基于基因组的分析表明，两株来自哥伦比亚的临床 Providencia rettgeri 分离株共同携带 NDM-1、VIM-2 和其他β-内酰胺酶。
Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases.
机构信息
Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia.
Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia.
出版信息
BMC Microbiol. 2020 Nov 12;20(1):345. doi: 10.1186/s12866-020-02030-z.
BACKGROUND
Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá - Colombia, 2015.
RESULTS
Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six β-lactamase genes in both isolates: bla, bla, bla, bla, bla and bla. Additionally, various resistance genes associated with antibiotic target alteration (arnA, PmrE, PmrF, LpxA, LpxC, gyrB, folP, murA, rpoB, rpsL, tet34) were found and four efflux pumps (RosAB, EmrD, mdtH and cmlA). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates. The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015.
CONCLUSIONS
We report the coexistence of the carbapenemase genes bla, and bla, together with the β-lactamase genes bla, bla, bla and bla, in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further.
背景
雷氏普罗威登斯菌是一种与尿路感染相关的医院获得性病原体，与医疗保健相关感染（HAI）有关。近年来，已经报道了产生新德里金属β-内酰胺酶（NDM）和其他β-内酰胺酶的分离株，这降低了临床抗菌治疗的效率。在这项研究中，我们分析了 2015 年从哥伦比亚波哥大同一医院收治的两名男性患者获得的两个雷氏普罗威登斯菌分离株的抗生素耐药性、耐药基因的存在和克隆关系。
结果
通过 Kirby-Bauer 方法评估的抗生素敏感性谱表明，两种分离株均对第三代碳青霉烯类和头孢菌素类药物耐药。全基因组测序（Illumina HiSeq），然后是 SPAdes 组装，Prokka 注释与内部 Python 程序相结合，以及通过 ResFinder 检测β-内酰胺酶基因，在两种分离株中均鉴定出相同的六个β-内酰胺酶基因：bla、bla、bla、bla、bla 和 bla。此外，还发现了各种与抗生素靶标改变相关的耐药基因（arnA、PmrE、PmrF、LpxA、LpxC、gyrB、folP、murA、rpoB、rpsL、tet34）和四个外排泵（RosAB、EmrD、mdth 和 cmlA）。其中一个分离株对庆大霉素的额外耐药性可以通过 CpxA（Cys191Arg）中的 SNP 解释，该 SNP 参与细菌包膜的应激反应。使用 CGView 进行基因组 BLAST 比较，ANI 值（99.99%）和 Roary 使用的泛基因组树（同一分支，小距离）显示两个分离株之间高度相似。rMLST 分析表明，两个分离株均为 rST-61，696 型，与 2013 年哥伦比亚布卡拉曼加分离的 RB151 分离株和 2015 年美国 FDAARGOS_330 分离株相同。
结论
我们报告了来自哥伦比亚两名患者的雷氏普罗威登斯菌分离株同时存在碳青霉烯酶基因 bla 和 bla，以及β-内酰胺酶基因 bla、bla、bla 和 bla。全基因组序列分析表明，美洲存在雷氏普罗威登斯菌 rST-61，696 菌株的循环，需要进一步调查。
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