Escherichia coli is a common commensal bacterial species of humans and animals that may become a troublesome pathogen causing serious diseases. The aim of this study was to characterize the quinolone resistance phenotypes and genotypes in E. coli isolates of different origin from one area of the Czech Republic. E. coli isolates were obtained from hospitalized patients and outpatients, chicken farms, retailed turkeys, rooks wintering in the area, and wastewaters. Susceptibility of the isolates grown on the MacConkey agar with ciprofloxacin (0.05 mg/L) to 23 antimicrobial agents was determined. The presence of plasmid-mediated quinolone resistance (PMQR) and ESBL genes was tested by PCR and sequencing. Specific mutations in gyrA, gyrB, parC, and parE were also examined. Multilocus sequence typing and pulsed-field gel electrophoresis were performed to assess the clonal relationship. In total, 1050 E. coli isolates were obtained, including 303 isolates from humans, 156 from chickens, 105 from turkeys, 114 from the rooks, and 372 from wastewater samples. PMQR genes were detected in 262 (25%) isolates. The highest occurrence was observed in isolates from retailed turkey (49% of the isolates were positive) and inpatients (32%). The qnrS1 gene was the most common PMQR determinant identified in 146 (56%) followed by aac(6')-Ib-cr in 77 (29%), qnrB19 in 41 (16%), and qnrB1 in 9 (3%) isolates. All isolates with high level of ciprofloxacin resistance (>32 mg/L) carried double or triple mutations in gyrA combined with single or double mutations in parC. The most frequently identified substitutions were Ser(83)Leu; Asp(87)Asn in GyrA, together with Ser(80)Ile, or Glu(84)Val in ParC. Majority of these isolates showed resistance to beta-lactams and multiresistance phenotype was found in 95% isolates. Forty-eight different sequence types among 144 isolates analyzed were found, including five major clones ST131 (26), ST355 (19), ST48 (13), ST95 (10), and ST10 (5). No isolates sharing 100% relatedness and originating from different areas were identified. In conclusion, our study identified PMQR genes in E. coli isolates in all areas studied, including highly virulent multiresistant clones such as ST131 producing CTX-M-15 beta-lactamases.

Central European Institute of Technology University of Veterinary and Pharmaceutical Sciences BrnoBrno Czechia; Department of Infectious Diseases and Microbiology Faculty of Veterinary Medicine University of Veterinary and Pharmaceutical Sciences BrnoBrno Czechia

Department of Biology and Wildlife Diseases Faculty of Veterinary Hygiene and Ecology University of Veterinary and Pharmaceutical Sciences Brno Brno Czechia

Department of Biology and Wildlife Diseases Faculty of Veterinary Hygiene and Ecology University of Veterinary and Pharmaceutical Sciences BrnoBrno Czechia; Central European Institute of Technology University of Veterinary and Pharmaceutical Sciences BrnoBrno Czechia

Department of Microbiology Faculty of Medicine and Dentistry Palacký University Olomouc Olomouc Czechia

Department of Microbiology Faculty of Medicine and Dentistry Palacký University OlomoucOlomouc Czechia; Department of Microbiology University Hospital OlomoucOlomouc Czechia

Institute of Applied Biotechnologies Prague Czechia

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Adams-Sapper S., Diep B. A., Perdreau-Remington F., Riley L. W. (2013). Clonal composition and community clustering of drug-susceptible and -resistant PubMed DOI PMC

Adler A., Baraniak A., Izdebski R., Fiett J., Salvia A., Samso J. V., et al. (2014). A multinational study of colonization with extended spectrum β-lactamase-producing Enterobacteriaceae in healthcare personnel and family members of carrier patients hospitalized in rehabilitation centres. Clin. Microbiol. Infect. 20, O516–O523. 10.1111/1469-0691.12560 PubMed DOI

Agabou A., Lezzar N., Ouchenane Z., Khemissi S., Satta D., Sotto A., et al. (2016). Clonal relationship between human and avian ciprofloxacin-resistant PubMed DOI

Alcalá L., Alonso C. A., Simón C., González-Esteban C., Orós J., Rezusta A., et al. (2016). Wild Birds, Frequent Carriers of Extended-Spectrum β-Lactamase (ESBL) producing PubMed DOI

Aldred K. J., Kerns R. J., Osheroff N. (2014). Mechanism of quinolone action and resistance. Biochemistry 53, 1565–1574. 10.1021/bi5000564 PubMed DOI PMC

Andriole V. T. (2005). The quinolones: past, present, and future. Clin. Infect. Dis. 15(Suppl. 2), S113–S119. 10.1086/428051 PubMed DOI

Balakrishnan S., Antony P. X., Mukhopadhyay H. K., Pillai R. M., Thanislass J., Padmanaban V., et al. (2016). Genetic characterization of fluoroquinolone-resistant PubMed DOI PMC

Ben Said L., Jouini A., Alonso C. A., Klibi N., Dziri R., Boudabous A., et al. (2016). Characteristics of extended-spectrum beta-lactamase (ESBL)- and pAmpC beta-lactamase-producing Enterobacteriaceae of water samples in Tunisia. Sci. Total. Environ. 550, 1103–1109. 10.1016/j.scitotenv.2016.01.042 PubMed DOI

Briñas L., Zarazaga M., Sáenz Y., Ruiz-Larrea F., Torres C. (2002). β-Lactamases in ampicillin-resistant PubMed DOI PMC

Castillo F. Y. R., González F. J. A., Garneau P., Díaz F. M., Barrera A. L. G., Harel J. (2013). Presence of multi-drug resistant pathogenic PubMed DOI PMC

Cattoir V., Poirel L., Nordmann P. (2007). Plasmid-mediated quinolone resistance determinant QnrB4 identified in France in an PubMed DOI PMC

Cavaco L. M., Hasman H., Xia S., Aarestrup F. M. (2009). qnrD, a novel gene conferring transferable quinolone resistance in PubMed DOI PMC

Cerquetti M., García-Fernández A., Giufré M., Fortini D., Accogli M., Graziani C., et al. (2009). First report of plasmid-mediated quinolone resistance determinant qnrS1 in an PubMed DOI PMC

Cerquetti M., Giufré M., García-Fernandez A., Accogli M., Fortini D., Luzzi I., et al. (2010). Ciprofloxacin-resistant, CTX-M-15-producing PubMed DOI

Clinical and Laboratory Standards Institute (CLSI) (2015). Performance Standards for Antimicrobial Susceptibility Testing. Twenty Fifth Informational Supplement Update. CLSI document M100-S25 U. Wayne, PA: Clinical and Laboratory Standards Institute.

Colomer-Lluch M., Mora A., López C., Mamani R., Dahbi G., Marzoa J., et al. (2013). Detection of quinolone-resistant PubMed DOI

Dalhoff A. (2012). Global fluoroquinolone resistance epidemiology and implictions for clinical use. Interdiscip. Perspect Infect. Dis. 2012:976273. 10.1155/2012/976273 PubMed DOI PMC

Dolejska M., Brhelova E., Dobiasova H., Krivdova J., Jurankova J., Sevcikova A., et al. (2012). Dissemination of IncFII(K)-type plasmids in multiresistant CTX-M-15-producing Enterobacteriaceae isolates from children in hospital paediatric oncology wards. Int. J. Antimicrob. Agents 40, 510–515. 10.1016/j.ijantimicag.2012.07.016 PubMed DOI

Dolejska M., Duskova E., Rybarikova J., Janoszowska D., Roubalova E., Dibdakova K., et al. (2011b). Plasmids carrying blaCTX-M-1 and qnr genes in PubMed DOI

Dolejska M., Frolkova P., Florek M., Jamborova I., Purgertova M., Kutilova I., et al. (2011a). CTX-M-15-producing PubMed DOI

Ewers C., Grobbel M., Stamm I., Kopp P. A., Diehl I., Semmler T., et al. (2010). Emergence of human pandemic O25:H4-ST131 CTX-M-15 extended-spectrum-beta-lactamase-producing PubMed DOI

ECDC (European Centre for Disease Prevention and Control), EFSA (European Food Safety Authority) and EMA (European Medicines Agency). (2015). ECDC/EFSA/EMA first joint report on the integrated analysis of the consumption of antimicrobial agents and occurrence of antimicrobial resistence in bacteria from humans and food-producing animals. Stockhom/parma/London: ECDC/EFSA/EMA. EFSA J. 13:4006 10.2903/j.efsa.2015.4006 DOI

European Centre for Disease Prevention and Control (2015). Antimicrobial Resistance Interactive Database (EARS-Net) [online]. Available online at: http://www.ecdc.europa.eu/en/Pages/home.aspx (Accessed on 10 July 2016).

Forcella C., Alessiani A., Perilli M., Zilli K., Di Giannatale E., Amicosante G. (2010). Characterization of quinolone resistance in PubMed DOI

Ghodousi A., Bonura C., Di Carlo P., van Leeuwen W. B., Mammina C. (2016). Extraintestinal pathogenic PubMed DOI

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 PubMed DOI

Gosling R. J., Clouting C. S., Randall L. P., Horton R. A., Davies R. H. (2012). Ciprofloxacin resistance in PubMed DOI

Hopkins K. L., Davies R. H., Threlfall E. J. (2005). Mechanisms of quinolone resistance in PubMed DOI

Htoutou Sedlakova M., Hanulik V., Chroma M., Hricova K., Kolar M., Latal T., et al. (2011). Phenotypic detection of broad-spectrum beta-lactamases in microbiological practice. Med. Sci. Monitor 17, BR 147–152. 10.12659/msm.881761 PubMed DOI PMC

Huijbers P. M., Graat E. A., Haenen A. P., van Santen M. G., van Essen-Zandbergen A., Mevius D. J., et al. (2014). Extended-spectrum and AmpC beta-lactamase-producing PubMed DOI

Husickova V., Cekanova L., Chroma M., Htoutou-Sedlakova M., Hricova K., Kolar M. (2012). Carriage of ESBL- and AmpC-positive Enterobacteriaceae in the gastrointestinal tract of community subjects and hospitalized patients in the Czech Republic. Biomed. Pap. Med. Fac. Univ. Palacky Olomouc Czech Repub. 156, 348–353. 10.5507/bp.2012.039 PubMed DOI

Hussain A., Ewers C., Nandanwar N., Guenther S., Jadhav S., Wieler L. H., et al. (2012). Multiresistant uropathogenic PubMed DOI PMC

Jacoby G. A., Strahilevitz J., Hooper D. C. (2014). Plasmid-mediated quinolone resistance. Microbiol. Spectr. 2:PLAS-0006-2013. 10.1128/microbiolspec.plas-0006-2013 PubMed DOI PMC

Jamborova I., Dolejska M., Vojtech J., Guenther S., Uricariu R., Drozdowska J., et al. (2015). Plasmid-mediated resistance to cephalosporins and fluoroquinolones in various PubMed DOI PMC

Jarlier V., Nicolas M. H., Fournier G., Philippon A. (1988). Extended broad-spectrum beta-lactamases conferring transferable resistance to newer beta-lactam agents in Enterobacteriaceae: hospital prevalence and susceptibility patterns. Rev. Infect. Dis. 10, 867–878. 10.1093/clinids/10.4.867 PubMed DOI

Jiménez Gómez P. A., García de los Rios J. E., Rojas Mendoza A., de Pedro Ramonet P., Garcia Albiach R., Reche Sainz M. P. (2004). Molecular basis of quinolone resistance in PubMed PMC

Johnning A., Kristiansson E., Fick J., Weijdegård B., Larsson D. G. (2015). Resistance mutations in gyrA and parC are common in escherichia communities of both fluoroquinolone-polluted and uncontaminated aquatic environments. Front. Microbiol. 6:1355. 10.3389/fmicb.2015.01355 PubMed DOI PMC

Johnson J. R., Gajewski A., Lesse A. J., Russo T. A. (2003). Extraintestinal pathogenic PubMed DOI PMC

Kim H. B., Park C. H., Kim C. J., Kim E. C., Jacoby G. A., Hooper D. C. (2009). Prevalence of plasmid-mediated quinolone resistance determinants over a 9-year period. Antimicrob. Agents Chemother. 53, 639–645. 10.1128/AAC.01051-08 PubMed DOI PMC

Koboldt D. C., Chen K., Wylie T., Larsen D. E., McLellan M. D., Mardis E. R., et al. (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25, 2283–2285. 10.1093/bioinformatics/btp373 PubMed DOI PMC

Lautenbach E., Strom B. L., Nachamkin I., Bilker W. B., Marr A. M., Larosa L. A., et al. (2004). Longitudinal trends in fluoroquinolone resistance among Enterobacteriaceae isolates from inpatients and outpatients, 1989-2000: differences in the emergence and epidemiology of resistance across organisms. Clin. Infect. Dis. 38, 655–662. 10.1086/381549 PubMed DOI

Lee M. Y., Choi H. J., Choi J. Y., Song M., Song Y., Kim S. W., et al. (2010). Dissemination of ST131 and ST393 community-onset, ciprofloxacin-resistant PubMed DOI

Lewis J. S., Herrera M., Wickes B., Patterson J. E., Jorgensen J. H. (2007). First report of the emergence of CTX-M-type extended-spectrum β-lactamases (ESBLs) as the predominant ESBL isolated in a U.S. health care system. Antimicrob. Agents Chemother. 51, 4015–4021. 10.1128/AAC.00576-07 PubMed DOI PMC

Li H., Durbin R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595. 10.1093/bioinformatics/btp698 PubMed DOI PMC

Literak I., Micudova M., Tausova D., Cizek A., Dolejska M., Papousek I., et al. (2012). Plasmid-mediated quinolone resistance genes in fecal bacteria from rooks commonly wintering throughout Europe. Microb. Drug. Resist. 18, 567–573. 10.1089/mdr.2012.0075 PubMed DOI

Literak I., Reitschmied T., Bujnakova D., Dolejska M., Cizek A., Bardon J., et al. (2013). Broilers as a source of quinolone-resistant and extraintestinal pathogenic PubMed DOI

Liu B. T., Liao X. P., Yang S. S., Wang X. M., Li L. L., Sun J., et al. (2012). Detection of mutations in the gyrA and parC genes in PubMed DOI

Manges A. R., Johnson J. R. (2012). Food-borne origins of PubMed DOI

Martínez-Martínez L., Pascual A., Jacoby G. A. (1998). Quinolone resistance from a transferable plasmid. Lancet. 351, 797–799. PubMed

Micenková L., Sišková P., Bosák J., Jamborová I., Cernohorská L., Smajs D. (2014). Characterization of human uropathogenic ESBL-producing PubMed DOI

Moore B., Perry E. L., Chard S. T. (1952). A survey by the sewage swab method of latent enteric infection in an urban area. J. Hyg. 50, 137–156. 10.1017/S0022172400019501 PubMed DOI PMC

Mora A., Viso S., López C., Alonso M. P., García-Garrote F., Dabhi G., et al. (2013). Poultry as reservoir for extraintestinal pathogenic PubMed DOI

Nicolas-Chanoine M. H., Bertrand X., Madec J. Y. (2014). PubMed DOI PMC

Nüesch-Inderbinen M., Stephan R. (2016). Epidemiology of extended-spectrum β-lactamase-producing DOI

Oh J. Y., Kwon Y. K., Tamang M. D., Jang H. K., Jeong O. M., Lee H. S., et al. (2016). Plasmid-mediated quinolone resistance in PubMed DOI

Oram M., Fisher L. M. (1991). 4-Quinolone resistance mutations in the DNA gyrase of PubMed DOI PMC

Paltansing S., Kraakman M. E., Ras J. M., Wessels E., Bernards A. T. (2013). Characterization of fluoroquinolone and cephalosporin resistance mechanisms in Enterobacteriaceae isolated in a Dutch teaching hospital reveals the presence of an PubMed DOI

Papagiannitsis C. C., Študentová V., Jakubu V., Španelová P., Urbášková P., Žemlicková H., et al. (2015). High prevalence of ST131 among CTX-M-producing PubMed DOI

Park C. H., Robicsek A., Jacoby G. A., Sahm D., Hooper D. C. (2006). Prevalence in the United States of aac(6′)-Ib-cr encoding a ciprofloxacin-modifying enzyme. Antimicrob. Agents Chemother. 50, 3953–3955. 10.1128/AAC.00915-06 PubMed DOI PMC

Peirano G., Costello M., Pitout J. D. (2010). Molecular characteristics of extended-spectrum beta-lactamase-producing PubMed DOI

Périchon B., Courvalin P., Galimand M. (2007). Transferable resistance to aminoglycosides by methylation of G1405 in 16S rRNA and to hydrophilic fluoroquinolones by QepA-mediated efflux in PubMed DOI PMC

Pitout J. D., Hossain A., Hanson N. D. (2004). Phenotypic and molecular detection of CTX-M-beta-lactamases produced by PubMed DOI PMC

Platell J. L., Cobbold R. N., Johnson J. R., Heisig A., Heisig Clabots, C., et al. (2011). Commonality among Fluoroquinolone-resistant sequence type st131 extraintestinal PubMed DOI PMC

Riley L. W. (2014). Pandemic lineages of extraintestinal pathogenic PubMed DOI

Robicsek A., Jacoby G. A., Hooper D. C. (2006). The worldwide emergence of plasmid-mediated quinolone resistance. Lancet Infect. Dis. 6, 629–640. 10.1016/S1473-3099(06)70599-0 PubMed DOI

Ruiz J. (2003). Mechanisms of resistance to quinolones: target alterations, decreased accumulation and DNA gyrase protection. J. Antimicrob. Chemother. 51, 1109–1117. 10.1093/jac/dkg222 PubMed DOI

Ruiz J., Casellas S., Jimenez de Anta M. T., Vila J. (1997). The region of the parE gene, homologous to the quinolone-resistant determining region of the gyrB gene, is not linked with the acquisition of quinolone resistance in PubMed DOI

Sáenz Y., Zarazaga M., Briñas L., Ruiz-Larrea F., Torres C. (2003). Mutations in gyrA and parC genes in nalidixic acid-resistant PubMed DOI

Strahilevitz J., Jacoby G. A., Hooper D. C., Robicsek A. (2009). Plasmid-mediated quinolone resistance: a multifaceted threat. Clin. Microbiol. Rev. 22, 664–689. 10.1128/CMR.00016-09 PubMed DOI PMC

Tamang M. D., Seol S. Y., Oh J. Y., Kang H. Y., Lee J. C., Lee Y. C., et al. (2008). Plasmid-mediated quinolone resistance determinants PubMed DOI PMC

Tartof S. Y., Solberg O. D., Riley L. W. (2007). Genotypic analyses of uropathogenic PubMed DOI

Tenover F. C., Arbeit R. D., Goering R. V., Mickelsen P. A., Murray B. E., Persing D. H., et al. (1995). Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33, 2233–2239. PubMed PMC

Varela A. R., Macedo G. N., Nunes O. C., Manaia C. M. (2015). Genetic characterization of fluoroquinolone resistant PubMed DOI

Veldman K., Cavaco L. M., Mevius D., Battisti A., Franco A., Botteldoorn N., et al. (2011). International collaborative study on the occurrence of plasmid-mediated quinolone resistance in PubMed DOI

Vila J., Ruiz J., Goñi P., De Anta M. T. (1996). Detection of mutations in parC in quinolone-resistant clinical isolates of PubMed PMC

Vila J., Ruiz J., Marco F., Barcelo A., Goñi P., Giralt E., et al. (1994). Association between double mutation in gyrA gene of ciprofloxacin-resistant clinical isolates of PubMed DOI PMC

Vincent C., Boerlin P., Daignault D., Dozois C. M., Dutil L., Galanakis C., et al. (2010). Food reservoir for PubMed DOI PMC

Wang J., Gibbons J. F., McGrath K., Bai L., Li F., Leonard F. C., et al. (2016). Molecular characterization of blaESBL-producing PubMed DOI

World Health Organization (2012). WHO Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR). Critically important antimicrobials for human medicine 3rd Revision 2011. WHO Document Production Services, Geneva, Switzerland. Clin. Infect. Dis. 55, 712–719.

Woodford N., Carattoli A., Karisik E., Underwood A., Ellington M. J., Livermore D. M. (2009). Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major PubMed DOI PMC

Yamane K., Wachino J., Suzuki S., Kimura K., Shibata N., Kato H., et al. (2008). New plasmid-mediated fluoroquinolone efflux pump, QepA, found in an PubMed DOI PMC

Escherichia coli from Human Wounds: Analysis of Resistance to β-Lactams and Expression of RND Efflux Pumps

Restoration of antibacterial activity of inactive antibiotics via combined treatment with a cyanographene/Ag nanohybrid

Bacterial Pathogens and Evaluation of a Cut-Off for Defining Early and Late Neonatal Infection

Deadly Puppy Infection Caused by an MDR Escherichia coli O39 bla CTX-M-15, bla CMY-2, bla DHA-1, and aac(6)-Ib-cr - Positive in a Breeding Kennel in Central Italy