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. 2023 Jun 1:14:1174200.
doi: 10.3389/fmicb.2023.1174200. eCollection 2023.

Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database

Jia Li  1 , Yang Li  2 , Xiaoli Cao  1 , Jie Zheng  1 , Yan Zhang  1 , Hui Xie  1 , Chuchu Li  3 , Chang Liu  1 , Han Shen  1
Affiliations

Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database

Jia Li et al. Front Microbiol. .

Abstract

Objective: To use genomic analysis to identify Acinetobacter spp. and to explore the distribution characteristics of ß-lactamase oxallicinases (blaOXA) among Acinetobacter species globally.

Methods: Genomes of global Acinetobacter spp. were downloaded from GenBank using Aspera batch. After quality check using CheckM and QUAST software, the genomes were annotated using Prokka software to investigate the distribution of blaOXAs across Acinetobacter spp.; a phylogenetic tree was constructed to explore the evolutionary relationship among the blaOXA genes in Acinetobacter spp. Average-nucleotide identification (ANI) was performed to re-type the Acinetobacter spp. BLASTN comparison analysis was implemented to determine the sequence type (ST) of Acinetobacter baumannii strain.

Results: A total of 7,853 genomes were downloaded, of which only 6,639 were left for further analysis after quality check. Among them, 282 blaOXA variants were identified from the genomes of 5,893 Acinetobacter spp.; blaOXA-23 (n = 3,168, 53.8%) and blaOXA-66 (2,630, 44.6%) were the most frequent blaOXAs, accounting for 52.6% (3,489/6639), and the co-carriage of blaOXA-23 and blaOXA-66 was seen in 2223 (37.7%) strains. The 282 blaOXA variants were divided into 27 clusters according to the phylogenetic tree. The biggest clade was blaOXA-51-family carbapenem-hydrolyzing enzymes composed of 108 blaOXA variants. Overall, 4,923 A. baumannii were identified out of the 6,639 Acinetobacter spp. strains and 291 distinct STs were identified among the 4,904 blaOXA-carrying A. baumannii. The most prevalent ST was ST2 (n = 3,023, 61.6%) followed by ST1 (n = 228, 4.6%).

Conclusion: OXA-like carbapenemases were the main blaOXA-type β-lactamase spread widely across Acinetobacter spp. Both blaOXA-23 and blaOXA-66 were the predominant blaOXAs, among all A. baumannii strains, with ST2 (belonging to CC2) being the main clone disseminated globally.

Keywords: Acinetobacter baumannii; Acinetobacter spp.; OXA-23; OXA-66; ST2.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The phylogenetic tree of 282 blaOXA variants detected across global Acinetobacter spp. The phylogenetic tree was constructed using MUSCLE and RAxML software, and finally visualized with iTOL software. The clades were calculated based on the function of OXA variants.
Figure 2
Figure 2
The prevalence of OXA-23 and OXA-66 combination in global Acinetobacter baumannii (The blue line); The distribution of OXA-producing Acinetobacter baumannii ST1 and ST2 during 1999–2021 (The dark red line and light red line); Analysis of the submitted and released genomes of Acinetobacter spp. per year (The green line).
Figure 3
Figure 3
The predominant sequence types of global OXA-producing Acinetobacter baumannii in 1996, 1999, and during 2001–2021 as well as the distribution of OXA variants among the three dominant clones of Acinetobacter baumannii. (A) The predominant sequence types of global OXA-producing Acinetobacter baumannii in 1996, 1999, and during 2001–2021; (B) The distribution of OXA variants among Acinetobacter baumannii ST1; (C) The distribution of OXA variants among Acinetobacter baumannii ST2; and (D) The distribution of OXA variants among Acinetobacter baumannii ST25.
Figure 4
Figure 4
Submitted and released genomes of Acinetobacter spp. by different countries worldwide.
See this image and copyright information in PMC

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