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Correa A, Shehreen S, Machado LC, Thesier J, Cunic L, Petassi M, Chu J, Kapili B, Jia Y, England K, Peters J. Novel mechanisms of diversity generation in Acinetobacter baumannii resistance islands driven by Tn7-like elements. Nucleic Acids Res 2024; 52:3180-3198. [PMID: 38407477 PMCID: PMC11014353 DOI: 10.1093/nar/gkae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
Mobile genetic elements play an important role in the acquisition of antibiotic and biocide resistance, especially through the formation of resistance islands in bacterial chromosomes. We analyzed the contribution of Tn7-like transposons to island formation and diversification in the nosocomial pathogen Acinetobacter baumannii and identified four separate families that recognize different integration sites. One integration site is within the comM gene and coincides with the previously described Tn6022 elements suggested to account for the AbaR resistance island. We established Tn6022 in a heterologous E. coli host and confirmed basic features of transposition into the comM attachment site and the use of a novel transposition protein. By analyzing population features within Tn6022 elements we identified two potential novel transposon-encoded diversification mechanisms with this dynamic genetic island. The activities of these diversification features were confirmed in E. coli. One was a novel natural gain-of-activity allele that could function to broaden transposition targeting. The second was a transposon-encoded hybrid dif-like site that parasitizes the host dimer chromosome resolution system to function with its own tyrosine recombinase. This work establishes a highly active Tn7-like transposon that harnesses novel features allowing the spread and diversification of genetic islands in pathogenic bacteria.
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Affiliation(s)
- Alberto Correa
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | | | - Jordan Thesier
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Lille M Cunic
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - Joshua Chu
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - Yu Jia
- College of Life Sciences and Engineering Research Center of Bioreactor and Pharmaceutical Development (Ministry of Education), Jilin Agricultural University, Changchun City, Jilin Province, China
| | - Kevin A England
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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2
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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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3
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Medeot D, Sannazzaro A, Estrella MJ, Torres Tejerizo G, Contreras-Moreira B, Pistorio M, Jofré E. Unraveling the genome of Bacillus velezensis MEP 218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis. Sci Rep 2023; 13:22168. [PMID: 38092837 PMCID: PMC10719345 DOI: 10.1038/s41598-023-49194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16-C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892 bp, with a total of 3474 coding sequences and a G + C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1-4 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16-C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.
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Affiliation(s)
- Daniela Medeot
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CCT-CONICET-Córdoba, Universidad Nacional de Río Cuarto, 5800, Córdoba, Argentina
| | - Analía Sannazzaro
- Instituto Tecnológico de Chascomús (INTECH), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín (UNSAM), 7130, Chascomús, Argentina
| | - María Julia Estrella
- Instituto Tecnológico de Chascomús (INTECH), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín (UNSAM), 7130, Chascomús, Argentina
| | - Gonzalo Torres Tejerizo
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, 1900, La Plata, Argentina
| | | | - Mariano Pistorio
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Universidad Nacional de La Plata, 1900, La Plata, Argentina
| | - Edgardo Jofré
- Instituto de Biotecnología Ambiental y Salud (INBIAS), CCT-CONICET-Córdoba, Universidad Nacional de Río Cuarto, 5800, Córdoba, Argentina.
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4
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Castanheira M, Mendes RE, Gales AC. Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis 2023; 76:S166-S178. [PMID: 37125466 PMCID: PMC10150277 DOI: 10.1093/cid/ciad109] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.
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Affiliation(s)
| | | | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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5
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Interspecies Horizontal Transfer and Specific Integration of the Mosquitocidal Toxin-Encoding Plasmid pTAND672-2 from Bacillus thuringiensis subsp. israelensis to Lysinibacillus sphaericus. Appl Environ Microbiol 2023; 89:e0165222. [PMID: 36749061 PMCID: PMC9973010 DOI: 10.1128/aem.01652-22] [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: 02/08/2023] Open
Abstract
pTAND672-2, a 144-kb resident plasmid of Bacillus thuringiensis serovar israelensis strain TAND672, was sequenced and characterized. This extrachromosomal element carries mosquitocidal toxin-, conjugation-, and recombinase-encoding genes, together with a putative arbitrium system, a genetic module recently discovered in temperate phages controlling lysogeny-lysis transition and in mobile genetic elements (MGEs) where its function remains clarified. Using conjugation experiments, pTAND672-2 is shown to be a novel integrative and conjugative element (ICE), which can horizontally transfer from B. thuringiensis serovar israelensis to Lysinibacillus sphaericus, another mosquitocidal bacterium, where it integrates into the chromosome. Its integration and circularization are reversible and involve a single-cross recombination between 33-bp specific sites, attB in the chromosome of L. sphaericus and attP in pTAND672-2. CDS143, coding for the putative tyrosine integrase Int143 distantly related to site-specific tyrosine Xer recombinases and phage integrases, can mediate the integration of pTAND672-2 to attB. The B. thuringiensis mosquito-killing genes carried by pTAND672-2 are efficiently transcribed and expressed in L. sphaericus, displaying a slight increased toxicity in this bacterium against Aedes albopictus larvae. The occurrence of pTAND672-2-like plasmids within the Bacillus cereus group was also explored and indicated that they all share a similar genetic backbone with diverse plasmid sizes, ranging from 58 to 225 kb. Interestingly, among them, the pEFR-4-4 plasmid of Bacillus paranthracis EFR-4 and p5 of B. thuringiensis BT-59 also display conjugative capability; moreover, like pTAND672-2 displays a chimeric structure between the pCH_133-e- and pBtoxis-like plasmids, pBTHD789-3 also appears to be mosaic of two plasmids. IMPORTANCE Horizontal transfer of mobile genetic elements carrying mosquitocidal toxin genes may play a driving role in the diversity of mosquitocidal bacteria. Here, the 144-kb mosquitocidal toxin-encoding plasmid pTAND672-2 is the first verified integrative and conjugative element (ICE) identified in Bacillus thuringiensis serovar israelensis. The key tyrosine integrase Int143, involved in the specific integration, is distantly related to other tyrosine recombinases. The study also reports the occurrence and potential interspecies transmission of pTAND672-2-like plasmids with varied sizes in B. thuringiensis, Bacillus paranthracis, and Bacillus wiedmannii isolates belonging to the Bacillus cereus group. This study is important for further understanding the evolution and ecology of mosquitocidal bacteria, as well as for providing new direction for the genetic engineering of biopesticides in the control of disease-transmitting mosquitoes.
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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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7
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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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8
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Noel HR, Petrey JR, Palmer LD. Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination. Ann N Y Acad Sci 2022; 1518:166-182. [PMID: 36316792 PMCID: PMC9771954 DOI: 10.1111/nyas.14918] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pathogenic Acinetobacter species, most notably Acinetobacter baumannii, are a significant cause of healthcare-associated infections worldwide. Acinetobacter infections are of particular concern to global health due to the high rates of multidrug resistance and extensive drug resistance. Widespread genome sequencing and analysis has determined that bacterial antibiotic resistance is often acquired and disseminated through the movement of mobile genetic elements, including insertion sequences (IS), transposons, integrons, and conjugative plasmids. In Acinetobacter specifically, resistance to carbapenems and cephalosporins is highly correlated with IS, as many ISAba elements encode strong outwardly facing promoters that are required for sufficient expression of β-lactamases to confer clinical resistance. Here, we review the role of mobile genetic elements in antibiotic resistance in Acinetobacter species through the framework of the mechanism of resistance acquisition and with a focus on experimentally validated mechanisms.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Jessica R. Petrey
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
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9
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Ashrafi S, Kuzmanović N, Patz S, Lohwasser U, Bunk B, Spröer C, Lorenz M, Elhady A, Frühling A, Neumann-Schaal M, Verbarg S, Becker M, Thünen T. Two New Rhizobiales Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies. Microbiol Spectr 2022; 10:e0109922. [PMID: 36005754 PMCID: PMC9603459 DOI: 10.1128/spectrum.01099-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/04/2022] [Indexed: 12/30/2022] Open
Abstract
Root nodules of legume plants are primarily inhabited by rhizobial nitrogen-fixing bacteria. Here, we propose two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia), as shown by core-gene phylogeny, overall genome relatedness indices, and pan-genome analysis. Mesorhizobium onobrychidis sp. nov. actively induces nodules and achieves atmospheric nitrogen and carbon dioxide fixation. This species appears to be depleted in motility genes and is enriched in genes for direct effects on plant growth performance. Its genome reveals functional and plant growth-promoting signatures, like a large unique chromosomal genomic island with high density of symbiotic genetic traits. Onobrychidicola muellerharveyae gen. nov. sp. nov. is described as a type species of the new genus Onobrychidicola in Rhizobiaceae. This species comprises unique genetic features and plant growth-promoting traits (PGPTs), which strongly indicate its function in biotic stress reduction and motility. We applied a newly developed bioinformatics approach for in silico prediction of PGPTs (PGPT-Pred), which supports the different lifestyles of the two new species and the plant growth-promoting performance of M. onobrychidis in the greenhouse trial. IMPORTANCE The intensive use of chemical fertilizers has a variety of negative effects on the environment. Increased utilization of biological nitrogen fixation (BNF) is one way to mitigate those negative impacts. In order to optimize BNF, suitable candidates for different legume species are required. Despite intensive search for new rhizobial bacteria associated with legumes, no new rhizobia have recently been identified from sainfoin (Onobrychis viciifolia). Here, we report on the discovery of two new rhizobial species associated with sainfoin, which are of high importance for the host and may help to increase sustainability in agricultural practices. We employed the combination of in silico prediction and in planta experiments, which is an effective way to detect promising plant growth-promoting bacteria.
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Affiliation(s)
- Samad Ashrafi
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Nemanja Kuzmanović
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Braunschweig, Germany
| | - Sascha Patz
- University of Tübingen, Institute for Bioinformatics and Medical Informatics, Algorithms in Bioinformatics, Tübingen, Germany
| | - Ulrike Lohwasser
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Genebank Department, Seeland, Germany
| | - Boyke Bunk
- Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig, Germany
| | - Maria Lorenz
- Technische Universität Braunschweig, Braunschweig, Germany
| | - Ahmed Elhady
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Anja Frühling
- Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig, Germany
| | - Susanne Verbarg
- Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), Braunschweig, Germany
| | - Matthias Becker
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Braunschweig, Germany
| | - Torsten Thünen
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Crop and Soil Science, Braunschweig, Germany
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10
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Gu Y, Zhang W, Lei J, Zhang L, Hou X, Tao J, Wang H, Deng M, Zhou M, Weng R, Xu J. Molecular epidemiology and carbapenem resistance characteristics of Acinetobacter baumannii causing bloodstream infection from 2009 to 2018 in northwest China. Front Microbiol 2022; 13:983963. [PMID: 36071964 PMCID: PMC9441628 DOI: 10.3389/fmicb.2022.983963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/26/2022] [Indexed: 01/10/2023] Open
Abstract
Bloodstream infection (BSI) caused by Acinetobacter baumannii poses a serious threat to health and is correlated with high mortality in patients with hospital-acquired infections, so the molecular epidemiology and antimicrobial resistance characteristics of this pathogen urgently need to be explored. A. baumannii isolates from BSI patients were collected in three tertiary hospitals in northwest China from 2009 to 2018. Antimicrobial susceptibility testing was used to determine the MICs of the A. baumannii isolates. Whole-genome sequencing based on the Illumina platform was performed for molecular epidemiological analyses and acquired resistance gene screening. The efflux pump phenotype was detected by examining the influence of an efflux pump inhibitor. The expression of efflux pump genes was evaluated by RT-PCR. In total, 47 A. baumannii isolates causing BSI were collected and they presented multidrug resistance, including resistance to carbapenems. Clone complex (CC) 92 was the most prevalent with 30 isolates, among which a cluster was observed in the phylogenetic tree based on the core genome multi-locus sequence type, indicating the dissemination of a dominant clone. BSI-related A. baumannii isolates normally harbour multiple resistance determinants, of which oxacillinase genes are most common. Except for the intrinsic blaOXA-51 family, there are some carbapenem-resistant determinants in these A. baumannii isolates, including blaOXA-23, which is encoded within the Tn2006, Tn2008 or Tn2009 transposon structures and blaOXA-72. The transfer of blaOXA-72 was suggested by XerC/D site-specific recombination. The AdeABC efflux pump system contributed to carbapenem resistance in A. baumannii isolates, as evidenced by the high expression of some of its encoding genes. Both the clone dissemination and carbapenem resistance mediated by oxacillinase or efflux pumps suggest an effective strategy for hospital infection control.
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Affiliation(s)
- Yihai Gu
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Wei Zhang
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Jine Lei
- Department of Clinical Laboratory, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lixia Zhang
- Department of Clinical Laboratory, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China
| | - Xuan Hou
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Junqi Tao
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Hui Wang
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Minghui Deng
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Mengrong Zhou
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Rui Weng
- Department of Microbiology, 3201 hospital, School of Medicine, Xi'an Jiaotong University, Hanzhong, Shaanxi, China
| | - Jiru Xu
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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11
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Tian C, Xing M, Fu L, Zhao Y, Fan X, Wang S. Emergence of uncommon KL38-OCL6-ST220 carbapenem-resistant Acinetobacter pittii strain, co-producing chromosomal NDM-1 and OXA-820 carbapenemases. Front Cell Infect Microbiol 2022; 12:943735. [PMID: 36034705 PMCID: PMC9411868 DOI: 10.3389/fcimb.2022.943735] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/12/2022] [Indexed: 11/23/2022] Open
Abstract
Objective To characterize one KL38-OCL6-ST220 carbapenem-resistant Acinetobacter pittii strain, co-producing chromosomal NDM-1 and OXA-820 carbapenemases. Methods A. pittii TCM strain was isolated from a bloodstream infection (BSI). Antimicrobial susceptibility tests were conducted via disc diffusion and broth microdilution. Stability experiments of blaNDM-1 and blaOXA-820 carbapenemase genes were further performed. Whole-genome sequencing (WGS) was performed on the Illumina and Oxford Nanopore platforms. Multilocus sequence typing (MLST) was analyzed based on the Pasteur and Oxford schemes. Resistance genes, virulence factors, and insertion sequences (ISs) were identified with ABRicate based on ResFinder 4.0, virulence factor database (VFDB), and ISfinder. Capsular polysaccharide (KL), lipooligosaccharide outer core (OCL), and plasmid reconstruction were tested using Kaptive and PLACNETw. PHASTER was used to predict prophage regions. A comparative genomics analysis of all ST220 A. pittii strains from the public database was carried out. Point mutations, average nucleotide identity (ANI), DNA–DNA hybridization (DDH) distances, and pan-genome analysis were performed. Results A. pittii TCM was ST220Pas and ST1818Oxf with KL38 and OCL6, respectively. It was resistant to imipenem, meropenem, and ciprofloxacin but still susceptible to amikacin, colistin, and tigecycline. WGS revealed that A. pittii TCM contained one circular chromosome and four plasmids. The Tn125 composite transposon, including blaNDM-1, was located in the chromosome with 3-bp target site duplications (TSDs). Many virulence factors and the blaOXA-820 carbapenemase gene were also identified. The stability assays revealed that blaNDM-1 and blaOXA-820 were stabilized by passage in an antibiotic-free medium. Moreover, 12 prophage regions were identified in the chromosome. Phylogenetic analysis showed that there are 11 ST220 A. pittii strains, and one collected from Anhui, China was closely related. All ST220 A. pittii strains presented high ANI and DDH values; they ranged from 99.85% to 100% for ANI and from 97.4% to 99.9% for DDH. Pan-genome analysis revealed 3,200 core genes, 0 soft core genes, 1,571 shell genes, and 933 cloud genes among the 11 ST220 A. pittii strains. Conclusions The coexistence of chromosomal NDM-1 and OXA-820 carbapenemases in A. pittii presents a huge challenge in healthcare settings. Increased surveillance of this species in hospital and community settings is urgently needed.
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Affiliation(s)
- Chongmei Tian
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, China
| | - Mengyu Xing
- Department of Pharmacy, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liping Fu
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, China
| | - Yaping Zhao
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, China
| | - Xueyu Fan
- Department of Clinical Laboratory, Quzhou People’s Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
| | - Siwei Wang
- Core Facility, Quzhou People’s Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- *Correspondence: Siwei Wang,
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12
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Moran RA, Liu H, Doughty EL, Hua X, Cummins EA, Liveikis T, McNally A, Zhou Z, van Schaik W, Yu Y. GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes. Microb Genom 2022; 8. [PMID: 35731562 PMCID: PMC9455709 DOI: 10.1099/mgen.0.000840] [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] [Indexed: 11/25/2022] Open
Abstract
Carbapenem and other antibiotic resistance genes (ARGs) can be found in plasmids in Acinetobacter, but many plasmid types in this genus have not been well-characterized. Here we describe the distribution, diversity and evolutionary capacity of rep group 13 (GR13) plasmids that are found in Acinetobacter species from diverse environments. Our investigation was prompted by the discovery of two GR13 plasmids in A. baumannii isolated in an intensive care unit (ICU). The plasmids harbour distinct accessory genes: pDETAB5 contains blaNDM-1 and genes that confer resistance to four further antibiotic classes, while pDETAB13 carries putative alcohol tolerance determinants. Both plasmids contain multiple dif modules, which are flanked by pdif sites recognized by XerC/XerD tyrosine recombinases. The ARG-containing dif modules in pDETAB5 are almost identical to those found in pDETAB2, a GR34 plasmid from an unrelated A. baumannii isolated in the same ICU a month prior. Examination of a further 41 complete, publicly available plasmid sequences revealed that the GR13 pangenome consists of just four core but 1186 accessory genes, 123 in the shell and 1063 in the cloud, reflecting substantial capacity for diversification. The GR13 core genome includes genes for replication and partitioning, and for a putative tyrosine recombinase. Accessory segments encode proteins with diverse putative functions, including for metabolism, antibiotic/heavy metal/alcohol tolerance, restriction-modification, an anti-phage system and multiple toxin–antitoxin systems. The movement of dif modules and actions of insertion sequences play an important role in generating diversity in GR13 plasmids. Discrete GR13 plasmid lineages are internationally disseminated and found in multiple Acinetobacter species, which suggests they are important platforms for the accumulation, horizontal transmission and persistence of accessory genes in this genus.
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Affiliation(s)
- Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Haiyang Liu
- 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
| | - Emma L Doughty
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - 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
| | - Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tomas Liveikis
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhihui Zhou
- 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
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - 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
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13
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Coexistence of blaOXA-58 and blaNDM-1 on a Novel Plasmid of GR59 from an Acinetobacter towneri Isolate. Antimicrob Agents Chemother 2022; 66:e0020622. [PMID: 35546112 DOI: 10.1128/aac.00206-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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14
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Vuillemenot JB, Bour M, Beyrouthy R, Bonnet R, Laaberki MH, Charpentier X, Ruimy R, Plésiat P, Potron A. Genomic analysis of CTX-M-115 and OXA-23/-72 co-producing Acinetobacter baumannii, and their potential to spread resistance genes by natural transformation. J Antimicrob Chemother 2022; 77:1542-1552. [PMID: 35412620 DOI: 10.1093/jac/dkac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/16/2022] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To characterize Acinetobacter baumannii strains co-producing the ESBL CTX-M-115 and carbapenem-hydrolysing class D β-lactamases (CHDLs), and to assess the potential diffusion of their resistance genes by horizontal transfer. METHODS Nineteen CTX-M-115/CHDL-positive A. baumannii were collected between 2015 and 2019 from patients hospitalized in France. Their whole-genome sequences were determined on Illumina and Oxford Nanopore platforms and were compared through core-genome MLST (cgMLST) and SNP analyses. Transferability of resistance genes was investigated by natural transformation assays. RESULTS Eighteen strains were found to harbour CHDL OXA-72, and another one CHDL OXA-23, in addition to CTX-M-115, narrow-spectrum β-lactamases and aminoglycoside resistance determinants including ArmA. cgMLST typing, as well as Oxford Scheme ST and K locus typing, confirmed that 17 out of the 18 CTX-M-115/OXA-72 isolates belonged to new subclades within clonal complex 78 (CC78). The chromosomal region carrying the blaCTX-M-115 gene appeared to vary greatly both in gene content and in length (from 20 to 79 kb) among the strains, likely because of IS26-mediated DNA rearrangements. The blaOXA-72 gene was localized on closely related plasmids showing structural variations that occurred between pdif sites. Transfer of all the β-lactamase genes, as well as aminoglycoside resistance determinants to a drug-susceptible A. baumannii recipient, was easily obtained in vitro by natural transformation. CONCLUSIONS This work highlights the propensity of CC78 isolates to collect multiple antibiotic resistance genes, to rearrange and to pass them to other A. baumannii strains via natural transformation. This process, along with mobile genetic elements, likely contributes to the considerable genomic plasticity of clinical strains, and to the diversity of molecular mechanisms sustaining their multidrug resistance.
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Affiliation(s)
- Jean-Baptiste Vuillemenot
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France.,Laboratoire de Bactériologie, UMR 6249 Chrono-Environnement, UFR Santé, Université Bourgogne Franche-Comté, Besançon, France
| | - Maxime Bour
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France
| | - Racha Beyrouthy
- UMR INSERM 1071 USC INRA2018, Université Clermont Auvergne, Clermont-Ferrand, France.,Laboratoire associé Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, France
| | - Richard Bonnet
- UMR INSERM 1071 USC INRA2018, Université Clermont Auvergne, Clermont-Ferrand, France.,Laboratoire associé Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, France
| | - Maria-Halima Laaberki
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Xavier Charpentier
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Raymond Ruimy
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Nice, UMR INSERM C3M, Université Côte d'Azur, Nice, France
| | - Patrick Plésiat
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France.,Laboratoire de Bactériologie, UMR 6249 Chrono-Environnement, UFR Santé, Université Bourgogne Franche-Comté, Besançon, France
| | - Anaïs Potron
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, France.,Laboratoire de Bactériologie, UMR 6249 Chrono-Environnement, UFR Santé, Université Bourgogne Franche-Comté, Besançon, France
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15
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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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16
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Frequency and diversity of small plasmids in mesophilic Aeromonas isolates from fish, water and sediment. Plasmid 2021; 118:102607. [PMID: 34800545 DOI: 10.1016/j.plasmid.2021.102607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022]
Abstract
Plasmids are autonomous genetic elements ubiquitously present in bacteria. In addition to containing genetic determinants responsible for their replication and stability, some plasmids may carry genes that help bacteria adapt to different environments, while others without a known function are classified as cryptic. In this work we identified and characterized plasmids from a collection of mesophilic Aeromonas spp. (N = 90) isolated from water, sediments and fish. A total of 15 small plasmids ranging from 2287 to 10,558 bp, with an incidence of 16.7% (15/90) was found. Plasmids were detected in A. hydrophila (6), A. veronii (4), A. taiwanensis (2), A. jandaei (1), A. media (1) and Aeromonas sp. (1). There were no large or megaplasmids in the strains studied in this work. Analysis of coding sequences identified proteins associated to replication, mobilization, antibiotic resistance, virulence and stability. A considerable number of hypothetical proteins with unknown functions were also found. Some strains shared identical plasmid profiles, however, only two of them were clones. Small plasmids could be acting as a gene repositories as suggested by the presence of a gene encoding for a putative zonula occludens toxin (Zot) that causes diarrhea and the qnrB gene involved in quinolone resistance harbored in plasmids pAerXII and pAerXIII respectively.
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17
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Bonnin RA, Dortet L, Naas T. Acquired carbapenemase in Acinetobacter during the pre-antibiotic era. THE LANCET MICROBE 2021; 2:e137. [DOI: 10.1016/s2666-5247(21)00032-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 10/21/2022] Open
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18
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Wilkowska K, Mruk I, Furmanek-Blaszk B, Sektas M. Low-level expression of the Type II restriction-modification system confers potent bacteriophage resistance in Escherichia coli. DNA Res 2021; 27:5804985. [PMID: 32167561 PMCID: PMC7315355 DOI: 10.1093/dnares/dsaa003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/09/2020] [Indexed: 01/21/2023] Open
Abstract
Restriction–modification systems (R–M) are one of the antiviral defense tools used by bacteria, and those of the Type II family are composed of a restriction endonuclease (REase) and a DNA methyltransferase (MTase). Most entering DNA molecules are usually cleaved by the REase before they can be methylated by MTase, although the observed level of fragmented DNA may vary significantly. Using a model EcoRI R–M system, we report that the balance between DNA methylation and cleavage may be severely affected by transcriptional signals coming from outside the R–M operon. By modulating the activity of the promoter, we obtained a broad range of restriction phenotypes for the EcoRI R–M system that differed by up to 4 orders of magnitude in our biological assays. Surprisingly, we found that high expression levels of the R–M proteins were associated with reduced restriction of invading bacteriophage DNA. Our results suggested that the regulatory balance of cleavage and methylation was highly sensitive to fluctuations in transcriptional signals both up- and downstream of the R–M operon. Our data provided further insights into Type II R–M system maintenance and the potential conflict within the host bacterium.
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Affiliation(s)
- Karolina Wilkowska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Beata Furmanek-Blaszk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Marian Sektas
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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19
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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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20
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Sykes EME, Deo S, Kumar A. Recent Advances in Genetic Tools for Acinetobacter baumannii. Front Genet 2020; 11:601380. [PMID: 33414809 PMCID: PMC7783400 DOI: 10.3389/fgene.2020.601380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
Acinetobacter baumannii is classified as a top priority pathogen by the World Health Organization (WHO) because of its widespread resistance to all classes of antibiotics. This makes the need for understanding the mechanisms of resistance and virulence critical. Therefore, tools that allow genetic manipulations are vital to unravel the mechanisms of multidrug resistance (MDR) and virulence in A. baumannii. A host of current strategies are available for genetic manipulations of A. baumannii laboratory-strains, including ATCC® 17978TM and ATCC® 19606T, but depending on susceptibility profiles, these strategies may not be sufficient when targeting strains newly obtained from clinic, primarily due to the latter's high resistance to antibiotics that are commonly used for selection during genetic manipulations. This review highlights the most recent methods for genetic manipulation of A. baumannii including CRISPR based approaches, transposon mutagenesis, homologous recombination strategies, reporter systems and complementation techniques with the spotlight on those that can be applied to MDR clinical isolates.
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Affiliation(s)
- Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Soumya Deo
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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21
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Camargo CH, Cunha MPV, de Barcellos TAF, Bueno MS, Bertani AMDJ, dos Santos CA, Nagamori FO, Takagi EH, Chimara E, de Carvalho E, Tiba-Casas MR. Genomic and phenotypic characterisation of antimicrobial resistance in carbapenem-resistant Acinetobacter baumannii hyperendemic clones CC1, CC15, CC79 and CC25. Int J Antimicrob Agents 2020; 56:106195. [DOI: 10.1016/j.ijantimicag.2020.106195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/29/2020] [Accepted: 10/04/2020] [Indexed: 12/17/2022]
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22
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Ayibieke A, Kobayashi A, Suzuki M, Sato W, Mahazu S, Prah I, Mizoguchi M, Moriya K, Hayashi T, Suzuki T, Iwanaga S, Ablordey A, Saito R. Prevalence and Characterization of Carbapenem-Hydrolyzing Class D β-Lactamase-Producing Acinetobacter Isolates From Ghana. Front Microbiol 2020; 11:587398. [PMID: 33281784 PMCID: PMC7691484 DOI: 10.3389/fmicb.2020.587398] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
Multidrug resistance, especially carbapenem resistance in Acinetobacter bacteria is a global healthcare concern. However, available data on the phenotypic and genotypic characteristics of Acinetobacter isolates from West Africa, including Ghana is scanty. Our aim was to investigate the antibiotic resistance profile and genotypic characteristics of Acinetobacter isolates from Ghana and to characterize carbapenemase producers using whole-genome sequencing (WGS). A total of 36 Acinetobacter isolates collected at three hospitals in Ghana between 2016 and 2017 were analyzed. MICs were determined by commercial antibiotic plates. Acinetobacter baumannii MLST was determined using the Pasteur scheme. WGS of OXA-carbapenemase producers was performed using short- and long-read sequencing strategies. The resistance rate was highest for trimethoprim/sulfamethoxazole (n = 22; 61%). Six (16.7%) and eight (22.2%) isolates were resistant to ceftazidime and colistin, respectively. Two (5.6%) isolates were resistant and one (2.8%) isolate had intermediate sensitivity to three carbapenems. Fifteen STs were identified in 24 A. baumannii isolates including six new STs (ST1467 ∼ ST1472). ST78 was the predominant (n = 6) followed by ST1469 (n = 3). Four carbapenemase-producing A. baumannii isolates also were identified. Isogenic ST103 isolates Ab-B004d-c and Ab-D10a-a harbored blaOXA–23 within Tn2007 on identical plasmids, pAb-B004d-c_3, and pAb-D10a-a_3. ST1472 isolate Ab-C102 and ST107 isolate Ab-C63 carried blaOXA–58 and blaOXA–420, a rare blaOXA–58 variant, respectively, within novel genetic contexts. Our results show that A. baumannii isolates of diverse and unique genotypes, including OXA-carbapenemase producers, are circulating in Ghana highlighting the need for a wider surveillance of antimicrobial resistance.
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Affiliation(s)
- Alafate Ayibieke
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayumi Kobayashi
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Wakana Sato
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Environmental Parasitology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Miyuki Mizoguchi
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Takaya Hayashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shiroh Iwanaga
- Department of Environmental Parasitology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ryoichi Saito
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
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23
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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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24
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Wang J, Wang Y, Wu H, Wang ZY, Shen PC, Tian YQ, Sun F, Pan ZM, Jiao X. Coexistence of bla OXA-58 and tet(X) on a Novel Plasmid in Acinetobacter sp. From Pig in Shanghai, China. Front Microbiol 2020; 11:578020. [PMID: 33042094 PMCID: PMC7530245 DOI: 10.3389/fmicb.2020.578020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/18/2020] [Indexed: 12/31/2022] Open
Abstract
The purpose of this study was to characterize the complete sequence of a novel plasmid carrying tigecycline resistance gene tet(X) and carbapenemase gene blaOXA-58 from a swine Acinetobacter sp. strain SH19PTT10. Minimal inhibitory concentration (MIC) was performed using microbroth dilution method. The isolate SH19PTT10 was highly resistant (16 mg/L) to tigecycline, and also exhibited resistance to ampicillin, streptomycin, tetracycline, chloramphenicol, florfenicol, ciprofloxacin, and sulfamethoxazole/trimethoprim. Although SH19PTT10 harbored blaOXA-58, it was susceptible to cefotaxime and meropenem. The genome sequence of SH19PTT10 was determined using PacBio single-molecule real-time sequencing. Plasmid pYUSHP10-1 had a size of 174,032 bp and showed partial homology to several plasmids found in Acinetobacter isolates. It contained two repA genes, putative toxin-antitoxin systems (HipA/HipB, RelE/RelB, and BrnT/BrnA), partitioning genes (parA and parB), and heavy metal resistance-associated genes (copA/copB, nrp, and czcA/czcD) but the transfer region or proteins was not found. pYUSHP10-1 carried 16 resistance genes, mainly clustered in two mosaic multiresistance regions (MRRs). The first MRR contained sul3, qacI-aadA1-clmA1-aadA2-blaCARB-2-dfrA16 cassette, aac(3)-IId, and blaOXA-58. The blaOXA-58 gene was associated with ISAba3, as previously described. The second MRR is the tet(X) region (ISAcsp12-aph(3')-Ia-IS26-ΔxerD-tet(X)-res-ISCR2-sul2) related to the corresponding region in other tet(X)-bearing plasmids. The pdif sites, as well as mobile elements, play an important role in mobilization of DNA modules and plasmid evolution. Coexistence of numerous resistance genes on a single plasmid may contribute to the dissemination of these genes under pressure posed by different agents, which may explain the presence of clinically crucial resistance genes tet(X) and blaOXA-58 in livestock. Thus, rational drug use and continued surveillance of tet(X) and blaOXA-58 in livestock are warranted.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yan Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Han Wu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhen-Yu Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Peng-Cheng Shen
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yu-Qi Tian
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Fan Sun
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhi-Ming Pan
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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25
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Monem S, Furmanek-Blaszk B, Łupkowska A, Kuczyńska-Wiśnik D, Stojowska-Swędrzyńska K, Laskowska E. Mechanisms Protecting Acinetobacter baumannii against Multiple Stresses Triggered by the Host Immune Response, Antibiotics and Outside-Host Environment. Int J Mol Sci 2020; 21:E5498. [PMID: 32752093 PMCID: PMC7432025 DOI: 10.3390/ijms21155498] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is considered one of the most persistent pathogens responsible for nosocomial infections. Due to the emergence of multidrug resistant strains, as well as high morbidity and mortality caused by this pathogen, A. baumannii was placed on the World Health Organization (WHO) drug-resistant bacteria and antimicrobial resistance research priority list. This review summarizes current studies on mechanisms that protect A. baumannii against multiple stresses caused by the host immune response, outside host environment, and antibiotic treatment. We particularly focus on the ability of A. baumannii to survive long-term desiccation on abiotic surfaces and the population heterogeneity in A. baumannii biofilms. Insight into these protective mechanisms may provide clues for the development of new strategies to fight multidrug resistant strains of A. baumannii.
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Affiliation(s)
- Soroosh Monem
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Beata Furmanek-Blaszk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Adrianna Łupkowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Dorota Kuczyńska-Wiśnik
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Karolina Stojowska-Swędrzyńska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
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26
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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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27
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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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28
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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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29
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Salgado-Camargo AD, Castro-Jaimes S, Gutierrez-Rios RM, Lozano LF, Altamirano-Pacheco L, Silva-Sanchez J, Pérez-Oseguera Á, Volkow P, Castillo-Ramírez S, Cevallos MA. Structure and Evolution of Acinetobacter baumannii Plasmids. Front Microbiol 2020; 11:1283. [PMID: 32625185 PMCID: PMC7315799 DOI: 10.3389/fmicb.2020.01283] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/20/2020] [Indexed: 11/24/2022] Open
Abstract
Acinetobacter baumannii is an emergent bacterial pathogen that provokes many types of infections in hospitals around the world. The genome of this organism consists of a chromosome and plasmids. These plasmids vary over a wide size range and many of them have been linked to the acquisition of antibiotic-resistance genes. Our bioinformatic analyses indicate that A. baumannii plasmids belong to a small number of plasmid lineages. The general structure of these lineages seems to be very stable and consists not only of genes involved in plasmid maintenance functions but of gene sets encoding poorly characterized proteins, not obviously linked to survival in the hospital setting, and opening the possibility that they improve the parasitic properties of plasmids. An analysis of genes involved in replication, suggests that members of the same plasmid lineage are part of the same plasmid incompatibility group. The same analysis showed the necessity of classifying the Rep proteins in ten new groups, under the scheme proposed by Bertini et al. (2010). Also, we show that some plasmid lineages have the potential capacity to replicate in many bacterial genera including those embracing human pathogen species, while others seem to replicate only within the limits of the Acinetobacter genus. Moreover, some plasmid lineages are widely distributed along the A. baumannii phylogenetic tree. Despite this, a number of them lack genes involved in conjugation or mobilization functions. Interestingly, only 34.6% of the plasmids analyzed here possess antibiotic resistance genes and most of them belong to fourteen plasmid lineages of the twenty one described here. Gene flux between plasmid lineages appears primarily limited to transposable elements, which sometimes carry antibiotic resistance genes. In most plasmid lineages transposable elements and antibiotic resistance genes are secondary acquisitions. Finally, broad host-range plasmids appear to have played a crucial role.
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Affiliation(s)
- Abraham D Salgado-Camargo
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Semiramis Castro-Jaimes
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Rosa-Maria Gutierrez-Rios
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis F Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis Altamirano-Pacheco
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jesús Silva-Sanchez
- Grupo de Resistencia Bacteriana, Centro de Investigaciones Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Ángeles Pérez-Oseguera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Patricia Volkow
- Departamento de Infectología, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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30
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Bonnin RA, Girlich D, Jousset AB, Gauthier L, Cuzon G, Bogaerts P, Haenni M, Madec JY, Couvé-Deacon E, Barraud O, Fortineau N, Glaser P, Glupczynski Y, Dortet L, Naas T. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales. Sci Rep 2020; 10:9160. [PMID: 32514057 PMCID: PMC7280188 DOI: 10.1038/s41598-020-66161-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
Abstract
In Enterobacterales, the most common carbapenemases are Ambler's class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The blaOXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the blaOXA-23 gene in that isolate. By contrast to the blaOXA-23 genes, the blaOXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the blaOXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.
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Affiliation(s)
- Rémy A Bonnin
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Delphine Girlich
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Agnès B Jousset
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Lauraine Gauthier
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Gaëlle Cuzon
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Pierre Bogaerts
- Belgian National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, B-5530, Yvoir, Belgium
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES Laboratoire de Lyon, 31 avenue Tony Garnier, 69364, Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES Laboratoire de Lyon, 31 avenue Tony Garnier, 69364, Lyon, France
| | | | - Olivier Barraud
- Université de Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France
| | - Nicolas Fortineau
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Philippe Glaser
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Youri Glupczynski
- Belgian National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, B-5530, Yvoir, Belgium
| | - Laurent Dortet
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France.
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.
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Hamidian M, Nigro SJ. Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii. Microb Genom 2020; 5. [PMID: 31599224 PMCID: PMC6861865 DOI: 10.1099/mgen.0.000306] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of high levels of resistance to many antibiotics, particularly those considered to be last-resort antibiotics, such as carbapenems. Although alterations in the efflux pump and outer membrane proteins can cause carbapenem resistance, the main mechanism is the acquisition of carbapenem-hydrolyzing oxacillinase-encoding genes. Of these, oxa23 is by far the most widespread in most countries, while oxa24 and oxa58 appear to be dominant in specific regions. Historically, much of the global spread of carbapenem resistance has been due to the dissemination of two major clones, known as global clones 1 and 2, although new lineages are now common in some parts of the world. The analysis of all publicly available genome sequences performed here indicates that ST2, ST1, ST79 and ST25 account for over 71 % of all genomes sequenced to date, with ST2 by far the most dominant type and oxa23 the most widespread carbapenem resistance determinant globally, regardless of clonal type. Whilst this highlights the global spread of ST1 and ST2, and the dominance of oxa23 in both clones, it could also be a result of preferential selection of carbapenem-resistant strains, which mainly belong to the two major clones. Furthermore, ~70 % of the sequenced strains have been isolated from five countries, namely the USA, PR China, Australia, Thailand and Pakistan, with only a limited number from other countries. These genomes are a vital resource, but it is currently difficult to draw an accurate global picture of this important superbug, highlighting the need for more comprehensive genome sequence data and genomic analysis.
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Affiliation(s)
- Mohammad Hamidian
- The ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Steven J Nigro
- Communicable Diseases Branch, Health Protection NSW, St Leonards, NSW 2065, Australia
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
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Walter T, Klim J, Jurkowski M, Gawor J, Köhling I, Słodownik M, Zielenkiewicz U. Plasmidome of an environmental Acinetobacter lwoffii strain originating from a former gold and arsenic mine. Plasmid 2020; 110:102505. [PMID: 32380021 DOI: 10.1016/j.plasmid.2020.102505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/20/2020] [Accepted: 04/12/2020] [Indexed: 02/08/2023]
Abstract
Emerging important Acinetobacter strains commonly accommodate a plethora of mobile elements including plasmids of different size. Plasmids, apart from encoding modules enabling their self-replication and/or transmission, can carry a diverse number of genes, allowing the host cell to survive in an environment that would otherwise be lethal or restrictive for growth. The present study characterizes the plasmidome generated from an arsenic-resistant strain named ZS207, classified as Acinetobacter lwoffii. Sequencing effort revealed the presence of nine plasmids in the size between 4.3 and 38.4 kb as well as one 186.6 kb megaplasmid. All plasmids, except the megaplasmid, do apparently not confer distinguishing phenotypic features. In contrast, the megaplasmid carries arsenic and heavy metals resistance regions similar to those found in permafrost A. lwoffii strains. In-depth in silico analyses have shown a significant similarity between the regions from these plasmids, especially concerning multiple transposable elements, transfer and mobilization genes, and toxin-antitoxin systems. Since ars genes encode proteins of major significance in terms of potential use in bioremediation, arsenic resistance level of ZS207 was determined and the functionality of selected ars genes was examined. Additionally, we checked the functionality of plasmid-encoded toxin-antitoxin systems and their impact on the formation of persister cells.
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Affiliation(s)
- Tomasz Walter
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Joanna Klim
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Marcin Jurkowski
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Iwona Köhling
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Małgorzata Słodownik
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland
| | - Urszula Zielenkiewicz
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a Str., 02-106 Warsaw, Poland.
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The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9040186. [PMID: 32316342 PMCID: PMC7235769 DOI: 10.3390/antibiotics9040186] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups.
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Novel IS26-mediated hybrid plasmid harbouring tet(X4) in Escherichia coli. J Glob Antimicrob Resist 2020; 21:162-168. [PMID: 32247809 DOI: 10.1016/j.jgar.2020.03.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/03/2020] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES As the spread of antimicrobial resistance genes becomes an increasing global threat, improved understanding of genetic structure and transferability of the resistant plasmids becomes more critical. The newly description of several plasmid-mediated tet(X) variant genes, tet(X3), tet(X4) and tet(X5), poses a considerable risk for public health. This study aimed to investigate the recombination event that occurred during the conjugation process of a tet(X4)-bearing plasmid. METHODS A Tet(X4)-producing Escherichia coli isolate, 2019XSD11, was subjected to susceptibility testing, S1-PFGE and whole genome sequencing. The genetic features of plasmids and the recombination event were analysed by sequence comparison and annotation. We performed electrotransformation assay to further test the transferability of the tet(X4)-bearing plasmid. RESULTS A novel type of fusion tet(X4)-bearing plasmid was discovered from the transconjugant, plasmid p2019XSD11-TC2-284 (∼280kbp). The sequence of this plasmid consisted of a hybrid episome of two plasmids p2019XSD11-190 (∼190kbp) harbouring tet(X4) and p2019XSD11-92 (∼92kbp) harbouring blaCTX-M-55 originated from 2019XSD11. The two plasmids were concatenated by IS26 elements. Analyses of the genetic constitution of the plasmids essential for transmission showed the plasmid p2019XSD11-190 lacked an intact type IV secretion system. Beyond this, the origin of transfer region and relaxase genes in plasmid p2019XSD11-190 had no sequence similarity with those in plasmid p2019XSD11-92. CONCLUSIONS The fusion of the two plasmids probably formed through IS26 homologous recombination. Such recombination events presumably play an important role in the dissemination of the tet(X4). Molecular surveillance of tet(X) variant genes and genetic structures warrants further investigation to evaluate the underlying public health risk.
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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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Brovedan M, Repizo GD, Marchiaro P, Viale AM, Limansky A. Characterization of the diverse plasmid pool harbored by the blaNDM-1-containing Acinetobacter bereziniae HPC229 clinical strain. PLoS One 2019; 14:e0220584. [PMID: 31743332 PMCID: PMC6863613 DOI: 10.1371/journal.pone.0220584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/24/2019] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter bereziniae is an environmental microorganism with increasing clinical incidence, and may thus provide a model for a bacterial species bridging the gap between the environment and the clinical setting. A. bereziniae plasmids have been poorly studied, and their characterization could offer clues on the causes underlying the leap between these two different habitats. Here we characterized the whole plasmid content of A. bereziniae HPC229, a clinical strain previously reported to harbor a 44-kbp plasmid, pNDM229, conferring carbapenem and aminoglycoside resistance. We identified five extra plasmids in HPC229 ranging from 114 to 1.3 kbp, including pAbe229-114 (114 kbp) encoding a MOBP111 relaxase and carrying heavy metal resistance, a bacteriophage defense BREX system and four different toxin-antitoxin (TA) systems. Two other replicons, pAbe229-15 (15.4 kbp) and pAbe229-9 (9.1 kbp), both encoding MOBQ1 relaxases and also carrying TA systems, were found. The three latter plasmids contained Acinetobacter Rep_3 superfamily replication initiator protein genes, and functional analysis of their transfer regions revealed the mobilizable nature of them. HPC229 also harbors two smaller plasmids, pAbe229-4 (4.4 kbp) and pAbe229-1 (1.3 kbp), the former bearing a ColE1-type replicon and a TA system, and the latter lacking known replication functions. Comparative sequence analyses against deposited Acinetobacter genomes indicated that the above five HPC229 plasmids were unique, although some regions were also present in other of these genomes. The transfer, replication, and adaptive modules in pAbe229-15, and the stability module in pAbe229-9, were bordered by sites potentially recognized by XerC/XerD site-specific tyrosine recombinases, thus suggesting a potential mechanism for their acquisition. The presence of Rep_3 and ColE1-based replication modules, different mob genes, distinct adaptive functions including resistance to heavy metal and other environmental stressors, as well as antimicrobial resistance genes, and a high content of XerC/XerD sites among HPC229 plasmids provide evidence of substantial links with bacterial species derived from both environmental and clinical habitats.
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Affiliation(s)
- Marco Brovedan
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Guillermo D. Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Patricia Marchiaro
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Alejandro M. Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (AMV); (AL)
| | - Adriana Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (AMV); (AL)
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Abstract
Although the blaOXA-58 gene has been infrequently described in Brazil, contrasting with other bordering South American countries, we verified the maintenance of this resistance determinant over time among carbapenem-resistant Acinetobacter species isolates, not only in nosocomial settings but also in the environment. In addition, to the best of our knowledge, this is the first study to have used WPS analysis to evaluate the genetic surroundings of blaOXA-58 in Brazil. Moreover, the A. seifertii and A. baumannii clinical strains evaluated in this study were recovered 17 years apart in hospitals located in distinct Brazilian geographic regions. We characterize by whole-plasmid-sequence (WPS) two-plasmid-borne blaOXA-58 obtained from Acinetobacter seifertii (Asp-1069) and A. baumannii (Acb-45063) clinical strains recovered 17 years apart from distinct Brazilian regions. Multilocus sequence type (MLST) analysis showed that the Asp-1069 and Acb-45063 strains belong to ST551 and ST15/CC15, respectively. WPS analysis demonstrated that blaOXA-58 was located in two distinct plasmids named pAs1069_a (24,672 bp/44 open reading frames [ORFs]) and pAb45063_b (19,808 bp/24 ORFs), which belong to the GR8/GR23 (repAci23) and GR4 (repAci4) incompatibility groups, respectively. The genetic environments surrounding blaOXA-58 revealed that it was flanked by two intact ISAba3 copies on pAb45063_b, which differed from pAs1069_a. In the latter, the upstream ISAba3 copy was truncated by insertion of ISAba825 element. Although Re27-specific recombination sites were found adjacent to ISAba3-blaOXA-58-ISAba3 arrangement on pAb45063_b, such structures were absent on pAs1069_a. The conserved ISAba125-araC1-lysE arrangement was disrupted by TnaphA6 harboring the aminoglycosides resistance gene aphA6 on pAs1069_a, while an IS26-blaTEM-1-aac(3)-IIa-IS26 genetic structure was found upstream from ISAba3-blaOXA-58-ISAba3 on pAb45063_b. Other two plasmids, pAb45063_a (183,767 bp/209 ORFs) and pAs1069_b (13,129 bp/14 ORFs), were also found in the OXA-58-producing Acinetobacter species strains, harboring the strA and strB genes and the sul2 gene, which confer resistance to streptomycin and sulfonamides, respectively. The plasmid-mediated virulence factors corresponding to genes tonB, spl, glmM, ppa, sulP, and map were found in both strains, as well distinct toxin-antitoxin system-encoding genes stbD and relE (pAs1069_a), brnT and brnA (pAb45063_b), and xreE (pAb45063_a). Although infrequently reported in Brazil, plasmid-borne blaOXA-58 showed a complex and diverse genetic backbone that confers stability in different Acinetobacter species that have been isolated from nosocomial settings over time. IMPORTANCE Although the blaOXA-58 gene has been infrequently described in Brazil, contrasting with other bordering South American countries, we verified the maintenance of this resistance determinant over time among carbapenem-resistant Acinetobacter species isolates, not only in nosocomial settings but also in the environment. In addition, to the best of our knowledge, this is the first study to have used WPS analysis to evaluate the genetic surroundings of blaOXA-58 in Brazil. Moreover, the A. seifertii and A. baumannii clinical strains evaluated in this study were recovered 17 years apart in hospitals located in distinct Brazilian geographic regions.
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Ramirez MS, Iriarte A, Reyes-Lamothe R, Sherratt DJ, Tolmasky ME. Small Klebsiella pneumoniae Plasmids: Neglected Contributors to Antibiotic Resistance. Front Microbiol 2019; 10:2182. [PMID: 31616398 PMCID: PMC6764390 DOI: 10.3389/fmicb.2019.02182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is the causative agent of community- and, more commonly, hospital-acquired infections. Infections caused by this bacterium have recently become more dangerous due to the acquisition of multiresistance to antibiotics and the rise of hypervirulent variants. Plasmids usually carry genes coding for resistance to antibiotics or virulence factors, and the recent sequence of complete K. pneumoniae genomes showed that most strains harbor many of them. Unlike large plasmids, small, usually high copy number plasmids, did not attract much attention. However, these plasmids may include genes coding for specialized functions, such as antibiotic resistance, that can be expressed at high levels due to gene dosage effect. These genes may be part of mobile elements that not only facilitate their dissemination but also participate in plasmid evolution. Furthermore, high copy number plasmids may also play a role in evolution by allowing coexistence of mutated and non-mutated versions of a gene, which helps to circumvent the constraints imposed by trade-offs after certain genes mutate. Most K. pneumoniae plasmids 25-kb or smaller replicate by the ColE1-type mechanism and many of them are mobilizable. The transposon Tn1331 and derivatives were found in a high percentage of these plasmids. Another transposon that was found in representatives of this group is the bla KPC-containing Tn4401. Common resistance determinants found in these plasmids were aac(6')-Ib and genes coding for β-lactamases including carbapenemases.
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Affiliation(s)
- Maria S. Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Universidad de la República de Uruguay, Montevideo, Uruguay
| | | | - David J. Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Kumar S, Patil PP, Singhal L, Ray P, Patil PB, Gautam V. Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii isolates reveals the emergence of bla OXA-23 and bla NDM-1 encoding international clones in India. INFECTION GENETICS AND EVOLUTION 2019; 75:103986. [PMID: 31362071 DOI: 10.1016/j.meegid.2019.103986] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 01/09/2023]
Abstract
Acinetobacter baumannii is a nosocomial pathogen increasingly affecting the critically ill patients and represents a major public health challenge. Carbapenem-resistant A. baumannii (CRAB) is found to be associated with International Clones (ICs) and different classes of carbapenemases. The objective of the present study was to investigate the prevalence of carbapenem resistance genes, clonal relationship and genetic structure of clinical isolates of A. baumannii. In the present study, multi-locus sequence typing (MLSTOX) and analysis were carried out using Oxford scheme for 86 clinical isolates of CRAB along with 11 carbapenem sensitive A. baumannii (CSAB) collected over a period of two years (2014-2016) from two tertiary care hospitals of North India. We observed a high prevalence of the blaOXA-23-like (97.7%) among the CRAB followed by blaNDM-1 (29.1%) and blaOXA58-like (3.5%). Forty-seven Sequence Types (STs) were represented by all 97 isolates, out of which, 28 (59.6%) were novel STs that were assigned to 41 isolates. STs 451 (13%), 447 (7%), 195 (6%) and 848 (5%) were the most common STs. The majority of CRAB isolates (44.3%) belonged to the CC92, followed by the CC447 (15.1%), CC109 (9.3%) and CC110 (3.4%), which corresponds to the IC2, 8, 1 and 7 respectively. Phylogenetic and recombination analysis suggested two major and one minor lineage in the population. Further linkage disequilibrium analysis suggested clonal nature of the population as recombination was noticed at a low frequency, which was not enough to split the clonal relationship. The knowledge of genetic structure of CRAB from this study will be invaluable to illustrate epidemiology, surveillance and understanding its global diversity.
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Affiliation(s)
- Sunil Kumar
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India; Department of Biotechnology, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, Haryana 133207, India
| | - Prashant P Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India
| | - Lipika Singhal
- Government Medical College and Hospital, Sector -32B, Chandigarh 160030, India
| | - Pallab Ray
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India.
| | - Vikas Gautam
- Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India.
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Mindlin S, Beletsky A, Mardanov A, Petrova M. Adaptive dif Modules in Permafrost Strains of Acinetobacter lwoffii and Their Distribution and Abundance Among Present Day Acinetobacter Strains. Front Microbiol 2019; 10:632. [PMID: 30984151 PMCID: PMC6449649 DOI: 10.3389/fmicb.2019.00632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/13/2019] [Indexed: 12/22/2022] Open
Abstract
The dif/Xer system of site-specific recombination allows resolution of chromosomal dimers during bacterial DNA replication. Recently, it was also shown to be involved in horizontal transfer of a few known Xer-dependent mobile elements. Here, we show that plasmids of various Acinetobacter species, including clinically important strains, often contain multiple pdif sites that are mainly located within their accessory regions. Chromosomes of Acinetobacter strains may also contain additional dif sites, and their similarity with plasmid pdif sites is higher than with the main chromosomal site dif1. We further identify putative mobile genetic elements containing pdif sites on both flanks of adaptive genes and analyze their distribution in Acinetobacter species. In total, we describe seven mobile elements containing genes with various adaptive functions from permafrost strains of A. lwoffii group. All of them are also spread in modern plasmids of different Acinetobacter species including A. baumannii. We could not detect pdif sites and corresponding mobile elements in closely related bacterial genera, including Psychrobacter and Moraxella. Thus, the widespread distribution of dif modules is a characteristic feature of Acinetobacter species and may contribute to their high adaptability both in the environment and in the clinic.
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Affiliation(s)
- Sofia Mindlin
- Laboratory of Molecular Genetics of Microorganisms, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Beletsky
- Laboratory of Microorganism Genomics and Metagenomics, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mardanov
- Laboratory of Microorganism Genomics and Metagenomics, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Mayya Petrova
- Laboratory of Molecular Genetics of Microorganisms, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Dionisio F, Zilhão R, Gama JA. Interactions between plasmids and other mobile genetic elements affect their transmission and persistence. Plasmid 2019; 102:29-36. [DOI: 10.1016/j.plasmid.2019.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 10/27/2022]
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Hamidian M, Hall RM. Genetic structure of four plasmids found in Acinetobacter baumannii isolate D36 belonging to lineage 2 of global clone 1. PLoS One 2018; 13:e0204357. [PMID: 30260997 PMCID: PMC6160057 DOI: 10.1371/journal.pone.0204357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/06/2018] [Indexed: 11/24/2022] Open
Abstract
Four plasmids ranging in size from 4.7 to 44.7 kb found in the extensively antibiotic resistant Acinetobacter baumannii isolate D36 that belongs to lineage 2 of global clone 1 were examined. D36 includes two cryptic plasmids and two carrying antibiotic resistance genes. The smallest plasmid pD36-1 (4.7 kb) carries no resistance genes but includes mobA and mobC mobilisation genes related to those found in pRAY* (pD36-2, 6,078 bp) that also carries the aadB gentamicin, kanamycin and tobramycin resistance gene cassette. These two plasmids do not encode a Rep protein. Plasmid pRAY* was found to be mobilised at high frequency by the large conjugative plasmid pA297-3 but a pRAY* derivative lacking the mobA and mobC genes was not. The two larger plasmids, pD36-3 and pD36-4, encode Rep_3 family proteins (Pfam1051). The cryptic plasmid pD36-3 (6.2 kb) has RepAci1 and pD36-4 (44.7 kb) encodes two novel Rep_3 family proteins suggesting a co-integrate. Plasmid pD36-4 includes the sul2 sulfonamide resistance gene, the aphA1a kanamycin/neomycin resistance gene in Tn4352::ISAba1 and a mer module in a hybrid Tn501/Tn1696 transposon conferring resistance to mercuric ions. New examples of dif modules flanked by pdif sites (XerC-XerD binding sites) that are part of many A. baumannii plasmids were also identified in pD36-3 and pD36-4 which carry three and two dif modules, respectively. Homologs of three dif modules, the sup sulphate permease module in pD36-3, and of the abkAB toxin-antitoxin module and the orf module in pD36-4, were found in different contexts in diverse Acinetobacter plasmids, consistent with module mobility. A novel insertion sequence named ISAba32 found next to the pdif site in the abkAB dif module is related to members of the ISAjo2 group which also are associated with the pdif sites of dif modules. Plasmids found in D36 were also found in some other members of GC1 lineage 2.
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Affiliation(s)
- Mohammad Hamidian
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, Australia
- * E-mail:
| | - Ruth M. Hall
- School of Life and Environmental Sciences, The University of Sydney, New South Wales, Australia
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