Epidemiology, genotyping and antibiotic resistance of zoonotic bacteria isolated from poultry in Egypt

Poultry and poultry products are considered as major reservoirs for many zoonotic pathogens that are incriminated in human foodborne diseases globally. Moreover, these pathogens have contributed to the actual global challenge of antimicrobial resistance (AMR) with the use of antibiotics in the food production industry.
The poultry industry is one of the mainstay sources of Egyptian economy. Nonetheless, turkey production is still limited to a small scale. Few studies have discussed the probability of transmission of zoonotic pathogens and AMR between turkeys and humans in Egypt.
The global rise of ESBL- and carbapenemase-producing Gram-negative bacteria demands intensified surveillance. ESBL-producing and colistin-resistant Escherichia (E.) coli in poultry farms in Egypt are of major concern that emphasizes the possibility of spread of such strains and associated resistance genes including plasmid-mediated mcr-1 gene to humans.
Enterobacteriaceae strains were isolated and identified as E. coli (87.5%), Enterobacter cloacae (6.9%), K. pneumoniae (2.8%) and Citrobacter spp. (2.8%). ESBL-producing was confirmed in 12.5% of E. coli isolates while only 1.8% of isolates were confirmed as ESBL/carbapenemase-producing E. coli. The mcr-1 gene was identified in 7.9% of phenotypically colistin resistant E. coli isolates. The most prevalent resistance gene was blaTEM, which was identified in 85.7% of ESBL and AmpC ß-lactamase-producing isolates, while blaCMY-2 and blaOXA-7 were detected in 3.2% of ESBL and AmpC ß-lactamase-producing isolates. Only 1.6% of ESBL-producing E. coli isolates possessed blaCTX-M9, blaCTX-M1-15, blaOXA-1, blaDHA-1, blaLAP-1 and blaSHV genes. The virulence-associated genes detected by microarray analysis were differently distributed among the isolated E. coli including secretion system (cif, espA, espF_O103H2, espJ, nleA, nleB O157:H7 and tccP), adhesion-involved genes (eae and iha genes) and serine protease autotransporter genes (tsh, pic and vat).
Several toxin genes were detected including astA, cma, hlyE, mchF, sat and senB and fimbriae virulence genes (lpfA and prfB). Miscellaneous genes encoding virulence factors including hemL, intI1, ireA, iroN, iss and tir genes were identified. It was shown that molecular biological methods such as microarray investigation are reliable and fast tools for detection of genoserotypes, resistance- and virulence-associated determinants (Chapter 2).
The coagulase negative staphylococci (CoNS) are implicated in serious infections in both, humans and animals. They show high resistance to several antibiotics and gain a great research interest. Nevertheless, there are very few data available on the prevalence and resistance profiles of CoNS in Egypt.
Different CoNS species were isolated from apparently healthy turkeys located in five governorates in Egypt. The CoNS species were identified using MALDI-TOF MS as S. lentus (41%), S. xylosus (20.5%), S. saprophyticus (12.8%), S. sciuri (7.7%), S. condimenti (5.12%), S. cohnii (5.12%), S. simulans (2.6%), S. epidermidis (2.6%) and S. arlettae (2.6%). The susceptibility testing of CoNS isolates was performed using the broth microdilution test. All isolates were phenotypically resistant to trimethoprim/sulfamethoxazole, penicillin, ampicillin and tetracycline. The resistance rates to erythromycin, chloramphenicol, oxacillin, daptomycin and tigecycline were 97.4%, 94.9%, 92.3%, 89.7% and 87.2%, respectively. Thirty-one isolates were resistant to linezolid (79.5%). Low resistance rate was detected for both, imipenem and vancomycin (12.8%). The presence of resistance-associated genes mecA, vanA, blaZ, erm(A), erm(B), erm(C), aac-aphD, optrA, valS and cfr was determined. The erm(C) gene was identified in all erythromycin phenotypically resistant isolates, whereas two resistant isolates possessed three resistance-conferring genes erm(A), erm(B) and erm(C). The cfr and optrA genes were detected in 35.5% and 38.7% of the phenotypically linezolid-resistant isolates. The mecA, aac-aphD and blaZ genes were identified in 22.2%, 41.9%, and 2.6% of phenotypically resistant isolates to oxacillin, gentamicin and penicillin, respectively. This is the first study revealing the correlation between linezolid resistance and presence of cfr and optrA genes in CoNS isolates in Egypt. This study has demonstrated that both human and poultry can act as a vector for CoNS harboring antimicrobial resistance genes. Multidrug-resistant CoNS are a threat in both, human and veterinary medicine (Chapter 3).
There are no geographical boundaries that can hamper the worldwide spread of AMR. If preventive measures are not applied from farm-to-fork locally, nationally and globally, the tottering situation in one country can easily compromise the efficacy and threaten AMR control policies in other parts of the world.