Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae.
Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae.
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DOI：
10.1371/journal.ppat.1010334
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发表时间：
2022-07
期刊：
影响因子：
6.7
通讯作者：
中科院分区：
文献类型：
--
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外膜孔蛋白的突变与碳青霉烯酶协同作用，增加了重要的医院病原体肺炎克雷伯菌（KP）对碳青霉烯的耐药性。一个关键的例子是在OmpK 36的细胞外环3（L3）区域中的二氨基酸插入，甘氨酸-天冬氨酸（GD），其收缩孔并限制碳青霉烯类进入细菌细胞。在这里，我们结合了基因组和实验方法来研究OmpK 36中不同L3插入类型的多样性，传播和影响。我们在全球收集的14，888个具有完整ompK 36基因的KP基因组中的3588个（24.1%）中鉴定了L3插入。GD插入是最常见的，在欧洲和美洲广泛传播的ST 258/512克隆中具有高浓度。天冬氨酸（D）和苏氨酸-天冬氨酸（TD）插入在亚洲基因组中普遍存在，部分原因是KP序列类型ST 16和ST 231的获得以及随后的克隆扩增。通过解析新型OmpK 36变体的晶体结构，我们发现TD插入导致41%的孔收缩，显著大于GD（10%）或D（8%）所实现的孔收缩，导致对所选抗生素的最高水平的抗性。我们表明，在没有抗生素KP突变体窝藏这些L3插入表现出在体外和体内的竞争劣势相对于表达野生型OmpK 36的同基因亲本菌株。我们认为这解释了在KP基因组中观察到的低频率GD和TD插入的逆转。最后，我们证明了表达L3插入的菌株仍然对靶向产碳青霉烯酶的KP的药物敏感，包括新型β内酰胺-β内酰胺酶抑制剂组合。这项研究提供了一个当代的全球视野OmpK 36介导的耐药机制在KP，整合监测和实验数据，以指导治疗和药物开发策略。肺炎克雷伯菌（KP）抗生素耐药率迅速上升，需要全面了解耐药突变的多样性，传播和临床影响。在KP中，外膜孔蛋白的突变在介导对碳青霉烯类抗生素的耐药性中起着重要作用。在这里，我们表明，在OmpK 36孔蛋白的细胞外环3（L3）区域的耐药突变被发现在临床基因组中的高患病率，我们验证了它们的多样性和耐药性和毒力的影响。它们包括天冬氨酸（D）、甘氨酸-天冬氨酸（GD）和苏氨酸-天冬氨酸（TD）的氨基酸插入，其通过减小孔径和限制碳青霉烯类进入细菌细胞来起作用。我们发现，这些L3插入与抗性谱系的大克隆扩张相关，并在体内竞争过程中施加明显的适应性成本。关键的是，携带L3插入的菌株仍然对新型药物敏感，包括β内酰胺-β内酰胺酶抑制剂组合。这项研究强调了监测OmpK 36 L3插入菌株的出现和传播对于控制耐药KP感染的重要性，并为药物开发和治疗策略提供了关键数据。
Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies. Rapidly rising rates of antibiotic resistance among Klebsiella pneumoniae (KP) necessitate a comprehensive understanding of the diversity, spread and clinical impact of resistance mutations. In KP, mutations in outer membrane porins play an important role in mediating resistance to carbapenems, a key class of antibiotics. Here we show that resistance mutations in the extracellular loop 3 (L3) region of the OmpK36 porin are found at high prevalence among clinical genomes and we characterise their diversity and impact on resistance and virulence. They include amino acid insertions of Aspartate (D), Glycine-Aspartate (GD) and Threonine-Aspartate (TD), which act by decreasing the pore size and restricting entry of carbapenems into the bacterial cell. We show that these L3 insertions are associated with large clonal expansions of resistant lineages and impose a fitness cost evident during in vivo competition. Critically, strains harbouring L3 insertions remain susceptible to novel drugs, including beta lactam-beta lactamase inhibitor combinations. This study highlights the importance of monitoring the emergence and spread of strains with OmpK36 L3 insertions for the control of resistant KP infections and provides crucial data for drug development and treatment strategies.
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DOI：
10.1093/cid/cix270
发表时间：
2017-07-15
期刊：
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
影响因子：
--
作者：
Gorrie CL;Mirceta M;Wick RR;Edwards DJ;Thomson NR;Strugnell RA;Pratt NF;Garlick JS;Watson KM;Pilcher DV;McGloughlin SA;Spelman DW;Jenney AWJ;Holt KE
通讯作者：
Holt KE
影响因子：
4.9
作者：
Haidar, Ghady;Clancy, Cornelius J.;Nguyen, M. Hong
通讯作者：
Nguyen, M. Hong
影响因子：
3.9
作者：
Argimón S;Abudahab K;Goater RJE;Fedosejev A;Bhai J;Glasner C;Feil EJ;Holden MTG;Yeats CA;Grundmann H;Spratt BG;Aanensen DM
通讯作者：
Aanensen DM
DOI：
10.1093/cid/ciab784
发表时间：
2021-12-01
期刊：
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
影响因子：
--
作者：
Argimón S;David S;Underwood A;Abrudan M;Wheeler NE;Kekre M;Abudahab K;Yeats CA;Goater R;Taylor B;Harste H;Muddyman D;Feil EJ;Brisse S;Holt K;Donado-Godoy P;Ravikumar KL;Okeke IN;Carlos C;Aanensen DM;NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
通讯作者：
NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
DOI：
10.1107/s0907444902016657
发表时间：
2002-11-01
影响因子：
2.2
作者：
Adams, PD;Grosse-Kunstleve, RW;Terwilliger, TC
通讯作者：
Terwilliger, TC