Surveillance and Genomic Analysis of Third-Generation Cephalosporin-Resistant and Carbapenem-Resistant Klebsiella pneumoniae Complex in Germany,Antibiotics

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Surveillance and Genomic Analysis of Third-Generation Cephalosporin-Resistant and Carbapenem-Resistant Klebsiella pneumoniae Complex in Germany
Antibiotics ( IF 4.3 ) Pub Date : 2022-09-21 , DOI: 10.3390/antibiotics11101286
Kyriaki Xanthopoulou _{1,

2} , Can Imirzalioglu _{1,

3} , Sarah V Walker _{1,

2} , Michael Behnke _{1,

4,

5} , Ariane G Dinkelacker _{1,

6} , Simone Eisenbeis _{1,

7} , Petra Gastmeier _{1,

4,

5} , Hanna Gölz _{1,

8} , Nadja Käding _{1,

9} , Winfried V Kern ₁₀ , Axel Kola _{1,

4,

5} , Evelyn Kramme _{1,

9} , Kai Lucassen ₂ , Alexander Mischnik _{1,

9,

10} , Silke Peter _{1,

6} , Anna M Rohde _{1,

4} , Jan Rupp _{1,

9} , Evelina Tacconelli _{1,

7} , David Tobys _{1,

2} , Maria J G T Vehreschild _{1,

11,

12} , Julia Wille _{1,

2} , Harald Seifert _{1,

2} , Paul G Higgins _{1,

2} ,

Affiliation

German Centre for Infection Research (DZIF), 38124 Braunschweig, Germany.
Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany.
Institute of Medical Microbiology, Justus Liebig University Giessen, 35392 Giessen, Germany.
Institute of Hygiene and Environmental Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 12203 Berlin, Germany.
National Reference Centre for the Surveillance of Nosocomial Infections, 12203 Berlin, Germany.
Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, 72074 Tübingen, Germany.
Division of Infectious Diseases, Department of Internal Medicine I, University Hospital Tübingen, 72076 Tübingen, Germany.
Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, 79104 Freiburg, Germany.
Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, 23538 Lübeck, Germany.
Division of Infectious Diseases, Department of Medicine II, Faculty of Medicine, Medical Centre, University of Freiburg, 79106 Freiburg, Germany.
Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany.
Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany.

To analyse the epidemiology and population structure of third-generation cephalosporin-resistant (3GCR) and carbapenem-resistant (CR) Klebsiella pneumoniae complex isolates, patients were screened for rectal colonisation with 3GCR/CR K. pneumoniae complex on admission to six German university hospitals (2016–2019). Also collected were 3GCR/CR and susceptible K. pneumoniae isolates from patients with bloodstream infections (2016–2018). Whole-genome sequencing was performed followed by multilocus sequencing typing (MLST), core-genome MLST, and resistome and virulome analysis. The admission prevalence of 3GCR K. pneumoniae complex isolates during the 4-year study period was 0.8%, and 1.0 bloodstream infection per 1000 patient admissions was caused by K. pneumoniae complex (3GCR prevalence, 15.1%). A total of seven K. pneumoniae complex bloodstream isolates were CR (0.8%). The majority of colonising and bloodstream 3GCR isolates were identified as K. pneumoniae, 96.7% and 98.8%, respectively; the remainder were K. variicola and K. quasipneumoniae. cgMLST showed a polyclonal population of colonising and bloodstream isolates, which was also reflected by MLST and virulome analysis. CTX-M-15 was the most prevalent extended-spectrum beta-lactamase, and 29.7% of the colonising and 48.8% of the bloodstream isolates were high-risk clones. The present study provides an insight into the polyclonal 3GCR K. pneumoniae population in German hospitals.

中文翻译：

德国第三代抗头孢菌素和抗碳青霉烯类肺炎克雷伯菌复合物的监测和基因组分析

为了分析第三代耐头孢菌素 (3GCR) 和耐碳青霉烯类 (CR) 肺炎克雷伯菌复合物分离株的流行病学和人群结构，在六家德国大学医院入院时筛查患者的直肠定植与 3GCR/CR肺炎克雷伯菌复合物（2016-2019）。还收集了来自血流感染患者（2016-2018 年）的 3GCR/CR 和易感肺炎克雷伯菌分离株。进行全基因组测序，然后进行多位点测序分型 (MLST)、核心基因组 MLST，以及抗性组和病毒组分析。在 4 年研究期间，3GCR肺炎克雷伯菌复合体分离株的入院流行率为 0.8%，每 1000 例入院患者中有 1.0 次血流感染是由以下原因引起的肺炎克雷伯菌复合体（3GCR 患病率，15.1%）。共有 7 个肺炎克雷伯菌复合体血流分离株为 CR (0.8%)。大多数定植和血流 3GCR 分离株被鉴定为肺炎克雷伯菌，分别为 96.7% 和 98.8%；其余为K. variicola 和K. quasipneumoniae。cgMLST 显示定植和血流分离株的多克隆群体，MLST 和病毒组分析也反映了这一点。CTX-M-15 是最普遍的超广谱 β-内酰胺酶，29.7% 的定植和 48.8% 的血流分离株是高风险克隆。本研究提供了对多克隆 3GCR肺炎克雷伯菌的深入了解德国医院的人口。

更新日期：2022-09-21

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