje, J. M. & Whittam, T. S. (2009). Cryptic lineages of the genus Escherichia. Appl Environ Microbiol 75, 6534–6544.
48. Woerther, P. L., Angebault, C., Jacquier, H., Clermont, O., El Mniai, A., Moreau, B., Djossou, F., Peroz, G., Catzeflis, F. & other authors (2013). Characterization of fecal extended-spectrum-b-lactamaseproducing Escherichia coli in a remote community during a long time period. Antimicrob Agents Chemother 57, 5060–5066.