Comparison of antimicrobial resistance of clinical and non-clinical Enterococcus cecorum from poultry using whole-genome sequencing

Authors: SHARMA, POONAM - Orise Fellow; GUPTA, SUSHIM - Orise Fellow; KARIYAWASAM, SUBHASHINIE - Pennsylvania State University; Barrett, John; Hiott, Lari; Woodley, Tiffanie; Frye, Jonathan; Jackson, Charlene

Submitted to: American Society for Microbiology General Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 2/22/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Enterococcus cecorum has been implicated as a possible cause of disease in poultry including spondylitis, vertebral osteoarthritis and femoral osteomyelitis. Antimicrobials have been used to treat the disease during outbreaks, but have been ineffective in controlling outbreak mortality possibly due to antimicrobial resistance (AR) in E. cecorum. To better define AR in E. cecorum, whole-genome sequencing (WGS) was used to identify and compare AR genes between E. cecorum from diseased (clinical) and healthy (non-clinical) poultry. Strains from each group were previously tested for antimicrobial susceptibility to a panel of 16 antimicrobials. Twenty strains were selected from this analysis and subjected to genome sequencing using Illumina MiSeq. The raw data was assembled using A5-miseq. The assembled contigs were analyzed for AR genes using the ARG-ANNOT database. Resistance to erythromycin was mediated by an erythromycin-resistance methylase, ermB and mefA, in non-clinical isolates and ermB, ermG, and mefA in clinical isolates. The bifunctional aminoglycoside resistance gene, aac(6’)-aph(2”), was present in a non-clinical isolate only. Kanamycin resistance was mediated by aminoglycoside-modifying enzyme, aph3-III, in both groups of isolates and aphA2 in one non-clinical isolate. Lincomycin resistance genes were identified as linB, lnuB, lnuC, and lnuD with lnuD found only in non-clinical E. cecorum. Tetracycline resistance genes for ribosomal protection (tetM, tetO) or efflux (tetL) was found in both sets of isolates; a fourth gene tetS (ribosomal protection) was also detected in one non-clinical E. cecorum. No mutations or known resistance genes were found for isolates resistant to either linezolid or chloramphenicol suggesting possible new mechanisms of resistance to these drugs. Comparison of WGS results confirmed that non-clinical isolates contained more resistance genes than clinical isolates. Resistance genes were both shared and exclusive to each group indicating varying genetic characteristics among E. cecorum isolates. Further investigation using WGS will assist in determining genes responsible for pathogenesis of E. cecorum in poultry.