Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits

Liangcai Xu; Bo Peng; Yuxiang He; Yujun Cui; Qinghua Hu; Yarong Wu; Hongbiao Chen; Xiaofeng Zhou; Lili Chen; Min Jiang; Le Zuo; Qiongcheng Chen; Shuang Wu; Yang Liu; Yanming Qin; Xiaolu Shi

doi:10.3389/fmicb.2021.799150

Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits

Front Microbiol. 2022 Jan 4:12:799150. doi: 10.3389/fmicb.2021.799150. eCollection 2021.

Authors

Liangcai Xu¹, Bo Peng², Yuxiang He², Yujun Cui³, Qinghua Hu², Yarong Wu³, Hongbiao Chen⁴, Xiaofeng Zhou⁴, Lili Chen¹, Min Jiang², Le Zuo², Qiongcheng Chen², Shuang Wu², Yang Liu⁵, Yanming Qin⁵, Xiaolu Shi^{1

2}

Affiliations

¹ Department of Public Health Laboratory Sciences, School of Public Health, University of South China, Hengyang, China.
² Microbiology Lab, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.
³ State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
⁴ Communicable Diseases Control and Prevention Division, Longhua District Center for Disease Control and Prevention, Shenzhen, China.
⁵ Institute for Disinfection and Vector Prevention and Control, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.

Abstract

Purpose: To investigate and characterize the putative Elizabethkingia anophelis contaminant isolated from throat and anal swab samples of patients from three fever epidemic clusters, which were not COVID-19 related, in Shenzhen, China, during COVID-19 pandemic. Methods: Bacteria were cultured from throat (n = 28) and anal (n = 3) swab samples from 28 fever adolescent patients. The isolated bacterial strains were identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) and the VITEK2 automated identification system. Nucleic acids were extracted from the patient samples (n = 31), unopened virus collection kits from the same manufacturer as the patient samples (n = 35, blank samples) and from unopened throat swab collection kits of two other manufacturers (n = 22, control samples). Metagenomic sequencing and quantitative real-time PCR (qPCR) detection were performed. Blood serum collected from patients (n = 13) was assessed for the presence of antibodies to E. anophelis. The genomic characteristics, antibiotic susceptibility, and heat resistance of E. anophelis isolates (n = 31) were analyzed. Results: The isolates were identified by MALDI-TOF/MS and VITEK2 as Elizabethkingia meningoseptica. DNA sequence analysis confirmed isolates to be E. anophelis. The patients' samples and blank samples were positive for E. anophelis. Control samples were negative for E. anophelis. The sera from a sub-sample of 13 patients were antibody-negative for isolated E. anophelis. Most of the isolates were highly homologous and carried multiple β-lactamase genes (bla _B, bla _GOB, and bla _CME). The isolates displayed resistance to nitrofurans, penicillins, and most β-lactam drugs. The bacteria survived heating at 56°C for 30 min. Conclusion: The unopened commercial virus collection kits from the same manufacturer as those used to swab patients were contaminated with E. anophelis. Patients were not infected with E. anophelis and the causative agent for the fevers remains unidentified. The relevant authorities were swiftly notified of this discovery and subsequent collection kits were not contaminated. DNA sequence-based techniques are the definitive method for Elizabethkingia species identification. The E. anophelis isolates were multidrug-resistant, with partial heat resistance, making them difficult to eradicate from contaminated surfaces. Such resistance indicates that more attention should be paid to disinfection protocols, especially in hospitals, to avoid outbreaks of E. anophelis infection.

Keywords: contamination; heat tolerance; identification; multidrug resistance; nosocomial infection.