Clinical characteristics of CRAB strains

A total of 92 unduplicated isolates were collected from ICU patients over a four-year period from 2019 to 2022 that were clinically documented with carbapenem-resistant A. baumannii infections. Isolates were predominantly of ICU origin (n = 81, 88%), with a small proportion of emergency ICU (EICU) origin (n = 11, 12%). Three CRAB samples were collected from ICUs in 2019, 18 from ICUs in 2020, as well as 19 isolates from ICUs and 1 isolate from an EICU in 2021. In 2022, 41 isolates were documented from ICU and 10 isolates were documented from EICU. Of these samples of CRAB isolates, the majority were from sputum (n = 87, 94.57%), with the remainder from blood (n = 3, 3.26%), ascites fluid (n = 1, 1.09%) and cerebrospinal fluid (n = 1, 1.09%) samples. The demographic information and clinical information of patients is shown in Fig. 1 and Table S1, respectively.

Fig. 1

Details of annual collections of CRAB isolates and sample types. A: Year of isolation and number of isolates, B: Type of sample from which the isolates originated

Statistical analysis of drug resistance in CRAB subjects

Our analysis showed that all 92 CRAB strains were resistant to carbapenem antibiotics. For example, we found 100% resistance to cefepime and ceftazidime, 96% resistance to Cefepime, 91% resistance to levofloxacin, 89% resistance to Tetracycline and to Gentamicin and 83% resistance to amikacin. Of the antibiotics tested, the CRAB samples were the least (28%) resistant to minocycline. We also found that the MIC50 and MIC90 of the antibiotics tested for the CRAB samples all varied considerably. For example, for imipenem and meropenem, their MIC50 and MIC90 featured a difference of greater than 4-fold, while an 8-fold difference in amikacin was also observed. The specific statistical results are shown in Table 1, and the resistance and MIC results are shown in Table S2.

Table 1 Drug resistance features of clinical isolates, alongside their MIC50, MIC90 valuesAnalysis of bacterial genomic data

When we analyzed the genomic data of the strains, we found that almost all of the strains were identified as ST2, while only one strain was identified as ST1336. In the ST2 lineage, all strains carried Class D carbapenemase blaOXA−23, and no blaKPC, blaNDM, blaIMP, or blaVIM were found in the genome. AB25 belonging to ST1336 not carrying blaOXA−23, blaKPC, blaNDM, blaIMP, and blaVIM. Evolutionary tree analysis was performed and we identified a temporal correlation of the strains. AB25 exhibits significant differences from the ST2 lineage. In particular, the isolates in this study were closely related to isolates from Guangzhou and Hangzhou, China (Biosample: SAMN10985290 and SAMN15232025). The results of evolutionary tree and distribution of resistance genes are shown in Fig. 2.

Fig. 2

Bacterial genome evolution tree. The blaOXA-23 carriage rate, isolation time and sequence type of the isolates are shown on the right. Green represents the isolates in this study, other strains were derived from A. baumannii isolates from other regions of China that were publicly available in the NCBI database

Bacterial genome virulence gene data analysis

Bacterial genomes were uploaded to VFDB for virulence gene analysis. Through this, we discovered a few number of deletions in csuA (n = 3, 3.26%), csuB (No absent), csuC (n = 1, 1.09%), csuD (n = 1, 1.09%), and csuE (No absent). We detected a small deletion to lpxC, a cell membrane lipid A biosynthesis gene, and no Polymyxin resistance was found in combination with bacterial resistance across the samples. In addition, we also detected isolated deletions in the group sensing system abaI and abaR genes, and the rhamnose synthase gene rmlD was found to be largely absent. The results of the distribution of virulence genes are shown in Fig. 3.

Fig. 3

Distribution of bacterial virulence genes that are present (dark blue) or absent (light blue)

Single nucleotide polymorphism analysis of CRAB genome

We found that single nucleotide polymorphisms (SNPs) showed tendency to gradually disperse that was associated with the year of sample collection. For example, isolates from 2019 tended to be homogeneous, while samples from 2020 had only one dispersed isolate, however the isolates tended to be dispersed from each other. Isolates from 2021 were the most dispersed. One caveat of these observations is that the variation in the number of samples collected between years is large. Detailed results of SNP analysis are shown in Figure S1.

Analysis of bla OXA−23gene environment

The genome was uploaded to NCBI search and the CRAB genome used in this study was compared with the database. The Acinetobacter baumannii pABT-AB4-1 plasmid carries the insertion sequence blaOXA−23 in ISAba1 with homology to blaOXA−23 in the AB002 genome. In the AB002 genome, blaOXA−23 is homologous to the insertion sequences and genes as the genomes of other clinical strains in the database. This is consistent with the interpretation that A.baumannii blaOXA−23 is widely transmissible and was transmitted to these samples. The results of gene environment analysis are shown in Fig. 4.

Fig. 4

Resistance gene-gene environment analysis. A: plasmid homologous gene environment analysis, B: chromosome homologous gene environment analysis