Abdullahi Idris Nasir, Lozano Carmen, Latorre-Fernández Javier, Zarazaga Myriam, Stegger Marc, Torres Carmen
Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain.
Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria.
Int Microbiol. 2024 Sep 17. doi: 10.1007/s10123-024-00577-9.
Coagulase-negative staphylococci (CoNS) are evolving as major reservoirs and vectors of unusual and critical antimicrobial resistance (AMR) mechanisms.
In this study, the genomic characterization of 26 multidrug-resistant (MDR)-CoNS (S. borealis, S. saprophyticus, S. sciuri, S. hominis, S. epidermidis, S. pasteuri, S. hyicus, S. simulans, S. haemolyticus, and S. arlettae) previously obtained from the nasal cavity of healthy nestling storks, humans who had no contact with animals, pigs, and pig farmers, as well as dogs and dog owners from Spain was performed. High-quality draft genomes obtained by Illumina sequencing technology were used to determine their resistome, virulome, mobile genetic elements, and CRISPR-Cas types. The relatedness of three CoNS species with publicly available genomes was assessed by core-genome single nucleotide polymorphisms (SNPs).
AMR genes to all classes of antibiotics in staphylococci were detected including unusual ones (mecC, ermT, and cfr), of which their corresponding genetic organizations were analyzed. About 96.1% of the MDR-CoNS strains harbored diverse adherence or immune evasion genes. Remarkably, one enterotoxin-C and -L-carrying S. epidermidis-ST595 strain from a nestling stork was detected. Moreover, various plasmid bound-biocide resistance genes (qacACGJ) were identified in 34.6% of the MDR-CoNS. Two genes that encode for cadmium and zinc resistance (cadD, czrC) were found, of which czrC predominated (42.3%). Complete CRISPR-Cas system was detected in 19.2% of the CoNS strains, of which cas-1, -2, and -9 predominated, especially in 75% of the S. borealis strains. The phylogenetic analysis identified clusters of related S. epidermidis lineages with those of other countries (SNP < 100). Also, highly related S. borealis isolates (SNP < 10) from pigs was confirmed for the first time in Spain.
These findings showed that various ecological niches harbor CoNS that presented MDR phenotypes mediated by multiple AMR genes carried by mobile genetic elements with relatively low frequency of intact CRISPR-Cas systems. Furthermore, the transmission of some CoNS species in humans and animals is strongly suggested.
凝固酶阴性葡萄球菌（CoNS）正逐渐成为不寻常且关键的抗菌耐药（AMR）机制的主要储存库和传播媒介。
在本研究中，对先前从健康雏鹳的鼻腔、未接触动物的人类、猪和养猪户以及来自西班牙的狗和狗主人中分离得到的26株多重耐药（MDR）-CoNS（北方葡萄球菌、腐生葡萄球菌、松鼠葡萄球菌、人葡萄球菌、表皮葡萄球菌、巴斯德葡萄球菌、猪葡萄球菌、模仿葡萄球菌、溶血葡萄球菌和阿氏葡萄球菌）进行了基因组特征分析。利用Illumina测序技术获得的高质量草图基因组来确定它们的耐药组、毒力组、移动遗传元件和CRISPR-Cas类型。通过核心基因组单核苷酸多态性（SNP）评估三种CoNS物种与公开可用基因组的相关性。
检测到葡萄球菌对所有类别的抗生素的耐药基因，包括不寻常的耐药基因（mecC、ermT和cfr），并对其相应的基因组织进行了分析。约96.1%的MDR-CoNS菌株携带多种黏附或免疫逃避基因。值得注意的是，从一只雏鹳中检测到一株携带肠毒素C和L的表皮葡萄球菌-ST595菌株。此外，在34.6%的MDR-CoNS中鉴定出各种质粒结合的杀生物剂耐药基因（qacACGJ）。发现了两个编码镉和锌抗性的基因（cadD、czrC），其中czrC占主导（42.3%）。在19.2%的CoNS菌株中检测到完整的CRISPR-Cas系统，其中cas-1、-2和-9占主导，尤其是在75%的北方葡萄球菌菌株中。系统发育分析确定了与其他国家相关的表皮葡萄球菌谱系簇（SNP < 100）。此外，首次在西班牙证实了来自猪的高度相关的北方葡萄球菌分离株（SNP < 10）。
这些发现表明，各种生态位中都存在CoNS，它们呈现出由移动遗传元件携带的多个AMR基因介导的MDR表型，且完整CRISPR-Cas系统的频率相对较低。此外，强烈提示某些CoNS物种在人和动物之间存在传播。
