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. 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: blaNDM-1, blaVIM-2, blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1. 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. We report the coexistence of the carbapenemase genes blaNDM-1, and blaVIM-2, together with the β-lactamase genes blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1, 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.

中文翻译：

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两种共同携带 NDM-1、VIM-2 和其他 β-内酰胺酶的哥伦比亚临床雷氏普罗威登斯菌分离株的基于基因组的表征


雷氏普罗维登斯菌是一种与尿路感染相关并与医疗保健相关感染 (HAI) 相关的医院病原体。近年来，据报道，产生新德里金属-β-内酰胺酶 (NDM) 和其他 β-内酰胺酶的分离株会降低临床抗菌治疗的效率。在这项研究中，我们分析了从 2015 年哥伦比亚波哥大同一家医院收治的男性患者中获得的两种雷氏假单胞菌分离株的抗生素耐药性、耐药基因的存在以及克隆关系。通过 Kirby-Bauer 方法评估抗生素敏感性概况结果表明，这两种分离株均对第三代碳青霉烯类药物和头孢菌素类药物具有耐药性。全基因组测序 (Illumina HiSeq)、SPAdes 组装、Prokka 注释与内部 Python 程序相结合以及 ResFinder 的抗性基因检测在两个分离株中鉴定出相同的 6 个 β-内酰胺酶基因：blaNDM-1、blaVIM-2、 blaCTX-M-15、blaOXA-10、blaCMY-2 和 blaTEM-1。此外，还发现了与抗生素靶点改变相关的各种耐药基因（arnA、PmrE、PmrF、LpxA、LpxC、gyrB、folP、murA、rpoB、rpsL、tet34）和四个外排泵（RosAB、EmrD、mdtH 和 cmlA）。两个分离株之一对庆大霉素的额外耐药性可以通过在 CpxA (Cys191Arg) 中检测到的 SNP 来解释，该 CpxA 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%）和全基因组（使用Roary）系统发育树（同一进化枝，小距离）显示分离株之间具有高度相似性。 rMLST 分析表明，这两种分离株的类型均为 rST-61,696，与之前 2013 年在哥伦比亚布卡拉曼加分离的 RB151 分离株以及 2015 年在美国分离的 FDAARGOS_330 分离株相同。我们报告了碳青霉烯酶基因 blaNDM-1 的共存、 blaVIM-2 以及 β-内酰胺酶基因 blaCTX-M-15、blaOXA-10、blaCMY-2 和 blaTEM-1，来自哥伦比亚两名患者的 P. rettgeri 分离物。全基因组序列分析表明 P. rettgeri rST-61,696 菌株在美国有传播，需要进一步研究。