Chromosome Mediated Fluoroquinolone and Extended Spectrum Beta-lactamase Resistant Genes in E. coli of Poultry Origin in Ekiti State
Microbiology Research Journal International,
Background: One health approach aimed at solving global health crisis links human, animal, and environmental health. This inclusive strategy has contributed to antibiotic classification in both human and animal medicine.
Aims: The aims of this research work are to determine the phylogenetic relationship of E. coli isolated from poultry and waste sources. The presence of chromosome mediated fluoroquinolone and extended spectrum beta-lactamase resistant genes will also be detected in the isolates.
Study Design: Experimental design.
Methodology: Data on farming attitudes of poultry farmers were collected using a questionnaire. E. coli was isolated from fresh poultry droppings and waste disposal sites using eosine methylene blue agar. The antibiotic sensitivity profile of the isolates was determined using the modified Kirby Bauer disc diffusion method. Phenotypic expression of fluoroquinolone (qnrS) and beta-lactamase (blaCMY) resistant traits were further detected using Polymerase Chain Reaction. The 16S rRNA gene sequencing was carried out followed by sequence alignment of E. coli genes with those from GenBank sources to determine the molecular identity of the isolates. Spearman’s correlation coefficient (rs) was run to determine the relationship between antibiotic treatment and resistant profile of the isolates. The phylogenetic relationship of the isolates was determined using Bio edit and Mega 6 software.
Results: Organic poultry farming was practiced by small-scaled, peasant farmers who raised free range birds while antibiotics were widely used on farms that adopted intensive mode of farming. The percentage occurrence of E. coli from waste disposal sources was lesser than that from fresh poultry droppings. Highest percentage of antibiotic resistance to the fluoroquinolones was found while the carbapenemase recorded the lowest. Statistical analysis shows that antibiotic treatment in poultry and resistant profile of isolates to antibiotics are directly related. The percentage similarity of gene sequence with those from Gene Data Bank (≥99.29%) validates the identity of the isolates as E. coli. About, 60% of the sampled population had the qnrS gene with a band size of approximately 322 base pair. Besides, 40% of the sampled isolates possessed the blaCMY gene with a band size of approximately 460 base pair. Both genes co-existed in the chromosome of 15% of the sampled isolates sourced from poultry droppings and waste sources. Phylogenetic classification links the origin of isolates from waste disposal sources to poultry production sites. Besides, variant strains of multiple antibiotic resistant E. coli from poultry with antibiotic treatment were more diverse compared to those obtained from birds raised without antibiotics.
Conclusion: The qnrS and blaCMY genes found in multiple antibiotic resistant E. coli mediated resistance to critically important antibiotics. The co-existence of these genes in variants strains of E. coli occupying different phylogenetic clusters suggests that antibiotics were widely used on the birds. Antibiotic treatment regimen in poultry may be responsible for the expression of antibiotic resistant genes found in the chromosome of the variant strains of E. coli.
- antibiotic resistant genes
- E. coli.
How to Cite
Available:http://www.who.int/mediacentre/factsheets/fs194/en/ 2017 a
Blázquez J, Couce A, Rodríguez-Beltrán J, Rodriguez-Rojas A. Antimicrobials as promoters of genetic variation. Current Opinions in Microbiology. 2012;15:561–569.
Davis GS, Waits K, Nordstrom L, Weaver B, Aziz M, Gauld L, et al. Intermingled Klebsiella pneumoniae populations between retail meats and human urinary tract infections. Clinical Infectious Diseases. 2015;61(6):892–899.
Börjesson S, Ny S, Egervärn M, Bergström J, Rosengrez Å, Englund S, et al. Limited dissemination of extended- spectrum β-lactamase and plasmid encoded AmpC–producing Escherichia coli from food and farm animals, Sweden. Emerging Infectious Diseases. 2016;22(4):15.
Kaiser G. Bookshelves microbiology book: Microbiology. Department of education open textbook pilot project, the UC Davis Office of the Provost, the UC Davis Library, the California State University; 2019.
Luby E, Ibekwe AM, Zilles J, Pruden A. Molecular methods for assessment of antibiotic resistance in agricultural ecosystems: Prospects and challenges. Journal of Environmental Quality. 2016;45:441-453.
Wang J, Tang P, Cui E, Wang L, Liu W, Ren J, et al. Characterization of antimicrobial resistance and related resistance genes in Escherichia coli strains isolated from chickens in China during 2007-2012. African Journal of Microbiology Research. 2013;7(46): 5238-5247.
Lentz SA, de Lima-Morales D, Cuppertino VM, Nunes LS, da Motta AS, Zavascki AP, et al. Letter to the editor: Escherichia coli harbouring mcr-1 gene isolated from poultry not exposed to polymyxins in Brazil. European Surveillance. 2016; 21(26):30267.
Jacoby GA, Griffin CM, Hooper DC. Citrobacter spp. as source of qnrB alleles. Antimicrobial Agents and Chemotherapy. 2011;55:4979-4984.
Enne VI, Delsol AA, Roe JM, Bennett PM. Evidence antibiotic resistance gene silencing in Escherichia coli. Antimicrobial Agents Chemotherapy. 2006;50:3003–3010.
Chen S, Larsson M, Robinson RC, Chen SL. Direct and convenient measurement of plasmid stability in lab and clinical isolates of Escherichia coli. Scientific Reports. 2017;7:4788.
Adelowo OO, Fagade OE, Agerso Y. Antibiotic resistance and resistance genes in Escherichia coli from poultry farms, southwest Nigeria. Journal of Infection in Developing Countries. 2014;8(9): 1103-1112.
Ieven ME, Vercauteren P, Descheemaeker F, Van Laer F, Goossens, H. Comparison of direct plating and broth enrichment culture for the detection of intestinal colonization by glycopeptide-resistant Enterococci among hospitalized patients. Journal of Clinical Microbiology.1999;37(5):1436–1440.
CLSI. Performance standards for antimicrobial disk susceptibility tests. Approved standard—eleventh edn. CLSI document M02-A11. Wayne, PA, USA; 2013.
Trindade LC, Marques E, Lopes DB, Marisa ÁSV, Ferreira. Development of a molecular method for detection and identification of Xanthomonas campestris pv. Viticola. Summa Phytopathologica. 2007;33(1):16-23.
Wawrik B, Kerkhof L, Zylstra GJ, Kukor J. Identification of unique type II polyketide synthase genes in Soil. Applied Environmental Microbiology. 2005;71(5): 2232–2238.
Promega Corporation, Madison, U.S.A. PCR master mix; 2016.
Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Applied and Environmental Microbiology. 2008;74: 2461–2470.
Wright MH, Adelskov J, Greene AC. Bacterial DNA extraction using individual enzymes and phenol/chloroform separation. Journal of Microbiology & Biology Education. 2017;18(2):1-3.
Almonacid AD, Kraal L, Ossandon FJ, Budovskaya YV, Cardenas JB, Bik EM, et al. 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. PLoS ONE. 2017;12(5): e0176555.
Cattoir V, Poirel L, Rotimi V, Soussy CJ, Nordmann P. Multiplex PCR for detection of plasmid-mediated quinolone resistance qnr genes in ESBL-producing enterobacterial isolates. Journal of Antimicrobial Chemotherapy. 2007;60(2): 394-397.
Mohammed F, AL-Marjani. Presence of qnr gene in environmental and clinical Pseudomonas aeruginosa isolates in Baghdad. International Journal of Current Microbiology and Applied Science. 2014; 3(7):853-857.
Shahad RM, Ayad Al-U, Mohammed HW. Detection of virulence genes (eae, blacmy-2, box) in Escherichia coli isolates from beta-thalasemic and non-thalasemic patients by using PCR technique. World Journal of Pharmaceutical Research. 2015;4(9):120-131.
Mahmud S, Nazir NH, Rahman MT. Prevalence and molecular detection of fluoroquinolone-resistant genes (qnrA and qnrS) in Escherichia coli isolated from healthy broiler chickens. Veterinary World. 2018;11(12):1720-1724.
Holmes AH, Moore LS, Sundsfjord A, Steinbakk M, Regmi S, Karley A. Understanding the mechanisms and drivers of antimicrobial resistance. Lancet. 2016;387:176–187.
WHO. Carbapenem-resistant Escherichia coli; Percentage of invasive isolates of Escherichia coli with resistance to carbapenems. Division of information, evidence, research and innovation, European health information gateway.
Available:https://gateway.euro.who.int/en/indicators/amr_1-carbapenem-resistant-Escherichia coli/ visualizations/#id=32511& tab= table. 2017b
Doregiraee F, Alebouyeh M, Fasaei BN, Charkhkar S, Tajeddin E, Zali MR. Changes in antimicrobial resistance patterns and dominance of extended spectrum β-lactamase genes among faecal Escherichia coli isolates from broilers and workers during two rearing periods. Italian Journal of Animal Science. 2018;17(3): 815-824.
Awogbemi J, Adeyeye M, Akinkunmi EO. A survey of antimicrobial agent’s usage in poultry farms and antibiotic resistance in Escherichia coli and Staphylococci isolates from the poultry in Ile-Ife, Nigeria. Journal of Infectious Disease and Epidemiology. 2018;4(1):047.
Fortini D, Fashae K, Garcia-Fernandez A, Villa L, Carattoli A. Plasmid mediated quinolone resistance and β-lactamases in E. coli from healthy animals from Nigeria. Journal of Antimicrobial Chemotherapy. 2011;66:1269-1272.
Poirel L, Naas T, Nordmann P. Diversity, epidemiology and genetics of class D beta-lactamases. Antimicrobial Agents Chemotherapy. 2010;54(1):24-38.
Li J, Zhang H, Ning J, Ning J, Sajid A, Cheng G, et al. The nature and epidemiology of OqxAB, a multidrug efflux pump. Antimicrobial Resistance and Infection. Control. 2019;8:44.
Pietsch M, Irrgang A, Roschanski N, Michael GV, Hamprecht A, Heime Rieber H, Kasbohrer et al. Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany. BioMed Central Genomics. 2018;19:601.
Ewers C, Bethe A, Semmler T, Guenther T, Wieler LH. Extended spectrum beta-lactamase producing and AmpC producing Escherichia coli from livestock and companion animals: And their putative impact on public health: a global perspective. Clinical Microbiology and Infection. 2012;18:646-655.
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