Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio’s SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having bla OXA-48-like and bla NDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (G A TC, G A TGNNNNNNTTG, CA A NNNNNNCATC motifs) and m4C (C C WGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both bla OXA-48 and bla NDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.

中文翻译：

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耐碳青霉烯肺炎克雷伯菌临床菌株的表观基因组学、基因组学、抗性组、移动组、病毒组和进化系统基因组学

耐碳青霉烯类肺炎克雷伯菌(CRKP) 仍然是主要的临床病原体和公共卫生威胁，几乎没有治疗选择。对南非和全球 CRKP 的移动组、抵抗组、甲基化组、病毒组和系统地理学进行了表征。2018 年收集的 CRKP 进行了抗菌药物敏感性测试、多重 PCR 筛选、重复元件回文 (REP)-PCR 基因分型、质粒大小、数量、不相容性和迁移率分析，以及 PacBio 的 SMRT 测序 ( n = 6)。有 56 种多重耐药 CRKP，在可自传播的 IncF、A/C、IncL/M 和 IncX 3 上具有bla OXA-48样和bla NDM-1/7碳青霉烯酶 具有原噬菌体、traT、抗性岛和 I 型和 II 型限制性修饰系统 (RMS) 的质粒。本研究中检测到的质粒和进化枝分别与全球建立/传播的质粒进化枝/克隆相关，表明跨界水平和垂直传播。23 个菌株对粘菌素的敏感性降低。常见克隆包括 ST307、ST607、ST17、ST39 和 ST3559。IncFII k毒力质粒复制子存在于 56 个菌株中。六株菌株的全基因组测序揭示了至少 41 个毒力基因、广泛的 ompK36 突变和四种不同的 K 和 O 位点类型：KL2、KL25、KL27、KL102、O1、O2、O4 和 O5。I、II 和 III 型 RMS，授予 m6A（G A TC、G A TGNNNNNNTTG、CA 发现了染色体和质粒上的NNNNNNCATC 基序）和 m4C（C C WGG）修饰。bla OXA-48样和 bla NDM-1的质粒介导、克隆和多克隆传播的性质反映了国际上对密切相关的质粒和序列类型观察到的流行病学趋势。令人担忧的是，在同一分离物中观察到bla OXA-48和bla NDM-1的存在。RMS、病毒体和原噬菌体的质粒介导传播影响细菌进化、流行病学、致病性和耐药性，威胁感染治疗。RMS 对抗菌和噬菌体治疗的影响需要紧急调查。