耐碳青霉烯肺炎克雷伯菌分离株的高分辨率基因组分析:一项多中心回顾性印度研究

G. Nagaraj, V. Shamanna, V. Govindan, Steffi Rose, D. Sravani, K. P. Akshata, M. Shincy, V. T. Venkatesha, M. Abrudan, S. Argimón, M. Kekre, A. Underwood, D. Aanensen, K. Ravikumar, Khalil Harry Dawn Ben Nicole Sophia Pilar Johan Fabian Al Abudahab Harste Muddyman Taylor Wheeler David Dona, Khalil AbuDahab, Harry Harste, Dawn Muddyman, Ben Taylor, Nicole Wheeler, S. David, P. Donado-Godoy, J. Bernal, A. Arévalo, M. F. Valencia, Erik C D Osma Castro, K. N. Ravishankar, I. Okeke, A. Oaikhena, A. O. Afolayan, Jolaade J. Ajiboye, E. E. Odih, C. Carlos, Marietta L Lagrada, P. K. Macaranas, Agnettah M. Olorosa, June M. Gayeta, Elmer M Herrera
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引用次数: 22

摘要

我们报道了对印度肺炎克雷伯菌分离株基因组序列的见解,突出了高风险国际克隆和遗传库的存在,不同于其他地区的主要克隆和遗传库。多药耐药和高致病性肺炎克雷伯菌的鉴定引起公共卫生关注。耐碳青霉烯肺炎克雷伯菌(CRKP)由于其高传播、高死亡率和有限的治疗选择,对印度的公共卫生构成威胁。其基因组变异性反映在序列类型、毒力因子和抗微生物药物耐药性(AMR)机制的多样性。本研究旨在描述印度CRKP分离株的克隆关系和抗性和毒力的遗传机制。材料与方法对2013-2019年从印度8个中心收集的344株回顾性肺炎克雷伯菌临床分离株进行了分析。采用VITEK 2检测抗生素敏感性。从它们的全基因组序列推断出荚膜类型、MLST、毒力基因、AMR决定因子、质粒复制子类型和单核苷酸多态性(SNP)系统发育。结果325株通过QC检测的克雷伯菌分离株的系统发育分析显示:严格感肺炎克雷伯菌(307株)、准肺炎克雷伯菌(17株)和水痘克雷伯菌(1株)。对307株严格感肺炎克雷伯菌进行测序和荚膜多样性分析,发现28个序列型,26个k位点型,11个o位点型,以ST231、KL51和O1V2为主。blaoxa -48 like和blaNDM-1/5分别为73.2%和24.4%。与碳青霉烯酶基因相关的质粒复制子类型主要为IncF组(51.0%)和Col组(35.0%)。结论本研究首次揭示了印度流行的K-和o -抗原的遗传多样性。结果表明,基因组监测技术在CRKP种群动态跟踪中的实用性。它提醒我们对这些毒性和传染性谱系进行纵向监测的紧迫性。这项工作得到了国家卫生研究院官方发展援助(ODA)资金的支持[拨款号16_136_111]。这项研究是由国家卫生研究所委托使用官方发展援助资金进行的。本出版物中表达的观点是作者的观点,不一定代表NHS、国家卫生研究所或卫生部的观点。利益冲突作者:无利益冲突报道。所有作者都提交了ICMJE潜在利益冲突披露表。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study
summary We report insights into genome sequences of Indian K. pneumoniae isolates, highlighting the presence of high-risk international clones and genetic pools different from those predominating in other regions. Identification of multidrug-resistant and hypervirulent K. pneumoniae elicits public health concerns. Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India due to its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India. Materials and Methods We characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013-2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, MLST, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism (SNP) phylogeny were inferred from their whole genome sequences. Results Phylogenetic analysis of the 325 Klebsiella isolates that passed QC revealed 3 groups: K. pneumoniae sensu stricto (n=307), K. quasipneumoniae (n=17), and K. varicolla (n=1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%), and Col group (35.0%). Conclusion Our study documents for the first time the genetic diversity of K- and O-antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these virulent and transmissible lineages. Funding This work was supported by Official Development Assistance (ODA) funding from the National Institute of Health Research [grant number 16_136_111]. This research was commissioned by the National Institute of Health Research using Official Development Assistance (ODA) funding. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research or the Department of Health. Conflict of Interest The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest.
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