Abstract：
BACKGROUND: Klebsiella pneumoniae (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.
METHODS: 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.
RESULTS: 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. blaKPC was dominant in CG258, blaKPC-2 was detected in 97 % of the ST11 CR-hvKp, blaNDM subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); blaOXA-48 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 %).
CONCLUSIONS: 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.
METHODS: 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.
RESULTS: 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. blaKPC was dominant in CG258, blaKPC-2 was detected in 97 % of the ST11 CR-hvKp, blaNDM subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); blaOXA-48 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 %).
CONCLUSIONS: 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.
摘要：
背景：肺炎克雷伯菌（Kp）是一种常见的社区获得性和院内病原体。耐碳青霉烯类和高毒力(CR-hvKp)变种可以在医疗机构中迅速出现，并受到其他感染因子如COVID-19病毒的影响。
方法：为了解COVID-19病毒对CR-hvKp流行的影响，我们使用来自GenBank的相应元数据访问了Kp基因组。序列类型(ST)，抗菌素抗性基因，和毒力基因，并确定了这些分数和CR-hvKp。我们分析了五种最常见的STs的种群多样性和系统发育特征，测量CR-hvKp的患病率，鉴定的CR-hvKp亚型，并确定碳青霉烯抗性基因亚型与STs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。
结果：在COVID-19大流行期间，不同大洲的多个ST中CR-hvKp分离株的比例增加，在常见的ST中发现了持续的CR-hvKp亚型。blaKPC在CG258中占主导地位，blaKPC-2在ST11CR-hvKp的97％中检测到，blaNDM亚型在ST147（87.4％）和ST307（70.8％）中突出；blaOXA-48及其亚型在ST15中普遍存在（80.5％）。碳青霉烯酶基因的拥有在每个ST内的不同时间段内来自不同起源的亚分化中不同。IncFIB/IncHI1B杂交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。
结论：在COVID-19大流行期间，CR-hvKp的患病率增加，当地特有克隆的增加证明了这一点。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。这些发现对呼吸道病毒暴发和大流行管理期间适当使用抗菌药物以及感染预防和控制具有重要意义。
方法：为了解COVID-19病毒对CR-hvKp流行的影响，我们使用来自GenBank的相应元数据访问了Kp基因组。序列类型(ST)，抗菌素抗性基因，和毒力基因，并确定了这些分数和CR-hvKp。我们分析了五种最常见的STs的种群多样性和系统发育特征，测量CR-hvKp的患病率，鉴定的CR-hvKp亚型，并确定碳青霉烯抗性基因亚型与STs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。
结果：在COVID-19大流行期间，不同大洲的多个ST中CR-hvKp分离株的比例增加，在常见的ST中发现了持续的CR-hvKp亚型。blaKPC在CG258中占主导地位，blaKPC-2在ST11CR-hvKp的97％中检测到，blaNDM亚型在ST147（87.4％）和ST307（70.8％）中突出；blaOXA-48及其亚型在ST15中普遍存在（80.5％）。碳青霉烯酶基因的拥有在每个ST内的不同时间段内来自不同起源的亚分化中不同。IncFIB/IncHI1B杂交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。
结论：在COVID-19大流行期间，CR-hvKp的患病率增加，当地特有克隆的增加证明了这一点。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。这些发现对呼吸道病毒暴发和大流行管理期间适当使用抗菌药物以及感染预防和控制具有重要意义。
