Open AccessWhole genome sequencing and characteristics of Escherichia coli with co-existence of ESBL and mcr genes from pigs
Author(s) -
Suthathip Trongjit,
Rungtip Chuanchuen
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0260011
Subject(s) - plasmid , biology , integron , escherichia coli , gene , contig , genome , genetics , insertion sequence , whole genome sequencing , microbiology and biotechnology , transposable element
This study aimed to analyze three ESBL-producing E . coli co-harboring mcr and ESBL genes from a healthy fattening pig (E. 431) and two sick pigs (ECP.81 and ECP.82) in Thailand using Whole Genome Sequencing (WGS) using either Illumina MiSeq or HiSeq PE150 platforms to determine their genome and transmissible plasmids. E. 431 carrying mcr-2 . 1 and mcr-3 . 1 belonged to serotype O142:H31 with ST29 sequence type. ECP.81 and ECP.82 from sick pigs harboring mcr-1 . 1 and mcr-3 . 1 were serotype O9:H9 with ST10. Two mcr-1 . 1 gene cassettes from ECP.81 and ECP.82 were located on IncI2 plasmid with 98% identity to plasmid pHNSHP45. The mcr-2 . 1 -carrying contig in E. 431 showed 100% identity to plasmid pKP37-BE with the upstream flanking sequence of IS 1595 . All three mcr-3 . 1 -carrying contigs contained the ΔTn As2 - mcr-3 . 1 - dgkA core segment and had high nucleotide similarity (85–100%) to mcr-3 . 1 -carrying plasmid, pWJ1. The mobile elements i.e. IS 4321 , ΔTn As2 , IS Kpn40 and IS 3 were identified in the flanking regions of mcr-3 . Several genes conferring resistance to aminoglycosides ( aac(3)-IIa , aadA1 , aadA2b , aph(3’’)-Ib , aph(3’)-IIa and aph(6)-Id ), macrolides ( mdf ( A )), phenicols ( cmlA1 ), sulphonamide ( sul3 ) and tetracycline ( tet(A) and tet(M) ) were located on plasmids, of which their presence was well corresponded to the host’s resistance phenotype. Amino acid substitutions S83L and D87G in GyrA and S80I and E62K in ParC were observed. The bla CTX-M-14 and bla CTX-M-55 genes were identified among these isolates additionally harbored bla TEM-1B . Co-transfer of mcr-1 . 1 / bla TEM-1B and mcr-3 . 1 / bla CTX-M-55 was observed in ECP.81 and ECP.82 but not located on the same plasmid. The results highlighted that application of advanced innovation technology of WGS in AMR monitoring and surveillance provide comprehensive information of AMR genotype that could yield invaluable benefits to development of control and prevention strategic actions plan for AMR.