A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China

Shaofu Qiu, Kangkang Liu, Chaojie Yang, Ying Xiang, Kaiyuan Min, Kunpeng Zhu, Hongbo Liu, Xinying Du, Mingjuan Yang, Ligui Wang, Yong Sun, Haijian Zhou, Muti Mahe, Jiayong Zhao, Shijun Li, Deshan Yu, Jane Hawkey, Kathryn E. Holt, Stephen Baker, Juntao Yang (), Xuebin Xu () and Hongbin Song ()
Additional contact information
Shaofu Qiu: The Chinese PLA Center for Disease Control and Prevention
Kangkang Liu: The Chinese PLA Center for Disease Control and Prevention
Chaojie Yang: The Chinese PLA Center for Disease Control and Prevention
Ying Xiang: The Chinese PLA Center for Disease Control and Prevention
Kaiyuan Min: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College
Kunpeng Zhu: The Chinese PLA Center for Disease Control and Prevention
Hongbo Liu: The Chinese PLA Center for Disease Control and Prevention
Xinying Du: The Chinese PLA Center for Disease Control and Prevention
Mingjuan Yang: The Chinese PLA Center for Disease Control and Prevention
Ligui Wang: The Chinese PLA Center for Disease Control and Prevention
Yong Sun: Anhui Provincial Center for Disease Control and Prevention
Haijian Zhou: Chinese Center for Disease Control and Prevention and State Key Laboratory for Infectious Disease Prevention and Control
Muti Mahe: Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region
Jiayong Zhao: Henan Provincial Center for Disease Control and Prevention
Shijun Li: Guizhou Provincial Center for Disease Control and Prevention
Deshan Yu: Gansu Provincial Center for Disease Control and Prevention
Jane Hawkey: Monash University
Kathryn E. Holt: Monash University
Stephen Baker: University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus
Juntao Yang: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College
Xuebin Xu: Shanghai Municipal Center for Disease Control and Prevention
Hongbin Song: The Chinese PLA Center for Disease Control and Prevention

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: Abstract Antimicrobial resistance of Shigella sonnei has become a global concern. Here, we report a phylogenetic group of S. sonnei with extensive drug resistance, including a combination of multidrug resistance, coresistance to ceftriaxone and azithromycin (cefRaziR), reduced susceptibility to fluoroquinolones, and even colistin resistance (colR). This distinct clone caused six waterborne shigellosis outbreaks in China from 2015 to 2020. We collect 155 outbreak isolates and 152 sporadic isolates. The cefRaziR isolates, including outbreak strains, are mainly distributed in a distinct clade located in global Lineage III. The outbreak strains form a recently derived monophyletic group that may have emerged circa 2010. The cefRaziR and colR phenotypes are attributed to the acquisition of different plasmids, particularly the IncB/O/K/Z plasmid coharboring the blaCTX-M-14, mphA, aac(3)-IId, dfrA17, aadA5, and sul1 genes and the IncI2 plasmid with an mcr-1 gene. Genetic analyses identify 92 accessory genes and 60 single-nucleotide polymorphisms associated with the cefRaziR phenotype. Surveillance of this clone is required to determine its dissemination and threat to global public health.

Date: 2022
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DOI: 10.1038/s41467-022-35136-1

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