Comparative distribution of extended-spectrum beta-lactamase–producing Escherichia coli from urine infections and environmental waters

Autoři: Anna Fagerström aff001;  Paula Mölling aff001;  Faisal Ahmad Khan aff002;  Martin Sundqvist aff001;  Jana Jass aff002;  Bo Söderquist aff001
Působiště autorů: Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden aff001;  The Life Science Centre–Biology, School of Science and Technology, Örebro University, Örebro, Sweden aff002
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224861


Extended-spectrum beta-lactamase (ESBL)–producing Escherichia coli have been reported in natural environments, and may be released through wastewater. In this study, the genetic relationship between ESBL-producing E. coli collected from patient urine samples (n = 45, both hospitalized patients and out-patients) and from environmental water (n = 82, from five locations), during the same time period, was investigated. Three independent water samples were collected from the municipal wastewater treatment plant, both incoming water and treated effluent water; the receiving river and lake; and a bird sanctuary near the lake, on two different occasions. The water was filtered and cultured on selective chromID ESBL agar plates in order to detect and isolate ESBL-producing E. coli. Illumina whole genome sequencing was performed on all bacterial isolates (n = 127). Phylogenetic group B2 was more common among the clinical isolates than the environmental isolates (44.4% vs. 17.1%, p < 0.01) due to a significantly higher prevalence of sequence type (ST) 131 (33.3% vs. 13.4%, p < 0.01). ST131 was, however, one of the most prevalent STs among the environmental isolates. There was no significant difference in diversity between the clinical isolates (DI 0.872 (0.790–0.953)) and the environmental isolates (DI 0.947 (0.920–0.969)). The distribution of ESBL genes was similar: blaCTX-M-15 dominated, followed by blaCTX-M-14 and blaCTX-M-27 in both the clinical (60.0%, 8.9%, and 6.7%) and the environmental isolates (62.2%, 12.2%, and 8.5%). Core genome multi-locus sequence typing showed that five environmental isolates, from incoming wastewater, treated wastewater, Svartån river and Hjälmaren lake, were indistinguishable or closely related (≤10 allele differences) to clinical isolates. Isolates of ST131, serotype O25:H4 and fimtype H30, from the environment were as closely related to the clinical isolates as the isolates from different patients were. This study confirms that ESBL-producing E. coli are common in the aquatic environment even in low-endemic regions and suggests that wastewater discharge is an important route for the release of ESBL-producing E. coli into the aquatic environment.

Klíčová slova:

Aquatic environments – Effluent – Genome analysis – Lakes – Phylogenetics – Surface water – Urine – Water pollution


1. Brolund A, Edquist PJ, Makitalo B, Olsson-Liljequist B, Soderblom T, Wisell KT, et al. Epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli in Sweden 2007–2011. Clinical microbiology and infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 2014;20(6):O344–52. Epub 2013/10/15. doi: 10.1111/1469-0691.12413 24118431.

2. Pitout JD, Laupland KB. Extended-spectrum beta-lactamase-producing Enterobacteriaceae: an emerging public-health concern. Lancet Infect Dis. 2008;8(3):159–66. Epub 2008/02/23. doi: 10.1016/S1473-3099(08)70041-0 18291338.

3. Dolejska M, Frolkova P, Florek M, Jamborova I, Purgertova M, Kutilova I, et al. CTX-M-15-producing Escherichia coli clone B2-O25b-ST131 and Klebsiella spp. isolates in municipal wastewater treatment plant effluents. J Antimicrob Chemother. 2011;66(12):2784–90. Epub 2011/09/29. doi: 10.1093/jac/dkr363 21954457.

4. Korzeniewska E, Harnisz M. Extended-spectrum beta-lactamase (ESBL)-positive Enterobacteriaceae in municipal sewage and their emission to the environment. J Environ Manage. 2013;128:904–11. Epub 2013/07/28. doi: 10.1016/j.jenvman.2013.06.051 23886578.

5. Zurfluh K, Hachler H, Nuesch-Inderbinen M, Stephan R. Characteristics of extended-spectrum beta-lactamase- and carbapenemase-producing Enterobacteriaceae Isolates from rivers and lakes in Switzerland. Appl Environ Microbiol. 2013;79(9):3021–6. Epub 2013/03/05. doi: 10.1128/AEM.00054-13 23455339; PubMed Central PMCID: PMC3623138.

6. Blaak H, de Kruijf P, Hamidjaja RA, van Hoek AH, de Roda Husman AM, Schets FM. Prevalence and characteristics of ESBL-producing E. coli in Dutch recreational waters influenced by wastewater treatment plants. Vet Microbiol. 2014;171(3–4):448–59. Epub 2014/04/03. doi: 10.1016/j.vetmic.2014.03.007 24690376.

7. Jorgensen SB, Soraas AV, Arnesen LS, Leegaard TM, Sundsfjord A, Jenum PA. A comparison of extended spectrum beta-lactamase producing Escherichia coli from clinical, recreational water and wastewater samples associated in time and location. PloS one. 2017;12(10):e0186576. Epub 2017/10/19. doi: 10.1371/journal.pone.0186576 29040337; PubMed Central PMCID: PMC5645111.

8. Literak I, Dolejska M, Radimersky T, Klimes J, Friedman M, Aarestrup FM, et al. Antimicrobial-resistant faecal Escherichia coli in wild mammals in central Europe: multiresistant Escherichia coli producing extended-spectrum beta-lactamases in wild boars. J Appl Microbiol. 2010;108(5):1702–11. Epub 2009/10/24. doi: 10.1111/j.1365-2672.2009.04572.x 19849769.

9. Goncalves A, Igrejas G, Radhouani H, Estepa V, Alcaide E, Zorrilla I, et al. Detection of extended-spectrum beta-lactamase-producing Escherichia coli isolates in faecal samples of Iberian lynx. Lett Appl Microbiol. 2012;54(1):73–7. Epub 2011/11/03. doi: 10.1111/j.1472-765X.2011.03173.x 22044404.

10. Stedt J, Bonnedahl J, Hernandez J, Waldenstrom J, McMahon BJ, Tolf C, et al. Carriage of CTX-M type extended spectrum beta-lactamases (ESBLs) in gulls across Europe. Acta Vet Scand. 2015;57:74. Epub 2015/11/04. doi: 10.1186/s13028-015-0166-3 26526188; PubMed Central PMCID: PMC4629291.

11. Li S, Song W, Zhou Y, Tang Y, Gao Y, Miao Z. Spread of extended-spectrum beta-lactamase-producing Escherichia coli from a swine farm to the receiving river. Environ Sci Pollut Res Int. 2015;22(17):13033–7. Epub 2015/04/30. doi: 10.1007/s11356-015-4575-7 25921760.

12. Gao L, Hu J, Zhang X, Ma R, Gao J, Li S, et al. Dissemination of ESBL-producing Escherichia coli of chicken origin to the nearby river water. J Mol Microbiol Biotechnol. 2014;24(4):279–85. Epub 2014/10/04. doi: 10.1159/000365786 25277838.

13. Wieler LH, Ewers C, Guenther S, Walther B, Lubke-Becker A. Methicillin-resistant staphylococci (MRS) and extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae in companion animals: nosocomial infections as one reason for the rising prevalence of these potential zoonotic pathogens in clinical samples. Int J Med Microbiol. 2011;301(8):635–41. Epub 2011/10/18. doi: 10.1016/j.ijmm.2011.09.009 22000738.

14. Gronthal T, Osterblad M, Eklund M, Jalava J, Nykasenoja S, Pekkanen K, et al. Sharing more than friendship—transmission of NDM-5 ST167 and CTX-M-9 ST69 Escherichia coli between dogs and humans in a family, Finland, 2015. Euro Surveill. 2018;23(27). Epub 2018/07/12. doi: 10.2807/1560-7917.Es.2018.23.27.1700497 29991384; PubMed Central PMCID: PMC6152158.

15. Ny S, Lofmark S, Borjesson S, Englund S, Ringman M, Bergstrom J, et al. Community carriage of ESBL-producing Escherichia coli is associated with strains of low pathogenicity: a Swedish nationwide study. J Antimicrob Chemother. 2017;72(2):582–8. Epub 2016/11/01. doi: 10.1093/jac/dkw419 27798205.

16. Ny S, Kozlov R, Dumpis U, Edquist P, Grondahl-Yli-Hannuksela K, Kling AM, et al. Large variation in ESBL-producing Escherichia coli carriers in six European countries including Russia. Eur J Clin Microbiol Infect Dis. 2018. Epub 2018/10/20. doi: 10.1007/s10096-018-3382-8 30338465.

17. Brechet C, Plantin J, Sauget M, Thouverez M, Talon D, Cholley P, et al. Wastewater treatment plants release large amounts of extended-spectrum beta-lactamase-producing Escherichia coli into the environment. Clin Infect Dis. 2014;58(12):1658–65. Epub 2014/05/06. doi: 10.1093/cid/ciu190 24795329.

18. Mathers AJ, Peirano G, Pitout JD. The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev. 2015;28(3):565–91. Epub 2015/05/01. doi: 10.1128/CMR.00116-14 25926236; PubMed Central PMCID: PMC4405625.

19. Platell JL, Johnson JR, Cobbold RN, Trott DJ. Multidrug-resistant extraintestinal pathogenic Escherichia coli of sequence type ST131 in animals and foods. Vet Microbiol. 2011;153(1–2):99–108. Epub 2011/06/11. doi: 10.1016/j.vetmic.2011.05.007 21658865.

20. Doi Y, Iovleva A, Bonomo RA. The ecology of extended-spectrum beta-lactamases (ESBLs) in the developed world. J Travel Med. 2017;24(suppl_1):S44–s51. Epub 2017/05/19. doi: 10.1093/jtm/taw102 28521000; PubMed Central PMCID: PMC5731446.

21. Onnberg A, Soderquist B, Persson K, Molling P. Characterization of CTX-M-producing Escherichia coli by repetitive sequence-based PCR and real-time PCR-based replicon typing of CTX-M-15 plasmids. APMIS. 2014;122(11):1136–43. Epub 2014/04/17. doi: 10.1111/apm.12270 24735173.

22. Egervarn M, Englund S, Ljunge M, Wiberg C, Finn M, Lindblad M, et al. Unexpected common occurrence of transferable extended spectrum cephalosporinase-producing Escherichia coli in Swedish surface waters used for drinking water supply. Sci Total Environ. 2017;587–588:466–72. Epub 2017/03/05. doi: 10.1016/j.scitotenv.2017.02.157 28258755.

23. Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S, Thammachote J, et al. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand. Genome Med. 2017;9(1):81. Epub 2017/09/08. doi: 10.1186/s13073-017-0471-8 28877757; PubMed Central PMCID: PMC5588602.

24. Onnberg A, Molling P, Zimmermann J, Soderquist B. Molecular and phenotypic characterization of Escherichia coli and Klebsiella pneumoniae producing extended-spectrum beta-lactamases with focus on CTX-M in a low-endemic area in Sweden. APMIS. 2011;119(4–5):287–95. Epub 2011/04/16. doi: 10.1111/j.1600-0463.2011.02730.x 21492229.

25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–77. Epub 2012/04/18. doi: 10.1089/cmb.2012.0021 22506599; PubMed Central PMCID: PMC3342519.

26. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol. 2000;66(10):4555–8. Epub 2000/09/30. doi: 10.1128/aem.66.10.4555-4558.2000 11010916; PubMed Central PMCID: PMC92342.

27. Simpson EH. Measurement of Diversity. Nature. 1949;163:688. doi: 10.1038/163688a0

28. Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol. 1988;26(11):2465–6. Epub 1988/11/01. 3069867; PubMed Central PMCID: PMC266921.

29. Grundmann H, Hori S, Tanner G. Determining confidence intervals when measuring genetic diversity and the discriminatory abilities of typing methods for microorganisms. J Clin Microbiol. 2001;39(11):4190–2. Epub 2001/10/30. doi: 10.1128/JCM.39.11.4190-4192.2001 11682558; PubMed Central PMCID: PMC88515.

30. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–4. Epub 2012/07/12. doi: 10.1093/jac/dks261 22782487; PubMed Central PMCID: PMC3468078.

31. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–903. Epub 2014/04/30. doi: 10.1128/AAC.02412-14 24777092; PubMed Central PMCID: PMC4068535.

32. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52(5):1501–10. Epub 2014/02/28. doi: 10.1128/JCM.03617-13 24574290; PubMed Central PMCID: PMC3993690.

33. Joensen KG, Tetzschner AM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J Clin Microbiol. 2015;53(8):2410–26. Epub 2015/05/15. doi: 10.1128/JCM.00008-15 25972421; PubMed Central PMCID: PMC4508402.

34. Stadler T, Meinel D, Aguilar-Bultet L, Huisman JS, Schindler R, Egli A, et al. Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland. BMJ Open. 2018;8(2):e021823. doi: 10.1136/bmjopen-2018-021823 29455172

35. Gomi R, Matsuda T, Matsumura Y. Occurrence of Clinically Important Lineages, Including the Sequence Type 131 C1-M27 Subclone, among Extended-Spectrum-beta-Lactamase-Producing Escherichia coli in Wastewater. 2017;61(9). doi: 10.1128/AAC.00564-17 28630184.

36. Alcala L, Alonso CA, Simon C, Gonzalez-Esteban C, Oros J, Rezusta A, et al. Wild Birds, Frequent Carriers of Extended-Spectrum beta-Lactamase (ESBL) Producing Escherichia coli of CTX-M and SHV-12 Types. 2016;72(4):861–9. doi: 10.1007/s00248-015-0718-0 26687342.

37. Liu H, Zhou H, Li Q, Peng Q, Zhao Q, Wang J, et al. Molecular characteristics of extended-spectrum β-lactamase-producing Escherichia coli isolated from the rivers and lakes in Northwest China. BMC microbiology. 2018;18(1):125–. doi: 10.1186/s12866-018-1270-0 30286725.

38. Karkman A, Parnanen K, Larsson DGJ. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments. Nat Commun. 2019;10(1):80. Epub 2019/01/10. doi: 10.1038/s41467-018-07992-3 30622259; PubMed Central PMCID: PMC6325112.

39. Zarfel G, Lipp M, Gurtl E, Folli B, Baumert R, Kittinger C. Troubled water under the bridge: Screening of River Mur water reveals dominance of CTX-M harboring Escherichia coli and for the first time an environmental VIM-1 producer in Austria. Sci Total Environ. 2017;593–594:399–405. Epub 2017/03/30. doi: 10.1016/j.scitotenv.2017.03.138 28351808.

40. Muller A, Stephan R, Nuesch-Inderbinen M. Distribution of virulence factors in ESBL-producing Escherichia coli isolated from the environment, livestock, food and humans. Sci Total Environ. 2016;541:667–72. Epub 2015/10/06. doi: 10.1016/j.scitotenv.2015.09.135 26437344.

41. Meric G, Kemsley EK, Falush D, Saggers EJ, Lucchini S. Phylogenetic distribution of traits associated with plant colonization in Escherichia coli. Environ Microbiol. 2013;15(2):487–501. Epub 2012/09/01. doi: 10.1111/j.1462-2920.2012.02852.x 22934605.

42. Walk ST, Alm EW, Calhoun LM, Mladonicky JM, Whittam TS. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ Microbiol. 2007;9(9):2274–88. Epub 2007/08/10. doi: 10.1111/j.1462-2920.2007.01341.x 17686024.

43. Kittinger C, Lipp M, Folli B, Kirschner A, Baumert R, Galler H, et al. Enterobacteriaceae Isolated from the River Danube: Antibiotic Resistances, with a Focus on the Presence of ESBL and Carbapenemases. PloS one. 2016;11(11):e0165820. Epub 2016/11/05. doi: 10.1371/journal.pone.0165820 27812159; PubMed Central PMCID: PMC5094594.

44. Caltagirone M, Nucleo E, Spalla M, Zara F, Novazzi F, Marchetti VM, et al. Occurrence of Extended Spectrum beta-Lactamases, KPC-Type, and MCR-1.2-Producing Enterobacteriaceae from Wells, River Water, and Wastewater Treatment Plants in Oltrepo Pavese Area, Northern Italy. Front Microbiol. 2017;8:2232. Epub 2017/11/28. doi: 10.3389/fmicb.2017.02232 29176971; PubMed Central PMCID: PMC5687051.

45. Price LB, Johnson JR, Aziz M, Clabots C, Johnston B, Tchesnokova V, et al. The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. MBio. 2013;4(6):e00377–13. Epub 2013/12/19. doi: 10.1128/mBio.00377-13 24345742; PubMed Central PMCID: PMC3870262.

46. Petty NK, Ben Zakour NL, Stanton-Cook M, Skippington E, Totsika M, Forde BM, et al. Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A. 2014;111(15):5694–9. Epub 2014/04/08. doi: 10.1073/pnas.1322678111 24706808; PubMed Central PMCID: PMC3992628.

47. Ludden C, Raven KE, Jamrozy D, Gouliouris T, Blane B, Coll F, et al. One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock. MBio. 2019;10(1). Epub 2019/01/24. doi: 10.1128/mBio.02693-18 30670621; PubMed Central PMCID: PMC6343043.

48. Borjesson S, Ny S, Egervarn M, Bergstrom J, Rosengren A, Englund S, et al. Limited Dissemination of Extended-Spectrum beta-Lactamase- and Plasmid-Encoded AmpC-Producing Escherichia coli from Food and Farm Animals, Sweden. Emerg Infect Dis. 2016;22(4):634–40. Epub 2016/03/18. doi: 10.3201/eid2204.151142 26982890; PubMed Central PMCID: PMC4806949.

49. Bonnedahl J, Drobni P, Johansson A, Hernandez J, Melhus A, Stedt J, et al. Characterization, and comparison, of human clinical and black-headed gull (Larus ridibundus) extended-spectrum beta-lactamase-producing bacterial isolates from Kalmar, on the southeast coast of Sweden. J Antimicrob Chemother. 2010;65(9):1939–44. Epub 2010/07/10. doi: 10.1093/jac/dkq222 20615928.

50. Atterby C, Borjesson S, Ny S, Jarhult JD, Byfors S, Bonnedahl J. ESBL-producing Escherichia coli in Swedish gulls-A case of environmental pollution from humans? PloS one. 2017;12(12):e0190380. Epub 2017/12/29. doi: 10.1371/journal.pone.0190380 29284053; PubMed Central PMCID: PMC5746268.

51. Khan FA, Hellmark B, Ehricht R, Soderquist B, Jass J. Related carbapenemase-producing Klebsiella isolates detected in both a hospital and associated aquatic environment in Sweden. Eur J Clin Microbiol Infect Dis. 2018;37(12):2241–51. Epub 2018/09/02. doi: 10.1007/s10096-018-3365-9 30171482.

52. Khan FA, Soderquist B, Jass J. Prevalence and Diversity of Antibiotic Resistance Genes in Swedish Aquatic Environments Impacted by Household and Hospital Wastewater. Front Microbiol. 2019;10:688. Epub 2019/04/26. doi: 10.3389/fmicb.2019.00688 31019498; PubMed Central PMCID: PMC6458280.

Článek vyšel v časopise


2019 Číslo 11