Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Feb 14;11(1):e0247822.
doi: 10.1128/spectrum.02478-22. Epub 2022 Dec 6.

Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins

Affiliations

Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins

Margaret M C Lam et al. Microbiol Spectr. .

Abstract

Plasmids found in Acinetobacter species contribute to the spread of antibiotic resistance genes. They appear to be largely confined to this genus and cannot be typed with available tools and databases. Here, a method for distinguishing and typing these plasmids was developed using a curated, non-redundant set of 621 complete sequences of plasmids from Acinetobacter baumannii. Plasmids were separated into 3 groups based on the Pfam domains of the encoded replication initiation (Rep) protein and a fourth group that lack an identifiable Rep protein. The rep genes of each Rep-encoding group (n = 13 Rep_1, n = 107 RepPriCT_1, n = 351 Rep_3) were then clustered using a threshold of >95% nucleotide identity to define 80 distinct types. Five Rep_1 subgroups, designated R1_T1 to R1-T5, were identified and a sixth reported recently was added. Each R1 type corresponded to a conserved small plasmid sequence. The RepPriCT_1 plasmids fell into 5 subgroups, designated RP-T1 to RP-T5 and the Rep_3 plasmids comprised 69 distinct types (R3-T1 to R3-T69). Three R1, 2 RP and 32 R3 types are represented by only a single plasmid. Over half of the plasmids belong to the 4 most abundant types: the RP-T1 plasmids (n = 97), which include conjugation genes and are often associated with various acquired antibiotic resistance genes, and R3-T1, R3-T2 and R3-T3 (n = 95, 30 and 45, respectively). To facilitate typing and the identification of plasmids in draft genomes using this framework, we established the Acinetobacter Typing database containing representative nucleotide and protein sequences of the type markers (https://github.com/MehradHamidian/AcinetobacterPlasmidTyping). IMPORTANCE Though they contribute to the dissemination of genes that confer resistance to clinically important carbapenem and aminoglycoside antibiotics used to treat life-threatening Acinetobacter baumannii infections, plasmids found in Acinetobacter species have not been well studied. As these plasmids do not resemble those found in other Gram-negative pathogens, available typing systems are unsuitable. The plasmid typing system developed for A. baumannii plasmids with an identifiable rep gene will facilitate the classification and tracking of sequenced plasmids. It will also enable the detection of plasmid-derived contigs present in draft genomes that are widely ignored currently. Hence, it will assist in the tracking of resistance genes and other genes that affect survival in the environment, as they spread through the population. As identical or similar plasmids have been found in other Acinetobacter species, the typing system will also be broadly applicable in identifying plasmids in other members of the genus.

Keywords: Acinetobacter baumannii; Rep protein, Rep_3; Rep_1 and RepPriCT_1; plasmid; replication initiation gene.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIG 1
FIG 1
Comparison of representatives of plasmids encoding Rep_1 family (Pfam01446) Rep proteins. Black horizontal arrows show indicate rep genes. White arrows encode hypothetical proteins. Regions with significant DNA identities are shown using shades of gray with % identities also labeled in red. p4ABAYE (GenBank accession number CU459139), pA85-1a (GenBank accession number CP021784), pAb-D10a-a_5 (GenBank accession number CP051874), p3AB5075 (GenBank accession number CP008709), pTS236 (GenBank accession number JN872565), and pMRSN56-1 (GenBank accession number CP080453) represent R1-T1, R1-T2, R1-T3, R1-T4, R1-T5, and R1-T6, respectively.
FIG 2
FIG 2
Schematic comparison of Rep_3 family (Pfam01051) plasmid structures. Horizontal arrows show the length and orientation of genes with rep genes colored black, resistance genes red, toxin/anti-toxins yellow and mobilization genes blue. Green boxes indicate insertion sequences with their transposase shown inside the box. Small thick vertical bar marked with “i” indicate iterons. Other vertical bards marked with “C/D or D/C” indicate the location of pdif sites. Regions with significant DNA identities are shown using shades of gray with % identities also shown using red numbers. Dotted lines draw the show the boundaries of pdif modules. (A) represents variations within five R3-T1 plasmids (p2ABAYE, pA1-1/pAB0055, pAB-NCGM253, and pD36-3 with GenBank accession numbers CU459138, CP010782/CP001183, AB823544, and CP012955, respectively) that carry different pdif modules. (B) compares two R3-T1 plasmids pABVA01 and pD72-1 (GenBank accession numbers FM210331.1 and KM051986, respectively) with pA1-1 (GenBank accession number CP010782) representing R3-T1. (C) represents the structure of plasmids representing R3-T12 (p1ATCC19606; GenBank accession number CP045108), R3-T4 (pMAC; AY541809) and R3-T11 (pVB473_1; GenBank accession number CP050389) with no significant DNA identity.
FIG 3
FIG 3
Maximum-likelihood phylogenetic relationship of replication initiation Rep sequences from the Rep_3 family. The tree comprises amino acid sequences encoded by n = 125 unique nucleotide sequence variants from the Rep_3 family generated in IQ-TREE. The shading show either sequence variants assigned to the same Rep3 family (unlabeled) or those detected in at least n = 5 plasmids (labeled). Columns are as follows: Rep types assigned based on a threshold of 95% nucleotide identity (those in light gray correspond to unique Rep types with a single nucleotide variant), clusters of Rep sequence variants grouped at 95% and 90% identity assigned with CD-HIT. The number of plasmids in which each Rep-encoding sequence variant was detected is shown on the right-hand side.

Similar articles

Cited by

References

    1. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi:10.1128/AAC.02412-14. - DOI - PMC - PubMed
    1. Bertini A, Poirel L, Mugnier PD, Villa L, Nordmann P, Carattoli A. 2010. Characterization and PCR-based replicon typing of resistance plasmids in Acinetobacter baumannii. Antimicrob Agents Chemother 54:4168–4177. doi:10.1128/AAC.00542-10. - DOI - PMC - PubMed
    1. Towner KJ, Evans B, Villa L, Levi K, Hamouda A, Amyes SG, Carattoli A. 2011. Distribution of intrinsic plasmid replicase genes and their association with carbapenem-hydrolyzing class D B-lactamase genes in European clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 55:2154–2159. doi:10.1128/AAC.01661-10. - DOI - PMC - PubMed
    1. Fu Y, Jiang J, Zhou H, Jiang Y, Fu Y, Yu Y, Zhou J. 2014. Characterization of a novel plasmid type and various genetic contexts of blaOXA-58 in Acinetobacter spp. from multiple cities in China. PLoS One 9:e84680. doi:10.1371/journal.pone.0084680. - DOI - PMC - PubMed
    1. Lean SS, Yeo CC. 2017. Small, enigmatic plasmids of the nosocomial pathogen, Acinetobacter baumannii: good, bad, who knows? Front Microbiol 8:1547. doi:10.3389/fmicb.2017.01547. - DOI - PMC - PubMed

Publication types

MeSH terms