Palmieri Mattia, D'Andrea Marco Maria, Pelegrin Andreu Coello, Mirande Caroline, Brkic Snezana, Cirkovic Ivana, Goossens Herman, Rossolini Gian Maria, van Belkum Alex
bioMérieux, Data Analytics Unit, La Balme-les-Grottes, France.
Department of Biology, University of "Tor Vergata", Rome, Italy.
Front Microbiol. 2020 Feb 21;11:294. doi: 10.3389/fmicb.2020.00294. eCollection 2020.
is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Carbapenem resistance is frequent, and colistin represents a key molecule to treat infections caused by such isolates. Here we evaluated the antimicrobial resistance (AMR) mechanisms and the genomic epidemiology of clinical isolates from Serbia. Consecutive non-replicate clinical isolates ( = 2,298) were collected from seven hospitals located in five Serbian cities and tested for carbapenem resistance by disk diffusion. Isolates resistant to at least one carbapenem ( = 426) were further tested for colistin resistance with Etest or Vitek2. Broth microdilution (BMD) was performed to confirm the colistin resistance phenotype, and colistin-resistant isolates ( = 45, 10.6%) were characterized by Vitek2 and whole genome sequencing. Three different clonal groups (CGs) were observed: CG101 (ST101, = 38), CG258 (ST437, = 4; ST340, = 1; ST258, = 1) and CG17 (ST336, = 1). genes, encoding for acquired colistin resistance, were not observed, while all the genomes presented mutations previously associated with colistin resistance. In particular, all strains had a mutated MgrB, with MgrB being the prevalent mutation and associated with ST101. Isolates belonging to ST101 harbored the carbapenemase OXA-48, which is generally encoded by an IncL/M plasmid that was no detected in our isolates. MinION sequencing was performed on a representative ST101 strain, and the obtained long reads were assembled together with the Illumina high quality reads to decipher the genetic background. The gene was located in a novel IncFIA-IncR hybrid plasmid, also containing the extended spectrum β-lactamase-encoding gene and several other AMR genes. Non-ST101 isolates presented different MgrB alterations (C28S, C28Y, K2, K3, Q30, adenine deletion leading to frameshift and premature termination, IS-mediated inactivation) and expressed different carbapenemases: OXA-48 (ST437 and ST336), NDM-1 (ST437 and ST340) and KPC-2 (ST258). Our study reports the clonal expansion of the newly emerging ST101 clone in Serbia. This high-risk clone appears adept at acquiring resistance, and efforts should be made to contain the spread of such clone.
是严重医疗保健相关感染的主要原因，且常表现出多重耐药表型。碳青霉烯耐药很常见，而黏菌素是治疗由此类分离株引起的感染的关键分子。在此，我们评估了塞尔维亚临床分离株的抗菌药物耐药（AMR）机制和基因组流行病学。从塞尔维亚五个城市的七家医院收集了连续的非重复临床分离株（n = 2298），并通过纸片扩散法检测碳青霉烯耐药性。对至少对一种碳青霉烯耐药的分离株（n = 426），进一步用Etest或Vitek2检测黏菌素耐药性。进行肉汤微量稀释（BMD）以确认黏菌素耐药表型，并用Vitek2和全基因组测序对黏菌素耐药分离株（n = 45，10.6%）进行特征分析。观察到三个不同的克隆群（CGs）：CG101（ST101，n = 38）、CG258（ST437，n = 4；ST340，n = 1；ST258，n = 1）和CG17（ST336，n = 1）。未观察到编码获得性黏菌素耐药的mcr基因，而所有基因组均呈现出先前与黏菌素耐药相关的突变。特别是，所有菌株的MgrB均发生突变，MgrB突变最为普遍且与ST101相关。属于ST101的分离株携带碳青霉烯酶OXA - 48，其通常由IncL/M质粒编码，但在我们的分离株中未检测到。对一株代表性的ST101菌株进行了MinION测序，并将获得的长读段与Illumina高质量读段组装在一起，以解析其遗传背景。mcr基因位于一个新型的IncFIA - IncR杂合质粒中，该质粒还包含编码超广谱β - 内酰胺酶的bla基因和其他几个AMR基因。非ST101分离株呈现出不同的MgrB改变（C28S、C28Y、K2、K3、Q30、腺嘌呤缺失导致移码和提前终止、IS介导的失活），并表达不同的碳青霉烯酶：OXA - 48（ST437和ST336）、NDM - 1（ST437和ST340）和KPC - 2（ST258）。我们的研究报告了塞尔维亚新出现的ST101克隆的克隆性扩张。这个高风险克隆似乎善于获得耐药性，应努力遏制此类克隆的传播。
