Whole-Genome Sequencing Elucidates the Epidemiology of Multidrug-Resistant Acinetobacter baumannii in an Intensive Care Unit.

Pu Mao,Leping Yan,Rong Zhang,Chun Yang,Yueting Jiang,Yimin Li,Yonghao Xu,Ya Wang,Xiaolong Deng,Xiaoqing Liu

doi:10.3389/fmicb.2021.715568

Abstract

The nosocomial pathogen Acinetobacter baumannii is a frequent cause of healthcare-acquired infections, particularly in critically ill patients, and is of serious concern due to its potential for acquired multidrug resistance. Whole-genome sequencing (WGS) is increasingly used to obtain a high-resolution view of relationships between isolates, which helps in controlling healthcare-acquired infections. Here, we conducted a retrospective study to identify epidemic situations and assess the percentage of transmission in intensive care units (ICUs). Multidrug-resistant A. baumannii (MDR-AB) were continuously isolated from the lower respiratory tract of different patients (at the first isolation in our ICU). We performed WGS, pulsed-field gel electrophoresis (PFGE), and multilocus-sequence typing (MLST) analyses to elucidate bacterial relatedness and to compare the performance of conventional methods with WGS for typing MDR-AB. From June 2017 to August 2018, A. baumannii complex strains were detected in 124 of 796 patients during their ICU stays, 103 of which were MDR-AB. Then we subjected 70 available MDR-AB strains to typing with WGS, PFGE, and MLST. Among the 70 A. baumannii isolates, 38 (54.29%) were isolated at admission, and 32(45.71%) were acquisition isolates. MLST identified 12 unique sequence types, a novel ST (ST2367) was founded. PFGE revealed 16 different pulsotypes. Finally, 38 genotypes and 23 transmissions were identified by WGS. Transmission was the main mode of MDR-AB acquisition in our ICU. Our results demonstrated that WGS was a discriminatory technique for epidemiological healthcare-infection studies. The technique should greatly benefit the identification of epidemic situations and controlling transmission events in the near future.

Highlights

Acinetobacter baumannii is a Gram-negative pathogen that causes serious nosocomial infections, especially in patients with advanced age, mechanical ventilation, respiratory failure, or a prolonged hospital stay in intensive care units (ICUs) (Vazquez-Lopez et al, 2020)
We aimed to describe the prevalence and molecular epidemiology of Multidrug-resistant A. baumannii (MDR-AB) in the ICU through wholegenome sequencing (WGS)-based typing and compare the performance of conventional methods with WGS for typing MDR-AB
This study spanned the period from June 2017 to August 2018, when 868 admissions to the ICU were recorded

Summary

Introduction

Acinetobacter baumannii is a Gram-negative pathogen that causes serious nosocomial infections, especially in patients with advanced age, mechanical ventilation, respiratory failure, or a prolonged hospital stay in intensive care units (ICUs) (Vazquez-Lopez et al, 2020). Multilocus-sequence typing (MLST), the partial sequence-based typing method, is usually considered as the gold standard for global epidemiological investigations It focuses on the clustering of isolates worldwide and is not sensitive to short duration and small-scale outbreaks (Tomaschek et al, 2016). Wholegenome sequencing (WGS) has become a promising method in microbiological laboratories for strain identification, molecular epidemiology and outbreak analysis (Makke et al, 2020). It has the highest discriminatory power and is likely to be widely used with cost reduction (Halachev et al, 2014; Salipante et al, 2015; Hwang et al, 2021)

Objectives

Methods

Results

Conclusion