Enterococcus cecorum is an emerging avian pathogen, particularly in chickens, but can be found in both diseased (clinical) and healthy (non-clinical) poultry. To better define differences between E. cecorum from the two groups, whole-genome sequencing (WGS) was used to identify and compare antimicrobial resistance genes as well as the pan-genome among the isolates. Eighteen strains selected from our previous study were subjected to WGS using Illumina MiSeq and comparatively analyzed. Assembled contigs were analyzed for resistance genes using ARG-ANNOT. Resistance to erythromycin was mediated by ermB, ermG, and mefA, in clinical isolates and ermB and mefA, in non-clinical isolates. Lincomycin resistance genes were identified as linB, lnuB, lnuC, and lnuD with lnuD found only in non-clinical E. cecorum; however, lnuB and linB were found in only one clinical isolate. For both groups of isolates, kanamycin resistance was mediated by aph3-III, while tetracycline resistance was conferred by tetM, tetO, and tetL. 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. A comparison of WGS results confirmed that non-clinical isolates contained more resistance genes than clinical isolates. The pan-genome of clinical and non-clinical isolates resulted in 3651 and 4950 gene families, respectively, whereas the core gene sets were comprised of 1559 and 1534 gene families in clinical and non-clinical isolates, respectively. Unique genes were found more frequently in non-clinical isolates than clinical. Phylogenetic analysis of the isolates and all the available complete and draft genomes showed no correlation between healthy and diseased poultry. Additional genomic comparison is required to elucidate genetic factors in E. cecorum that contribute to disease in poultry.

中文翻译：

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使用全基因组测序对家禽临床和非临床肠球菌的抗菌素耐药性和泛基因组进行比较。

盲肠肠球菌是一种新兴的禽类病原体，尤其是在鸡中，但在患病（临床）和健康（非临床）家禽中均可发现。为了更好地确定两组之间的盲肠大肠杆菌之间的差异，使用全基因组测序（WGS）来鉴定和比较分离株之间的抗菌素耐药基因以及全基因组。使用Illumina MiSeq对从我们先前研究中选择的十八个菌株进行WGS并进行比较分析。使用ARG-ANNOT分析组装的重叠群的抗性基因。在临床分离株以及ermB和mefA中，ermB，ermG和mefA介导了对红霉素的耐药性， 在非临床分离物中。林可霉素抗性基因被鉴定为铌酸锂，lnuB，lnuC， 和lnuD与lnuD发现，只有在非临床E. cecorum ; 但是，仅在一种临床分离物中发现了lnuB和linB。对于两组分离株，卡那霉素抗性由aph3-III介导，而四环素抗性由tet M，tet O和tet赋予L.对利奈唑胺或氯霉素耐药的分离株未发现突变或已知的耐药基因，表明对这些药物耐药的新机制。WGS结果的比较证实，非临床分离株比临床分离株包含更多的抗性基因。临床和非临床分离株的全基因组分别产生3651和4950个基因家族，而核心基因集分别由临床和非临床分离株的1559和1534个基因家族组成。在非临床分离物中比在临床中发现独特基因的频率更高。对分离物以及所有可用的完整基因组和原始基因组进行的系统发育分析表明，健康家禽和患病家禽之间没有相关性。需要额外的基因组比较来阐明遗传因素导致家禽疾病的大肠杆菌。