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. 2024 Feb 21;90(2):e0165423.
doi: 10.1128/aem.01654-23. Epub 2024 Jan 11.

Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains

Affiliations

Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains

Liam A Tobin et al. Appl Environ Microbiol. .

Abstract

Acinetobacter baumannii, an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates. Consequently, data on environmental A. baumannii and other Acinetobacter species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 Acinetobacter isolates representing 6 different species sourced from aquatic environments in South Australia. All 10 isolates were phylogenetically distinct compared to clinical and other non-clinical Acinetobacter strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified pdif modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than A. baumannii, including carbapenemase oxa58, tetracycline resistance gene tet(39), and macrolide resistance genes msr(E)-mph(E). These pdif modules were located on plasmids with high sequence identity to those circulating in globally distributed A. baumannii ST1 and ST2 clones. The environmental A. baumannii isolate characterized here (SAAb472; ST350) did not possess any native plasmids; however, it could capture two clinically important plasmids (pRAY and pACICU2) with high transfer frequencies. Furthermore, A. baumannii SAAb472 possessed virulence genes and a capsular polysaccharide type analogous to clinical strains. Our findings highlight the potential for environmental Acinetobacter species to acquire and disseminate clinically important antimicrobial resistance genes, underscoring the need for further research into the ecology and evolution of this important genus.IMPORTANCEAntimicrobial resistance (AMR) is a global threat to human, animal, and environmental health. Studying AMR in environmental bacteria is crucial to understand the emergence and dissemination of resistance genes and pathogens, and to identify potential reservoirs and transmission routes. This study provides novel insights into the genomic diversity and AMR potential of environmental Acinetobacter species. By comparing the genomes of aquatic Acinetobacter isolates with clinical and non-clinical strains, we revealed that they are highly divergent yet carry pdif modules that encode resistance to antibiotics commonly used in clinical settings. We also demonstrated that an environmental A. baumannii isolate can acquire clinically relevant plasmids and carries virulence factors similar to those of hospital-associated strains. These findings suggest that environmental Acinetobacter species may serve as reservoirs and vectors of clinically important genes. Consequently, further research is warranted to comprehensively understand the ecology and evolution of this genus.

Keywords: Acinetobacter baumannii; Acinetobacter chinensis; Acinetobacter gerneri; Acinetobacter johnsonii; Acinetobacter towneri; antibiotic resistance; environmental; mobile genetic elements; plasmid; virulence.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig 1
Fig 1
Genetic relatedness of A. baumannii clinical, environmental, and animal-sourced isolates. (A) Maximum likelihood phylogenetic tree of 171 A. baumannii genomes built using a core genome alignment (2,846,563 bp length). The colored outer ring denotes isolate geographic location, and isolate sources are marked as either a circle (human), rectangle (animal), or star (environmental). Tree branches belonging to STs with more than three isolates are highlighted—ST2 isolates in blue, ST1 in red, ST52 in purple, and ST49 in green. Bootstrap values of >0.95 marked by dots on branches. Isolate from this study is highlighted in yellow. (B) Heatmap illustrating pairwise SNP distances between A. baumannii isolates. (C) Bubble chart depicting highly sensitive and specific genes identified clinical isolates (shown in red) and environmental isolates (blue). The size of each bubble relates P-values and ranges from 2.31E−10 to 9.58E−19. HP, hypothetical protein.
Fig 2
Fig 2
Genetic relatedness of A. johnsonii and A. towneri isolates. (A) Maximum likelihood phylogenetic tree of 52 A. johnsonii genomes built using a core genome alignment (1,948,641 bp length). Isolate from this study in bold and highlighted in yellow. Isolates shown in red mark those that fall under the ANI threshold for an A. johnsonii conclusive identification. (B) Heatmap illustrating pairwise SNP distances between A. johnsonii isolates. (C) Maximum likelihood phylogenetic tree of 34 A. towneri genomes built using a core genome alignment (1,758,026 bp length). The three A. towneri isolates from this study are in bold and highlighted in yellow. The isolate shown in red fell under the ANI threshold for an A. towneri conclusive identification. (D) Heatmap illustrating pairwise SNP distances between A. towneri isolates.
Fig 3
Fig 3
Genetic structure of p2SAAc573 compared to pAb-C36_1, p1_010052, p5637, and pRCH52-1. Filled arrows indicate the orientation and extent of genes. Resistance genes are colored red, and the filled boxes colored green indicate ISAto1. Black arrows are putative replication initiation genes, and toxin/antitoxin genes are yellow. Vertical black lines indicate pdif sites. Scale bar is shown.

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References

    1. Koong J, Johnson C, Rafei R, Hamze M, Myers GSA, Kenyon JJ, Lopatkin AJ, Hamidian M. 2021. Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1. Microb Genom 7:000705. doi:10.1099/mgen.0.000705 - DOI - PMC - PubMed
    1. Prity FT, Tobin LA, Maharajan R, Paulsen IT, Cain AK, Hamidian M. 2023. The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate. Microb Genom 9:001010. doi:10.1099/mgen.0.001010 - DOI - PMC - PubMed
    1. Furlan JPR, de Almeida OGG, De Martinis ECP, Stehling EG. 2019. Characterization of an environmental multidrug-resistant Acinetobacter seifertii and comparative genomic analysis reveals co-occurrence of antimicrobial resistance and metal tolerance determinants. Front Microbiol 10:2151. doi:10.3389/fmicb.2019.02151 - DOI - PMC - PubMed
    1. Dekić S, Klobučar G, Ivanković T, Zanella D, Vucić M, Bourdineaud J-P, Hrenović J. 2018. Emerging human pathogen Acinetobacter baumannii in the natural aquatic environment: a public health risk. Int J Environ Health Res 28:315–322. doi:10.1080/09603123.2018.1472746 - DOI - PubMed
    1. Adewoyin MA, Okoh AI. 2018. The natural environment as a reservoir of pathogenic and non-pathogenic Acinetobacter species. Rev Environ Health 33:265–272. doi:10.1515/reveh-2017-0034 - DOI - PubMed

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