Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia

Raouia Ben Rhouma, Ahlem Jouini, Amira Klibi, Safa Hamrouni, Aziza Boubaker, Souhir Kmiha, Abderrazek Maaroufi

Abstract

The purpose of this study was to identify Escherichia coli isolates in diarrhoeic and healthy rabbits in Tunisia and characterise their virulence and antibiotic resistance genes. In the 2014-2015 period, 60 faecal samples from diarrhoeic and healthy rabbits were collected from different breeding farms in Tunisia. Susceptibility to 14 antimicrobial agents was tested by disc diffusion method and the mechanisms of gene resistance were evaluated using polymerase chain reaction and sequencing methods. Forty E. coli isolates were recovered in selective media. High frequency of resistance to tetracycline (95%) was detected, followed by different levels of resistance to sulphonamide (72.5%), streptomycin (62.5%), trimethoprim-sulfamethoxazole (60%), nalidixic acid (32.5%), ampicillin (37.5%) and ticarcillin (35%). E. coli strains were susceptible to cefotaxime, ceftazidime and imipenem. Different variants of blaTEM, tet, sul genes were detected in most of the strains resistant to ampicillin, tetracycline and sulphonamide, respectively. The presence of class 1 integron was studied in 29 sulphonamide-resistant E. coli strains from which 15 harboured class 1 integron with four different arrangements of gene cassettes, dfrA17+aadA5 (n=9), dfrA1 + aadA1 (n=4), dfrA12 + addA2 (n=1), dfrA12+orf+addA2 (n=1). The qnrB gene was detected in six strains out of 13 quinolone-resistant E. coli strains. Seventeen E. coli isolates from diarrhoeic rabbits harboured the enteropathogenic eae genes associated with different virulence genes tested (fimA, cnf1, aer), and affiliated to B2 (n=8) and D (n=9) phylogroups. Isolated E. coli strains from healthy rabbit were harbouring fim A and/or cnf1 genes and affiliated to A and B1 phylogroups. This study showed that E. coli strains from the intestinal tract of rabbits are resistant to the widely prescribed antibiotics in medicine. Therefore, they constitute a reservoir of antimicrobial-resistant genes, which may play a significant role in the spread of antimicrobial resistance. In addition, the eae virulence gene seemed to be implicated in diarrhoea in breeder rabbits in Tunisia.

Keywords

antibiotic resistance genes; breeding rabbits; E. coli isolates; integrons; virulence genes; Tunisia

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References

Allen H.K., Donato J., Wang H.H, Cloud-Hansen K.A., Davies J. 2010. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol., 8: 251-259. https://doi.org/10.1038/nrmicro2312

Allocatti N., Masulli M., Alexeyev M.F., Di Ilio C. 2013. Escherichia coli in Europe: An overview. Int. J. Environ. Res. Public Health., 10: 6235-6254. https://doi.org/10.3390/ijerph10126235

Alonso C.A., Zarazaga M., Ben Sallem R., Jouini A., Ben Slama K., Torres C. 2017. Antibiotic resistance in Escherichia coli in Husbandry animals. The African perspective. Lett. Appl. Microbiol., 64: 318-334. https://doi.org/10.1111/lam.12724

Barbosa T.M., Levy S.B. 2000. The impact of antibiotic use on resistance development and persistence. Drug Resist. Updates, 5: 303-311. https://doi.org/10.1054/drup.2000.0167

Ben Said L., Jouini A., Klibi N., Dziri R., Alonso C.A., Boudabous A., Ben Slama K., Torres C. 2015. Detection of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in vegetables, soil and water of farm environment in Tunisia. Int. J. Food Microbiol., 203: 86-92. https://doi.org/10.1016/j.ijfoodmicro.2015.02.023

Ben Sallem R.B., Gharsa H., Slama K.B.., Rojo-Bezares B, Estepa V., Porres-Osante N., Jouini A., Klibi N., Sáenz Y., Boudabous A., Torres C. 2013. First detection of CTX-M-, CMY-2, and QnrB19 resistance mechanisms in fecal Escherichia coli isolates from healthy pets in Tunisia. Vector Borne Zoonotic Dis., 13: 98-102. https://doi.org/10.1089/vbz.2012.1047

Ben Slama K., Jouini A., Ben Sallem R., Somalo S., Sáenz Y., Estepa V., Boudabous A., Torres C. 2010. Prevalence of broad-spectrum cephalosporin-resistant Escherichia coli isolates in food samples in Tunisia and characterization of integrons and antimicrobial resistance mechanisms implicated. Int. J. Food Microbiol., 13: 281-286. https://doi.org/10.1016/j.ijfoodmicro.2009.12.003

Ben Slama K., Ben Sallem R., Jouini A., Rachid S., Moussa L., Saenz Y., Estepa V., Somalo S., Boudabous A., Torres C. 2011. Diversity of genetic lineages among CTX-M-15 and CTX-M-14 producing Escherichia coli strains in a Tunisian hospital. Curr. Microbiol., 62: 1794-1801. https://doi.org/10.1007/s00284-011-9930-4

Blanco J.E., Blanco M., Blanco J., Mora A., Balaguer L., Mourino M., JuÁrez A., Jansen W.H. 1996. O serogroups, biotypes, and eae genes in Escherichia coli strains isolated from diarrheic and healthy rabbits. J. Clin. Microbiol., 34: 3101- 3107. https://doi.org/10.1128/JCM.34.12.3101-3107.1996

Blanco M., Blanco J.E., Dahbi G., Alonso M.P., Mora A., Corira M.A.A., Madrid C., Juárez A., Bernárdez M.I., González E.A., Blanco J. 2006. Identification of two new intimin types in atypical enteropathogenic Escherichia coli. Int. Microbiol., 9: 103-110.

Brinas L., Zarazaga M., Saenz Y., Ruiz-Larrea F., Torres C. 2002. Beta-lactamases in ampicillin-resistant Escherichia coli isolates from foods, humans, and healthy animals. Antimicrob. Agents Chemother., 46: 3156-3163. https://doi.org/10.1128/AAC.46.10.3156-3163.2002

Bryan A., Shapir N., Sadowsky M.J. 2004. Frequency and distribution of tetracycline resistance genes in genetically diverse, nonselected and nonclinical Escherichia coli strains isolated from diverse human and animal sources. Appl. Environ. Microbiol., 70: 2503-2507. https://doi.org/10.1128/AEM.70.4.2503-2507.2004

Camarda A., Pennelli D., Battista P., Martella V., Greco L., Alloggio I., Mazzolini E. 2004. Virulence genes and antimicrobial resistance patterns of enteropathogenic Escherichia coli from rabbits in southern Italy. In Proc.: 8th World Rabbit Congress., September 7-10, 2004, Puebla, Mexico, 470-476.

Clermont O., Bonacorsi S., Bingen E., 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microb., 66: 4555-4558. https://doi.org/10.1128/AEM.66.10.4555-4558.2000

Clermont O., Lavolly M., Vimont S., Deschamps C., Forestier C., Branger C., Denamur E., Arlet G. 2008. The CTX-M15-producing Escherichia coli diffusing clone belongs to a highly virulent B2 phylogenic subgroup. J. Antimicrob. Chemother., 61: 1024-1028. https://doi.org/10.1093/jac/dkn084

Clinical and Laboratory Standards Institute. 2015. Performance standards for antimicrobial susceptibility testing. Twenty-fifth informational supplement. Clinical and Laboratory Standards Institute document M100-S25, CLSI, Wayne, PA.

Coque T.M., Novais A., Carattoli A., Poirel L., Pitout J., Peixe L., Baquero F., Cantón R., Nordmann P. 2008. Dissemination of clonally related Escherichia coli strains expressing extendedspectrum β-lactamase CTX-M-15. Emerg. Infect. Dis., 14: 195-200. https://doi.org/10.3201/eid1402.070350

Da Costa P.M., Loureiro L., Matos A.J.F. 2013. Transfer of Multidrug-Resistant Bacteria between intermingled ecological niches: the interface between Humans, Animals and the environment. Int. J. Environ. Res. Public Health., 10: 278-294. https://doi.org/10.3390/ijerph10010278

Dotto G., Giacomelli M., Grilli G., Ferrazzi V., Carattoli A., Fortini D., Piccirillo A. 2014. High prevalence of oqxAB in Escherichia coli isolates from domestic and wild lagomorphs in Italy. Microb. Drug Resist., 20: 118-123. https://doi.org/10.1089/mdr.2013.0141

Eager H., Swan G., van Vuuren M. 2015. A survey of antimicrobial usage in animals in South Africa 479 with specific reference to food animals. J. S. Afr. Vet. Assoc., 83: 16. https://doi.org/10.4102/jsava.v83i1.16

Guardabassi L., Schwarz S., Lloyd D.H., 2004. Pet animals as reservoirs of antimicrobial-resistant bacteria. J. Antimicrob. Chemother., 54: 321-332. https://doi.org/10.1093/jac/dkh332

Hai S.W., Qi R.P., Y. Gao M. et al. 2014. Study on molecular characterization of Class I integron and integron-associated antimicrobial resistance in Escherichia coli from beef cattle. China Animal Husbandry Veterinary Medicine., 41: 63-67.

Jacoby G.A., Griffin C., Hooper D.C. 2011. Citrobacter spp. as a source of qnrB alleles. Antimicrob. Agents Chemother., 55: 4979-4984. https://doi.org/10.1128/AAC.05187-11

Johnson T.J., Logue C.M., Johnson J.R., Kuskowski M.A., Sherwood J.S., Barnes H.J., DebRoy C., Wannemuehler Y.M., Obata-Yasuoka M., Spanjaard L., Nolan L.K. 2012. Associations between multidrug resistance, plasmid content, and virulence potential among extra-intestinal pathogenic and commensal Escherichia coli from humans and poultry. Foodborne Pathog. Dis., 9: 37-46. https://doi.org/10.1089/fpd.2011.0961

Jouini A., Ben Slama K., Saenz Y., Klibi N., Costa D., Vinué L., Zarazaga M., Boudabous A., Torres C. 2009. Detection of Multiple-Antimicrobial Resistance and Characterization of the Implicated Genes in Escherichia coli isolates from Foods of Animal Origin in Tunis. J. Food Protect., 72: 1082-1088. https://doi.org/10.4315/0362-028X-72.5.1082

Kaper J.B., Nataro J.P., Mobley H.L. 2004. Pathogenic Escherichia coli. Nat. Rev. Microbiol., 2: 123-140. https://doi.org/10.1038/nrmicro818

Lauková A., Strompfová V., Szabóová R., Bónai A., Matics Z., Kovács M., Pogány Simonová M. 2019. Enterococci from pannon white rabbits: detection, identification, biofilm and screening for virulence factors. World Rabbit Sci., 27: 31-39. https://doi.org/10.4995/wrs.2019.10875

Marinho C., Igrejas G., Gonçalves A., Silva N., Santos T., Monteiro R., Gonçalves D., Rodrigues T., Poeta P. 2014. Azorean wild rabbits as reservoirs of antimicrobial resistant Escherichia coli. Anaerobe, 30: 116-119. https://doi.org/10.1016/j.anaerobe.2014.09.009

Panteado A.S., Ugrinivich L.A., Blanco J., Blanco M., Andrade J.R.C., Correa S.S., De Castro A.F.P. 2002. Serobiotypes and virulence genes of Escherichia coli strains isolated from diarrheic and healthy rabbits in Brazil. Vet. Microb., 89: 41-51. https://doi.org/10.1016/S0378-1135(02)00148-7

Pohl P.H., Peeters J.E.E., Jacquemin R., Lintermans P.F., Mainil J.G. 1993. Identification of eae sequences in enteropathogenic Escherichia coli strains from rabbits. Infect. Immun., 61: 2203-2206. https://doi.org/10.1128/IAI.61.5.2203-2206.1993

Poirel L., Bonnin R.A., Nordmann P. 2012. Genetic support and diversity of acquired extended-spectrum beta-lactamases in Gram-negative rods. Infect. Genet. Evol., 12: 883-893. https://doi.org/10.1016/j.meegid.2012.02.008

Qing F.K., Yi G., Ze H.Y., YA J.L., Wei H.M., Zhao B.D., Yu W.Z., Guan W. 2006. Detection of quinolone resistance and plasmid mediated quinolone gene in Escherichia coli isolated from rabbit. Chin. J. Prev. Vet. Med., 38: 944-948.

Ruiz J., Simon K., Horcajada J.P., Velasco M., Barranco M., Roig G., Moreno-Martínez A., Martínez J.A., Jiménez de Anta T., Mensa J., Vila J. 2002. Differences in virulence factors among clinical isolates of Escherichia coli causing cystitis and pyelonephritis in women and prostatitis in men. J. Clin. Microbiol., 40: 4445-4449. https://doi.org/10.1128/JCM.40.12.4445-4449.2002

Sáenz Y., Zarazaga M., Briñas L., Lantero M., Ruiz-Larrea F., Torres C. 2001. Antibiotic resistance in Escherichia coli isolates obtained from animals, foods and humans in Spain. Int. J. Antimicrob. Agents.,18: 353-358. https://doi.org/10.1016/S0924-8579(01)00422-8

Saenz Y., Briñas L., Domínguez E., Ruiz J., Zarazaga M., Vila J., Torres C. 2004. Mechanisms of resistance in multiple-antibio resistant Escherichia coli strains of human, animal, and food origins. Antimicrob. Agents Chemother., 48: 3996-4001. https://doi.org/10.1128/AAC.48.10.3996-4001.2004

Santos T., Silva N., Igrejas G, Rodrigues P., Micael J., Rodrigues T., Resendes R., Gonçalves A., Marinho C., Gonçalves D., Cunha R., Poeta P. 2013. Dissemination of antibiotic resistant Enterococcus spp. and Escherichia coli from wild birds of Azores Archipielago. Anaerobe., 24: 25-31. https://doi.org/10.1016/j.anaerobe.2013.09.004

Silva N., Igrejas G., Figueiredo N., Gonçalves, A., Radhouani H., Rodrigues J., Poeta P. 2010. Molecular characterization of antimicrobial resistance in enterococci and Escherichia coli isolates from European wild rabbit (Oryctolagus cuniculus). Sci Total Environ., 408: 4871-4876. https://doi.org/10.1016/j.scitotenv.2010.06.046

Swennes A.G., Buckley E.M., Parry N.M.A., Madden C.M., Garcia A., Morgan P.B., Astrofsky K.M., Fox J.G. 2012. Enzootic Enteropathogenic Escherichia coli Infection in Laboratory Rabbits. J. Clin. Microbiol., 50: 2353-2358. https://doi.org/10.1128/JCM.00832-12

Teshager T., Herrero I.A., Porrero M.C., Garde J., Moreno M.A., Domínguez L. 2000. Surveillance of antimicrobial resistance in Escherichia coli strains isolated from pigs at Spanish slaughterhouses. Int. J. Antimicrob. Agents, 15: 137-142. https://doi.org/10.1016/S0924-8579(00)00153-9

Van den Bogaard A.E., London N., Stobberingh E.E. 2000. Antimicrobial resistance in pig faecal samples from The Netherlands (five abattoirs) and Sweden. J. Antimicrobial Chemother., 45: 663-671. https://doi.org/10.1093/jac/45.5.663

Wang J., Sang L., Chen Y., Sun S., Chen D., Xie X. 2019. Characterisation of Staphylococcus aureus strain causing severe respiratory disease in rabbits. World Rabbit Sci., 27: 41-48. https://doi.org/10.4995/wrs.2019.10454

Werner G., Gfrörer S., Fleige C., Witte W., Klare I. 2008. Tigecycline-resistant Enterococcus faecalis strain isolated from a German ICU patient. J. Antimicrob Chemother., 61: 1182-1183. https://doi.org/10.1093/jac/dkn065

Yoon S.H., Jeong H., Kwon S.K., Kim J.F. 2009. Genomics, Biological Features, and Biotechnological Applications of Escherichia coli B: Is B for better. In: Lee S.Y. (eds). Systems Biology and Biotechnology of Escherichia coli., 1-17. https://doi.org/10.1007/978-1-4020-9394-4_1

Zhao X., Yang J., Ju Z., Chang W., Sun S. 2018. Molecular characterization of antimicrobial resistance in Escherichia coli from rabbit farms in Tai'an, China. Hindawi, Biomed Research International., 2018: 1-7. https://doi.org/10.1155/2018/8607647

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