Table 3.
Associations detected between A. baumannii clonal lineages and ompA variants described in this work. For details see Fig. 3, Tables S1 and S2
Clonal lineage |
Observations |
---|---|
CC2 |
Among 502 CC2 isolates (474 ST2, 27 SLV, 1 DLV), 484 (96.4 %) carried V1(lct)a1; 2 (0.4 %) V2(lct)a2; and 16 (3.2 %) V1(lct)a3. CC2 thus contained 99.6 % (484/486) of all V1(lct)a1‐carrying isolates found in the A. baumannii population analysed. Only V1(lct)a1 was found in two other isolates branching separately from the CC2 cluster: AB_2007‐09‐110‐01‐7 and NIPH70, providing evidences of V1(lct) exchanges between CC2 and other lineages. |
CC1 |
Among 73 CC1 isolates (60 ST1, 12 SLV, 1 DLV), 67 (91.8 %) carried V2(lct)a1 (91.8 %); 3 V2(lct)a6 (4.1 %); and other 3 V1(lct)a14 (4.1 %). CC1 thus contained 45.6 % (67/147) of all V2(lct)a1‐carrying isolates found in the A. baumannii population analyzed. In addition, all isolates assigned to the main L1 sublineage of CC1 carried V2(lct)a1, the few detected V2(lct)a6‐ and V1(lct)a14‐containing isolates were restricted to the L2 sublineage. Evidences of exchanges of different variants and variant alleles during the evolution of this global clone. |
ST3 |
All eight ST3 isolates carried V2(lct)a1. ST3 contained 5.4 % (8/147) of all V2(lct)a1‐carrying isolates found in the A. baumannii population analysed. |
CC500 |
All 14 CC500 (13 ST500, 1 SLV) carried V2(lct)a1. CC500 contained 9.5 % of all V2(lct)a1‐carrying isolates found in the A. baumannii population. This CC lineage is phylogenetically close to ST3. |
CC416 |
All 30 CC416 isolates (13 ST416, 17 SLV) carried V2(lct)a1. CC416 contained 20.4 % of all V2(lct)a1‐carrying isolates found in the A. baumannii population analysed. |
CC417 |
All 19 CC417 isolates (14 ST417, 3 SLV, 2 DLV) carried V2(lct)a1. CC417 contained 12.9 % of all V2(lct)a1‐carrying isolates found in the A. baumannii population analysed. |
CC79 |
All 20 CC79 isolates (9 ST79, 11 SLV) carried V1(lct)a5. CC79 thus contained 90.9 % (20/22) of all V1(lct)a5‐carrying isolates found in the A. baumannii population analysed. |
CC10 |
All 48 CC10 strains (43 ST10, 5 SLV) carried V1(lct)a27. CC10 thus contained 98 % (48/49) of all V1(lct)a27‐carrying isolates found in the A. baumannii population analysed. |
CC15 |
All seven CC15 isolates (six ST15, one SLV) carried V1(lct)a8. CC15 contained 16.3 % (7/43) of all V1(lct)a8‐carrying isolates found in the A. baumannii population. |
ST406 |
All nine ST406 isolates carried V2(lct)a2. Thus, ST406 contained all V2(lct)a2‐carrying isolates found in the A. baumannii population. |
ST499 |
All 20 ST499 isolates carried V1(lct)a30. Thus, ST499 contained all V1(lct)a30‐carrying isolates found in the A. baumannii population. |
CC52 |
Composed by four ST52 isolates all carrying V1(lct)a14, isolated worldwide during a time period spanning 66 years: ATCCT19606 (USA, 1948), MSP4‐16 (India, 2010), GTC 03324 and GTC 03329 (Japan, 2014). CC52 includes another SLV isolate, AB_TG19617, carrying V1(lct)a6. |
ST49 |
All four ST49 isolates carried V4(lct)a1 alleles. ST49 thus contained 44.4 % (4/9) of all V4(lct)a1 isolates found in the A. baumannii population. |
CC25 |
The 47 CC25 isolates carried different ompA variants: 2 (ST25) carried V1(lct)a5, 31 (21 ST25, 10 SLV) carried V1(lct)a8, 4 (ST25) carried V2(lct)a1, and 10 (8 ST25, 1 SLV, 1 DLV) carried V3(sct)a1. Evidence of exchanges of different ompA variants and variant alleles. |
ST16 |
The eight ST16 isolates analyzed carried different V4(lct) alleles: 5 carried V4(lct)a1 (55.5 % of all V4(lct)a1 alleles), 2 carried V4(lct)a4, and one carried V4(lct)a7. Evidence of different V4(lct) allele exchanges. |
CC497 |
The six CC497 isolates carried different variants: Naval‐82 (SLV), TG27391 (SLV), 1 106 579 (SLV) and 83 444 (DLV) carried V1(sct)a1; A200 (SLV) carried V5(sct)a1, and AB_2007‐09‐110‐01‐7 (DLV) carried V1(lct)a1. Evidence of different ompA variant exchanges. |
CC516 |
The five CC516 isolates carried different variants: AB405E4 (ST516) and CR‐ D1 (SLV) carried V1(lct)a32, A9 (DLV) carried V1(sct)a1, NIPH 80 (DLV) and 1 440 422 (DLV) carried V1(lct)a14. Evidence of different variant and variant allele exchanges. |
CC33 |
The three CC33 isolates carried different variants: NIPH615 (DLV) and A219 (SLV) both carried V1(lct)a24, TG02017 (ST33) carried V1(sct)a2. Evidences of ompA variant exchanges. |
ST32 |
ST32 encompassed six isolates carrying different V1(lct) alleles: OIFC032, OIFC087, and OIFC099 carried V1(lct)a12, while 781 407, 1 525 283 and A147 displayed V1(lct)a13. The two V1(lct) alleles translate to identical proteins: G52S replacement as compared to V1(lct)a1. Evidence of V1(lct) allele exchange while maintaining the same OmpA characteristics. |
CC216 |
This CC encompassed ten isolates: WC‐A‐92 (DLV); A185, A181, A134 and A173, (all four ST216) bearing V1(lct)a11; AB405E4 (DLV) bearing V1(lct)a32; A9 (ST216) containing V1(sct)a1; NCIMB8209 (SLV) containing V1(lct)a32; NIPH80 (DLV) and 1 440 422 (SLV) carrying V1(lct)a14. Evidence of ompA variant exchanges. |
CC240 |
CC240 encompassed two avian isolates carrying different V1(lct) alleles: 01D3‐2 (ST240) carried V1(lct)a10 while 86II/2C (DLV) carried V1(lct)a16. All alleles translate to identical proteins: G52S replacement as compared to V1(lct)a1. Evidence of V1(lct) allele replacement while maintaining the OmpA protein characteristics. |
CC821 |
CC821 encompassed four isolates, including three avian isolates carrying V1(lct)a14: LoGest3‐1 (ST821), 151/C (SLV), and Ganse Ei‐1 (DLV); and the clinical isolate A166B (SLV) displaying V1(lct)a10. Both alleles translate to the same protein: G52S replacement as compared to V1(lct)a1. Evidence of V1(lct) allele replacement while maintaining the same OmpA protein characteristics. |