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

Peini Yang

Peini Yang

Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical UniversityKunming, China
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Yang, Peini
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Jiang Li

Jiang Li

Department of Blood Transfusion, The Second Affiliated Hospital of Kunming Medical UniversityKunming, China
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Li, Jiang
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Mei Lv

Mei Lv

Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical UniversityKunming, China
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Lv, Mei
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Pingan He

Pingan He

Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical UniversityKunming, China
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He, Pingan
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Guibo Song

Guibo Song

Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
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Song, Guibo
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Bin Shan

Bin Shan

Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
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Shan, Bin
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Xu Yang

Xu Yang

Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical UniversityKunming, China
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Yang, Xu
  
13 sept. 2024
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Catégorie d'article: ORIGINAL PAPER
Publié en ligne: 13 sept. 2024
Pages: 349 - 362
Reçu: 01 avr. 2024
Accepté: 06 juil. 2024
DOI: https://doi.org/10.33073/pjm-2024-031
Mots clés
© 2024 Peini Yang et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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_

Isolate Ward Type of specimen Isolation time ST LZD MIC (ug/ml) Resistance genes Virulence genes
1 A1 urology blood 2018/10/19 16 8 aac(6’)-aph(2”), str, erm(A), erm(B), lsa(A), fexA, cat, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, cylA, cylL, cylM
2 A2 urology urine 2018/11/02 585 8 aac(6’)-aph(2”), erm(A), erm(B), fexA, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, cylA, cylL, cylM, fsrB, gelE
3 A3 urology urine 2018/11/18 330 16 aac(6’)-aph(2”), aph(3’)-III, Str, erm(A), lnu(G), fexA, cat, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, fsrB, gelE, hylA, hylB
4 A5 urology urine 2019/01/12 974 8 erm(A), erm(B), fexA, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, fsrB, gelE, hylA, hylB, cylA, cylL, cylM
5 A6 ICU drainage 2019/01/17 123 8 aph(3’)-III, erm(B), cat, fexA, tet(L), dfrG elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, fsrB, gelE, hylA, hylB
6 A7 urology urine 2019/03/13 16 8 ant(6’)-la, erm(A), erm(B), lsa(A), fexA, cat, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
7 A8 ICU urine 2019/03/17 16 8 aac(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 A9 urology urine 2019/04/09 16 8 aac(6’)-aph(2”), erm(B), lsa(A), fexA, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA, fsrB, gelE
9 A10 urology urine 2019/04/22 69 8 aac(6’)-aph(2”), aph(3’)-III, erm(A), erm(B), lsa(A), lsa(E), fexA, cat(PC233), tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
10 A13 urology urine 2019/07/01 16 8 erm(A), lsa(A), fexA, tet(M) elrA, srtA, ace, agg, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
11 A15 urology urine 2019/07/23 16 8 aac(6’)-aph(2”), aph(3’)-III, erm(A), erm(B), lsa(A), fexA, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, cylA, cylL, cylM
12 A20 general surgery drainage 2019/12/20 902 8 aac(6’)-aph(2”), ant(6’)-la, str, erm(A), lsa(A), cat, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, hylB
13 A22 hepatobiliary surgery drainage 2020/07/07 535 16 erm(B), fexA, cat, tet(M) elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, gelE, efaAfs, hylB, hylA, fsrB
14 A23 urology urine 2020/07/29 1287 8 aac(6’)-aph(2”), ant(6’)-la, erm(A), erm(B), lsa(A), fexA, tet(M), dfrG srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, gelE, efaAfs, hylB, fsrB
15 A26 ICU drainage 2020/06/05 619 16 aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, erm(B), lnu(G), fexA, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpB, tpx, gelE, efaAfs, hylB, hylA, fsrB
16 L3 burn wound secretion 2020/11/06 480 8 aph(3’)-III, ant(6’)-la, erm(A), erm(B), fexA, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpB, fsrB, tpx, efaAfs, gelE, hylA, hylB
17 L4 hepatobiliary surgery pus 2020/10/21 902 8 ant(6’)-la, erm(A), lsa(E), cat, fexA, tet(M), dfrG hylB, ace, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpC, tpx
18 L9 nephrology urine 2020/12/01 585 8 aac(6’)-aph(2”), aph(3’)-III, str, lsa(E), fexA, cat, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, cylB, cylL, cylM, ebpA, ebpC, fsrB, tpx, efaAfs, gelE
19 L13 urology urine 2020/09/27 480 8 aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(E), erm(A), erm(B), fexA, cat, tet(M), dfrG hylA, ace, efaAfs, elrA, srtA, ccf, cob, cad, camE, ebpA, ebpB, tpx, agg
20 B2 urology urine 2021/08/12 16 8 aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(A), lsa(E), lnu(B), erm(A), erm(B), fexA, tet(L), tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA, cylA, cylL, cylM
21 B3 dermatovenereology wound secretion 2021/08/30 207 8 aac(6’)-aph(2”), aph(3’)-III, erm(A), erm(B), lsa(A), lsa(E), fexA, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
22 B7 urology urine 2021/10/09 632 8 ant(6’)-la, erm(A), erm(B), fexA, tet(M), dfrG elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
23 B9 urology urine 2021/10/14 816 16 cat(pC233), fexA, tet(M) elrA, srtA, ace, agg, ccf, cob, cad, camE, ebpA, ebpB, tpx, efaAfs, hylB, hylA, fsrB, gelE, cylA, cylL, cylM
24 B10 ICU bile 2021/10/23 968 8 aac(6’)-aph(2”), aph(3’)-III, ant(6’)-la, erm(A), lsa(A), lsa(E), cat, fexA, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylA
25 B11 burn wound secretion 2021/10/23 300 8 ant(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 B12 urology urine 2021/11/06 179 8 aac(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 B13 hematology wound secretion 2021/11/07 16 8 aac(6’)-aph(2”), aph(3’)-III, str, erm(A), erm(B), lsa(A), lsa(E), fexA, cat, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, cylA, cylL, cylM, ebpA, ebpC, tpx, efaAfs, hylA
28 B15 urology drainage 2021/12/05 660 8 ant(6’)-la, aph(3’)-III, erm(A), erm(B), fexA, tet(M), dfrG elrA, srtA, ace, ccf, cob, cad, camE, ebpA, ebpC, tpx, efaAfs, hylB, fsrB, gelE
29 B18 TCM pus 2021/08/13 631 8 aph(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 B19 gastroenterology urine 2021/12/03 585 8 ant(6’)-la, str, erm(A), erm(B), cat, fexA, tet(M), dfrG elrA, 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_

Antibiotics Abbreviations Measurement range (μg/ml)
1 Linezolid LZD 0.5–8
2 Ampicillin AMP 2–32
3 Penicillin PEN 0.12–64
4 Erythromycin ERY 0.25–8
5 Clindamycin CLI 0.25–8
6 Tigecycline TGC 0.12–2
7 Tetracycline TET 1–16
8 Gentamicin – high concentration GEH S/R
9 Streptomycin – high concentration STH S/R
10 Ciprofloxacin CIP 0.5–8
11 Levofloxacin LVX 0.12–8
12 Moxifloxacin MFX 0.25–8
13 Vancomycin VAN 0.5
14 Nitrofurantoin NIT 16–512

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

Strain MIC (μg/ml) ST Conjugation frequency Resistance genes
RA FFC LZD CHL ERY CLI TET GEH STH
Enterococcus faecalis JH2–2 128 8 2 S ≤ 0.25 ≤ 6 ≤ 0.12 < 500 (S) ≤ 1,000 (S) 8 – –
Enterococcus faecalis B2 2 128 8 6 (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-B2 128 128 8 6 (R) ≥ 8 (R) ≥ 8 (R) ≥ 16 (R) ≥ 500 (R) ≥ 1,000 (R) 8 1.2 × 10−4 aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(A), lsa(E), lnu(B), erm(A), erm(B), optrA, fexA, dfrG
Enterococcus faecalis B3 2 128 8 6 (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-B3 128 128 8 6 (R) ≥ 8 (R) ≥ 8 (R) ≥ 16 (S) ≥ 500 (S) < 1,000 (S) 8 2.0 × 10−4 aac(6’)-aph(2”), ant(6’)-la, aph(3’)-III, lsa(A), lsa(E), lnu(B), erm(A), erm(B), optrA, fexA, dfrG
Enterococcus faecalis B10 0.5 128 8 7 (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-B10 128 128 8 6 (R) ≥ 8 (R) ≥ 8 (R) ≥ 16 (R) ≥ 500 (R) < 1,000 (S) 8 1.2 × 10−5 aac(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 Features Enterococcus faecalis B2 Enterococcus faecalis TC-B2
Genome size (bp) 3,171,404 2,989,374
Number of plasmids 2 1
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 gene 46108–48021 97914–99827
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