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Molecular Epidemiology and Horizontal Transfer Mechanism of optrA-Carrying Linezolid-Resistant Enterococcus faecalis

Polish Journal of Microbiology
Volume 73 (2024): Issue 3 (September 2024)
By:
Open Access
|Sep 2024

Figures & Tables

Fig. 1.

Electrophoresis of polymerase chain reaction products of the optrA gene in the selected strains: M is a DNA Marker, C is a blank control; B10, A6, B2, A15, L13, L4 are strain numbers. Marker bands from top to bottom are in the order of 2,000 bp, 1,000 bp, 750 bp, 500 bp, 250 bp, 100 bp.
Electrophoresis of polymerase chain reaction products of the optrA gene in the selected strains: M is a DNA Marker, C is a blank control; B10, A6, B2, A15, L13, L4 are strain numbers. Marker bands from top to bottom are in the order of 2,000 bp, 1,000 bp, 750 bp, 500 bp, 250 bp, 100 bp.

Fig. 2.

Phylogenetic tree of 30 optrA gene-positive LREfs. The columns to the right side of the phylogenetic tree sequentially refer to strain names, sequence types, source departments, specimen types, and linezolid minimal inhibitory concentrations from left to right.
Phylogenetic tree of 30 optrA gene-positive LREfs. The columns to the right side of the phylogenetic tree sequentially refer to strain names, sequence types, source departments, specimen types, and linezolid minimal inhibitory concentrations from left to right.

Fig. 3.

Evolutionary tree constructed using SNP comparison files of 30 optrA gene-positive LREfs. A9, A8, A13, A15, A7, A1, B2, B12, B13 on same branch.
Evolutionary tree constructed using SNP comparison files of 30 optrA gene-positive LREfs. A9, A8, A13, A15, A7, A1, B2, B12, B13 on same branch.

Fig. 4.

Genetic background of the optrA gene located on plasmids PB2-1 (above) and PTC-B2 (below). Genes and their orientations are indicated and labeled with arrows; colored arrows indicate genes and gray arrows indicate hypothetical proteins of unknown function, with ferrodoxin representing the gene encoding ferredoxin proteins.
Genetic background of the optrA gene located on plasmids PB2-1 (above) and PTC-B2 (below). Genes and their orientations are indicated and labeled with arrows; colored arrows indicate genes and gray arrows indicate hypothetical proteins of unknown function, with ferrodoxin representing the gene encoding ferredoxin proteins.

Characteristics of 30 optrA-positive linezolid-resistant Enterococcus faecalis_

IsolateWardType of specimenIsolation timeSTLZD MIC (ug/ml)Resistance genesVirulence genes
1 A1urologyblood2018/10/19168aac(6’)-aph(2”), str, erm(A), erm(B), lsa(A), fexA, cat, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, cylA, cylL, cylM
2 A2urologyurine2018/11/025858aac(6’)-aph(2”), erm(A), erm(B), fexA, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, cylA, cylL, cylM, fsrB, gelE
3 A3urologyurine2018/11/1833016aac(6’)-aph(2”), aph(3’)-III, Str, erm(A), lnu(G), fexA, cat, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, fsrB, gelE, hylA, hylB
4 A5urologyurine2019/01/129748erm(A), erm(B), fexA, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, fsrB, gelE, hylA, hylB, cylA, cylL, cylM
5 A6ICUdrainage2019/01/171238aph(3’)-III, erm(B), cat, fexA, tet(L), dfrGelrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, fsrB, gelE, hylA, hylB
6 A7urologyurine2019/03/13168ant(6’)-la, erm(A), erm(B), lsa(A), fexA, cat, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
7 A8ICUurine2019/03/17168aac(6’)-aph(2”), ant(6’)-la, erm(A), erm(B), lsa(E), fexA, cat, tet(M)elrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
8 A9urologyurine2019/04/09168aac(6’)-aph(2”), erm(B), lsa(A), fexA, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA, fsrB, gelE
9 A10urologyurine2019/04/22698aac(6’)-aph(2”), aph(3’)-III, erm(A), erm(B), lsa(A), lsa(E), fexA, cat(PC233), tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
10 A13urologyurine2019/07/01168erm(A), lsa(A), fexA, tet(M)elrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
11 A15urologyurine2019/07/23168aac(6’)-aph(2”), aph(3’)-III, erm(A), erm(B), lsa(A), fexA, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, cylA, cylL, cylM
12 A20general surgerydrainage2019/12/209028aac(6’)-aph(2”), ant(6’)-la, str, erm(A), lsa(A), cat, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, hylB
13 A22hepatobiliary surgerydrainage2020/07/0753516erm(B), fexA, cat, tet(M)elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, gelE, efaAfs, hylB, hylA, fsrB
14 A23urologyurine2020/07/2912878aac(6’)-aph(2”), ant(6’)-la, erm(A), erm(B), lsa(A), fexA, tet(M), dfrGsrtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, gelE, efaAfs, hylB, fsrB
15 A26ICUdrainage2020/06/0561916aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, erm(B), lnu(G), fexA, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpB, tpx, gelE, efaAfs, hylB, hylA, fsrB
16 L3burnwound secretion2020/11/064808aph(3’)-III, ant(6’)-la, erm(A), erm(B), fexA, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpB, fsrB, tpx, efaAfs, gelE, hylA, hylB
17 L4hepatobiliary surgerypus2020/10/219028ant(6’)-la, erm(A), lsa(E), cat, fexA, tet(M), dfrGhylB, ace, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpC, tpx
18 L9nephrologyurine2020/12/015858aac(6’)-aph(2”), aph(3’)-III, str, lsa(E), fexA, cat, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, cylB, cylL, cylM, ebpA, ebpC, fsrB, tpx, efaAfs, gelE
19 L13urologyurine2020/09/274808aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(E), erm(A), erm(B), fexA, cat, tet(M), dfrGhylA, ace, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, tpx, agg
20 B2urologyurine2021/08/12168aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(A), lsa(E), lnu(B), erm(A), erm(B), fexA, tet(L), tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, cylA, cylL, cylM
21 B3dermatovenereologywound secretion2021/08/302078aac(6’)-aph(2”), aph(3’)-III, erm(A), erm(B), lsa(A), lsa(E), fexA, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
22 B7urologyurine2021/10/096328ant(6’)-la, erm(A), erm(B), fexA, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
23 B9urologyurine2021/10/1481616cat(pC233), fexA, tet(M)elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpB, tpx, efaAfs, hylB, hylA, fsrB, gelE, cylA, cylL, cylM
24 B10ICUbile2021/10/239688aac(6’)-aph(2”), aph(3’)-III, ant(6’)-la, erm(A), lsa(A), lsa(E), cat, fexA, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA
25 B11burnwound secretion2021/10/233008ant(6’)-la, erm(A), erm(B), lsa(A), fexA, tet(M)srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, hylB, fsrB, gelE
26 B12urologyurine2021/11/061798aac(6’)-aph(2”), aph(3’)-III, ant(6’)-la, erm(A), erm(B), lsa(A), lsa(E), cat, fexA, tet(M)elrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
27 B13hematologywound secretion2021/11/07168aac(6’)-aph(2”), aph(3’)-III, str, erm(A), erm(B), lsa(A), lsa(E), fexA, cat, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
28 B15urologydrainage2021/12/056608ant(6’)-la, aph(3’)-III, erm(A), erm(B), fexA, tet(M), dfrGelrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
29 B18TCMpus2021/08/136318aph(3’)-III, ant(6’)-la, erm(A), erm(B), cat, fexA, tet(M)elrA, srtA, ace, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpB, ebpC, tpx, efaAfs, hylB, fsrB, gelE
30 B19gastroenterologyurine2021/12/035858ant(6’)-la, str, erm(A), erm(B), cat, fexA, tet(M), dfrGelrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, fsrB, gelE

The composition of the AST-GP67 card, drug names, and MIC ranges tested_

AntibioticsAbbreviationsMeasurement range (μg/ml)
1 LinezolidLZD0.5–8
2 AmpicillinAMP2–32
3 PenicillinPEN0.12–64
4 ErythromycinERY0.25–8
5 ClindamycinCLI0.25–8
6 TigecyclineTGC0.12–2
7 TetracyclineTET1–16
8 Gentamicin – high concentrationGEHS/R
9 Streptomycin – high concentrationSTHS/R
10 CiprofloxacinCIP0.5–8
11 LevofloxacinLVX0.12–8
12 MoxifloxacinMFX0.25–8
13 VancomycinVAN0.5
14 NitrofurantoinNIT16–512

Resistance phenotypes, genotypes and STs of recipient bacteria, donor bacteria and transconjugants_

StrainMIC (μg/ml)STConjugation frequencyResistance genes
RAFFCLZDCHLERYCLITETGEHSTH
Enterococcus faecalis JH2–212882S≤ 0.25≤ 6≤ 0.12< 500 (S)≤ 1,000 (S)8––
Enterococcus faecalis B2212886 (R)≥ 8 (R)≥ 8 (R)≥ 16 (R)< 500 (S)≥ 1,000 (R)16–aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(A), lsa(E), lnu(B), erm(A), erm(B), optrA, fexA, tet(L), tet(M), dfrG
Enterococcus faecalis TC-B212812886 (R)≥ 8 (R)≥ 8 (R)≥ 16 (R)≥ 500 (R)≥ 1,000 (R)81.2 × 10−4aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(A), lsa(E), lnu(B), erm(A), erm(B), optrA, fexA, dfrG
Enterococcus faecalis B3212886 (R)≥ 8 (R)≥ 8 (R)≥ 17 (R)≥ 500 (R)< 1,000 (S)207–aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, erm(A), erm(B), lnu(B), lsa(A), lsa(E), optrA, fexA, tet(L), tet(M), dfrG
Enterococcus faecalis TC-B312812886 (R)≥ 8 (R)≥ 8 (R)≥ 16 (S)≥ 500 (S)< 1,000 (S)82.0 × 10−4aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(A), lsa(E), lnu(B), erm(A), erm(B), optrA, fexA, dfrG
Enterococcus faecalis B100.512887 (R)≥ 8 (R)≥ 8 (R)≥ 16 (R)≥ 500 (R)≥ 1,000 (R)968–aac(6’)-aph(2”), aph(3’)-III, ant(6’)-la, erm(A), erm(B), lsa(A), lsa(E), lnu(B), cat, optrA, fexA, tet(L), tet(M), dfrG
Enterococcus faecalis TC-B1012812886 (R)≥ 8 (R)≥ 8 (R)≥ 16 (R)≥ 500 (R)< 1,000 (S)81.2 × 10−5aac(6’)-aph(2”), aph(3’)-III, ant(6’)-la, erm(A), erm(B), lsa(A), lsa(E), lnu(B), optrA, fexA, dfrG

Genomic characterization of Enterococcus faecalis B2 and Enterococcus faecalis TC-B2_

Genomic FeaturesEnterococcus faecalis B2Enterococcus faecalis TC-B2
Genome size (bp)3,171,4042,989,374
Number of plasmids21
Size range of plasmid(s) (bp)62,351 (PB2-1)105,222
GC content of plasmid(s) (%)34.89 (PB2-1)34.32
Coding genes of plasmid(s)70 (PB2-1)115
Location of the optrA gene46108–4802197914–99827
DOI: https://doi.org/10.33073/pjm-2024-031 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
Journal RSS Feed
Language: English
Page range: 349 - 362
Submitted on: Apr 1, 2024
Accepted on: Jul 6, 2024
Published on: Sep 13, 2024
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 times per year
Keywords:
horizontal transfer,
linezolid,
whole genome sequencing
Related subjects:
Life sciences,
Microbiology and virology

© 2024 Peini Yang, Jiang Li, Mei Lv, Pingan He, Guibo Song, Bin Shan, Xu Yang, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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