Multidrug resistant (MDR) Klebsiella pneumoniae is a common cause of nosocomial infections worldwide. Recent years have seen an explosion of resistance to extended-spectrum β-lactamases (ESBLs) and emergence of carbapenem resistance. Here, we examine 198 invasive K. pneumoniae isolates collected from over a decade in Kilifi County Hospital (KCH) in Kenya. We observe a significant increase in MDR K. pneumoniae isolates, particularly to third generation cephalosporins conferred by ESBLs. Using whole-genome sequences, we describe the population structure and the distribution of antimicrobial resistance genes within it. More than half of the isolates examined in this study were ESBL-positive, encoding CTX-M-15, SHV-2, SHV-12 and SHV-27, and 79% were MDR conferring resistance to at least three antimicrobial classes. Although no isolates in our dataset were found to be resistant to carbapenems we did find a plasmid with the genetic architecture of a known New Delhi metallo-β-lactamase-1 (NDM)-carrying plasmid in 25 isolates. In the absence of carbapenem use in KCH and because of the instability of the NDM-1 gene in the plasmid, the NDM-1 gene has been lost in these isolates. Our data suggests that isolates that encode NDM-1 could be present in the population; should carbapenems be introduced as treatment in public hospitals in Kenya, resistance is likely to ensue rapidly.

中文翻译：

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肯尼亚基利菲县医院十多年来的肺炎克雷伯菌侵袭性感染分子流行病学研究。

耐多药（MDR）肺炎克雷伯菌是全球医院感染的常见原因。近年来，人们对广谱β-内酰胺酶（ESBLs）的耐药性呈爆炸性增长，对碳青霉烯类药物也产生了耐药性。在这里，我们检查了十多年来在肯尼亚的基利菲县医院（KCH）收集到的198种侵袭性肺炎克雷伯菌分离株。我们观察到耐多药肺炎克雷伯菌的分离株显着增加，特别是ESBLs赋予的第三代头孢菌素。使用全基因组序列，我们描述了种群结构和其中的抗菌素耐药基因的分布。在这项研究中检查的分离株中，有一半以上为ESBL阳性，编码CTX-M-15，SHV-2，SHV-12和SHV-27，其中79％为MDR，对至少三种抗菌剂具有耐药性。尽管在我们的数据集中未发现任何分离株对碳青霉烯类药物有抗性，但我们确实在25个分离物中找到了具有已知新德里金属-β-内酰胺酶-1（NDM）携带质粒的遗传结构的质粒。在KCH中不使用碳青霉烯的情况下，由于质粒中NDM-1基因的不稳定性，这些分离物中NDM-1基因已经丢失。我们的数据表明，人群中可能存在编码NDM-1的分离株。如果将碳青霉烯类药物引入肯尼亚的公立医院进行治疗，很可能会很快产生耐药性。这些分离物中已经丢失了NDM-1基因。我们的数据表明，人群中可能存在编码NDM-1的分离株。如果将碳青霉烯类药物引入肯尼亚的公立医院进行治疗，很可能会很快产生耐药性。这些分离物中已经丢失了NDM-1基因。我们的数据表明，人群中可能存在编码NDM-1的分离株。如果将碳青霉烯类药物引入肯尼亚的公立医院进行治疗，很可能会很快产生耐药性。