Jiang Jianping, Cienfuegos-Gallet Astrid V, Long Tengfei, Peirano Gisele, Chu Tingyu, Pitout Johann D D, Kreiswirth Barry N, Chen Liang
Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.
School of Microbiology, University of Antioquia, Medellín, Colombia.
Genome Med. 2025 Jan 30;17(1):9. doi: 10.1186/s13073-025-01428-6.
Klebsiella pneumoniae is one of the most prevalent pathogens responsible for multiple infections in healthcare settings and the community. K. pneumoniae CG147, primarily including ST147 (the founder ST), ST273, and ST392, is one of the most globally successful MDR clone linked to various carbapenemases.
One hundred and one CG147 strains were sequenced and additional 911 publicly available CG147 genome sequences were included for analysis. The molecular epidemiology, population structure, and time phylogeny were investigated. The virulome, resistome, and mobilome were analyzed, and the recombination in the capsular region was studied. The CRISPR-Cas and anti-CRISPR were identified. The interplay between CRISPR-Cas, anti-CRISPR, and carbapenemase-encoding plasmids was analyzed and experimentally validated.
We analyzed 1012 global CG147 genomes, with 80.4% encoding at least one carbapenemase (NDM [529/1012, 52.3%], OXA-48-like [182/1012, 17.7%], and KPC [105/1012, 10.4%]). Surprisingly, almost all CG147 strains (99.7%, 1009/1,012) harbor a chromosomal type I-E CRISPR-Cas system, with 41.8% (423/1012) containing an additional plasmid-borne type IV-A3 CRISPR-Cas system, and both target IncF plasmids, e.g., the most prevalent KPC-encoding pKpQIL-like plasmids. We found the presence of IV-A3 CRISPR-Cas system showed a negative correlation with the presence of KPC. Interestingly, a prophage-encoding anti-CRISPR AcrIE8.1 and a plasmid-borne anti-CRISPR AcrIE9.2 were detected in 40.1% (406/1012) and 54.2% (548/1012) of strains, respectively, which displayed positive correlations with the presence of a carbapenemase. Plasmid transfer experiments confirmed that the I-E and IV-A3 CRISPR-Cas systems significantly decreased (p < 0.001) KPC-encoding pKpQIL plasmid conjugation frequencies, while the AcrIE8.1 and AcrIE9.2 significantly increased (p < 0.001) pKpQIL conjugation frequencies and protected plasmids from elimination by CRISPR-Cas I-E system.
Our results indicated a complex interplay between CRISPR-Cas, anti-CRISPR, and mobile genetic elements that shape the evolution of CG147. Our findings advance the understanding of multi-drug resistance mechanisms and will aid in preventing the emergence of future MDR clones.
肺炎克雷伯菌是医疗机构和社区中导致多种感染的最常见病原体之一。肺炎克雷伯菌CG147主要包括ST147（始祖序列类型）、ST273和ST392，是全球最成功的与各种碳青霉烯酶相关的多重耐药克隆之一。
对101株CG147菌株进行测序，并纳入另外911条公开可得的CG147基因组序列进行分析。研究分子流行病学、群体结构和时间系统发育。分析毒力组、耐药组和可移动基因组，并研究荚膜区域的重组。鉴定CRISPR-Cas和抗CRISPR。分析并通过实验验证CRISPR-Cas、抗CRISPR与碳青霉烯酶编码质粒之间的相互作用。
我们分析了1012个全球CG147基因组，其中80.4%编码至少一种碳青霉烯酶（NDM [529/1012，52.3%]、OXA-48样酶 [182/1012，17.7%] 和KPC [105/1012，10.4%]）。令人惊讶的是，几乎所有CG147菌株（99.7%，1009/1012）都含有染色体I-E型CRISPR-Cas系统，41.8%（423/1012）还含有额外的质粒携带的IV-A3型CRISPR-Cas系统，两者都靶向IncF质粒，例如最常见的编码KPC的pKpQIL样质粒。我们发现IV-A3型CRISPR-Cas系统的存在与KPC的存在呈负相关。有趣的是，分别在40.1%（406/1012）和54.2%（548/1012）的菌株中检测到一种噬菌体编码的抗CRISPR AcrIE8.1和一种质粒携带的抗CRISPR AcrIE9.2，它们与碳青霉烯酶的存在呈正相关。质粒转移实验证实，I-E和IV-A3型CRISPR-Cas系统显著降低（p < 0.001）编码KPC的pKpQIL质粒的接合频率，而AcrIE8.1和AcrIE9.2显著增加（p < 0.001）pKpQIL的接合频率，并保护质粒不被CRISPR-Cas I-E系统消除。
我们的结果表明CRISPR-Cas、抗CRISPR和可移动遗传元件之间存在复杂的相互作用，这些相互作用塑造了CG147的进化。我们的发现推进了对多药耐药机制的理解，并将有助于预防未来多重耐药克隆的出现。
