Houkes K M G, Weterings V, Verweij J J, Murk J L, van den Bijllaardt W, Stohr J J J M
Microvida, Laboratory of Medical Microbiology, Amphia Hospital, Breda, Netherlands.
Microvida, Laboratory of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands.
Microb Genom. 2025 Jul;11(7). doi: 10.1099/mgen.0.001458.
Multidrug-resistant Enterobacterales isolates carrying extended-spectrum beta-lactamases (ESBLs) and mobile colistin resistance () genes pose a significant healthcare threat as they can lead to difficult-to-treat infections. This study investigates the prevalence of isolates co-harbouring ESBL and genes and characterizes the plasmids co-harbouring those genes. ESBL-producing Enterobacterales (ESBL-E) isolates identified during point prevalence surveys (PPS) in a Dutch hospital were screened for genes. Plasmids co-harbouring and ESBL genes were identified using long- and short-read sequencing data, while detecting resistance and replicon genes using AMRFinderPlus and PlasmidFinder. The plasmid database PLSDB was searched for plasmids containing the same and ESBL gene(s), and SNP and DCJ-Indel distance analyses were conducted to examine plasmid diversity. The most recent common ancestor (MRCA) was inferred through timed phylogeny analyses in BEAST, and putative composite transposons containing the or ESBL genes were identified. Among 188 screened ESBL-E, 11 harboured genes: 9 with and 2 with and . All plasmids containing and ESBL genes were IncHI plasmids harbouring , and/or . The plasmid database search resulted in 128 similar plasmids. SNP analysis showed ≤10 SNPs among the PPS study plasmids and up to 924 SNPs among all plasmids. Structural relatedness and phylogenetic analyses revealed clustering of the PPS study plasmids but no additional taxonomical or geographical clustering. The MRCA of the PPS study plasmids likely emerged between 1986 and 2008. Finally, composite transposon analysis indicated that matching complete insertion sequences rarely flanked genes, whereas and frequently were. The prevalence of genes among ESBL-E in this study is 5.9%, with being the most prevalent. Limited plasmid diversity suggests a single introduction event followed by regional and global dissemination across related bacterial species. Persistent ESBL gene mobility suggests a more recent introduction of these genes compared to the genes.
携带超广谱β-内酰胺酶（ESBLs）和可移动性黏菌素耐药（mcr）基因的多重耐药肠杆菌科分离株对医疗保健构成了重大威胁，因为它们可导致难以治疗的感染。本研究调查了同时携带ESBL和mcr基因的分离株的流行情况，并对携带这些基因的质粒进行了特征分析。在一家荷兰医院的现患率调查（PPS）期间鉴定出的产ESBL肠杆菌科（ESBL-E）分离株被筛查是否携带mcr基因。利用长读长和短读长测序数据鉴定同时携带mcr和ESBL基因的质粒，同时使用AMRFinderPlus和PlasmidFinder检测耐药基因和复制子基因。在质粒数据库PLSDB中搜索含有相同mcr和ESBL基因的质粒，并进行单核苷酸多态性（SNP）和双切割连接（DCJ）-插入缺失距离分析，以检查质粒多样性。通过在BEAST中进行的定时系统发育分析推断最近共同祖先（MRCA），并鉴定出含有mcr或ESBL基因的假定复合转座子。在188株经筛查的ESBL-E中，有11株携带mcr基因：9株携带mcr-1，2株携带mcr-3和mcr-4。所有含有mcr和ESBL基因的质粒均为携带mcr、blaCTX-M和/或blaTEM的IncHI质粒。质粒数据库搜索结果显示有128个相似质粒。SNP分析显示，PPS研究质粒之间的SNP≤10个，而所有质粒之间最多有924个SNP。结构相关性和系统发育分析揭示了PPS研究质粒的聚类，但没有额外的分类学或地理聚类。PPS研究质粒的MRCA可能出现在1986年至2008年之间。最后，复合转座子分析表明，匹配的完整插入序列很少位于mcr基因两侧，而blaCTX-M和blaTEM则经常位于两侧。本研究中ESBL-E中mcr基因的流行率为5.9%，其中mcr-1最为普遍。有限的质粒多样性表明存在一次单一引入事件，随后在相关细菌物种中进行区域和全球传播。与mcr基因相比，ESBL基因持续的移动性表明这些基因是较近期引入的。
