Whole genome sequencing and characteristics of Escherichia coli with co-existence of ESBL and mcr genes from pigs.
Amino Acid Substitution
Animals
Drug Resistance, Bacterial
Escherichia coli
/ classification
Escherichia coli Infections
/ veterinary
Escherichia coli Proteins
/ genetics
High-Throughput Nucleotide Sequencing
Interspersed Repetitive Sequences
Phylogeny
Plasmids
/ genetics
Serogroup
Swine
Swine Diseases
/ microbiology
Thailand
Whole Genome Sequencing
/ methods
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2021
2021
Historique:
received:
16
07
2021
accepted:
30
10
2021
entrez:
16
11
2021
pubmed:
17
11
2021
medline:
31
12
2021
Statut:
epublish
Résumé
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 IS1595. All three mcr-3.1-carrying contigs contained the ΔTnAs2-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. IS4321, ΔTnAs2, ISKpn40 and IS3 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 blaCTX-M-14 and blaCTX-M-55 genes were identified among these isolates additionally harbored blaTEM-1B. Co-transfer of mcr-1.1/blaTEM-1B and mcr-3.1/blaCTX-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.
Identifiants
pubmed: 34784400
doi: 10.1371/journal.pone.0260011
pii: PONE-D-21-23097
pmc: PMC8594834
doi:
Substances chimiques
Escherichia coli Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0260011Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Clin Microbiol Infect. 2017 Jan;23(1):51.e1-51.e4
pubmed: 27615718
Euro Surveill. 2017 Aug 3;22(31):
pubmed: 28797325
J Antimicrob Chemother. 2012 Nov;67(11):2640-4
pubmed: 22782487
Appl Environ Microbiol. 2004 Jan;70(1):1-7
pubmed: 14711619
Front Microbiol. 2018 Jun 12;9:1217
pubmed: 29951045
Int J Antimicrob Agents. 2016 Oct;48(4):445-8
pubmed: 27526978
mBio. 2018 Feb 13;9(1):
pubmed: 29440577
Expert Rev Anti Infect Ther. 2012 Aug;10(8):917-34
pubmed: 23030331
J Clin Microbiol. 2014 May;52(5):1501-10
pubmed: 24574290
J Clin Microbiol. 2012 Apr;50(4):1355-61
pubmed: 22238442
Vet World. 2019 Nov;12(11):1735-1746
pubmed: 32009752
Microb Drug Resist. 2021 Jul;27(7):971-979
pubmed: 33325796
Sci Rep. 2015 Feb 10;5:8365
pubmed: 25666585
Lancet Infect Dis. 2016 Mar;16(3):281
pubmed: 26774246
Emerg Microbes Infect. 2020 Dec;9(1):508-516
pubmed: 32116151
Nucleic Acids Res. 2021 Jan 8;49(D1):D644-D650
pubmed: 33010178
Euro Surveill. 2019 Sep;24(37):
pubmed: 31530344
Front Microbiol. 2021 Jan 11;11:586368
pubmed: 33505364
J Antimicrob Chemother. 2017 Oct 1;72(10):2745-2749
pubmed: 29091227
Antimicrob Agents Chemother. 2005 Apr;49(4):1319-22
pubmed: 15793104
mBio. 2019 May 7;10(3):
pubmed: 31064835
Int J Food Microbiol. 2014 Feb 3;171:8-14
pubmed: 24296257
Vet Microbiol. 2019 Mar;230:56-61
pubmed: 30827405
Lancet Infect Dis. 2016 Oct;16(10):1102-1103
pubmed: 27676338
Emerg Infect Dis. 2016 Sep;22(9):1689-91
pubmed: 27322919
J Antimicrob Chemother. 2011 Jun;66(6):1263-8
pubmed: 21415040
Antimicrob Agents Chemother. 2017 Oct 24;61(11):
pubmed: 28848017
J Antimicrob Chemother. 2018 May 1;73(5):1121-1137
pubmed: 29370371
J Antimicrob Chemother. 2005 Jul;56(1):115-21
pubmed: 15941775
Int J Antimicrob Agents. 2016 Dec;48(6):581-582
pubmed: 27939183
Genome Res. 2020 Jan;30(1):138-152
pubmed: 31809257
mBio. 2017 Jun 27;8(3):
pubmed: 28655818
Front Microbiol. 2017 Nov 17;8:2262
pubmed: 29250039
J Clin Microbiol. 2015 Aug;53(8):2410-26
pubmed: 25972421
Lancet Infect Dis. 2016 Mar;16(3):281-2
pubmed: 26774244
Sci Rep. 2017 Nov 10;7(1):15364
pubmed: 29127343
J Antimicrob Chemother. 2020 Dec 1;75(12):3491-3500
pubmed: 32780112
Euro Surveill. 2016 Jul 7;21(27):
pubmed: 27416987
Int J Antimicrob Agents. 2018 Jul;52(1):104-108
pubmed: 29635007
Clin Microbiol Rev. 2017 Apr;30(2):557-596
pubmed: 28275006
J Antimicrob Chemother. 2015 Jan;70(1):71-4
pubmed: 25150146
Bioinformatics. 2005 Feb 15;21(4):537-9
pubmed: 15479716
Front Microbiol. 2020 Mar 24;11:387
pubmed: 32265859
Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903
pubmed: 24777092
Sci Rep. 2019 Jan 24;9(1):696
pubmed: 30679636
Int J Food Microbiol. 2013 Apr 15;163(1):14-8
pubmed: 23474653
Front Microbiol. 2018 Feb 27;9:331
pubmed: 29535696
Antimicrob Agents Chemother. 2013 Jun;57(6):2824-7
pubmed: 23478963
Sci Rep. 2018 Feb 27;8(1):3705
pubmed: 29487327
Pathology. 2015 Apr;47(3):199-210
pubmed: 25730631
Plasmid. 2018 Sep;99:72-81
pubmed: 30194944
J Antimicrob Chemother. 2016 Aug;71(8):2336-8
pubmed: 27330065
BMJ Glob Health. 2020 Feb 28;5(2):e001918
pubmed: 32180998
Front Microbiol. 2019 Nov 01;10:2469
pubmed: 31736909
J Comput Biol. 2013 Oct;20(10):714-37
pubmed: 24093227
Emerg Microbes Infect. 2018 Jul 4;7(1):122
pubmed: 29970891
Euro Surveill. 2017 Aug 3;22(31):
pubmed: 28797329
J Antimicrob Chemother. 2017 Feb;72(2):393-401
pubmed: 28073961
Antimicrob Agents Chemother. 2015 Aug;59(8):5026-8
pubmed: 26014934
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Lancet Infect Dis. 2016 Feb;16(2):161-8
pubmed: 26603172
Euro Surveill. 2017 Aug 3;22(31):
pubmed: 28797328