PDF(Pubmed)
Abstract：
Linezolid resistance in Enterococcus spp. is increasingly considered critically important and a public health threat which mandates the need to understand their genomic contents and dissemination patterns. Here, we used whole-genome sequencing to characterize the resistome, virulome and mobile genetic elements of nine linezolid-resistant (LZDR) enterococci (seven optrA-E. faecalis, one poxtA-E. faecium and one optrA-E. casseliflavus) previously obtained from the nares of healthy dogs, pigs, pig farmers and tracheal samples of nestling storks in Spain. Also, the relatedness of the isolates with publicly available genomes was accessed by core-genome single nucleotide polymorphism (SNP) analysis. The optrA gene of the E. faecalis and E. casseliflavus isolates was located downstream of the fexA gene. The optrA gene in the E. casseliflavus isolate was carried in a plasmid (pURX4962), while those in the seven E. faecalis isolates were chromosomally located. The OptrA proteins were mostly variants of wild type (DP-2: Y176D/T481P; RDK: I104R/Y176D/E256K; DD-3: Y176D/G393D; and EDD: K3E/Y176D/G393D), except two that were wild type (one E. faecalis and one E. casseliflavus). The poxtA gene in the E. faecium isolate was found alone within its contig. The cfrD was upstream of ermB gene in the E. casseliflavus isolate and flanked by ISNCY and IS1216. All the LZDR enterococci carried plasmid rep genes (2-3) containing tetracycline, chloramphenicol and aminoglycoside resistance genes. All isolates except E. casseliflavus carried at least one intact prophage, of which E. faecalis-ST330 (X4957) from a pig carried the highest (n = 5). Tn6260 was associated with lnuG in E. faecalis-ST330 while Tn554 was with fexA in E. feaecalis-ST59 isolates. All except E. casseliflavus (n = 0) carried at least two metal resistance genes (MRGs), of which poxtA-carrying E. faecium-ST1739 isolate contained the most (arsA, copA, fief, ziaA, znuA, zosA, zupT, and zur). SNP-based analyses identified closely related optrA-E. faecalis isolates from a pig and a pig farmer on the same farm (SNP = 4). Moreover, optrA- carrying E. faecalis-ST32, -ST59, and -ST474 isolates from pigs were related to those previously described from humans (sick and healthy) and cattle in Spain, Belgium, and Switzerland (SNP range 43-86). These findings strongly suggest the transmission of LZDR-E. faecalis between a pig and a pig farmer and potential inter-country dissemination. These highlight the need to strengthen molecular surveillance of LZDR enterococci in all ecological niches and body parts to direct appropriate control strategies.
摘要：
肠球菌属对利奈唑胺的耐药性。越来越被认为是至关重要的公共健康威胁，这要求需要了解其基因组内容和传播模式。这里,我们使用全基因组测序来表征抗性组，九种利奈唑胺抗性（LZDR）肠球菌的病毒组和移动遗传元件（七个optrA-E。粪肠,一个poxtA-E.屎和一个optrA-E。卡塞利黄）以前从健康狗的鼻孔中获得，猪,养猪户和西班牙雏鸟的气管样本。此外，通过核心基因组单核苷酸多态性(SNP)分析获得了分离株与公开基因组的相关性.粪肠球菌和卡塞利黄大肠杆菌分离株的optrA基因位于fexA基因的下游。E.casseliflavus分离物中的optrA基因携带在质粒（pURX4962）中，而七个粪肠球菌分离株中的那些位于染色体上。OptrA蛋白主要是野生型变体（DP-2：Y176D/T481P;RDK：I104R/Y176D/E256K;DD-3：Y176D/G393D;和EDD：K3E/Y176D/G393D），除了两个是野生型(一个粪肠球菌和一个卡萨利黄)。在屎肠球菌分离物中的poxtA基因在其重叠群中单独发现。cfrD位于E.casseliflavus分离物中ermB基因的上游，侧翼为ISNCY和IS1216。所有的LZDR肠球菌携带含有四环素的质粒rep基因（2-3），氯霉素和氨基糖苷类耐药基因。除E.casselifatus外，所有分离株都携带至少一个完整的原种，其中猪的粪肠球菌-ST330(X4957)含量最高(n=5)。Tn6260在粪肠球菌-ST330中与lnuG相关，而Tn554在粪肠球菌-ST59分离株中与fexA相关。除E.casseliflavus（n=0）外，所有携带至少两个金属抗性基因（MRGs），其中携带痘痘的屎肠球菌-ST1739分离株含量最高(arsA，COPA,Fief,ziaA,znuA,zosA,zupt,和zur）。基于SNP的分析确定了密切相关的optrA-E。来自同一农场的猪和养猪户的粪菌分离物（SNP=4）。此外，来自猪的携带optrA的粪肠球菌-ST32，-ST59和-ST474分离株与先前从西班牙的人类（患病和健康）和牛中描述的分离株有关，比利时,和瑞士（SNP范围为43-86）。这些发现强烈暗示了LZDR-E的传播。猪和养猪户之间的粪便和潜在的跨国传播。这些强调需要加强对所有生态位和身体部位的LZDR肠球菌的分子监测，以指导适当的控制策略。
