(Kp) is a common community-acquired and nosocomial pathogen. Carbapenem-resistant and hypervirulent (CR-hvKp) variants can emerge rapidly within healthcare facilities and impacted by other infectious agents such as COVID-19 virus. To understand the impact of COVID-19 virus on the prevalence of CR-hvKp, we accessed Kp genomes with corresponding metadata from GenBank. Sequence types (STs), antimicrobial resistance genes, and virulence genes, and those scores and CR-hvKp were identified. We analyzed population diversity and phylogenetic characteristics of five most common STs, measured the prevalence of CR-hvKp, identified CR-hvKp subtypes, and determined associations between carbapenem resistance gene subtypes with STs and plasmid types. These variables were compared pre- and during the COVID-19 pandemic. The proportion of CR-hvKp isolates increased within multiple STs in different continents during the COVID-19 pandemic and persistent CR-hvKp subtypes were found in common STs. was dominant in CG258, was detected in 97 % of the ST11 CR-hvKp, subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); and its subtypes were prevalent in ST15 (80.5 %). The possession of carbapenemase genes was different among subclades from different origins in different periods of time within each ST. IncFIB/IncHI1B hybrid plasmids contained virulence genes and carbapenemase genes and were predominant in ST147 (67.37 %) and ST307 (56.25 %). The prevalence of CR-hvKp increased during the COVID-19 pandemic, which was evident by an increase in local endemic clones. This process was facilitated by the convergence of plasmids containing carbapenemase genes and virulence genes. These findings have implications for the appropriate use of antimicrobials and infection prevention and control during outbreaks of respiratory viruses and pandemic management.

中文翻译：

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与 COVID-19 大流行相关的耐碳青霉烯类高毒力肺炎克雷伯菌患病率增加


(Kp) 是一种常见的社区获得性和医院内病原体。碳青霉烯类抗药性和高毒力 (CR-hvKp) 变种可能在医疗机构内迅速出现，并受到其他传染源（例如 COVID-19 病毒）的影响。为了了解 COVID-19 病毒对 CR-hvKp 流行的影响，我们访问了 Kp 基因组以及 GenBank 中的相应元数据。序列类型 (ST)、抗菌素耐药性基因和毒力基因以及这些评分和 CR-hvKp 均已确定。我们分析了五种最常见 ST 的种群多样性和系统发育特征，测量了 CR-hvKp 的患病率，鉴定了 CR-hvKp 亚型，并确定了碳青霉烯类抗性基因亚型与 ST 和质粒类型之间的关联。这些变量在 COVID-19 大流行之前和期间进行了比较。在 COVID-19 大流行期间，不同大陆的多个 ST 中 CR-hvKp 分离株的比例有所增加，并且在常见 ST 中发现了持续的 CR-hvKp 亚型。在 CG258 中占主导地位，在 97% 的 ST11 CR-hvKp 中检测到，亚型在 ST147 (87.4%) 和 ST307 (70.8%) 中突出；其亚型在 ST15 中普遍存在（80.5%）。每个ST内不同时期不同来源的亚支所拥有的碳青霉烯酶基因是不同的。 IncFIB/IncHI1B 杂合质粒含有毒力基因和碳青霉烯酶基因，在 ST147 (67.37%) 和 ST307 (56.25%) 中占主导地位。在 COVID-19 大流行期间，CR-hvKp 的患病率有所增加，当地流行克隆的增加就证明了这一点。含有碳青霉烯酶基因和毒力基因的质粒的融合促进了这一过程。 这些发现对于呼吸道病毒爆发期间抗菌药物的适当使用以及感染预防和控制以及大流行管理具有重要意义。