Chao Liu , Jun Guo , Shuaihua Fan , Wei Guo , Huaiqing Qi , Stephen Baker , Pengcheng Du , Bin Cao
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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.</p></div><div><h3>Findings</h3><p>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. <em>bla</em><sub>KPC</sub> was dominant in CG258, <em>bla</em><sub>KPC-2</sub> was detected in 97 % of the ST11 CR-hvKp, <em>bla</em><sub>NDM</sub> subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); <em>bla</em><sub>OXA-48</sub> 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 %).</p></div><div><h3>Interpretation</h3><p>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.</p></div>","PeriodicalId":51022,"journal":{"name":"Drug Resistance Updates","volume":"77 ","pages":"Article 101124"},"PeriodicalIF":15.8000,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"An increased prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae associated with the COVID-19 pandemic\",\"authors\":\"Chao Liu , Jun Guo , Shuaihua Fan , Wei Guo , Huaiqing Qi , Stephen Baker , Pengcheng Du , Bin Cao\",\"doi\":\"10.1016/j.drup.2024.101124\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><p><em>Klebsiella pneumoniae</em> (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.</p></div><div><h3>Methods</h3><p>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.</p></div><div><h3>Findings</h3><p>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. <em>bla</em><sub>KPC</sub> was dominant in CG258, <em>bla</em><sub>KPC-2</sub> was detected in 97 % of the ST11 CR-hvKp, <em>bla</em><sub>NDM</sub> subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); <em>bla</em><sub>OXA-48</sub> 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 %).</p></div><div><h3>Interpretation</h3><p>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. 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引用次数: 0
摘要
(Kp）是一种常见的社区获得性和医院内病原体。耐碳青霉烯类和高病毒性（CR-hvKp）变种可在医疗机构内迅速出现，并受到 COVID-19 病毒等其他传染源的影响。为了了解 COVID-19 病毒对 CR-hvKp 流行的影响，我们从 GenBank 获取了 Kp 基因组及相应的元数据。我们确定了序列类型（ST）、抗菌药耐药性基因和毒力基因，以及这些得分和 CR-hvKp。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 的流行率，确定了 CR-hvKp 亚型，并确定了碳青霉烯耐药基因亚型与 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，各大洲多个 ST 中的 CR-hvKp 分离物比例增加，在常见的 ST 中发现了持续的 CR-hvKp 亚型。CG258 中 CR-hvKp 占主导地位，97% 的 ST11 中检测到 CR-hvKp，其亚型在 ST147（87.4%）和 ST307（70.8%）中表现突出；其亚型在 ST15（80.5%）中普遍存在。碳青霉烯酶基因的拥有情况在每个 ST 的不同时期不同来源的亚支系中有所不同。IncFIB/IncHI1B杂交质粒含有毒力基因和碳青霉烯酶基因，主要存在于ST147（67.37%）和ST307（56.25%）中。在 COVID-19 大流行期间，CR-hvKp 的流行率有所上升，当地流行克隆的增加就是明证。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。这些发现对在呼吸道病毒爆发和大流行管理期间适当使用抗菌药物、预防和控制感染具有重要意义。
An increased prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae associated with the COVID-19 pandemic
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.
Findings
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 %).
Interpretation
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.
期刊介绍：
Drug Resistance Updates serves as a platform for publishing original research, commentary, and expert reviews on significant advancements in drug resistance related to infectious diseases and cancer. It encompasses diverse disciplines such as molecular biology, biochemistry, cell biology, pharmacology, microbiology, preclinical therapeutics, oncology, and clinical medicine. The journal addresses both basic research and clinical aspects of drug resistance, providing insights into novel drugs and strategies to overcome resistance. Original research articles are welcomed, and review articles are authored by leaders in the field by invitation.
Articles are written by leaders in the field, in response to an invitation from the Editors, and are peer-reviewed prior to publication. Articles are clear, readable, and up-to-date, suitable for a multidisciplinary readership and include schematic diagrams and other illustrations conveying the major points of the article. The goal is to highlight recent areas of growth and put them in perspective.
*Expert reviews in clinical and basic drug resistance research in oncology and infectious disease
*Describes emerging technologies and therapies, particularly those that overcome drug resistance
*Emphasises common themes in microbial and cancer research
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