Clinical Characteristics of Patients and Whole Genome Sequencing-Based Surveillance of Escherichia coli Community-Onset Bloodstream Infections at a Non-tertiary Hospital in CHINA

Fenghong Chen; Tao Lv; Yupeng Xiao; Aizhi Chen; Yonghong Xiao; Yunbo Chen

doi:10.3389/fmicb.2021.748471

Clinical Characteristics of Patients and Whole Genome Sequencing-Based Surveillance of Escherichia coli Community-Onset Bloodstream Infections at a Non-tertiary Hospital in CHINA

Front Microbiol. 2021 Oct 7:12:748471. doi: 10.3389/fmicb.2021.748471. eCollection 2021.

Authors

Fenghong Chen¹, Tao Lv^{2

3}, Yupeng Xiao¹, Aizhi Chen¹, Yonghong Xiao^{2

3}, Yunbo Chen^{2

3}

Affiliations

¹ Clinical Laboratory, The First Hospital of Putian City, Putian, China.
² State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
³ Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.

Abstract

Background: Escherichia coli is the most common pathogens in patients with community-onset blood stream infections (COBSI). Knowledge of the epidemiology of this disease is crucial to improve allocation of health resources, formulate isolation strategies that prevent transmission, and guide empirical antibiotic therapy. Methods: This retrospective observational study examined patients with E. coli COBSI (EC-COBSI) at a non-tertiary hospital in China. Whole-genome sequencing and analysis of the isolates was performed. The relationships of clinical variables with antimicrobial resistance and the genetic background of the isolates were examined. Results: There were 148 isolates in patients with EC-COBSI. All isolates were susceptible to ceftazidime/avibactam, carbapenems, and tigecycline; 35.1% were positive for extended spectrum β-lactamase (ESBL+); and bla _CTX _- _M _- ₁₄ was the most common ESBL gene. Patients with ESBL- isolates were more likely to receive appropriate empiric treatment than those with ESBL+ isolates (61.5% vs. 91.4%, p < 0.001), but these two groups had similar mortality rates. The overall 30-day mortality rate was 9.5%. Phylogenetic analysis showed that the isolates were diverse, and that the main sequence types (STs) were ST95, ST131, and ST69. Intra-abdominal infection was the primary source of disease, and isolates from these patients had lower frequencies of virulence genes. Conclusion: The mortality rate of patients with EC-COBSI was unrelated to ESBL status of the isolates. Most isolates had low resistance to most of the tested antimicrobial agents. The isolates were diverse, and multiple strains were related. Prevention and control of EC-COBSI should target prevention of patient colonization and the living environment.

Keywords: Escherichia coli; community-onset blood stream infection; epidemiology; virulence genes; whole-genome sequencing.