Among obtained STs, the number of alleles in each locus varied from 5 to 14 and that of SNPs ranged from 5 to 63. The sequence diversity of each locus ranged from 2.98–6.40% with average value of 3.83%. Furthermore, nucleotide diversity (π) in this study was in the range of 0.00413 to 0.03514 (Table 1).
Table 1
Property of the MLST loci in A baumannii in this study.
Locus | No. of nucleotide analyzed | No. of alleles | No. of SNP | SNP Frequency | No. of variable sites | Nucleotide diversity π | Sequence diversity rate |
Oxf_gltA | 484 | 5 | 5 | 1.03% | 5 | 0.00413 | 2.98% |
Oxf_gyrB | 457 | 10 | 20 | 4.38% | 19 | 0.01255 | 3.92% |
Oxf_gdhB | 344 | 10 | 20 | 5.81% | 20 | 0.01628 | 3.73% |
Oxf_recA | 371 | 11 | 63 | 16.98% | 60 | 0.03514 | 6.40% |
Oxf_cpn60 | 421 | 7 | 11 | 2.61% | 11 | 0.00882 | 3.87% |
Oxf_gpi | 305 | 14 | 48 | 15.74% | 44 | 0.03967 | 3.38% |
Oxf_rpoD | 513 | 7 | 6 | 1.17% | 6 | 0.00464 | 3.29% |
2.1. Antimicrobial susceptibility
The result of antimicrobial susceptibility is shown in supporting information (Table S1). Totally, the resistant portions of Jilin isolates to ertapenem, imipenem, meropenem, tigecycline, and colistin B are 91.01% (n = 81), 87.64% (n = 78), 89.89% (n = 80), 7.86% (n = 7), and 13.48% (n = 12), respectively. Twelve isolates were found to be sensitive to at least one of tested carbapenems. The overwhelming majority in our Jilin isolates (77/89) were resistant to all tested carbapenems, and 75 of them were at least sensitive to one or both of tigecycline and colistin B. But one isolate was resistant to all tested antibiotics including tigecycline and colistin B.
2.2. MLST analysis
Among 89 Jilin isolates, 22 STs were identified, among them ten STs including ST2370, ST2393, ST2395, ST2396, ST2397 ST2398, ST2399, ST2400, ST2401, and ST2402 were found for the first time. It should be noted, ST1779, with 6 isolates, was not recognized as novel ST in MLST Database, but the clues to the existence of ST1779 was hardly to be founded. The frequencies of STs ranged from 1–34 with ST195 (n = 34), ST208 (n = 14), ST540 (n = 13), ST1779 (n = 6), ST368 (n = 3), ST218 (n = 2) and ST369 (n = 2) as the majority. All newly discovered STs just occupied one isolate in this study. The previously registered ST75 was not found in this study.
2.3 The association between Jilin STs and carbapenem resistance
ST 195 (n = 3), ST373 (n = 1), ST699 (n = 1), ST2395 (n = 1), ST2396 (n = 1), ST2397 (n = 1), ST2398 (n = 1), ST2399 (n = 1), ST2401 (n = 1), and ST2402 (n = 1) were found to be sensitive to at least one of tested carbapenems, and among them just ST195, ST373 and ST699 were previously discovered STs. The occupation of carbapenems sensitive isolates in all previously discovered STs was about 7.6% (6/79), while that in newly discovered STs was 70% (7/10). The attempts have been done to ensure the association between the STs and the antimicrobial susceptibility. In this study, ST373 (n = 1), ST699 (n = 1), ST2395 (n = 1), ST2396 (n = 1), ST2397 (n = 1), ST2399 (n = 1), ST2401 (n = 1), ST2402 (n = 1) were found to be sensitive to ertapenem, imipenem and meropenem in general, the overwhelming majority isolates of other STs are non-sensitive to three carbapenems antimicrobial, and association was statistically significant (P༜0.001, by Fisher’s precision probability test). The association between the STs and the carbapenem sensitivity was showed in Fig. 1.
2.3. Genetic relatedness
ST195, ST208, ST218, ST368, ST369, and ST540, which are predominant STs in Jilin could be classified into CC92 group. However, other main STs in Jilin including ST1779, ST1926, and ST2370, could not be classified into CC92 group because of lacking sufficient alleles of the loci in housekeeping genes. It must be pointed out that although ST1779 (n = 6) is not a novel ST, it has never been founded in MLST database before.
The goeBURST analysis within the scope of Jilin isolates showed that 78 our isolates in nine STs and six previous isolates in ST75 could be classified into a big group with ST369 as group founder and ST195, ST540 as subgroup founders (Fig. 2A). And among 10 novel STs, 8 newly identified STs are singletons without any association with other Jilin isolates (Fig. 2A). The details of locus variation in goeBURST algorithm was displayed in supporting document (Table S2).
In the nationwide analysis, ST369 was also a group founder with ST136, ST195, ST208, ST350 and ST540 as subgroup founders (Fig. 2B). The locations and distribution of Jilin STs in nation wide unrooted tree were similar to that in Jilin tree, but there was no nation wide subgroup founders ST136, ST350 and their downstream branches in Jilin tree. Subgroup founder ST208 had several variant STs, which located in three downstream branches. But in Jilin, as a predominant ST (14/89), ST208 did not occupy any variant and branches. This phenomenon suggested that ST208 in Jilin possibly was a traveler which traveled to Jilin and induced an outbreak in sample-taking hospital. Same to ST469, which was identified as a singleton in Jilin, but in nation wide, ST469 was variant of ST350, which was not detected in Jilin isolates (Fig. 2).
In worldwide analysis (Fig. 3), the majority of Jilin STs are classified in Group 1 along with predominant STs from Australia, France, Germany, Iraq, Italy, Japan, Malaysia, Russia, Saudi Arabia, Singapore, South Korea, Thailand, and the USA. And some Jilin STs are closely related to predominant STs from Australia, Bolivia, Brazil, India, South Korea, Russia, Iraq, and the USA in Group 4. ST2397 from Jilin had close relationship with French predominant ST2289 in Group 2. ST2402 is grouped in ‘Group 8’ along with predominant ST (ST2225) from Saudi Arabia. Among the novel STs in Jilin, only ST2399 without closely related strains in other countries, and it is divided into group 7 alone.
2.4. Genetic relatedness and geographical distribution
By 19th of June, 2021, total number of A. baumannii isolates was 3303 in MLST database, among them 653 were Chinese isolates.
In China, 653 isolates distributed in 329 STs with frequency range 1–56, and major STs were ST1145 (n = 56), ST195 (n = 36), ST92 (n = 32), ST208 (n = 25), ST75 (n = 22), ST540 (n = 19), ST1417 (n = 17), ST138 (n = 10), ST191 (n = 10) and ST368 (n = 8). Jilin predominant STs shared same group founder ST369 with all STs of Guizhou (south east China), and some sporadic isolates from other regions. But predominant STs in Guizhou were ST1646, ST1417, ST1145, ST2200, ST2208, ST2207, ST2204, ST1658, and ST1144 in Guizhou, which showed different origin and evolution trend from Jilin. The aggregation trend was not found in STs isolated from Zhejiang (east China), Shanghai (east China), Guangdong (south China), Fujian (south China), and Beijing (north China) (Fig. 4).
If the analysis was performed worldwide, all STs were divided into six groups as shown in Fig. 5. All Chinese A. baumannii predominant STs belonged to Group F.