Table 3.
Results of the metagenomic sequencing of the 24 samples analysed in this study and antibiotic resistance determinants.
| Patient | Sample number | Monomicrobial or polymicrobial | Main species identified in metagenomic sequencing (≥1% abundance) | Antibiotic resistance genes (Resfinder) | Antibiotic resistance genes (functional metagenomic studies) | GyrA | ParC | RpoB |
|---|---|---|---|---|---|---|---|---|
| A | 2 | Polymicrobial | Staphylococcus aureus (99.6) | blaZ, norA | None | WT (S. aureus) | WT (S. aureus) | D320N (S. aureus) |
| A | 28 | Polymicrobial | Staphylococcus aureus (90.3), Finegoldia magna (4.3), Peptoniphilus harei (3.7) | ant(6)-Ia, aph(3′)-III, norA | tet(O) | WT (S. aureus) | WT (S. aureus) | D320N (S. aureus) |
| A | 66 | Polymicrobial | Staphylococcus aureus (99.9) | blaZ, norA | None | WT (S. aureus) | WT (S. aureus) | D320N (S. aureus) |
| B | 4 | Polymicrobial | Morganella morganii (5.6), Propionibacterium propionicum (71.5), Bacteroides fragilis (14.2), Prevotella bivia (4.1), Atopobium rimae (3.0) | aadA1, aph(3′)-Ia, blaDHA-1, catA1, catA2, cepA, cfxA3, dfrA1, erm(A), erm(B), strA, sul2, tet(D), tet(M), tet(Q) | dfr, dfr, van, tet(B) | |||
| B | 140 | Polymicrobial | Morganella morganii (14.6), Prevotella bivia (6.6), Propionibacterium propionicum (43.2), Bacteroides fragilis (24.4), Atopobium rimae (8.3), Parvimonas unclassified (1.2), Dermabacter sp HFH0086 (1.0) | aadA1, aph(3′)-Ia, blaMOR, blaTEM-1A, catA1, catA2, cepA, cfxA3, dfrA1, dfrA14, erm(B), QnrS1, strA, sul1, sul2, tet(D), tet(M), tet(Q) | dfr, dfr, tet(B), van | |||
| C | 19 | Polymicrobial | Acinetobacter baumanii complex (22.1), Streptococcus agalactiae (73.1), Finegoldia magna (1.7) | blaADC-25, blaOXA-328, erm(B), tet(M) | None | WT (A. baumannii, S. agalactiae) | WT (A. baumannii, S. agalactiae) | WT (S. agalactiae) |
| C | 103 | Polymicrobial | Acinetobacter baumanii complex (66.9), Streptococcus agalactiae (26.9), Acinetobacter pittii calcoaceticus nosocomialis (2.7), Finegoldia magna (1.5) | blaADC-25, blaOXA-328, erm(B), tet(M) | None | WT (A. baumannii, S. agalactiae) | WT (A. baumannii, S. agalactiae) | WT (S. agalactiae) |
| C | 104 | Polymicrobial | Acinetobacter baumanii complex (70.1), Streptococcus agalactiae (24.2), Acinetobacter pittii calcoaceticus nosocomialis (3.9), Corynebacterium resistens (1.1) | blaADC-25, blaOXA-328, tet(M) | None | WT (A. baumannii, S. agalactiae) | WT (A. baumannii, S. agalactiae) | WT (S. agalactiae) |
| D | 110 | Monomicrobial | Staphylococcus aureus (98.2), Propionibacterium acnes (1.7) | blaZ, norA | None | WT | WT | WT |
| E | 42 | Polymicrobial | Staphylococcus epidermidis (99.1) | aac(6′)-aph(2′′), aph(3′)-Ia, blaZ, erm(C), fosB, mecA | blaTEM | S84Y (S. epidermidis) | S80F, D84Y (S. epidermidis) | T700S, D837E (S. epidermidis) |
| F | 46 | Monomicrobial | Streptococcus anginosus (2.2), Mogibacterium sp CM50 (34.5), Olsenella uli (13.8), Atopobium sp oral taxon 199 (13.0), Peptostreptococcus stomatis (6.9), Parvimonas unclassified (6.7), Fretibacterium fastidiosum (6.3), Pseudoramibacter alactolyticus (5.6), Slackia unclassified (3.2), Slackia exigua (2.2), Alloprevotella tannerae (2.0) | cfxA3, lsa(C), tet(M) | dfr, dfr, dfr, tet(M), van | C96Y | WT | D492A |
| G | 59 | Monomicrobial | Streptococcus agalactiae (99.9) | erm(B), tet(M) | None | WT | WT | WT |
| G | 117 | Monomicrobial | Streptococcus agalactiae (99.9) | erm(B), tet(M) | None | WT | WT | WT |
| G | 136 | Monomicrobial | Streptococcus agalactiae (99.8) | erm(B), tet(M), tet(M) | None | WT | WT | WT |
| H | 90 | Polymicrobial | Olsenella sp oral taxon 809 (55.9), Pseudoramibacter alactolyticus (9.6), Atopobium sp oral taxon 199 (8.4), Eggerthella unclassified (6.6), Slackia unclassified (5.8), Mogibacterium sp CM50 (5.3), Slackia exigua (1.8), Peptoniphilus sp oral taxon 375 (1.6), Anaerococcus lactolyticus (1.0) | ant(6)-Ia, aph(3′)-III, erm(A), erm(B), erm(X), strA, sul2, tet(32), tet(M), tet(W) | dfr, tet(O) | |||
| H | 158 | Polymicrobial | Enterococcus faecalis (3.8), Streptococcus anginosus (1.3), Olsenella sp oral taxon 809 (69.8), Mogibacterium sp CM50 (6.5), Slackia unclassified (3.8), Peptoniphilus harei (1.6), Atopobium sp oral taxon 199 (1.5), Finegoldia magna (1.4), Pseudoramibacter alactolyticus (1.2), Anaerococcus lactolyticus (1.2), Peptoniphilus sp oral taxon 375 (1.1), Slackia exigua (1.0) | ant(6)-Ia, aph(3′)-III, cmx, erm(A), erm(B), erm(X), lsa(A), strA, strB, tet(M) | cfxA, dfr, dfr, dfr, tet(O), tet(O) | |||
| I | 108 | Polymicrobial | Peptoniphilus harei (98.7) | None | tet(M), tet(M) | NA | NA | NA |
| I | 181 | Polymicrobial | Enterococcus faecalis (62.5), Propionimicrobium (1.2), Anaerococcus vaginalis (0.5), Peptoniphilus harei (20.7), Actinomyces neuii (7.5), Finegoldia magna (7.1) | aph(3′)-III, lsa(A) | dfr, blaTEM, tet(M) | WT (E. faecalis) | WT (E. faecalis) | WT (E. faecalis) |
| J | 121 | Monomicrobial | Staphylococcus aureus (99.6) | blaZ, norA | None | WT | NA | WT |
| J | 172 | Monomicrobial | Staphylococcus aureus (94.6), Micrococcus luteus (3.1), Propionibacterium acnes (2.2) | norA | blaTEM | WT | NA | WT |
| K | 128 | Polymicrobial | Klebsiella oxytoca (74.2), Pseudomonas aeruginosa (0.8), Klebsiella unclassified (23.5) | aac(3)-IIa, aac(6′)Ib-cr, blaCTX-M-11, blaOXA-1, blaOXY-2–8, dfrA14, fosA, oqxA, oqxB, QnrB1, | Putative beta-lactamase, blaTEM, vanB | T83I (K. oxytoca) | S80I (K. oxytoca) | |
| L | 171 | Polymicrobial | Staphylococcus aureus (97.8), Anaerococcus vaginalis (1.6) | blaZ, norA | None | WT (S. aureus) | WT (S. aureus) | WT (S. aureus) |
| M | 178 | Monomicrobial | Staphylococcus epidermidis (99.7) | aac(6′)-aph(2′′), blaZ, erm(A), fusB, mecA, spc, vat(B), vga(A), vga(B) | None | S84F | S80Y | WT |
| N | 184 | Polymicrobial | Enterococcus faecalis (2.3), Corynebacterium striatum (4.7), Finegoldia magna (53.6), Dermabacter sp HFH0086 (13.7), Peptoniphilus harei (10.3), Varibaculum cambriense (8.6), Anaerococcus vaginalis (2.3), Propionibacterium acnes (2.0) | erm(A), erm(X) | tet(M), tet(O) | S83I (F. magna) |
WT: wild-type. NA: not assembled.