1
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Ambrose SJ, Hall RM. Variation in the plasmid backbone and dif module content of R3-T33 Acinetobacter plasmids. Plasmid 2024; 129-130:102722. [PMID: 38631562 DOI: 10.1016/j.plasmid.2024.102722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
The predominant type of plasmids found in Acinetobacter species encode a Rep_3 initiation protein and many of these carry their accessory genes in dif modules. Here, available sequences of the 14 members of the group of Rep_3 plasmids typed as R3-T33, using a threshold of 95% identity in the repA gene, were compiled and compared. These plasmids were from various Acinetobacter species. The pdif sites were identified allowing the backbone and dif modules to be defined. As for other Rep_3 plasmids carrying dif modules, orfX encoding a protein of unknown function was found downstream of repA followed by a pdif site in the orientation XerC binding site-spacer-XerD binding site. Most backbones (n = 12) also included mobA and mobC genes but the two plasmids with the most diverged repA and orfX genes had different backbone contents. Although the gene content of the plasmid backbone was largely conserved, extensive recombinational exchange was detected and only two small groups carried identical or nearly identical backbones. Individual plasmids were associated with 1 to 13 dif modules. Many different dif modules were identified, including ones containing antibiotic or chromate resistance genes and several toxin/antitoxin gene pairs. In some cases, modules carrying the same genes were significantly diverged. Generally, the orientation of the pdif sites alternated such that C modules (XerC binding sites internal) alternated with D modules (XerD binding sites internal). However, fusions of two dif modules via mutational inactivation or loss of a pdif site were also detected.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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2
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Siguier P, Rousseau P, Cornet F, Chandler M. A subclass of the IS1202 family of bacterial insertion sequences targets XerCD recombination sites. Plasmid 2023; 127:102696. [PMID: 37302728 DOI: 10.1016/j.plasmid.2023.102696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
We describe here a new family of IS which are related to IS1202, originally isolated from Streptococcus pneumoniae in the mid-1990s and previously tagged as an emerging IS family in the ISfinder database. Members of this family have impacted some important properties of their hosts. We describe here another potentially important property of certain family members: specific targeting of xrs recombination sites. The family could be divided into three subgroups based on their transposase sequences and the length on the target repeats (DR) they generate on insertion: subgroup IS1202 (24-29 bp); ISTde1 (15-18 bp); and ISAba32 (5-6 bp). Members of the ISAba32 subgroup were repeatedly found abutting Xer recombinase recombination sites (xrs), separated by an intervening copy of a DR. These xrs sites, present in multiple copies in a number of Acinetobacter plasmids flanking antibiotic resistance genes, were proposed to form a new type of mobile genetic element using the chromosomally-encoded XerCD recombinase for mobility. Transposase alignments identified subgroup-specific indels which may be responsible for the differences in the transposition properties of the three subgroups (i.e. DR length and target specificity). We propose that this collection of IS be classed as a new insertion sequence family: the IS1202 family composed of three subgroups, only one of which specifically targets plasmid-borne xrs. We discuss the implications of xrs targeting for gene mobility.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France.
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France
| | - François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, France
| | - Michael Chandler
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA.
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3
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Harmer CJ, Pong CH, Hall RM. Insertion sequences related to ISAjo2 target p dif and dif sites and belong to a new IS family, the IS 1202 family. Microb Genom 2023; 9. [PMID: 36880881 PMCID: PMC10132070 DOI: 10.1099/mgen.0.000953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Several insertion sequences (IS) found in various Acinetobacter species exhibit target specificity. They are found, in the same orientation, 5 bp from the XerC binding site of the pdif sites associated with dif modules in Acinetobacter plasmids, and searches revealed they are also found near chromosomal dif sites of Acinetobacter species. These IS are 1.5 kb long, bounded by 24-26 bp imperfect terminal inverted repeats (TIRs) and encode a large transposase of 441-457 aa. They generate 5 bp target site duplications (TSDs). Structural predictions of the ISAjo2 transposase, TnpAjo2, modelled on TnsB of Tn7 revealed two N-terminal HTH domains followed by an RNaseH fold (DDE domain), a β barrel and a C-terminal domain. Similar to Tn7, the outer IS ends are 5'-TGT and ACA-3', and an additional Tnp binding site, corresponding to the internal portion of the IR, is found near each end. However, the Acinetobacter IS do not encode further proteins related to those required by Tn7 for targeted transposition, and the transposase may interact directly with XerC bound to a dif-like site. We propose that these IS, currently in the IS1202 group in the not characterized yet (NCY) category in ISFinder, are part of a distinct IS1202 family. Other IS listed as in the IS1202 group encode transposases related to TnpAjo2 (25-56 % amino acid identity) and have similar TIRs but fall into three groups based on the TSD length (3-5, >15, 0 bp). Those with 3-5 bp TSDs may also target dif-like sites but targets were not found for the other groups.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Carol H Pong
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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4
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Lam MMC, Koong J, Holt KE, Hall RM, Hamidian M. Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins. Microbiol Spectr 2023; 11:e0247822. [PMID: 36472426 PMCID: PMC9927589 DOI: 10.1128/spectrum.02478-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
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.
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Affiliation(s)
- Margaret M. C. Lam
- Department of Infectious Diseases, Monash University, Melbourne, Australia
| | - Jonathan Koong
- Australian Institute for Microbiology and Infection, University of Technology Sydney, New South Wales, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Monash University, Melbourne, Australia
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ruth M. Hall
- School of Life and Environmental Sciences, The University of Sydney, New South Wales, Australia
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, New South Wales, Australia
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5
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Giacone L, Cameranesi MM, Sanchez RI, Limansky AS, Morán-Barrio J, Viale AM. Dynamic state of plasmid genomic architectures resulting from XerC/D-mediated site-specific recombination in Acinetobacter baumannii Rep_3 superfamily resistance plasmids carrying blaOXA-58 - and Tn aphA6-resistance modules. Front Microbiol 2023; 14:1057608. [PMID: 36846794 PMCID: PMC9947245 DOI: 10.3389/fmicb.2023.1057608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
The acquisition of bla OXA genes encoding different carbapenem-hydrolyzing class-D β-lactamases (CHDL) represents a main determinant of carbapenem resistance in the nosocomial pathogen Acinetobacter baumannii. The blaOXA-58 gene, in particular, is generally embedded in similar resistance modules (RM) carried by plasmids unique to the Acinetobacter genus lacking self-transferability. The ample variations in the immediate genomic contexts in which blaOXA-58 -containing RMs are inserted among these plasmids, and the almost invariable presence at their borders of non-identical 28-bp sequences potentially recognized by the host XerC and XerD tyrosine recombinases (pXerC/D-like sites), suggested an involvement of these sites in the lateral mobilization of the gene structures they encircle. However, whether and how these pXerC/D sites participate in this process is only beginning to be understood. Here, we used a series of experimental approaches to analyze the contribution of pXerC/D-mediated site-specific recombination to the generation of structural diversity between resistance plasmids carrying pXerC/D-bounded bla OXA-58- and TnaphA6-containing RM harbored by two phylogenetically- and epidemiologically-closely related A. baumannii strains of our collection, Ab242 and Ab825, during adaptation to the hospital environment. Our analysis disclosed the existence of different bona fide pairs of recombinationally-active pXerC/D sites in these plasmids, some mediating reversible intramolecular inversions and others reversible plasmid fusions/resolutions. All of the identified recombinationally-active pairs shared identical GGTGTA sequences at the cr spacer separating the XerC- and XerD-binding regions. The fusion of two Ab825 plasmids mediated by a pair of recombinationally-active pXerC/D sites displaying sequence differences at the cr spacer could be inferred on the basis of sequence comparison analysis, but no evidence of reversibility could be obtained in this case. The reversible plasmid genome rearrangements mediated by recombinationally-active pairs of pXerC/D sites reported here probably represents an ancient mechanism of generating structural diversity in the Acinetobacter plasmid pool. This recursive process could facilitate a rapid adaptation of an eventual bacterial host to changing environments, and has certainly contributed to the evolution of Acinetobacter plasmids and the capture and dissemination of bla OXA-58 genes among Acinetobacter and non-Acinetobacter populations co-residing in the hospital niche.
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Affiliation(s)
| | | | - Rocío I. Sanchez
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Adriana S. Limansky
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario (UNR), Rosario, Argentina
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6
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Shao M, Ying N, Liang Q, Ma N, Leptihn S, Yu Y, Chen H, Liu C, Hua X. Pdif-mediated antibiotic resistance genes transfer in bacteria identified by pdifFinder. Brief Bioinform 2023; 24:6873868. [PMID: 36470841 DOI: 10.1093/bib/bbac521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Modules consisting of antibiotic resistance genes (ARGs) flanked by inverted repeat Xer-specific recombination sites were thought to be mobile genetic elements that promote horizontal transmission. Less frequently, the presence of mobile modules in plasmids, which facilitate a pdif-mediated ARGs transfer, has been reported. Here, numerous ARGs and toxin-antitoxin genes have been found in pdif site pairs. However, the mechanisms underlying this apparent genetic mobility is currently not understood, and the studies relating to pdif-mediated ARGs transfer onto most bacterial genera are lacking. We developed the web server pdifFinder based on an algorithm called PdifSM that allows the prediction of diverse pdif-ARGs modules in bacterial genomes. Using test set consisting of almost 32 thousand plasmids from 717 species, PdifSM identified 481 plasmids from various bacteria containing pdif sites with ARGs. We found 28-bp-long elements from different genera with clear base preferences. The data we obtained indicate that XerCD-dif site-specific recombination mechanism may have evolutionary adapted to facilitate the pdif-mediated ARGs transfer. Through multiple sequence alignment and evolutionary analyses of duplicated pdif-ARGs modules, we discovered that pdif sites allow an interspecies transfer of ARGs but also across different genera. Mutations in pdif sites generate diverse arrays of modules which mediate multidrug-resistance, as these contain variable numbers of diverse ARGs, insertion sequences and other functional genes. The identification of pdif-ARGs modules and studies focused on the mechanism of ARGs co-transfer will help us to understand and possibly allow controlling the spread of MDR bacteria in clinical settings. The pdifFinder code, standalone software package and description with tutorials are available at https://github.com/mjshao06/pdifFinder.
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Affiliation(s)
- Mengjie Shao
- School of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Nanjiao Ying
- School of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Qian Liang
- Hangzhou Digital Micro Biotech Co., Ltd., Hangzhou, 311215, China
| | - Nan Ma
- School of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Sebastian Leptihn
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Zhejiang University-University of Edinburgh Institute, School of Medicine, Zhejiang University, Hangzhou, China.,University of Edinburgh Medical School, Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, 310016, PR China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China
| | - Huan Chen
- Hangzhou Digital Micro Biotech Co., Ltd., Hangzhou, 311215, China.,College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chengzhi Liu
- Hangzhou Digital Micro Biotech Co., Ltd., Hangzhou, 311215, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, 310016, PR China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, PR China.,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare
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7
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Plasmids as Key Players in Acinetobacter Adaptation. Int J Mol Sci 2022; 23:ijms231810893. [PMID: 36142804 PMCID: PMC9501444 DOI: 10.3390/ijms231810893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
This review briefly summarizes the data on the mechanisms of development of the adaptability of Acinetobacters to various living conditions in the environment and in the clinic. A comparative analysis of the genomes of free-living and clinical strains of A. lwoffii, as well as the genomes of A. lwoffii and A. baumannii, has been carried out. It has been shown that plasmids, both large and small, play a key role in the formation of the adaptability of Acinetobacter to their living conditions. In particular, it has been demonstrated that the plasmids of various strains of Acinetobacter differ from each other in their structure and gene composition depending on the lifestyle of their host bacteria. Plasmids of modern strains are enriched with antibiotic-resistant genes, while the content of genes involved in resistance to heavy metals and arsenic is comparable to plasmids from modern and ancient strains. It is concluded that Acinetobacter plasmids may ensure the survival of host bacteria under conditions of various types of environmental and clinical stresses. A brief overview of the main mechanisms of horizontal gene transfer on plasmids inherent in Acinetobacter strains is also given.
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8
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Jones NI, Harmer CJ, Hamidian M, Hall RM. Evolution of Acinetobacter baumannii plasmids carrying the oxa58 carbapenemase resistance gene via plasmid fusion, IS26-mediated events and dif module shuffling. Plasmid 2022; 121:102628. [DOI: 10.1016/j.plasmid.2022.102628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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9
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Alattraqchi AG, Mohd Rani F, A Rahman NI, Ismail S, Cleary DW, Clarke SC, Yeo CC. Complete Genome Sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 Unveils a Large Multidrug-Resistant Plasmid Encoding the NDM-1 and OXA-58 Carbapenemases. mSphere 2021; 6:e01076-20. [PMID: 33504662 PMCID: PMC7885321 DOI: 10.1128/msphere.01076-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/08/2021] [Indexed: 11/20/2022] Open
Abstract
Carbapenem-resistant Acinetobacter spp. are considered priority drug-resistant human-pathogenic bacteria. The genomes of two carbapenem-resistant Acinetobacter spp. clinical isolates obtained from the same tertiary hospital in Terengganu, Malaysia, namely, A. baumannii AC1633 and A. nosocomialis AC1530, were sequenced. Both isolates were found to harbor the carbapenemase genes blaNDM-1 and blaOXA-58 in a large (ca. 170 kb) plasmid designated pAC1633-1 and pAC1530, respectively, that also encodes genes that confer resistance to aminoglycosides, sulfonamides, and macrolides. The two plasmids were almost identical except for the insertion of ISAba11 and an IS4 family element in pAC1633-1, and ISAba11 along with relBE toxin-antitoxin genes flanked by inversely orientated pdif (XerC/XerD) recombination sites in pAC1530. The blaNDM-1 gene was encoded in a Tn125 composite transposon structure flanked by ISAba125, whereas blaOXA-58 was flanked by ISAba11 and ISAba3 downstream and a partial ISAba3 element upstream within a pdif module. The presence of conjugative genes in plasmids pAC1633-1/pAC1530 and their discovery in two distinct species of Acinetobacter from the same hospital are suggestive of conjugative transfer, but mating experiments failed to demonstrate transmissibility under standard laboratory conditions. Comparative sequence analysis strongly inferred that pAC1633-1/pAC1530 was derived from two separate plasmids in an IS1006-mediated recombination or transposition event. A. baumannii AC1633 also harbored three other plasmids designated pAC1633-2, pAC1633-3, and pAC1633-4. Both pAC1633-3 and pAC1633-4 are cryptic plasmids, whereas pAC1633-2 is a 12,651-bp plasmid of the GR8/GR23 Rep3-superfamily group that encodes the tetA(39) tetracycline resistance determinant in a pdif module.IMPORTANCE Bacteria of the genus Acinetobacter are important hospital-acquired pathogens, with carbapenem-resistant A. baumannii listed by the World Health Organization as the one of the top priority pathogens. Whole-genome sequencing of carbapenem-resistant A. baumannii AC1633 and A. nosocomialis AC1530, which were isolated from the main tertiary hospital in Terengganu, Malaysia, led to the discovery of a large, ca. 170-kb plasmid that harbored genes encoding the New Delhi metallo-β-lactamase-1 (NDM-1) and OXA-58 carbapenemases alongside genes that conferred resistance to aminoglycosides, macrolides, and sulfonamides. The plasmid was a patchwork of multiple mobile genetic elements and comparative sequence analysis indicated that it may have been derived from two separate plasmids through an IS1006-mediated recombination or transposition event. The presence of such a potentially transmissible plasmid encoding resistance to multiple antimicrobials warrants vigilance, as its spread to susceptible strains would lead to increasing incidences of antimicrobial resistance.
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Affiliation(s)
- Ahmed Ghazi Alattraqchi
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
| | - Farahiyah Mohd Rani
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
| | - Nor Iza A Rahman
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
| | - Salwani Ismail
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
| | - David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, United Kingdom
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, United Kingdom
- Global Health Research Institute, University of Southampton, Southampton, United Kingdom
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
- Centre for Translational Research, IMU Institute for Research, Development and Innovation (IRDI), Kuala Lumpur, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengganu, Malaysia
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10
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Mindlin S, Beletsky A, Rakitin A, Mardanov A, Petrova M. Acinetobacter Plasmids: Diversity and Development of Classification Strategies. Front Microbiol 2020; 11:588410. [PMID: 33304332 PMCID: PMC7693717 DOI: 10.3389/fmicb.2020.588410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Acinetobacter, with their numerous species common in various habitats, play a significant role as pathogens. Their ability to adapt to different living conditions is largely due to the presence of numerous plasmids containing the necessary adaptive genes. At the same time the diversity of Acinetobacter plasmids and their evolutionary dynamics have not been sufficiently studied. Here, we characterized 44 plasmids isolated from five permafrost Acinetobacter lwoffii strains, examined their relationship with plasmids of modern Acinetobacter strains and identified groups of related plasmids. For this purpose, we have developed a combined approach for classifying all known Acinetobacter plasmids. The classification took into account the size of plasmids, the presence and structure of the rep and mob genes, as well as the structure of their backbone and accessory regions. Based on the analysis, 19 major groups (lineages) of plasmids were identified, of which more than half were small plasmids. The plasmids of each group have common features of the organization of the backbone region with a DNA identity level of at least 80%. In addition, plasmids of the same group have similarities in the organization of accessory regions. We also described a number of plasmids with a unique structure. The presence of plasmids in clinical strains that are closely related to those of environmental permafrost strains provides evidence of the origin of the former from the latter.
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Affiliation(s)
- Sofia Mindlin
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Alexey Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Mayya Petrova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow, Russia
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11
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Balalovski P, Grainge I. Mobilization of p
dif
modules in
Acinetobacter
: A novel mechanism for antibiotic resistance gene shuffling? Mol Microbiol 2020; 114:699-709. [DOI: 10.1111/mmi.14563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Phillip Balalovski
- Biological Sciences School of Environmental and Life Sciences University of Newcastle Callaghan NSW Australia
| | - Ian Grainge
- Biological Sciences School of Environmental and Life Sciences University of Newcastle Callaghan NSW Australia
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12
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Lin DL, Traglia GM, Baker R, Sherratt DJ, Ramirez MS, Tolmasky ME. Functional Analysis of the Acinetobacter baumannii XerC and XerD Site-Specific Recombinases: Potential Role in Dissemination of Resistance Genes. Antibiotics (Basel) 2020; 9:antibiotics9070405. [PMID: 32668667 PMCID: PMC7399989 DOI: 10.3390/antibiotics9070405] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 12/12/2022] Open
Abstract
Modules composed of a resistance gene flanked by Xer site-specific recombination sites, the vast majority of which were found in Acinetobacter baumannii, are thought to behave as elements that facilitate horizontal dissemination. The A. baumanniixerC and xerD genes were cloned, and the recombinant clones used to complement the cognate Escherichia coli mutants. The complemented strains supported the resolution of plasmid dimers, and, as is the case with E. coli and Klebsiella pneumoniae plasmids, the activity was enhanced when the cells were grown in a low osmolarity growth medium. Binding experiments showed that the partially purified A. baumannii XerC and XerD proteins (XerCAb and XerDAb) bound synthetic Xer site-specific recombination sites, some of them with a nucleotide sequence deduced from existing A. baumannii plasmids. Incubation with suicide substrates resulted in the covalent attachment of DNA to a recombinase, probably XerCAb, indicating that the first step in the recombination reaction took place. The results described show that XerCAb and XerDAb are functional proteins and support the hypothesis that they participate in horizontal dissemination of resistant genes among bacteria.
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Affiliation(s)
- David L. Lin
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA; (D.L.L.); (M.S.R.)
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
| | - German M. Traglia
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República (UDeLaR), Montevideo 11600, Uruguay;
| | - Rachel Baker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
| | - David J. Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA; (D.L.L.); (M.S.R.)
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA; (D.L.L.); (M.S.R.)
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
- Correspondence:
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Brovedan MA, Cameranesi MM, Limansky AS, Morán-Barrio J, Marchiaro P, Repizo GD. What do we know about plasmids carried by members of the Acinetobacter genus? World J Microbiol Biotechnol 2020; 36:109. [PMID: 32656745 DOI: 10.1007/s11274-020-02890-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/04/2020] [Indexed: 02/07/2023]
Abstract
Several Acinetobacter spp. act as opportunistic pathogens causing healthcare-associated infections worldwide, and in this respect their ability to resist antimicrobial compounds has certainly boosted up their global propagation. Acinetobacter clinical strains have demonstrated a remarkable ability to evolve and become resistant to almost all available drugs in the antimicrobial arsenal, including the last-resort carbapenem β-lactams. The dissemination of antimicrobial resistant genes (ARG), heavy metals-detoxification systems and other traits such as virulence factors is facilitated by mobile genetic elements (MGE) through horizontal gene transfer. Among them, plasmids have been shown to play a critical role in this genus. Despite the continuous increase of Acinetobacter plasmid sequences present in databases, there are no reports describing the basic traits carried by these MGE. To fill this gap, a broad analysis of the Acinetobacter plasmidome was performed. A search for Acinetobacter complete plasmids indicated that 905 sequences have been deposited in the NCBI-GenBank public database, of which 492 are harbored by Acinetobacter baumannii strains. Plasmid-classification schemes based on Rep proteins homology have so far described 23 different groups for A. baumannii (GR1-23), and 16 Acinetobacter Rep3 Groups (AR3G1-16) for the complete genus. Acinetobacter plasmids size ranges from 1.3 to 400 kb. Interestingly, widespread plasmids which are < 20 kb make up 56% of the total present in members of this genus. This led to the proposal of Acinetobacter plasmid assignation to two groups according to their size (< 20 kb and > 20 kb). Usually, smaller plasmids are not self-transmissible, and thereby employ alternative mechanisms of dissemination. For instance, a subgroup of < 20 kb-plasmids belonging to the pRAY-family, lack a rep gene, but encode a relaxase enabling their mobilization by conjugative plasmids. Other subgroup, including small GR2 Acinetobacter plasmids, does not encode a relaxase gene. However, they could still be mobilized by conjugative plasmids which recognize an oriT region carried by these small plasmids. Also, these < 20 kb-plasmids usually carry accessory genes bordered by XerC/D-recombinases recognition sites which have been hypothesized to mediate plasmid plasticity. Conversely, many cases of larger plasmids are self-transmissible and might encode virulence factors and their regulators, thus controlling strain pathogenicity. The ARGs carried by the > 20 kb-plasmids are usually encoded within other MGEs such as transposons, or as part of integrons. It has been recently noted that some of the > 20 kb-plasmids are derived from excised phages, and thus dubbed as phage-like plasmids. All in all, the plethora of plasmids found in strains of this genus and the multiple strategies promoting their evolution and dissemination have certainly contributed to survival of the Acinetobacter members in different habitats, including the clinical environment.
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Affiliation(s)
- Marco A Brovedan
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María M Cameranesi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana S Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina Morán-Barrio
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Patricia Marchiaro
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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Cameranesi MM, Paganini J, Limansky AS, Moran-Barrio J, Salcedo SP, Viale AM, Repizo GD. Acquisition of plasmids conferring carbapenem and aminoglycoside resistance and loss of surface-exposed macromolecule structures as strategies for the adaptation of Acinetobacter baumannii CC104 O/CC15 P strains to the clinical setting. Microb Genom 2020; 6. [PMID: 32213259 PMCID: PMC7643966 DOI: 10.1099/mgen.0.000360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Acinetobacter baumannii (Aba) is an emerging opportunistic pathogen associated to nosocomial infections. The rapid increase in multidrug resistance (MDR) among Aba strains underscores the urgency of understanding how this pathogen evolves in the clinical environment. We conducted here a whole-genome sequence comparative analysis of three phylogenetically and epidemiologically related MDR Aba strains from Argentinean hospitals, assigned to the CC104O/CC15P clonal complex. While the Ab244 strain was carbapenem-susceptible, Ab242 and Ab825, isolated after the introduction of carbapenem therapy, displayed resistance to these last resource β-lactams. We found a high chromosomal synteny among the three strains, but significant differences at their accessory genomes. Most importantly, carbapenem resistance in Ab242 and Ab825 was attributed to the acquisition of a Rep_3 family plasmid carrying a blaOXA-58 gene. Other differences involved a genomic island carrying resistance to toxic compounds and a Tn10 element exclusive to Ab244 and Ab825, respectively. Also remarkably, 44 insertion sequences (ISs) were uncovered in Ab825, in contrast with the 14 and 11 detected in Ab242 and Ab244, respectively. Moreover, Ab825 showed a higher killing capacity as compared to the other two strains in the Galleria mellonella infection model. A search for virulence and persistence determinants indicated the loss or IS-mediated interruption of genes encoding many surface-exposed macromolecules in Ab825, suggesting that these events are responsible for its higher relative virulence. The comparative genomic analyses of the CC104O/CC15P strains conducted here revealed the contribution of acquired mobile genetic elements such as ISs and plasmids to the adaptation of A. baumannii to the clinical setting.
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Affiliation(s)
- María M Cameranesi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julian Paganini
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana S Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina Moran-Barrio
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Suzana P Salcedo
- Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR5086, University of Lyon, LyonF-69367, France
| | - Alejandro M Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.,Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR5086, University of Lyon, LyonF-69367, France
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