1
|
Karampatakis T, Tsergouli K, Behzadi P. Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove for Acinetobacter baumannii. Antibiotics (Basel) 2024; 13:257. [PMID: 38534692 DOI: 10.3390/antibiotics13030257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/17/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative pathogen responsible for a variety of community- and hospital-acquired infections. It is recognized as a life-threatening pathogen among hospitalized individuals and, in particular, immunocompromised patients in many countries. A. baumannii, as a member of the ESKAPE group, encompasses high genomic plasticity and simultaneously is predisposed to receive and exchange the mobile genetic elements (MGEs) through horizontal genetic transfer (HGT). Indeed, A. baumannii is a treasure trove that contains a high number of virulence factors. In accordance with these unique pathogenic characteristics of A. baumannii, the authors aim to discuss the natural treasure trove of pan-genome and virulence factors pertaining to this bacterial monster and try to highlight the reasons why this bacterium is a great concern in the global public health system.
Collapse
Affiliation(s)
| | - Katerina Tsergouli
- Microbiology Department, Agios Pavlos General Hospital, 55134 Thessaloniki, Greece
| | - Payam Behzadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran 37541-374, Iran
| |
Collapse
|
2
|
Minnick MF. Functional Roles and Genomic Impact of Miniature Inverted-Repeat Transposable Elements (MITEs) in Prokaryotes. Genes (Basel) 2024; 15:328. [PMID: 38540387 PMCID: PMC10969869 DOI: 10.3390/genes15030328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
Prokaryotic genomes are dynamic tapestries that are strongly influenced by mobile genetic elements (MGEs), including transposons (Tn's), plasmids, and bacteriophages. Of these, miniature inverted-repeat transposable elements (MITEs) are undoubtedly the least studied MGEs in bacteria and archaea. This review explores the diversity and distribution of MITEs in prokaryotes and describes what is known about their functional roles in the host and involvement in genomic plasticity and evolution.
Collapse
Affiliation(s)
- Michael F Minnick
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Zheng L, Zhang X, Zhu L, Lu G, Guan J, Liu M, Jing J, Sun S, Wang Y, Sun Y, Ji X, Jiang B, Chen J, Liu J, Chen P, Guo X. A clinical Pseudomonas juntendi strain with blaIMP−1 carried by an integrative and conjugative element in China. Front Microbiol 2022; 13:929800. [PMID: 35966707 PMCID: PMC9374279 DOI: 10.3389/fmicb.2022.929800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Objective To precisely determine the species of a carbapenem-resistant Pseudomonas strain 1809276 isolated from the urine of a Chinese patient and analyze its integrative and conjugative element (ICE) 1276 formation mechanism. Methods Single-molecule real-time (SMRT) sequencing was carried out on strain 18091276 to obtain the complete chromosome and plasmid (pCN1276) sequences, and average nucleotide identity (ANI) was used for precise species identification. The ICEs in GenBank with the same integrase structure as ICE 1276 were aligned. At the same time, the transfer ability of blaIMP−1 and the antibiotic sensitivity of Pseudomonas juntendi 18091276 were tested. Results This bacterium was P. juntendi, and its drug resistance mechanism is the capture of the accA4' gene cassette by the Tn402-like type 1 integron (IntI1-blaIMP−1) to form In1886 before its capture by the ΔTn4662a-carrying ICE 1276. The acquisition of blaIMP−1 confers carbapenem resistance to P. juntendi 18091276. Conclusion The formation of blaIMP−1-carrying ICE 1276, its further integration into the chromosomes, and transposition and recombination of other elements promote bacterial gene accumulation and transmission.
Collapse
Affiliation(s)
- Lin Zheng
- School of Food and Engineering, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xinfang Zhang
- China-Japan Union Hospital, Jilin University, Changchun, China
| | - Lingwei Zhu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Gejin Lu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jiayao Guan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Mingwei Liu
- School of Food and Engineering, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jie Jing
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shiwen Sun
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ying Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yang Sun
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xue Ji
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bowen Jiang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jun Chen
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jun Liu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ping Chen
- School of Food and Engineering, Jilin Agricultural University, Changchun, China
- *Correspondence: Ping Chen
| | - Xuejun Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
- Xuejun Guo
| |
Collapse
|
6
|
Mindlin S, Maslova O, Beletsky A, Nurmukanova V, Zong Z, Mardanov A, Petrova M. Ubiquitous Conjugative Mega-Plasmids of Acinetobacter Species and Their Role in Horizontal Transfer of Multi-Drug Resistance. Front Microbiol 2021; 12:728644. [PMID: 34621254 PMCID: PMC8490738 DOI: 10.3389/fmicb.2021.728644] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/25/2021] [Indexed: 02/05/2023] Open
Abstract
Conjugative mega-plasmids play a special role in adaptation since they carry a huge number of accessory genes, often allowing the host to develop in new niches. In addition, due to conjugation they are able to effectively spread themselves and participate in the transfer of small mobilizable plasmids. In this work, we present a detailed characterization of a recently discovered family of multiple-drug resistance mega-plasmids of Acinetobacter species, termed group III-4a. We describe the structure of the plasmid backbone region, identify the rep gene and the origin of plasmid replication, and show that plasmids from this group are able not only to move between different Acinetobacter species but also to efficiently mobilize small plasmids containing different mob genes. Furthermore, we show that the population of natural Acinetobacter strains contains a significant number of mega-plasmids and reveal a clear correlation between the living conditions of Acinetobacter strains and the structure of their mega-plasmids. In particular, comparison of the plasmids from environmental and clinical strains shows that the genes for resistance to heavy metals were eliminated in the latter, with the simultaneous accumulation of antibiotic resistance genes by incorporation of transposons and integrons carrying these genes. The results demonstrate that this group of mega-plasmids plays a key role in the dissemination of multi-drug resistance among Acinetobacter species.
Collapse
Affiliation(s)
- Sofia Mindlin
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, Russia
| | - Olga Maslova
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, Russia
| | - Alexey Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Varvara Nurmukanova
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, Russia
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - 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 Center "Kurchatov Institute", Moscow, Russia
| |
Collapse
|
7
|
Zong G, Zhong C, Fu J, Zhang Y, Zhang P, Zhang W, Xu Y, Cao G, Zhang R. The carbapenem resistance gene bla OXA-23 is disseminated by a conjugative plasmid containing the novel transposon Tn6681 in Acinetobacter johnsonii M19. Antimicrob Resist Infect Control 2020; 9:182. [PMID: 33168102 PMCID: PMC7653874 DOI: 10.1186/s13756-020-00832-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background Carbapenem resistant Acinetobacter species have caused great difficulties in clinical therapy in the worldwide. Here we describe an Acinetobacter johnsonii M19 with a novel blaOXA-23 containing transposon Tn6681 on the conjugative plasmid pFM-M19 and the ability to transferand carbapenem resistance.
Methods A. johnsonii M19 was isolated under selection with 8 mg/L meropenem from hospital sewage, and the minimum inhibitory concentrations (MICs) for the representative carbapenems imipenem, meropenem and ertapenem were determined. The genome of A. johnsonii M19 was sequenced by PacBio RS II and Illumina HiSeq 4000 platforms. A homologous model of OXA-23 was generated, and molecular docking models with imipenem, meropenem and ertapenem were constructed by Discovery Studio 2.0. Type IV secretion system and conjugation elements were identified by the Pathosystems Resource Integration Center (PATRIC) server and the oriTfinder. Mating experiments were performed to evaluate transfer of OXA-23 to Escherichia coli 25DN. Results MICs of A. johnsonii M19 for imipenem, meropenem and ertapenem were 128 mg/L, 48 mg/L and 24 mg/L, respectively. Genome sequencing identified plasmid pFM-M19, which harbours the carbapenem resistance gene blaOXA-23 within the novel transposon Tn6681. Molecular docking analysis indicated that the elongated hydrophobic tunnel of OXA-23 provides a hydrophobic environment and that Lys-216, Thr-217, Met-221 and Arg-259 were the conserved amino acids bound to imipenem, meropenem and ertapenem. Furthermore, pFM-M19 could transfer blaOXA-23 to E. coli 25DN by conjugation, resulting in carbapenem-resistant transconjugants.
Conclusions Our investigation showed that A. johnsonii M19 is a source and disseminator of blaOXA-23 and carbapenem resistance. The ability to transfer blaOXA-23 to other species by the conjugative plasmid pFM-M19 raises the risk of spread of carbapenem resistance. Graphic abstract The carbapenem resistance gene blaOXA-23 is disseminated by a conjugative plasmid containing the novel transposon Tn6681 in Acinetobacter johnsonii M19.![]()
Collapse
Affiliation(s)
- Gongli Zong
- Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Department of Epidemiology, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, China.,Shandong Medicinal Biotechnology Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Chuanqing Zhong
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Jiafang Fu
- Department of Epidemiology, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, China.,Shandong Medicinal Biotechnology Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250062, China.,Key Lab for Biotech-Drugs of National Health Commission, Jinan, 250062, China
| | - Yu Zhang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Peipei Zhang
- Department of Epidemiology, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, China.,Shandong Medicinal Biotechnology Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250062, China.,Key Lab for Biotech-Drugs of National Health Commission, Jinan, 250062, China
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guangxiang Cao
- Department of Epidemiology, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250062, China. .,Shandong Medicinal Biotechnology Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250062, China.
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
8
|
MITE Aba12 , a Novel Mobile Miniature Inverted-Repeat Transposable Element Identified in Acinetobacter baumannii ATCC 17978 and Its Prevalence across the Moraxellaceae Family. mSphere 2019; 4:4/1/e00028-19. [PMID: 30787115 PMCID: PMC6382973 DOI: 10.1128/mspheredirect.00028-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
One of the most important weapons in the armory of Acinetobacter is its impressive genetic plasticity, facilitating rapid genetic mutations and rearrangements as well as integration of foreign determinants carried by mobile genetic elements. Of these, IS are considered one of the key forces shaping bacterial genomes and ultimately evolution. We report the identification of a novel nonautonomous IS-derived element present in multiple bacterial species from the Moraxellaceae family and its recent translocation into the hns locus in the A. baumannii ATCC 17978 genome. The latter finding adds new knowledge to only a limited number of documented examples of MITEs in the literature and underscores the plastic nature of the hns locus in A. baumannii. MITEAba12, and its predicted parent(s), may be a source of substantial adaptive evolution within environmental and clinically relevant bacterial pathogens and, thus, have broad implications for niche-specific adaptation. Insertion sequences (IS) are fundamental mediators of genome plasticity with the potential to generate phenotypic variation with significant evolutionary outcomes. Here, a recently active miniature inverted-repeat transposon element (MITE) was identified in a derivative of Acinetobacter baumannii ATCC 17978 after being subjected to stress conditions. Transposition of the novel element led to the disruption of the hns gene, resulting in a characteristic hypermotile phenotype. DNA identity shared between the terminal inverted repeats of this MITE and coresident ISAba12 elements, together with the generation of 9-bp target site duplications, provides strong evidence that ISAba12 elements were responsible for mobilization of the MITE (designated MITEAba12) within this strain. A wider genome-level survey identified MITEAba12 in 30 additional Acinetobacter genomes at various frequencies and one Moraxella osloensis genome. Ninety MITEAba12 copies could be identified, of which 40% had target site duplications, indicating recent transposition events. Elements ranged between 111 and 114 bp; 90% were 113 bp in length. Using the MITEAba12 consensus sequence, putative outward-facing Escherichia coli σ70 promoter sequences in both orientations were identified. The identification of transcripts originating from the promoter in one direction supports the proposal that the element can influence neighboring host gene transcription. The location of MITEAba12 varied significantly between and within genomes, preferentially integrating into AT-rich regions. Additionally, a copy of MITEAba12 was identified in a novel 8.5-kb composite transposon, Tn6645, in the M. osloensis CCUG 350 chromosome. Overall, this study shows that MITEAba12 is the most abundant nonautonomous element currently found in Acinetobacter. IMPORTANCE One of the most important weapons in the armory of Acinetobacter is its impressive genetic plasticity, facilitating rapid genetic mutations and rearrangements as well as integration of foreign determinants carried by mobile genetic elements. Of these, IS are considered one of the key forces shaping bacterial genomes and ultimately evolution. We report the identification of a novel nonautonomous IS-derived element present in multiple bacterial species from the Moraxellaceae family and its recent translocation into the hns locus in the A. baumannii ATCC 17978 genome. The latter finding adds new knowledge to only a limited number of documented examples of MITEs in the literature and underscores the plastic nature of the hns locus in A. baumannii. MITEAba12, and its predicted parent(s), may be a source of substantial adaptive evolution within environmental and clinically relevant bacterial pathogens and, thus, have broad implications for niche-specific adaptation.
Collapse
|
9
|
Ebmeyer S, Kristiansson E, Larsson DGJ. PER extended-spectrum β-lactamases originate from Pararheinheimera spp. Int J Antimicrob Agents 2018; 53:158-164. [PMID: 30395985 DOI: 10.1016/j.ijantimicag.2018.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 10/23/2018] [Accepted: 10/27/2018] [Indexed: 10/27/2022]
Abstract
To investigate the origin of PER extended-spectrum β-lactamases, publicly available sequence databases were searched for blaPER-like genes. Three genomes from Pararheinheimera, a genus associated with water and soil environments, were found to carry blaPER-like genes but lacked the ISCR1/ISPa12/ISPa13 insertion sequences commonly associated with blaPER in clinical isolates. Sequence analysis revealed 78-96% nucleotide identity and conserved synteny between the clinical mobile genetic elements (MGEs) encoding blaPER-1 and the blaPER locus in the Pararheinheimera genomes. Notably, blaPER genes were only identified in 3 of 21 Pararheinheimera and Rheinheimera genomes, whereas the genetic environment of blaPER genes as found in clinical MGEs was conserved in all Pararheinheimera and Rheinheimera genomes. These findings indicate that blaPER genes were likely acquired by a branch of the Pararheinheimera genus long before the antibiotic era. Later, blaPER genes were mobilised, likely through the involvement of insertion sequences, from one or several Pararheinheimera species, allowing their dissemination into human pathogens.
Collapse
Affiliation(s)
- Stefan Ebmeyer
- Center for Antibiotic Resistance Research, University of Gothenburg, SE-413 46 Göteborg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE-413 46 Göteborg, Sweden
| | - Erik Kristiansson
- Center for Antibiotic Resistance Research, University of Gothenburg, SE-413 46 Göteborg, Sweden; Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, SE-412 96 Göteborg, Sweden
| | - D G Joakim Larsson
- Center for Antibiotic Resistance Research, University of Gothenburg, SE-413 46 Göteborg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE-413 46 Göteborg, Sweden.
| |
Collapse
|
10
|
Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1139] [Impact Index Per Article: 189.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
Collapse
Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
| |
Collapse
|
11
|
Xu Y, Niu Y, Sun F, Yang Y, Luo W, Wang Z. The novel Pseudomonas putida plasmid p12969-2 harbors an In127-carrying multidrug-resistant region. Future Microbiol 2017; 12:573-584. [PMID: 28660784 DOI: 10.2217/fmb-2016-0201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aim: This study aims to characterize a multidrug-resistant (MDR) plasmid p12969-2 coexistent with the previously reported one p12969-DIM in clinical Pseudomonas putida. Materials & methods: The complete sequence of p12969-2 was determined using next-generation sequencing technology. Results: p12969-2 contains a 29.2 kb MDR region, which carries In127 harboring three resistance genes aadA2, qacED1 and sul1. The MDR region is derived from the connection of Tn5041D and Tn5045, which is facilitated by two copies of miniature inverted-repeat transposable element. Conclusion & future perspective: p12969-2 represents a novel lineage with the highest but limited nucleotide sequence similarity with the plasmid pGRT1 that does not carry any of the resistance genes. This is the first report of coexistence of two MDR plasmids in P. putida.
Collapse
Affiliation(s)
- Yang Xu
- Department of Gynaecology & Obstetrics, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Yong Niu
- Criminal Investigation Bureau, Ministry of Public Security, Beijing 100741, China
| | - Fengjun Sun
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University, Chongqing 400038, China
| | - Ying Yang
- Department of Gynaecology & Obstetrics, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Wenbo Luo
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University, Chongqing 400038, China
| | - Zhe Wang
- Department of Oncology & Southwest Cancer Center, Southwest Hospital, The Third Military Medical University, Chongqing 400038, China
| |
Collapse
|
12
|
GES-14-Producing Acinetobacter baumannii Isolates in a Neonatal Intensive Care Unit in Tunisia Are Associated with a Typical Middle East Clone and a Transferable Plasmid. Antimicrob Agents Chemother 2017; 61:AAC.00142-17. [PMID: 28348158 DOI: 10.1128/aac.00142-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
|
13
|
Unique Features of Aeromonas Plasmid pAC3 and Expression of the Plasmid-Mediated Quinolone Resistance Genes. mSphere 2017; 2:mSphere00203-17. [PMID: 28567445 PMCID: PMC5444012 DOI: 10.1128/msphere.00203-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/07/2017] [Indexed: 11/29/2022] Open
Abstract
In the present study, plasmid pAC3 isolated from a highly fluoroquinolone-resistant isolate of Aeromonas species was sequenced and found to contain two fluoroquinolone resistance genes, aac(6′)-Ib-cr and qnrS2. Comparative analyses of plasmid pAC3 and other Aeromonas sp. IncU-type plasmids revealed a mobile insertion cassette element with a unique structure containing a qnrS2 gene and a typical miniature inverted-repeat transposable element (MITE) structure. This study also revealed that this MITE sequence appears in other Aeromonas species plasmids and chromosomes. Our results also demonstrate that the fluoroquinolone-dependent expression of qnrS2 is associated with rsd in E. coli DH5α harboring plasmid pAC3. Our findings suggest that the mobile element may play an important role in qnrS2 dissemination and that Aeromonas species constitute an important reservoir of fluoroquinolone resistance determinants in the environment. A highly fluoroquinolone-resistant isolate of Aeromonas species was isolated from a wastewater treatment plant and found to possess multiple resistance mechanisms, including mutations in gyrA and parC, efflux pumps, and plasmid-mediated quinolone resistance (PMQR) genes. Complete sequencing of the IncU-type plasmid, pAC3, present in the strain revealed a circular plasmid DNA 15,872 bp long containing two PMQR genes [qnrS2 and aac(6′)-Ib-cr]. A mobile insertion cassette element containing the qnrS2 gene and a typical miniature inverted-repeat transposable element (MITE) structure was identified in the plasmid. The present study revealed that this MITE sequence appears in other Aeromonas species plasmids and chromosomes. Plasmid pAC3 was introduced into Escherichia coli, and its PMQR genes were expressed, resulting in the acquisition of resistance. Proteome analysis of the recipient E. coli strain harboring the plasmid revealed that aac(6′)-Ib-cr expression was constitutive and that qnrS2 expression was dependent upon fluoroquinolone stress through regulation by regulator of sigma D (Rsd). To the best of our knowledge, this is the first report to characterize a novel MITE sequence upstream of the PMQR gene within a mobile insertion cassette, as well as the regulation of qnrS2 expression. Our results suggest that this mobile element may play an important role in qnrS2 dissemination. IMPORTANCE In the present study, plasmid pAC3 isolated from a highly fluoroquinolone-resistant isolate of Aeromonas species was sequenced and found to contain two fluoroquinolone resistance genes, aac(6′)-Ib-cr and qnrS2. Comparative analyses of plasmid pAC3 and other Aeromonas sp. IncU-type plasmids revealed a mobile insertion cassette element with a unique structure containing a qnrS2 gene and a typical miniature inverted-repeat transposable element (MITE) structure. This study also revealed that this MITE sequence appears in other Aeromonas species plasmids and chromosomes. Our results also demonstrate that the fluoroquinolone-dependent expression of qnrS2 is associated with rsd in E. coli DH5α harboring plasmid pAC3. Our findings suggest that the mobile element may play an important role in qnrS2 dissemination and that Aeromonas species constitute an important reservoir of fluoroquinolone resistance determinants in the environment.
Collapse
|
14
|
Montaña S, Schramm STJ, Traglia GM, Chiem K, Parmeciano Di Noto G, Almuzara M, Barberis C, Vay C, Quiroga C, Tolmasky ME, Iriarte A, Ramírez MS. The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer. PLoS One 2016; 11:e0161528. [PMID: 27548264 PMCID: PMC4993456 DOI: 10.1371/journal.pone.0161528] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/08/2016] [Indexed: 02/08/2023] Open
Abstract
Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.
Collapse
Affiliation(s)
- Sabrina Montaña
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Sareda T. J. Schramm
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - German Matías Traglia
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Kevin Chiem
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - Gisela Parmeciano Di Noto
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Marisa Almuzara
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Claudia Barberis
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Carlos Vay
- Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Marcelo E. Tolmasky
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
| | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - María Soledad Ramírez
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States of America
- * E-mail:
| |
Collapse
|
15
|
Tian S, Ali M, Xie L, Li L. Genome-sequence analysis of Acinetobacter johnsonii MB44 reveals potential nematode-virulent factors. SPRINGERPLUS 2016; 5:986. [PMID: 27429894 PMCID: PMC4932006 DOI: 10.1186/s40064-016-2668-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/25/2016] [Indexed: 02/05/2023]
Abstract
Acinetobacter johnsonii is generally recognized as a nonpathogenic bacterium although it is often found in hospital environments. However, a newly identified isolate of this species from a frost-plant-tissue sample, namely, A. johnsonii MB44, showed significant nematicidal activity against the model organism Caenorhabditis elegans. To expand our understanding of this bacterial species, we generated a draft genome sequence of MB44 and analyzed its genomic features related to nematicidal attributes. The 3.36 Mb long genome contains 3636 predicted protein-coding genes and 95 RNA genes (including 14 rRNA genes), with a G + C content of 41.37 %. Genomic analysis of the prediction of nematicidal proteins using the software MP3 revealed a total of 108 potential virulence proteins. Some of these proteins were homologous to the known virulent proteins identified from Acinetobacter baumannii, a pathogenic species of the genus Acinetobacter. These virulent proteins included the outer membrane protein A, the phospholipase D, and penicillin-binding protein 7/8. Moreover, one siderophore biosynthesis gene cluster and one capsular polysaccharide gene cluster, which were predicted to be important virulence factors for C. elegans, were identified in the MB44 genome. The current study demonstrated that A. johnsonii MB44, with its nematicidal activity, could be an opportunistic pathogen to animals.
Collapse
Affiliation(s)
- Shijing Tian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Muhammad Ali
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China ; Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Li Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| |
Collapse
|
16
|
Molecular Epidemiology and Genetic Characteristics of Various blaPER Genes in Shanghai, China. Antimicrob Agents Chemother 2016; 60:3849-53. [PMID: 27067315 DOI: 10.1128/aac.00258-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/21/2016] [Indexed: 01/03/2023] Open
Abstract
We describe the genetic characteristics and possible transmission mechanism of blaPER in 25 clinical Gram-negative bacilli in Shanghai. blaPER, including blaPER-1, blaPER-3, and blaPER-4, was located chromosomally or in different plasmids. Tn1213 harboring blaPER-1 was first identified in two Proteus mirabilis isolates in China. The other blaPER variants were preceded by an ISCR1 element inside the complex class 1 integron associated with IS26, Tn21, Tn1696, and a miniature inverted-repeat transposable element.
Collapse
|
17
|
Li R, Chan EWC, Chen S. Characterisation of a chromosomally-encoded extended-spectrum β-lactamase gene blaPER-3 in Aeromonas caviae of chicken origin. Int J Antimicrob Agents 2015; 47:103-5. [PMID: 26674256 DOI: 10.1016/j.ijantimicag.2015.10.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Affiliation(s)
- Ruichao Li
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shenzhen Research Institute, Shenzhen, PR China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shenzhen Research Institute, Shenzhen, PR China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shenzhen Research Institute, Shenzhen, PR China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| |
Collapse
|
18
|
Feng Y, Yang P, Wang X, Zong Z. Characterization of Acinetobacter johnsonii isolate XBB1 carrying nine plasmids and encoding NDM-1, OXA-58 and PER-1 by genome sequencing. J Antimicrob Chemother 2015; 71:71-5. [PMID: 26462992 DOI: 10.1093/jac/dkv324] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 09/07/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES To obtain the complete genome sequence of an Acinetobacter johnsonii isolate, which encodes the NDM-1 and OXA-58 carbapenemases. METHODS Genome sequencing was performed using the 454 and HiSeq 2000 platforms. Reads were assembled into scaffolds and gaps between scaffolds were filled by PCR and Sanger sequencing. Phylogenetic analyses of A. johnsonii isolates and their intrinsic blaOXA genes were performed using Harvest and MEGA. The context of blaOXA-58 was analysed in detail. RESULTS Isolate XBB1 has one 3.5 Mb chromosome (38.5% GC content) and nine plasmids in the range 3.9-398.9 kb. Isolate XBB1 appears to be distinct from other A. johnsonii isolates. Five of the nine plasmids contained genes encoding for mobilization. The largest contains four XerC/XerD-like binding sites and five Re27 regions. Alignment revealed that Re27 regions are variants of XerC/XerD-like sites. Besides blaNDM-1 and blaOXA-58, isolate XBB1 has an ESBL gene blaPER-1 and a few other genes conferring resistance to aminoglycosides, chloramphenicol, rifampicin, sulphonamides and tetracycline. blaOXA-58 is located in a Russian doll-type structure, as it is flanked by ISAba3, then by two copies of a newly identified element ISAjo2 and bracketed by a pair of Re27 regions. The intrinsic blaOXA of XBB1 is a new variant, blaOXA-311, which is most closely related to blaOXA-333 in an Australian A. johnsonii isolate. CONCLUSIONS We present the first completely assembled genome sequence of A. johnsonii. The ability of A. johnsonii to harbour nine plasmids suggests this species could generate various platforms to mediate the dissemination of antimicrobial resistance.
Collapse
Affiliation(s)
- Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Ping Yang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Xiaohui Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
19
|
Grosso F, Silva L, Sousa C, Ramos H, Quinteira S, Peixe L. Extending the reservoir of bla IMP-5: the emerging pathogen Acinetobacter bereziniae. Future Microbiol 2015; 10:1609-13. [PMID: 26439605 DOI: 10.2217/fmb.15.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Acinetobacter bereziniae clinical relevance is starting to be recognized; however, very few descriptions of its carbapenem resistance currently exist. Here we characterize two carbapenem-resistant A. bereziniae isolates. MATERIALS & METHODS Isolates were obtained from environmental and clinical samples. Carbapenemases were searched by phenotypic, biochemical and PCR assays. Clonality was studied by ApaI-PFGE and genetic location for carbapenemase genes were assessed by I-CeuI and S1 hybridizations. RESULTS Isolates were not clonally related but both produced the 'exclusively Portuguese' IMP-5, with the clinical isolate also producing an OXA-58. The carbapenemase genes were plasmid located. CONCLUSION Our results emphasize the role of non-baumannii Acinetobacter species as important reservoirs of clinically relevant resistance genes that could also contribute to their emergence as nosocomial pathogens.
Collapse
Affiliation(s)
- Filipa Grosso
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Liliana Silva
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.,Escola Superior de Saúde Dr. Lopes Dias, Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal
| | - Clara Sousa
- CEB- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Helena Ramos
- Hospital Geral de Santo António, Porto, Portugal
| | - Sandra Quinteira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos. Universidade do Porto (CIBIO/UP)/InBio Laboratório Associado, Vairão, Portugal.,Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Porto, Portugal.,CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| |
Collapse
|
20
|
Hamidian M, Holt KE, Hall RM. Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate. J Antimicrob Chemother 2015; 70:2519-23. [PMID: 26023211 DOI: 10.1093/jac/dkv137] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/24/2015] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES The objective of this study was to locate the antibiotic resistance determinants in the multiply antibiotic-resistant Acinetobacter baumannii isolate D4. METHODS The genome was sequenced using Illumina HiSeq and assembled de novo using Velvet. PCR was used to link the relevant contigs and fill the gaps. Sequences were compared with ones in GenBank and annotated. RESULTS A sporadic A. baumannii isolate D4, recovered in Sydney in 2006 from a wound, was multiply antibiotic resistant. D4 is ST25 (Institut Pasteur scheme) and exhibited resistance to third-generation cephalosporins and reduced susceptibility to ciprofloxacin, as well as resistance to aminoglycosides (gentamicin, kanamycin, neomycin and tobramycin) and further older antibiotics, nalidixic acid, sulfamethoxazole, streptomycin, spectinomycin and trimethoprim. The gyrA gene has a mutation consistent with nalidixic acid resistance. The bla PER conferring cephalosporin resistance, together with the aadB, aadA13/2, aadA2, strAB and sul1 resistance genes, are located within a 29 173 bp complex class 1 integron that includes three copies of intI1, three cassette arrays and two copies of the 3'-conserved segment. This integron is adjacent to the resG gene of an integrative genomic resistance island, AGI1 (Acinetobacter genomic island 1), with a backbone related to that of islands in the SGI1, SGI2 and PGI1 families. AGI1 is located at the 3'-end of the chromosomal trmE (formerly thdF) gene. CONCLUSIONS AGI1 represents a new lineage of genomic resistance islands that belongs in the same broad group as members of the SGI1, SGI2 and PGI1 families. Genes conferring resistance to cephalosporins, aminoglycosides and sulphonamides are located in a complex class 1 integron within AGI1.
Collapse
Affiliation(s)
- Mohammad Hamidian
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ruth M Hall
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| |
Collapse
|
21
|
Sun F, Yin Z, Feng J, Qiu Y, Zhang D, Luo W, Yang H, Yang W, Wang J, Chen W, Xia P, Zhou D. Production of plasmid-encoding NDM-1 in clinical Raoultella ornithinolytica and Leclercia adecarboxylata from China. Front Microbiol 2015; 6:458. [PMID: 26052314 PMCID: PMC4439573 DOI: 10.3389/fmicb.2015.00458] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/27/2015] [Indexed: 12/17/2022] Open
Abstract
Raoultella ornithinolytica YNKP001 and Leclercia adecarboxylata P10164, which harbor conjugative plasmids pYNKP001-NDM and pP10164-NDM, respectively, were isolated from two different Chinese patients, and their complete nucleotide sequences were determined. Production of NDM-1 enzyme by these plasmids accounts for the carbapenem resistance of these two strains. This is the first report of bla NDM in L. adecarboxylata and third report of this gene in R. ornithinolytica. pYNKP001-NDM is very similar to the IncN2 NDM-1-encoding plasmids pTR3, pNDM-ECS01, and p271A, whereas pP10164-NDM is similar to the IncFIIY bla NDM-1-carrying plasmid pKOX_NDM1. The bla NDM-1 genes of pYNKP001-NDM and pP10164-NDM are embedded in Tn125-like elements, which represent two distinct truncated versions of the NDM-1-encoding Tn125 prototype observed in pNDM-BJ01. Flanking of these two Tn125-like elements by miniature inverted repeat element (MITE) or its remnant indicates that MITE facilitates transposition and mobilization of bla NDM-1 gene contexts.
Collapse
Affiliation(s)
- Fengjun Sun
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University Chongqing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China ; Laboratory Animal Center, Academy of Military Medical Sciences Beijing, China
| | - Yefeng Qiu
- Laboratory Animal Center, Academy of Military Medical Sciences Beijing, China
| | - Defu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Wenbo Luo
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University Chongqing, China ; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Jie Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University Chongqing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| |
Collapse
|
22
|
Molecular characterization of ISCR1-mediated blaPER-1 in a non-O1, non-O139 Vibrio cholerae strain from China. Antimicrob Agents Chemother 2015; 59:4293-5. [PMID: 25870070 DOI: 10.1128/aac.00166-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/06/2015] [Indexed: 11/20/2022] Open
Abstract
We report the detection of PER-1 extended-spectrum β-lactamase (ESBL) in a clinical non-O1, non-O139 Vibrio cholerae strain from China. ISCR1-mediated bla(PER-1) was embedded in a complex In4 family class 1 integron belonging to the lineage of Tn1696 on a conjugative IncA/C plasmid. A free 8.98-kb circular molecule present with the ISCR1-bla(PER-1)-truncated 3'-conserved sequence (CS) structure was detected in this isolate. These findings may provide insight into the mobilization of bla(PER-1).
Collapse
|
23
|
Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii. J Bacteriol 2015; 197:2027-35. [PMID: 25845845 DOI: 10.1128/jb.00131-15] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/31/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for A. baumannii strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make A. baumannii a formidable public health threat. IMPORTANCE Acinetobacter baumannii is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of A. baumannii that is highly virulent and representative of current outbreak strains.
Collapse
|
24
|
Complete nucleotide sequence of a conjugative plasmid carrying bla(PER-1). Antimicrob Agents Chemother 2015; 59:3582-4. [PMID: 25779581 DOI: 10.1128/aac.00518-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
The nucleotide sequence of a self-transmissible plasmid pVPH1 harboring bla(PER-1) from Vibrio parahaemolyticus was determined. pVPH1 was 183,730 bp in size and shared a backbone similar to pAQU1 and pAQU2, differing mainly in an ∼40-kb multidrug resistance (MDR) region. A complex class 1 integron was identified together with ISCR1 and bla(PER-1) (ISCR1-bla(PER-1)-gst-abct-qacEΔ1-sul1), which was shown to form a circular intermediate playing an important role in the dissemination of bla(PER-1).
Collapse
|
25
|
First isolation of Acinetobacter johnsonii co-producing PER-2 and OXA-58 β-lactamases. Diagn Microbiol Infect Dis 2014; 80:341-2. [PMID: 25294301 DOI: 10.1016/j.diagmicrobio.2014.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 09/12/2014] [Accepted: 09/14/2014] [Indexed: 11/22/2022]
|