Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, 630 W 168th St, New York City, NY 10032, USA.
Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 W 168th St, New York City, NY 10032, USA.
J Antimicrob Chemother. 2021 Jan 19;76(2):380-384. doi: 10.1093/jac/dkaa466.
Patients with COVID-19 may be at increased risk for secondary bacterial infections with MDR pathogens, including carbapenemase-producing Enterobacterales (CPE).
We sought to rapidly investigate the clinical characteristics, population structure and mechanisms of resistance of CPE causing secondary infections in patients with COVID-19.
We retrospectively identified CPE clinical isolates collected from patients testing positive for SARS-CoV-2 between March and April 2020 at our medical centre in New York City. Available isolates underwent nanopore sequencing for rapid genotyping, antibiotic resistance gene detection and phylogenetic analysis.
We identified 31 CPE isolates from 13 patients, including 27 Klebsiella pneumoniae and 4 Enterobacter cloacae complex isolates. Most patients (11/13) had a positive respiratory culture and 7/13 developed bacteraemia; treatment failure was common. Twenty isolates were available for WGS. Most K. pneumoniae (16/17) belonged to ST258 and encoded KPC (15 KPC-2; 1 KPC-3); one ST70 isolate encoded KPC-2. E. cloacae isolates belonged to ST270 and encoded NDM-1. Nanopore sequencing enabled identification of at least four distinct ST258 lineages in COVID-19 patients, which were validated by Illumina sequencing data.
While CPE prevalence has declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a re-emergence of these highly resistant pathogens in the wake of the global pandemic. Increased surveillance and antimicrobial stewardship efforts, as well as identification of optimal treatment approaches for CPE, will be needed to mitigate their future impact.
COVID-19 患者可能因耐多药病原体（包括产碳青霉烯酶肠杆菌科（CPE））而导致继发性细菌感染的风险增加。
我们旨在快速研究 COVID-19 患者继发性感染中 CPE 的临床特征、种群结构和耐药机制。
我们回顾性地从 2020 年 3 月至 4 月在纽约市我们的医疗中心检测出 SARS-CoV-2 阳性的患者中收集了 CPE 临床分离株。对可用的分离株进行纳米孔测序，以进行快速基因分型、抗生素耐药基因检测和系统发育分析。
我们从 13 名患者中鉴定出 31 株 CPE 分离株，包括 27 株肺炎克雷伯菌和 4 株阴沟肠杆菌复合体分离株。大多数患者（11/13）呼吸道培养阳性，7/13 发生菌血症；治疗失败很常见。20 株分离株可进行 WGS。大多数肺炎克雷伯菌（16/17）属于 ST258 并编码 KPC（15 株 KPC-2；1 株 KPC-3）；1 株 ST70 分离株编码 KPC-2。阴沟肠杆菌分离株属于 ST270 并编码 NDM-1。纳米孔测序能够鉴定出 COVID-19 患者中至少 4 种不同的 ST258 谱系，这些谱系通过 Illumina 测序数据得到了验证。
尽管近年来在纽约市 CPE 的流行率已大幅下降，但在 COVID-19 患者中检测到的增加可能表明这些高度耐药病原体在全球大流行后再次出现。需要加强监测和抗菌药物管理措施，以及确定治疗 CPE 的最佳方法，以减轻其未来的影响。
