Multidrug Resistant Genome Analysis of E.coli isolated from Avian Species

Abstract

Escherichia coli are commensal adherent of the gastrointestinal tract of both human and animals. Although most E. coli strains are harmless, however, some strains are pathogenic for both human and animals as well. Pathogenic E. coli are usually categorized as intestinal pathogenic or extra intestinal pathogenic E. coli. The pathogenic group is further divided into further sub-pathotypes, e.g., enterohemorrhagicE. coli (EHEC), enterotoxigenicE. coli (ETEC), entero-aggregative E. coli (EAEC) and enteropathogenicE. coli (EPEC). Multidrug resistant (MDR) bacteria, usually described as those impervious to three or more antibiotic classes, especially are of great concern because MDR E. coli tends to harbor numerous resistance genes and shifts its resistance determinants to other strains, species or genera. The current study was designed to evaluate AMR in E. coli isolated from healthy chicken. A total 785 samples wereobtained from which 621 E. coli were isolated. About 221 (35%) isolates were subjected to Antimicrobial Susceptibility Tests using CLSI protocols. Phenotypically 100% resistant to Penicillin was observed in tested E. coli isolates. More than 50% resistance in tested E. coli isolates was observed against 18 (58%) out of 31 antibiotics analyzed by AST and these include Ampicillin, Ampicillin-Sulbactam, Azithromycin, Chloramphenicol, Ciprofloxacin, Clindamycin, Doxycycline, Enrofloxacin, Erythromycin, Florfenicol, Linezolid, Nalidixic acid, Penicillin, Quinupritin-Dalfopristin, Streptomycin, Co-trimoxazole, Tetracycline, and Teicoplanin. Highest sensitivity was observed against Pepracilline/Tazobactam, Amikacin and Meropenem antibiotics showing sensitivity in 88%, 80% and 79% respectively. Based on the phenotypic AMR pattern, 24 isolates were subjected to genotypic characterization against 20 AMR genes of 4 antibiotic classes which include Β-lactams, Aminoglycosides, Tetracyclines and Polypeptides (Colistin). Among Beta-lactamase blaTEM was found in 22 (92%) isolates, while blaCTX-M was found in 4 (17%) isolates. The beta-lactamase producing blaOXA and blaFOX, were found in 2 (8%) isolates while blaNDM-1, blaSHV-1, weredetected in 1 (4%) isolate. Among Tetracycline tetA showed highest prevalence with 92% and detected in 22 isolates while tetM was detected in 2 (8%) isolates. The prevalence of aac(6')-Ib was found to be 46% as it was detected in 11 isolates while of aac(3)-II, aph(3)-II was 8% each with detection in 2 isolates. For Colistin resistance producing genes, mcr 1 to mcr 9 were tested and only mcr-9, mcr-5 and mcr-2 were detected vi Abstract with mcr-9 was found in 12 (50%), mcr-5 detected in 6 (25%) and mcr-2 was detected in 3 (13%) isolates, however, mcr-1 reported previously was not detected in any of the isolates tested. On the basis of these results, it could be concluded that the chickens sold in retail sectors of Pakistan are harboring significant population of multi-drug resistant E. coli. The presence of MDR E. coli may be resulted by the persistent exposure of birds to multiple antibiotics during the rearing period. To relieve this issue, the public health authority ought to control non-judicial utilization of antibiotics at poultry production and stringent measure need to be adopted for future control of AMR issue in the country as well as globally. Further a surveillance network for detection of AMR in healthy poultry and other food animals need to be established on sustainable basis. While data collection and analysis needs to be carried out at larger scale for exact depiction of the AMR situation in the country. The control measures may be devised according to the situation of AMR in the country. Key words:E. coli, antimicrobial resistance, isolation and identification, phenotypic antimicrobial resistance profile, genotypic antimicrobial resistance profile