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Yuan Q, Xia P, Xiong L, Xie L, Lv S, Sun F, Feng W. First report of coexistence of bla KPC-2-, bla NDM-1- and mcr-9-carrying plasmids in a clinical carbapenem-resistant Enterobacter hormaechei isolate. Front Microbiol 2023; 14:1153366. [PMID: 37032905 PMCID: PMC10076803 DOI: 10.3389/fmicb.2023.1153366] [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: 01/29/2023] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Colistin is regarded as one of the last-resort antibiotics against severe infections caused by carbapenem-resistant Enterobacteriaceae. Strains with cooccurrence of mcr-9 and carbapenemase genes are of particular concern. This study aimed to investigate the genetic characteristics of a bla KPC-2-carrying plasmid, bla NDM-1-carrying plasmid and mcr-9-carrying plasmid coexisting in a carbapenem-resistant Enterobacter hormaechei isolate. Methods E. hormaechei strain E1532 was subjected to whole-genome sequencing, and the complete nucleotide sequences of three resistance plasmids identified in the strain were compared with related plasmid sequences. The resistance phenotypes mediated by these plasmids were analyzed by plasmid transfer, carbapenemase activity and antimicrobial susceptibility testing. Results Whole-genome sequencing revealed that strain E1532 carries three different resistance plasmids, pE1532-KPC, pE1532-NDM and pE1532-MCR. pE1532-KPC harboring bla KPC-2 and pE1532-NDM harboring bla NDM-1 are highly identical to the IncR plasmid pHN84KPC and IncX3 plasmid pNDM-HN380, respectively. The mcr-9-carrying plasmid pE1532-MCR possesses a backbone highly similar to that of the IncHI2 plasmids R478 and p505108-MDR, though their accessory modules differ. These three coexisting plasmids carry a large number of resistance genes and contribute to high resistance to almost all antibiotics tested, except for amikacin, trimethoprim/sulfamethoxazole, tigecycline and polymyxin B. Most of the plasmid-mediated resistance genes are located in or flanked by various mobile genetic elements, facilitating horizontal transfer of antibiotic resistance genes. Discussion This is the first report of a single E. hormaechei isolate with coexistence of three resistance plasmids carrying mcr-9 and the two most common carbapenemase genes, bla KPC-2 and bla NDM-1. The prevalence and genetic features of these coexisting plasmids should be monitored to facilitate the establishment of effective strategies to control their further spread.
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Salam LB, Obayori OS. Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome. Folia Microbiol (Praha) 2022; 68:299-314. [PMID: 36329216 DOI: 10.1007/s12223-022-01012-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology Unit, Elizade University, Ilara-Mokin, Ondo State, Nigeria.
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Roy PH, Partridge SR, Hall RM. Comment on "Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection" by A.N. Zhang et al. MICROBIOME 2021; 9:3. [PMID: 33397505 PMCID: PMC7784347 DOI: 10.1186/s40168-020-00950-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/06/2020] [Indexed: 05/31/2023]
Abstract
An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.
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Affiliation(s)
- Paul H Roy
- Centre de Recherche en Infectiologie, CHU de Québec, Québec, QC, Canada.
- Department de Biochimie, de Microbiologie, et de Bio-informatique, Université Laval, Québec, QC, Canada.
| | - 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, 2145, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, 2006, Australia
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Kitao T. [Molecular biological studies toward controlling infectious diseases caused by multidrug-resistant Pseudomonas aeruginosa]. Nihon Saikingaku Zasshi 2020; 74:177-189. [PMID: 31902822 DOI: 10.3412/jsb.74.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that causes serious acute, persistent, and relapsing infections. Recent year, the effectiveness of antibiotics for eliminating P. aeruginosa infections has been further complicated by the emergence of multidrug-resistant strains. Thus, new approaches for the rapid detection and novel antimicrobial drug discovery are urgently needed to control such intractable infections caused by the pathogen. Also, we do need deep understanding of the drug resistance mechanisms to overcome this issue. Here I describe a brief review on my biological studies toward controlling infectious diseases caused by multidrug-resistant P. aeruginosa.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University
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5
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Hossain S, Dahanayake P, De Silva B, Wickramanayake M, Wimalasena S, Heo G. Multidrug resistantAeromonasspp. isolated from zebrafish (Danio rerio): antibiogram, antimicrobial resistance genes and class 1 integron gene cassettes. Lett Appl Microbiol 2019; 68:370-377. [DOI: 10.1111/lam.13138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Affiliation(s)
- S. Hossain
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - P.S. Dahanayake
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - B.C.J. De Silva
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - M.V.K.S. Wickramanayake
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
| | - S.H.M.P. Wimalasena
- Bio‐Safety Research Institute and College of Veterinary Medicine Chonbuk National University Jeonju Korea
| | - G.‐J. Heo
- Veterinary Medical Center and College of Veterinary Medicine Chungbuk National University Cheongju Korea
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Chan AP, Choi Y, Brinkac LM, Krishnakumar R, DePew J, Kim M, Hinkle MK, Lesho EP, Fouts DE. Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells. Sci Rep 2018; 8:8656. [PMID: 29872152 PMCID: PMC5988826 DOI: 10.1038/s41598-018-26738-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022] Open
Abstract
In light of the ongoing antimicrobial resistance crisis, there is a need to understand the role of co-pathogens, commensals, and the local microbiome in modulating virulence and antibiotic resistance. To identify possible interactions that influence the expression of virulence or survival mechanisms in both the multidrug-resistant organisms (MDROs) and human host cells, unique cohorts of clinical isolates were selected for whole genome sequencing with enhanced assembly and full annotation, pairwise co-culturing, and transcriptome profiling. The MDROs were co-cultured in pairwise combinations either with: (1) another MDRO, (2) skin commensals (Staphylococcus epidermidis and Corynebacterium jeikeium), (3) the common probiotic Lactobacillus reuteri, and (4) human fibroblasts. RNA-Seq analysis showed distinct regulation of virulence and antimicrobial resistance gene responses across different combinations of MDROs, commensals, and human cells. Co-culture assays demonstrated that microbial interactions can modulate gene responses of both the target and pathogen/commensal species, and that the responses are specific to the identity of the pathogen/commensal species. In summary, bacteria have mechanisms to distinguish between friends, foe and host cells. These results provide foundational data and insight into the possibility of manipulating the local microbiome when treating complicated polymicrobial wound, intra-abdominal, or respiratory infections.
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Affiliation(s)
- Agnes P Chan
- J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, United States.
| | - Yongwook Choi
- J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, United States
| | - Lauren M Brinkac
- J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, United States
| | - Radha Krishnakumar
- J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, United States
| | - Jessica DePew
- J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, United States
| | - Maria Kim
- J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, United States
| | - Mary K Hinkle
- Multidrug-resistant organism Repository and Surveillance Network, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States
| | - Emil P Lesho
- Multidrug-resistant organism Repository and Surveillance Network, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, United States.,Infectious Diseases Unit, Rochester Regional Health, Rochester, NY, 14621, United States
| | - Derrick E Fouts
- J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD, 20850, United States.
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Mindlin SZ, Petrova MA. On the Origin and Distribution of Antibiotic Resistance: Permafrost Bacteria Studies. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2018. [DOI: 10.3103/s0891416817040048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hossain S, De Silva BCJ, Wimalasena SHMP, Pathirana HNKS, Dahanayake PS, Heo GJ. Distribution of Antimicrobial Resistance Genes and Class 1 Integron Gene Cassette Arrays in Motile Aeromonas spp. Isolated from Goldfish (Carassius auratus). Microb Drug Resist 2018; 24:1217-1225. [PMID: 29420133 DOI: 10.1089/mdr.2017.0388] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aeromonas spp. are opportunistic pathogens related to multiple infectious diseases in ornamental fishes. In the present study, the antimicrobial susceptibility, resistance genes, and integrons of 65 goldfish-borne Aeromonas spp. were evaluated. The isolates were identified as A. hydrophila (n = 30), A. veronii (n = 32), and A. punctata (n = 3) by gyrB sequencing. The antimicrobial susceptibility testing of the isolates designated that most of the isolates were resistant to amoxicillin (100.00%), nalidixic acid (100.00%), ampicillin (98.46%), tetracycline (92.31%), rifampicin (86.15%), and cephalothin (61.54%) and each of the isolates showed multiple antimicrobial resistance phenotype (resistant to ≥3 classes of antimicrobials). PCR amplification of antimicrobial resistance genes revealed that the plasmid-mediated quinolone resistance gene, qnrS, was the most prevalent (73.85%) among the isolates. The other antimicrobial resistance genes were detected in the following proportions: qnrB (26.15%), aac(6')-Ib-cr (4.60%), tetA (16.92%), tetE (21.54%), aac(6')-Ib (29.23%), and aphAI-IAB (7.69%). The IntI gene was found in 64.62% isolates, and four class 1 integron gene cassette profiles (incomplete dfrA1, catB3-aadA1, dfrA1-orfC, and qacE2-orfD) were identified. These data suggest that goldfish-borne Aeromonas spp. serve as a reservoir of antimicrobial resistance genes and class 1 integrons.
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Affiliation(s)
- Sabrina Hossain
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University , Cheongju, Korea
| | | | | | | | - Pasan Sepala Dahanayake
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University , Cheongju, Korea
| | - Gang-Joon Heo
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University , Cheongju, Korea
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Wang D, Zhu J, Zhou K, Chen J, Yin Z, Feng J, Ma L, Zhou D. Genetic characterization of novel class 1 Integrons In0, In1069 and In1287 to In1290, and the inference of In1069-associated integron evolution in Enterobacteriaceae. Antimicrob Resist Infect Control 2017; 6:84. [PMID: 28852475 PMCID: PMC5567636 DOI: 10.1186/s13756-017-0241-9] [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: 05/31/2017] [Accepted: 08/09/2017] [Indexed: 11/25/2022] Open
Abstract
Background This study aims to characterize genetically related class 1 integrons In1069, In893 and In1287 to In1290, and to further propose a scheme of stepwise integration or excision of individual gene cassettes (GCs) to generation of these integron variations. Methods Six of 139 non-redundant Enterobacteriaceae strains were studied by bacterial antimicrobial susceptibility testing, detection of carbapenemase activity, and integron sequencing and sequence comparison. Results Six novel class 1 integrons, In0, In1069, and In1287 to In1290, together with the previously characterized In893, were determined from the above strains. An unusual blaKPC-2-carrying In0 and the blaIMP-30-carrying In1069 coexists in a single isolate of Escherichia coli. In0 contains a PcH1 promoter and a truncated aacA4’-3 gene cassette (GCaacA4’-3), as well as a blaKPC-2-containing region of Tn6296 integrated between PcH1 and GCaacA4’-3. In1069 carries GCblaIMP-30 and GCaacA4’-3 in this order. The other five integrons, In893 and In1287 to In1290, are genetically related to In1069, and all possess a core GCaacA4’-3. The integration or excision of one or more individual gene cassettes, such as GCblaIMP-30, GCaadA16, GCcatB3, GCarr3 and GCdfrA27, upstream or downstream of GCaacA4’-3 generates various gene cassettes arrays among these five integrons. Conclusions These findings provide the insight into stepwise and parallel evolution of In1069-associated integron variations likely under antibiotic selection pressure in clinical settings. Electronic supplementary material The online version of this article (doi:10.1186/s13756-017-0241-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dongguo Wang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital affiliated with Taizhou University and the Institute of Molecular Diagnostics of Taizhou University, 381 Zhongshan Eastern Road, Taizhou, Zhejiang, 318000 China
| | - Jianfeng Zhu
- Department of Clinical Laboratory Medicine, Yinzhou No. 2 Hospital of Ningbo, 1 Qianhe Road, Ningbo, Zhejiang, 315100 China
| | - Kaiyu Zhou
- Department of the Neurosurgery, Taizhou Municipal Hospital affiliated to Medical College of Taizhou University, 381 Zhongshan Eastern Road, Taizhou, Zhejiang, 318000 China
| | - Jiayu Chen
- Basic Department, Medical College of Shaoxing University, 508 Huancheng western Road, Shaoxing, Zhejiang, 312099 China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071 China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071 China
| | - Liman Ma
- Department of Laboratory medicine, Medical College of Taizhou University, 1139 Shifu Avenue, Taizhou, Zhejiang, 318000 China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071 China
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Oliveira-Pinto C, Diamantino C, Oliveira PL, Reis MP, Costa PS, Paiva MC, Nardi RMD, Magalhães PP, Chartone-Souza E, Nascimento AMA. Occurrence and characterization of class 1 integrons in Escherichia coli from healthy individuals and those with urinary infection. J Med Microbiol 2017; 66:577-583. [DOI: 10.1099/jmm.0.000468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Clarisse Oliveira-Pinto
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Cristiane Diamantino
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia L Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Magna C Paiva
- Campus Dona Lindu, Universidade Federal de São João del Rei, Divinópolis, Minas Gerais, Brazil
| | - Regina M. D Nardi
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Paula P Magalhães
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | - Andréa M. A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
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Touwendsida SB, Bissoume SB, Hadiza BI, Gertrude BT, Rene D, Abdoul AW, Evariste B, Alfred ST, Nicolas B, Amy GS. Isolation and characterization of enteropathogenic and enterotoxinogenic Escherichia coli from dairy products consumed in Burkina Faso. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajmr2017.8485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Cury J, Jové T, Touchon M, Néron B, Rocha EP. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res 2016; 44:4539-50. [PMID: 27130947 PMCID: PMC4889954 DOI: 10.1093/nar/gkw319] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/13/2016] [Indexed: 12/13/2022] Open
Abstract
Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.
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Affiliation(s)
- Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
| | - Thomas Jové
- Univ. Limoges, INSERM, CHU Limoges, UMR_S 1092, F-87000 Limoges, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
| | - Bertrand Néron
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, Paris, France
| | - Eduardo Pc Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
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Guo Y, Zhou H, Qin L, Pang Z, Qin T, Ren H, Pan Z, Zhou J. Frequency, Antimicrobial Resistance and Genetic Diversity of Klebsiella pneumoniae in Food Samples. PLoS One 2016; 11:e0153561. [PMID: 27078494 PMCID: PMC4831839 DOI: 10.1371/journal.pone.0153561] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/31/2016] [Indexed: 12/01/2022] Open
Abstract
This study aimed to assess the frequency of Klebsiella pneumoniae in food samples and to detect antibiotic resistance phenotypes, antimicrobial resistance genes and the molecular subtypes of the recovered isolates. A total of 998 food samples were collected, and 99 (9.9%) K. pneumoniae strains were isolated; the frequencies were 8.2% (4/49) in fresh raw seafood, 13.8% (26/188) in fresh raw chicken, 11.4% (34/297) in frozen raw food and 7.5% (35/464) in cooked food samples. Antimicrobial resistance was observed against 16 antimicrobials. The highest resistance rate was observed for ampicillin (92.3%), followed by tetracycline (31.3%), trimethoprim-sulfamethoxazole (18.2%), and chloramphenicol (10.1%). Two K. pneumoniae strains were identified as extended-spectrum β-lactamase (ESBL)–one strain had three beta-lactamases genes (blaSHV, blaCTX-M-1, and blaCTX-M-10) and one had only the blaSHV gene. Nineteen multidrug-resistant (MDR) strains were detected; the percentage of MDR strains in fresh raw chicken samples was significantly higher than in other sample types (P<0.05). Six of the 18 trimethoprim-sulfamethoxazole-resistant strains carried the folate pathway inhibitor gene (dhfr). Four isolates were screened by PCR for quinolone resistance genes; aac(6’)-Ib-cr, qnrB, qnrA and qnrS were detected. In addition, gyrA gene mutations such as T247A (Ser83Ile), C248T (Ser83Phe), and A260C (Asp87Ala) and a parC C240T (Ser80Ile) mutation were identified. Five isolates were screened for aminoglycosides resistance genes; aacA4, aacC2, and aadA1 were detected. Pulsed-field gel electrophoresis-based subtyping identified 91 different patterns. Our results indicate that food, especially fresh raw chicken, is a reservoir of antimicrobial-resistant K. pneumoniae, and the potential health risks posed by such strains should not be underestimated. Our results demonstrated high prevalence, antibiotic resistance rate and genetic diversity of K. pneumoniae in food in China. Improved control and prevention strategies are urgently needed.
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Affiliation(s)
- Yumei Guo
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
- * E-mail: (HZ); (JZ)
| | - Liyun Qin
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Zhizhao Pang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Tian Qin
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
| | - Hongyu Ren
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zhuo Pan
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Jikun Zhou
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
- * E-mail: (HZ); (JZ)
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Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC, Murphy C, Feldgarden M, Wortman J, Clermont D, Lambert T, Grillot-Courvalin C, Nemec A, Courvalin P, Rocha EPC. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol 2014; 6:2866-82. [PMID: 25313016 PMCID: PMC4224351 DOI: 10.1093/gbe/evu225] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens.
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Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France CNRS, UMR3525, Paris, France
| | - Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France CNRS, UMR3525, Paris, France
| | - Eun-Jeong Yoon
- Unité des Agents Antibactériens, Institut Pasteur, Paris, France
| | - Lenka Krizova
- Laboratory of Bacterial Genetics, National Institute of Public Health, Prague, Czech Republic
| | | | - Cheryl Murphy
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | | | | | - Thierry Lambert
- Unité des Agents Antibactériens, Institut Pasteur, Paris, France
| | | | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Prague, Czech Republic.
| | | | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France CNRS, UMR3525, Paris, France
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15
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Tseng SP, Tsai WC, Liang CY, Lin YS, Huang JW, Chang CY, Tyan YC, Lu PL. The contribution of antibiotic resistance mechanisms in clinical Burkholderia cepacia complex isolates: an emphasis on efflux pump activity. PLoS One 2014; 9:e104986. [PMID: 25153194 PMCID: PMC4143217 DOI: 10.1371/journal.pone.0104986] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022] Open
Abstract
Due to the limited information of the contribution of various antibiotic resistance mechanisms in clinical Burkholderia cepacia complex isolates, Antibiotic resistance mechanisms, including integron analysis, identification of quinolone resistance-determining region mutations, measurement of efflux pump activity, and sequence analysis of efflux pump regulators, were investigated in 66 clinical B. cepacia complex isolates. Species were identified via recA-RFLP and MALDI-TOF. Four genomovars were identified by recA-RFLP. B. cenocepacia (genomovar III) was the most prevalent genomovar (90.1%). Most isolates (60/66, 90.9%) were correctly identified by MALDI-TOF analysis. Clonal relatedness determined by PFGE analysis revealed 30 pulsotypes, including two major pulsotypes that comprised 22.7% and 18.2% of the isolates, respectively. Seventeen (25.8%) isolates harboured class 1 integron with various combinations of resistance genes. Among six levofloxacin-resistant isolates, five had single-base substitutions in the gyrA gene and three demonstrated efflux pump activities. Among the 42 isolates exhibiting resistance to at least one antimicrobial agent, 94.4% ceftazidime-resistant isolates (17/18) and 72.7% chloramphenicol-resistant isolates (16/22) demonstrated efflux pump activity. Quantitation of efflux pump RNA level and sequence analysis revealed that over-expression of the RND-3 efflux pump was attributable to specific mutations in the RND-3 efflux pump regulator gene. In conclusion, high-level expression of efflux pumps is prevalent in B. cepacia complex isolates. Mutations in the RND-3 efflux pump regulator gene are the major cause of efflux pump activity, resulting in the resistance to antibiotics in clinical B. cepacia complex isolates.
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Affiliation(s)
- Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC
| | - Wan-Chi Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Chih-Yuan Liang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Yin-Shiou Lin
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Jun-Wei Huang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Chung-Yu Chang
- College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Yu-Chang Tyan
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Po-Liang Lu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC
- College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Taiwan, ROC
- * E-mail:
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Lima AMS, Melo MESD, Alves LC, Brayner FA, Lopes ACS. Investigation of class 1 integrons in Klebsiella pneumoniae clinical and microbiota isolates belonging to different phylogenetic groups in Recife, State of Pernambuco. Rev Soc Bras Med Trop 2014; 47:165-9. [DOI: 10.1590/0037-8682-0021-2014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/11/2014] [Indexed: 11/22/2022] Open
Affiliation(s)
- Alexsandra Maria Silva Lima
- Universidade Federal de Pernambuco, Brasil; Universidade Federal de Pernambuco, Brasil; Universidade Federal de Pernambuco, Brasil
| | | | - Luiz Carlos Alves
- Universidade Federal de Pernambuco, Brasil; Universidade Federal de Pernambuco, Brasil
| | - Fábio André Brayner
- Universidade Federal de Pernambuco, Brasil; Universidade Federal de Pernambuco, Brasil
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17
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El-Mahdy TS. Identification of a Novel Metallo-^|^beta;-Lactamase VIM-28 Located within Unusual Arrangement of Class 1 Integron Structure in Pseudomonas aeruginosa Isolates from Egypt. Jpn J Infect Dis 2014. [DOI: 10.7883/yoken.67.382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Analysis of drug resistance determinants in Klebsiella pneumoniae isolates from a tertiary-care hospital in Beijing, China. PLoS One 2012; 7:e42280. [PMID: 22860106 PMCID: PMC3409176 DOI: 10.1371/journal.pone.0042280] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 07/02/2012] [Indexed: 12/21/2022] Open
Abstract
Background The rates of multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) isolates among Enterobacteriaceae isolates, particularly Klebsiella pneumoniae, have risen substantially worldwide. Methodology/Principal Findings To better understand the molecular mechanisms of drug resistance in K. pneumoniae, we analyzed the drug resistance determinants for K. pneumoniae isolates collected from the 306 Hospital, a tertiary-care hospital in Beijing, China, for the period of September 1, 2010-October 31, 2011. Drug susceptibility testing, PCR amplification and sequencing of the drug resistance determinants were performed. Conjugation experiments were conducted to examine the natural ability of drug resistance to disseminate among Enterobacteriaceae strains using a sodium azide-resistant Escherichia coli J53 strain as a recipient. Among the 223 consecutive non-repetitive K. pneumoniae isolates included in this study, 101 (45.3%) were extended-spectrum beta-lactamases (ESBLs) positive. The rates of MDR, XDR, and PDR isolates were 61.4% (n = 137), 22.0% (n = 49), and 1.8% (n = 4), respectively. Among the tested drug resistance-associated genes, the following ones were detected at relatively high rates blaCTX-M-10 (80, 35.9%), aacC2 (73, 32.7%), dhfr (62, 27.8%), qnrS (58, 26.0%), aacA4 (57, 25.6%), aadA1 (56, 25.1%). Results from conjugation experiments indicate that many of the drug resistance genes were transmissible. Conclusions/Significance Our data give a “snapshot” of the complex genetic background responsible for drug resistance in K. pneumoniae in China and demonstrate that a high degree of awareness and monitoring of those drug resistance determinants are urgently needed in order to better control the emergence and transmission of drug-resistant K. pneumoniae isolates in hospital settings.
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20
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Solomenny AP, Lyapunov YE, Kuzyaev RZ. Genetic Variability of Enterobacterial Resistant Integrons. Bull Exp Biol Med 2011; 151:619-21. [DOI: 10.1007/s10517-011-1397-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Skippington E, Ragan MA. Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 2011; 35:707-35. [DOI: 10.1111/j.1574-6976.2010.00261.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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22
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Zhao KL, Liu Y, Zhang XY, Palahati P, Wang HN, Yue BS. Detection and characterization of antibiotic-resistance genes in Arcanobacterium pyogenes strains from abscesses of forest musk deer. J Med Microbiol 2011; 60:1820-1826. [PMID: 21852523 DOI: 10.1099/jmm.0.033332-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arcanobacterium pyogenes is commonly isolated from ruminant animals as an opportunistic pathogen that co-infects with other bacteria, normally causing surface or internal abscesses. Twenty-eight strains of A. pyogenes isolated from forest musk deer suppurative samples were identified by their 16S rRNA gene sequences, and confirmed by amplification of the pyolysin-encoding gene (plo) in all isolates. The MICs of 14 commonly used antibiotics were determined by an agar dilution method. Class 1 and 2 intI genes were amplified to determine whether integrons were present in the A. pyogenes genome. Class 1 gene cassettes were detected by specific primers and analysed by sequencing. All of the strains were susceptible to most fluoroquinolone antibiotics; however, high resistance rates were observed for β-lactams and trimethoprim. A total of 18 of the isolates (64.3%) were positive for the class 1 intI gene, and 16 (57.1%) contained class 1 gene cassettes with the aacC, aadA1, aadA2, blaP1 and dfr2a genes. Most were present in the multi-resistant isolates, indicating a general concordance between the presence of gene cassettes and antibiotic resistance, and that the integrons have played an important role in the dissemination of antimicrobial resistance in this species.
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Affiliation(s)
- Ke-Lei Zhao
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Science, Sichuan University, 610064 Chengdu, PR China
| | - Yang Liu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Science, Sichuan University, 610064 Chengdu, PR China
| | - Xiu-Yue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Science, Sichuan University, 610064 Chengdu, PR China
| | - Paha'erding Palahati
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Science, Sichuan University, 610064 Chengdu, PR China
| | - Hong-Ning Wang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), Bioengineering Research Center for Animal Disease Prevention and Control, College of Life Science, Sichuan University, 610064 Chengdu, PR China
| | - Bi-Song Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Science, Sichuan University, 610064 Chengdu, PR China
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Tn5045, a novel integron-containing antibiotic and chromate resistance transposon isolated from a permafrost bacterium. Res Microbiol 2011; 162:337-45. [PMID: 21262357 DOI: 10.1016/j.resmic.2011.01.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 12/21/2010] [Indexed: 11/21/2022]
Abstract
A novel antibiotic and chromate resistance transposon, Tn5045, was isolated from a permafrost strain of Pseudomonas sp. Tn5045 is a compound transposon composed of three distinct genetic elements. The backbone element is a Tn1013-like Tn3 family transposon, termed Tn1013∗, that contains the tnpA and the tnpR genes, encoding the transposase and resolvase, respectively, the res-site and four genes (orfA, B, C, D) related to different house-keeping genes. The second element is class 1 integron, termed InC∗, which is inserted into the Tn1013∗ res-region and contains 5'-CS-located integrase, 3'-CS-located qacE∆1 and sulfonamide resistance sulI genes, and a single cassette encoding the streptomycin resistance aadA2-gene. The third element is a TnOtChr-like Tn3 family transposon termed TnOtChr∗, which is inserted into the transposition module of the integron and contains genes of chromate resistance (chrB, A, C, F). Tn5045 is the first example of an ancient integron-containing mobile element and also the first characterized compound transposon coding for both antibiotic and chromate, resistance. Our data demonstrate that antibiotic and chromate resistance genes were distributed in environmental bacteria independently of human activities and provide important insights into the origin and evolution of antibiotic resistance integrons.
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24
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Extended-spectrum Beta-lactamase gene sequences in gram-negative saprophytes on retail organic and nonorganic spinach. Appl Environ Microbiol 2011; 77:1601-7. [PMID: 21216903 DOI: 10.1128/aem.02506-10] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A substantial proportion of infections caused by drug-resistant Gram-negative bacteria (GNB) in community and health care settings are recognized to be caused by evolutionarily related GNB strains. Their global spread has been suggested to occur due to human activities, such as food trade and travel. These multidrug-resistant GNB pathogens often harbor mobile drug resistance genes that are highly conserved in their sequences. Because they appear across different GNB species, these genes may have origins other than human pathogens. We hypothesized that saprophytes in common human food products may serve as a reservoir for such genes. Between July 2007 and April 2008, we examined 25 batches of prepackaged retail spinach for cultivatable GNB population structure by 16S rRNA gene sequencing and for antimicrobial drug susceptibility testing and the presence of extended-spectrum beta-lactamase (ESBL) genes. We found 20 recognized GNB species among 165 (71%) of 231 randomly selected colonies cultured from spinach. Twelve strains suspected to express ESBLs based on resistance to cefotaxime and ceftazidime were further examined for bla(CTX-M) and bla(TEM) genes. We found a 712-bp sequence in Pseudomonas teessidea that was 100% identical to positions 10 to 722 of an 876-bp bla(CTX-M-15) gene of an E. coli strain. Additionally, we identified newly recognized ESBL bla(RAHN-2) sequences from Rahnella aquatilis. These observations demonstrate that saprophytes in common fresh produce can harbor drug resistance genes that are also found in internationally circulating strains of GNB pathogens; such a source may thus serve as a reservoir for drug resistance genes that ultimately enter pathogens to affect human health.
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25
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Léon G, Quiroga C, Centrón D, Roy PH. Diversity and strength of internal outward-oriented promoters in group IIC-attC introns. Nucleic Acids Res 2010; 38:8196-207. [PMID: 20716518 PMCID: PMC3001079 DOI: 10.1093/nar/gkq709] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Integrons are genetic elements that incorporate mobile gene cassettes by site-specific recombination and express them as an operon from a promoter (Pc) located upstream of the cassette insertion site. Most gene cassettes found in integrons contain only one gene followed by an attC recombination site. We have recently shown that a specific lineage of group IIC introns, named group IIC-attC introns, inserts into the bottom strand sequence of attC sites. Here, we show that S.ma.I2, a group IIC-attC intron inserted in an integron cassette array of Serratia marcescens, impedes transcription from Pc while allowing expression of the following antibiotic resistance cassette using an internal outward-oriented promoter (Pout). Bioinformatic analyses indicate that one or two putative Pout, which have sequence similarities with the Escherichia coli consensus promoters, are conserved in most group IIC-attC intron sequences. We show that Pout with different versions of the −35 and −10 sequences are functionally active in expressing a promoterless chloramphenicol acetyltransferase (cat) reporter gene in E. coli. Pout in group IIC-attC introns may therefore play a role in the expression of one or more gene cassettes whose transcription from Pc would otherwise be impeded by insertion of the intron.
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Affiliation(s)
- Grégory Léon
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Québec, Canada
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26
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Lopes ACS, Veras DL, Lima AMS, Melo RDCA, Ayala J. bla(CTX-M-2) and bla(CTX-M-28) extended-spectrum beta-lactamase genes and class 1 integrons in clinical isolates of Klebsiella pneumoniae from Brazil. Mem Inst Oswaldo Cruz 2010; 105:163-7. [PMID: 20428675 DOI: 10.1590/s0074-02762010000200009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 02/03/2010] [Indexed: 11/22/2022] Open
Abstract
Twenty-eight Klebsiella pneumoniae clinical isolates that exhibited an extended-spectrum cephalosporin-resistance profile from a city in the Northeast of Brazil were analysed by PCR and DNA sequencing in order to determine the occurrence of blaCTX-M genes and class 1 integrons. We determined the occurrence of the blaCTX-M-2 gene in six K. pneumoniae isolates and describe the first detection of the blaCTX-M-28 gene in South America. Seven isolates carried class 1 integrons. Partial sequencing analysis of the 5'-3'CS variable region in the class 1 integrons of three isolates revealed the presence of aadA1, blaOXA-2 and dfr22 gene cassettes.
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Affiliation(s)
- Ana Catarina S Lopes
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, PE, Brasil.
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27
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Petrovski S, Stanisich VA. Tn502 and Tn512 are res site hunters that provide evidence of resolvase-independent transposition to random sites. J Bacteriol 2010; 192:1865-74. [PMID: 20118251 PMCID: PMC2838034 DOI: 10.1128/jb.01322-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 01/21/2010] [Indexed: 11/20/2022] Open
Abstract
In this study, we report on the transposition behavior of the mercury(II) resistance transposons Tn502 and Tn512, which are members of the Tn5053 family. These transposons exhibit targeted and oriented insertion in the par region of plasmid RP1, since par-encoded components, namely, the ParA resolvase and its cognate res region, are essential for such transposition. Tn502 and, under some circumstances, Tn512 can transpose when par is absent, providing evidence for an alternative, par-independent pathway of transposition. We show that the alternative pathway proceeds by a two-step replicative process involving random target selection and orientation of insertion, leading to the formation of cointegrates as the predominant product of the first stage of transposition. Cointegrates remain unresolved because the transposon-encoded (TniR) recombination system is relatively inefficient, as is the host-encoded (RecA) system. In the presence of the res-ParA recombination system, TniR-mediated (and RecA-mediated) cointegrate resolution is highly efficient, enabling resolution both of cointegrates involving functional transposons (Tn502 and Tn512) and of defective elements (In0 and In2). These findings implicate the target-encoded accessory functions in the second stage of transposition as well as in the first. We also show that the par-independent pathway enables the formation of deletions in the target molecule.
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Affiliation(s)
- Steve Petrovski
- Department of Microbiology, La Trobe University, Victoria 3086, Australia
| | - Vilma A. Stanisich
- Department of Microbiology, La Trobe University, Victoria 3086, Australia
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Umamaheswara Reddy C, Arun A, Amalraj A, Reddy BSR. Polymeric drug based on sulfanilamide: synthesis, antimicrobial and drug releasing studies. J Pharm Pharmacol 2010; 59:1207-13. [PMID: 17883891 DOI: 10.1211/jpp.59.9.0004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Abstract
N-((4-amino sulfonyl)phenyl)acrylamide (APA) was synthesized using sulfanilamide and acryloyl chloride in the presence of triethyl amine at 0–5°C. Homo- and co-polymerization of 2-hydroxyethyl acrylate (HEA) and acrylic acid (AA) were done by adopting a solution polymerization technique using methyl ethyl ketone (MEK) as a solvent and benzoyl peroxide (BPO) as a free radical initiator at 70+1°C. All the monomers and polymers were characterized by IR and NMR techniques. These monomers and polymers were tested for their antimicrobial activity against five different ATCC strain microorganisms (Escherichia coli (25922), Pseudomonas aeruginosa (27853), Klebsiella (70063), Salmonella typhi (6539) and Staphylococcus aureus (25923)). The effect of co-monomer, other than the active drug moiety present in the polymeric drug, is discussed. The antimicrobial activity of APA on Gram-positive bacteria was enhanced when copolymerized with AA and HEA. The polymer was made into a film form and that film was used for drug releasing study. The drug releasing rate was monitored by the absorption at 268 nm using a UV spectrophotometer. The effect of pH and the temperature on the drug releasing rate was monitored and found that the releasing rate was dependent on the co-monomer, pH and temperature of the medium.
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Niwa H, Anzai T, Izumiya H, Morita-Ishihara T, Watanabe H, Uchida I, Tozaki T, Hobo S. Antimicrobial resistance and genetic characteristics of Salmonella Typhimurium isolated from horses in Hokkaido, Japan. J Vet Med Sci 2010; 71:1115-9. [PMID: 19721370 DOI: 10.1292/jvms.71.1115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this study, we examined the antimicrobial susceptibility of 16 Salmonella Typhimurium isolates obtained from horses, and applied several genetic methods, namely polymerase chain reaction (PCR) for detecting class 1 integrons, multiplex PCR for detecting multidrug resistant S. Typhimurium definitive phage type 104 (MR-DT104), and fluorescent amplified-fragment length polymorphism (FAFLP). Seven isolates with an ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline (ACSSuT) type resistance pattern, harbored two class 1 integrons with sizes of 1.2 and 1.0 kb, and were identified as DT104 by bacteriophage typing. These isolates also showed a typical MR-DT104 amplification pattern, which was positive for flo(st), spvC, invA and int, in multiplex PCR. In the FAFLP analysis, the equine DT104 isolates and the previously reported ACSSuT-type resistant bovine isolates, which were also isolated in Hokkaido were included in the same genetic cluster. Our results retrospectively indicate that MR-DT104 infection has existed in horses in Japan at least since 1996, and it was suggested that there is a highly epidemiological relationship between the equine MR-DT104 isolates and certain multidrug resistant bovine isolates in the same area.
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Affiliation(s)
- Hidekazu Niwa
- Equine Research Institute, Japan Racing Association, Tochigi, Japan.
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30
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Solomenny AP. Class 1 integron-associated promoters for gene cassette transcription. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409070187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Jacquier H, Zaoui C, Sanson-le Pors MJ, Mazel D, Berçot B. Translation regulation of integrons gene cassette expression by the attC sites. Mol Microbiol 2009; 72:1475-86. [PMID: 19486293 DOI: 10.1111/j.1365-2958.2009.06736.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Integron are genetic elements able to carry, capture and shuffle the genes embedded in gene cassettes. The attC recombination sites adopt a stable secondary structure when single-stranded that is necessary for their recombination. In this study, we evaluated the impact of the structure of the attC site on expression of the 3' gene in class 1 integrons. This was analysed by substituting the attC of the bla(IMP-8) gene cassette with various mutated attC sites spanning a wide range of sizes and secondary structures, and measuring the integron-dependent translation of the 3'aac(6')-Ib7 gene. In the resulting constructs, the 5'-attC site differentially affected the expression of the aac(6')-Ib7 gene. Contrary to what was expected from their proposed role as Rho-independent transcription terminators, the transcription of the aac(6')-Ib7 gene was not affected by the various attC sites. Mutations of natural sites revealed that destabilization of the potential stem-loop structure of the attC site in the transcript could enhance the expression of the 3' gene. In particular, the presence of a translated open reading frame was shown to increase translation of the 3' gene. These findings might be explained by the capacity of the stem-loop structures to impede ribosome progression.
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Affiliation(s)
- Hervé Jacquier
- Assistance Publique Hôpitaux de Paris, Hôpital Lariboisière, Service de Bactériologie-Virologie, Université Paris VII, 2 rue Ambroise Paré, 75010 Paris, France
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Cabrera R, Ruiz J, Sánchez-Céspedes J, Goñi P, Gómez-Lus R, Jiménez de Anta MT, Gascón J, Vila J. Characterization of the enzyme aac(3)-Id in a clinical isolate of Salmonella enterica serovar Haifa causing traveler's diarrhea. Enferm Infecc Microbiol Clin 2009; 27:453-6. [PMID: 19403206 DOI: 10.1016/j.eimc.2008.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 10/13/2008] [Accepted: 11/11/2008] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The objective of this investigation was to identify the mechanism of decreased susceptibility to gentamicin in a Salmonella clinical isolate, leading to the detection of a aminoglycoside acetyltransferase gene found in a class 1 integron. METHODS A multidrug-resistant Salmonella strain was recovered from feces of a traveler to Egypt. The antimicrobial susceptibility test to 12 antimicrobial agents was performed with the Kirby-Bauer method. The presence of class 1 integron was determined by PCR. The amplified product was recovered and sequenced in order to establish the genes carried. In addition, susceptibility to gentamicin C1a, gentamicin C1, sisomicin, neomycin, dibekacin, kanamycin, tobramycin, amikacin, netilmicin, apramycin, dactimicin, spectinomycin, streptomycin, lividomycin and butirosin, was established. The Champion pET101 Directional TOPO Expression Kit was used to clone and express the aac(3)-I gene. RESULTS The isolate was identified as Salmonella enterica serovar Haifa, showing resistance to nalidixic acid, tetracycline and decreased susceptibility to gentamicin. One integron with a size circa 1,500 bp, encoding an aac(3)-Id plus aadA7 genes was observed. The analysis of the susceptibility to different aminoglycosides in the E. coli TOP10F' transformed with the vector carrying aac(3)-Id gene showed resistance to gentamicin C1a, gentamicin C1, and dactimicin, in accordance with the presence of this enzyme but, was susceptible to sisomicin. The homology of the amino acid and nucleotide sequences with the AAC(3)-Id enzyme was of 100%. CONCLUSION The presence of the AAC(3)-Id enzyme was described for the first time in a S. Haifa.
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Affiliation(s)
- Roberto Cabrera
- Servicio de Microbiología, IDIBAPS, Hospital Clínic, Barcelona, Spain
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AAC(6')-Iaf, a novel aminoglycoside 6'-N-acetyltransferase from multidrug-resistant Pseudomonas aeruginosa clinical isolates. Antimicrob Agents Chemother 2009; 53:2327-34. [PMID: 19349516 DOI: 10.1128/aac.01360-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here the characterization of a novel aminoglycoside resistance gene, aac(6')-Iaf, present in two multidrug-resistant (MDR) Pseudomonas aeruginosa clinical isolates. These isolates, IMCJ798 and IMCJ799, were independently obtained from two patients, one with a urinary tract infection and the other with a decubitus ulcer, in a hospital located in the western part of Japan. Although the antibiotic resistance profiles of IMCJ798 and IMCJ799 were similar to that of MDR P. aeruginosa IMCJ2.S1, which caused outbreaks in the eastern part of Japan, the pulsed-field gel electrophoresis patterns for these isolates were different from that for IMCJ2.S1. Both IMCJ798 and IMCJ799 were found to contain a novel chromosomal class 1 integron, In123, which included aac(6')-Iaf as the first cassette gene. The encoded protein, AAC(6')-Iaf, was found to consist of 183 amino acids, with 91 and 87% identity to AAC(6')-Iq and AAC(6')-Im, respectively. IMCJ798, IMCJ799, and Escherichia coli transformants carrying a plasmid containing the aac(6')-Iaf gene and its upstream region were highly resistant to amikacin, dibekacin, and kanamycin but not to gentamicin. The production of AAC(6')-Iaf in these strains was confirmed by Western blot analysis. Thin-layer chromatography indicated that AAC(6')-Iaf is a functional acetyltransferase that specifically modifies the amino groups at the 6' positions of aminoglycosides. Collectively, these findings indicate that AAC(6')-Iaf contributes to aminoglycoside resistance.
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Lee JE, Park SJ, Kim SH, Kim MN, Lee NY, Lee BK, Lee SO, Kim YS, Woo JH, Choi SH. Detection and Characterization of Integrons in Nontyphoid Salmonella Clinical Isolates. Infect Chemother 2009. [DOI: 10.3947/ic.2009.41.3.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Jung Eun Lee
- Center for Antimicrobial Resistance and Microbial Genomics, University of Ulsan, Seoul, Korea
- Department of Infectious Diseases, Asan Medical Center, Seoul, Korea
| | - Su Jin Park
- Center for Antimicrobial Resistance and Microbial Genomics, University of Ulsan, Seoul, Korea
- Department of Infectious Diseases, Asan Medical Center, Seoul, Korea
| | - Sung Han Kim
- Center for Antimicrobial Resistance and Microbial Genomics, University of Ulsan, Seoul, Korea
- Department of Infectious Diseases, Asan Medical Center, Seoul, Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Bok Kwon Lee
- Division of Enteric Bacterial Infection, Korean Center for Disease Control and Prevention, Seoul, Korea
| | - Sang-Oh Lee
- Center for Antimicrobial Resistance and Microbial Genomics, University of Ulsan, Seoul, Korea
- Department of Infectious Diseases, Asan Medical Center, Seoul, Korea
| | - Yang Soo Kim
- Center for Antimicrobial Resistance and Microbial Genomics, University of Ulsan, Seoul, Korea
- Department of Infectious Diseases, Asan Medical Center, Seoul, Korea
| | - Jun-Hee Woo
- Center for Antimicrobial Resistance and Microbial Genomics, University of Ulsan, Seoul, Korea
- Department of Infectious Diseases, Asan Medical Center, Seoul, Korea
| | - Sang-Ho Choi
- Center for Antimicrobial Resistance and Microbial Genomics, University of Ulsan, Seoul, Korea
- Department of Infectious Diseases, Asan Medical Center, Seoul, Korea
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Fihman V, Lartigue M, Jacquier H, Meunier F, Schnepf N, Raskine L, Riahi J, Sanson-le Pors MJ, Berçot B. Appearance of aac(6′)-Ib-cr gene among extended-spectrum β-lactamase-producing Enterobacteriaceae in a French hospital. J Infect 2008; 56:454-9. [DOI: 10.1016/j.jinf.2008.03.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Revised: 03/14/2008] [Accepted: 03/17/2008] [Indexed: 10/22/2022]
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Chang YC, Shih DYC, Wang JY, Yang SS. Molecular characterization of class 1 integrons and antimicrobial resistance in Aeromonas strains from foodborne outbreak-suspect samples and environmental sources in Taiwan. Diagn Microbiol Infect Dis 2007; 59:191-7. [PMID: 17908616 DOI: 10.1016/j.diagmicrobio.2007.04.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 04/09/2007] [Accepted: 04/18/2007] [Indexed: 10/22/2022]
Abstract
One hundred thirty-three Aeromonas spp. isolates were examined for multiple antibiotic resistance phenotypes and prevalence of class 1 integron sequences. Twenty-four (18.0%) of these isolates contained class 1 integron. Seven different class 1 integrons were found among 24strains, with a total of 10 different gene cassettes encoding for resistance to trimethoprim (dfr12 and dfr2d), aminoglycosides (aadA1 and aadA2), beta-lactam antibiotics (oxa2), chloramphenicol (catB3 and catB8), quaternary ammonium amines (qacE2), and 2 ORFs (orfD and orfF) with unknown function. Rate of antibiotic resistance was different between integron-positive and integron-negative strains. Trimethoprim and trimethoprim-sulphamethoxazole resistances were commonly associated with integron, and all of integron-positive isolates were multiple resistant to more than 3 agents. Resistance to as many as 10 antimicrobial agents were observed in integron-positive strains. Several cassette arrays of class 1 integrons identified in this study were not previously reported in Aeromonas strains. This study demonstrates the wide distribution of class 1 integron in Aeromonas spp. isolated from foodborne outbreak-suspect samples and environmental sources in Taiwan.
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Affiliation(s)
- Yu-Chang Chang
- Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 106, Taiwan
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Hall RM, Collis CM. Antibiotic resistance in gram-negative bacteria: the role of gene cassettes and integrons. Drug Resist Updat 2007; 1:109-19. [PMID: 16904397 DOI: 10.1016/s1368-7646(98)80026-5] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/1998] [Revised: 02/10/1998] [Accepted: 02/20/1998] [Indexed: 11/24/2022]
Abstract
Resistance of gram-negative organisms to antibiotics such as beta-lactams, aminoglycosides, trimethoprim and chloramphenicol is caused by many different acquired genes, and a substantial proportion of these are part of small mobile elements known as gene cassettes. A gene cassette consists of the gene and a downstream sequence, known as a 59-base element (59-be), that acts as a specific recombination site. Gene cassettes can move into or out of a specific receptor site (attl site) in a companion element called an integron, and integration or excision of the cassettes is catalysed by a site-specific recombinase (Intl) that is encoded by the integron. At present count there are 40 different cassette-associated resistance genes and three distinct classes of integron, each encoding a distinct Intl integrase. The same cassettes are found in all three classes of integron, indicating that cassettes can move freely between different integrons. Integrons belonging to class I often contain a further antibiotic resistance gene, sull, conferring resistance to sulphonamides. The sull gene is found in a conserved region (3'-CS) that is not present in all members of this class. Class I integrons of the sull type are most prevalent in clinical isolates and have been found in many different organisms. Even though most of them are defective transposon derivatives, having lost at least one of the transposition genes, they are none the less translocatable and consequently found in many different locations. The transposon Tn7 is the best known representative of class 2 integrons, and Tn7 and relatives are also found in many different species.
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Affiliation(s)
- R M Hall
- CSIRO Molecular Science, Sydney Laboratory, New South Wales, Australia.
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Poppe C, Martin L, Muckle A, Archambault M, McEwen S, Weir E. Characterization of antimicrobial resistance of Salmonella Newport isolated from animals, the environment, and animal food products in Canada. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2006; 70:105-14. [PMID: 16639942 PMCID: PMC1410721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Multi-drug-resistant (MDR) Salmonella enterica serovar Newport strains are increasingly isolated from animals and food products of animal origin and have caused septicemic illness in animals and humans. The purpose of this study was to determine the occurrence and the epidemiologic, phenotypic, and genotypic characteristics of S. Newport of animal origin that may infect humans, either via the food chain or directly. During the 1993-2002 period, the Office International des Epizooties Reference Laboratory for Salmonellosis in Guelph, Ontario, received 36 841 Salmonella strains for serotyping that had been isolated from animals, environmental sources, and food of animal origin in Canada. Of these, 119 (0.3%) were S. Newport. Before 2000, none of 49 S. Newport strains was resistant to more than 3 antimicrobials. In contrast, between January 2000 and December 2002, 35 of 70 isolates, primarily of bovine origin, were resistant to at least 11 antimicrobials, including the extended-spectrum cephalosporins. The blaCMY-2', flo(st'), strA, strB, sulII, and tetA resistance genes were located on plasmids of 80 to 90 MDa that were self-transmissible in 25% of the strains. Conserved segments of the integron 1 gene were found on the large MDR-encoding plasmids in 3 of 35 strains additionally resistant to gentamicin and spectinomycin or to spectinomycin, sulfamethoxazole-trimethoprim, and trimethoprim. Resistance to kanamycin and neomycin was encoded by the aphA-1 gene, located on small plasmids (2.3 to 6 MDa). The increase in bovine-associated MDR S. Newport infections is cause for concern since it indicates an increased risk of human acquisition of the infection via the food chain.
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Affiliation(s)
- Cornelius Poppe
- Office International des Epizooties Reference Laboratory for Salmonellosis, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, Ontario N1G 3W4
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Haines AS, Jones K, Cheung M, Thomas CM. The IncP-6 plasmid Rms149 consists of a small mobilizable backbone with multiple large insertions. J Bacteriol 2005; 187:4728-38. [PMID: 15995187 PMCID: PMC1169491 DOI: 10.1128/jb.187.14.4728-4738.2005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmid Rms149, the archetype of Pseudomonas plasmid incompatibility group IncP-6, was identified in Pseudomonas aeruginosa as an agent conferring resistance to streptomycin, sulfanilamide, gentamicin, and carbenicillin in 1975. It has been classed as a broad-host-range plasmid due to its ability to replicate in both Escherichia coli (where it is designated IncG) and Pseudomonas species, although both species are gamma-proteobacteria. To provide reference information on this Inc group, we have determined the complete sequence of Rms149 and found that, although the genome comprises 57,121 bp, it is essentially a small mobilizable plasmid carrying multiple mobile elements, which make up 79% (>45 kb) of its genome. A replicon has been identified which encodes a single polypeptide with moderate identity to other replication proteins. The region encoding this protein can replicate in Pseudomonas putida and E. coli. This sequence is directly downstream of a putative partitioning region highly similar to that of pRA2. A functional IncQ-type mobilization region is also present. Thus, the backbone appears to be a novel combination of modules already identified in other plasmid systems. Analysis of the segments that fall outside this core of stable inheritance and transfer functions show that this plasmid has been subject to multiple insertion events and that the plasmid appears to carry a considerable load of DNA that no longer should be phenotypically advantageous. The plasmid therefore functions not just as a vehicle for spread of selective traits but also as a store for DNA that is not currently under selection.
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Szczepanowski R, Krahn I, Linke B, Goesmann A, Pühler A, Schlüter A. Antibiotic multiresistance plasmid pRSB101 isolated from a wastewater treatment plant is related to plasmids residing in phytopathogenic bacteria and carries eight different resistance determinants including a multidrug transport system. MICROBIOLOGY-SGM 2005; 150:3613-3630. [PMID: 15528650 DOI: 10.1099/mic.0.27317-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ten different antibiotic resistance plasmids conferring high-level erythromycin resistance were isolated from an activated sludge bacterial community of a wastewater treatment plant by applying a transformation-based approach. One of these plasmids, designated pRSB101, mediates resistance to tetracycline, erythromycin, roxythromycin, sulfonamides, cephalosporins, spectinomycin, streptomycin, trimethoprim, nalidixic acid and low concentrations of norfloxacin. Plasmid pRSB101 was completely sequenced and annotated. Its size is 47 829 bp. Conserved synteny exists between the pRSB101 replication/partition (rep/par) module and the pXAC33-replicon from the phytopathogen Xanthomonas axonopodis pv. citri. The second pRSB101 backbone module encodes a three-Mob-protein type mobilization (mob) system with homology to that of IncQ-like plasmids. Plasmid pRSB101 is mobilizable with the help of the IncP-1alpha plasmid RP4 providing transfer functions in trans. A 20 kb resistance region on pRSB101 is located within an integron-containing Tn402-like transposon. The variable region of the class 1 integron carries the genes dhfr1 for a dihydrofolate reductase, aadA2 for a spectinomycin/streptomycin adenylyltransferase and bla(TLA-2) for a so far unknown Ambler class A extended spectrum beta-lactamase. The integron-specific 3'-segment (qacEDelta1-sul1-orf5Delta) is connected to a macrolide resistance operon consisting of the genes mph(A) (macrolide 2'-phosphotransferase I), mrx (hydrophobic protein of unknown function) and mphR(A) (regulatory protein). Finally, a putative mobile element with the tetracycline resistance genes tetA (tetracycline efflux pump) and tetR was identified upstream of the Tn402-specific transposase gene tniA. The second 'genetic load' region on pRSB101 harbours four distinct mobile genetic elements, another integron belonging to a new class and footprints of two more transposable elements. A tripartite multidrug (MDR) transporter consisting of an ATP-binding-cassette (ABC)-type ATPase and permease, and an efflux membrane fusion protein (MFP) of the RND-family is encoded between the replication/partition and the mobilization module. Homologues of the macrolide resistance genes mph(A), mrx and mphR(A) were detected on eight other erythromycin resistance-plasmids isolated from activated sludge bacteria. Plasmid pRSB101-like repA amplicons were also obtained from plasmid-DNA preparations of the final effluents of the wastewater treatment plant indicating that pRSB101-like plasmids are released with the final effluents into the environment.
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Affiliation(s)
- Rafael Szczepanowski
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Irene Krahn
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Burkhard Linke
- Center for Biotechnology (CeBiTec), Bioinformatics Resource Facility, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
| | - Alexander Goesmann
- Center for Biotechnology (CeBiTec), Bioinformatics Resource Facility, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Andreas Schlüter
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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Coleman N, Tetu S, Wilson N, Holmes A. An unusual integron in Treponema denticola. MICROBIOLOGY-SGM 2005; 150:3524-3526. [PMID: 15528643 DOI: 10.1099/mic.0.27569-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Nick Coleman
- School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW, 2006, Australia
| | - Sasha Tetu
- School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW, 2006, Australia
| | - Neil Wilson
- School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW, 2006, Australia
| | - Andrew Holmes
- School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW, 2006, Australia
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Michael CA, Gillings MR, Holmes AJ, Hughes L, Andrew NR, Holley MP, Stokes HW. Mobile Gene Cassettes: A Fundamental Resource for Bacterial Evolution. Am Nat 2004; 164:1-12. [PMID: 15266366 DOI: 10.1086/421733] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2003] [Accepted: 03/30/2004] [Indexed: 11/03/2022]
Abstract
Horizontal gene transfer increases genetic diversity in prokaryotes to a degree not allowed by the limitations of reproduction by binary fission. The integron/gene cassette system is one of the most recently characterized examples of a system that facilitates horizontal gene transfer. This system, discovered in the context of multidrug resistance, is recognized in a clinical context for its role in allowing pathogens to adapt to the widespread use of antibiotics. Recent studies suggest that gene cassettes are common and encode functions relevant to many adaptive traits. To estimate the diversity of mobile cassettes in a natural environment, a molecular technique was developed to provide representative distributions of cassette populations at points within a sampling area. Subsequently, statistical methods analogous to those used for calculating species diversity were employed to assess the diversity of gene cassettes within the sample area in addition to gaining an estimate of cassette pool size. Results indicated that the number of cassettes within a 5x10-m sample area was large and that the overall mobile cassette metagenome was likely to be orders of magnitude larger again. Accordingly, gene cassettes appear to be capable of mobilizing a significant genetic resource and consequently have a substantial impact on bacterial adaptability.
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Affiliation(s)
- Carolyn A Michael
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.
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Abstract
Integrons are genetic elements composed of a gene encoding an integrase, gene cassettes and an integration site for the gene cassettes (att). The integrase excises and integrates the gene cassettes from and into the integron, but integrons themselves are not mobile. Two groups of integrons are known: resistance integrons and super-integrons. Nearly all known gene cassettes from resistance integrons encode resistance to antibiotics or disinfectants. These integrons are found on transposons, plasmids and the bacterial chromosome. Gene cassettes in super-integrons encode a variety of different functions. Super-integrons are located on the bacterial chromosome. More than 100 gene cassettes may be present, in contrast to resistance integrons where less than ten cassettes are present. Many species harbour super-integrons, which are species-specific, whereas particular resistance integrons can be found in a variety of species. The gene cassettes in resistance integrons probably originated from super-integrons. In the last few years, a variety of new gene cassettes have been described. Many of these encode resistance against newer antibiotics such as cephalosporins and carbapenems. Resistance integrons have been found in isolates from a wide variety of sources, including food.
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Affiliation(s)
- A C Fluit
- Eijkman-Winkler Center, P.O. Box 85500, 3508 GA Utrecht, The Netherlands.
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Nemergut DR, Martin AP, Schmidt SK. Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. Appl Environ Microbiol 2004; 70:1160-8. [PMID: 14766601 PMCID: PMC348930 DOI: 10.1128/aem.70.2.1160-1168.2004] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA. The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. First, using culture-independent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metal-contaminated mine tailings. Using degenerate primers, we amplified integron integrase genes from the tailings. We discovered 14 previously undescribed integrase genes, including six novel gene lineages. In addition, we found 11 novel gene cassettes in this sample. One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity. This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics. We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects. We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.
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Affiliation(s)
- D R Nemergut
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
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Nandi S, Maurer JJ, Hofacre C, Summers AO. Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter. Proc Natl Acad Sci U S A 2004; 101:7118-22. [PMID: 15107498 PMCID: PMC406475 DOI: 10.1073/pnas.0306466101] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Accepted: 03/15/2004] [Indexed: 11/18/2022] Open
Abstract
Reversing the spread of antibiotic multiresistant bacteria is hampered by ignorance of the natural history of resistance genes, the mobile elements carrying them, and the bacterial hosts harboring them. Using traditional cultivation and cultivation-independent molecular techniques, we quantified antibiotic resistance genes and mobile elements called integrons in poultry house litter from commercial poultry farms. Unexpectedly, the major reservoir for Class 1 integrons in poultry litter is not their previously identified hosts, Gram-negative Enterobacteriaceae such as Escherichia coli. Rather, integrons and associated resistance genes abound in several genera of Gram-positive bacteria that constitute >85% of the litter community compared with Enterobacteriaceae that comprise <2% of this ecosystem. This finding warrants reexamination of our assumptions about the persistence and spread of antibiotic resistance genes.
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Affiliation(s)
- Sobhan Nandi
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Ruiz J, Navia MM, Casals C, Sierra JM, Jiménez De Anta MT, Vila J. Integron-mediated antibiotic multiresistance in Acinetobacter baumannii clinical isolates from Spain. Clin Microbiol Infect 2003; 9:907-11. [PMID: 14616677 DOI: 10.1046/j.1469-0691.2003.00561.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To determine whether non-epidemiologically related, antibiotic-resistant isolates of Acinetobacter baumannii from different geographical origins possess common type 1 integrons. METHODS The epidemiologic relationships between seven A. baumannii strains recovered from different Spanish hospitals were established by pulsed-field gel electrophoresis, the presence of integrons being determined by PCR and DNA sequencing. RESULTS Integron analysis showed the presence of four different integrons, containing six different known genes (aacC1, aacA4, aadA1, aadB, oxa21 and oxa37) plus an ORF. It was found that the same integron was present in different unrelated strains and that related strains could have different integrons. CONCLUSION These results show the potential risk of integron dissemination among different strains of A. baumannii.
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Affiliation(s)
- J Ruiz
- Institut Clinic d'Infeccions i Immunologia Clínica, IDIBAPS, Hospital Clínic, Facultat de Medicina, Universitat de Barcelona, Villaroel 170, 08036-Barcelona, Spain
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Abstract
Aminoglycoside antibiotics have had a major impact on our ability to treat bacterial infections for the past half century. Whereas the interest in these versatile antibiotics continues to be high, their clinical utility has been compromised by widespread instances of resistance. The multitude of mechanisms of resistance is disconcerting but also illuminates how nature can manifest resistance when bacteria are confronted by antibiotics. This article reviews the most recent knowledge about the mechanisms of aminoglycoside action and the mechanisms of resistance to these antibiotics.
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Affiliation(s)
- Sergei B Vakulenko
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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Navia MM, Ruiz J, Vila J. Characterization of an integron carrying a new class D beta-lactamase (OXA-37) in Acinetobacter baumannii. Microb Drug Resist 2003; 8:261-5. [PMID: 12523622 DOI: 10.1089/10766290260469516] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Integrons from a clinical strain of Acinetobacter baumannii highly resistant to beta-lactams have been analyzed. The largest (2.2 kb) contained three gene cassettes: an aacA4, an open reading frame of 417 nucleotides, and an OXA-type encoding gene. The oxa gene nucleotide sequence differed from that of the oxa-20 in 2 bp, one of the mutations being silent. The nonsilent mutationgenerated a substitution of glutamic acid for aspartic acid. The new OXA has been named OXA-37.
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Affiliation(s)
- Margarita M Navia
- Laboratori de Microbiologia, Institut Clinic Infeccions i Immunologia, Hospital Clinic i Provincial, Institut d'Investigacions Biomédiques August Pi I Sunyer (IDIBAPS), Universitat de Barcelona, Spain
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Casin I, Hanau-Berçot B, Podglajen I, Vahaboglu H, Collatz E. Salmonella enterica serovar Typhimurium bla(PER-1)-carrying plasmid pSTI1 encodes an extended-spectrum aminoglycoside 6'-N-acetyltransferase of type Ib. Antimicrob Agents Chemother 2003; 47:697-703. [PMID: 12543680 PMCID: PMC151738 DOI: 10.1128/aac.47.2.697-703.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have studied the aminoglycoside resistance gene, which confers high levels of resistance to both amikacin and gentamicin, that is carried by plasmid pSTI1 in the PER-1 beta-lactamase-producing strain of Salmonella enterica serovar Typhimurium previously isolated in Turkey. This gene, called aac(6')-Ib(11), was found in a class 1 integron and codes for a protein of 188 amino acids, a fusion product between the N-terminal moiety (8 amino acids) of the signal peptide of the beta-lactamase OXA-1 and the acetyltransferase. The gene lacked a plausible Shine-Dalgarno (SD) sequence and was located 45 nucleotides downstream from a small open reading frame, ORF-18, with a coding capacity of 18 amino acids and a properly spaced SD sequence likely to direct the initiation of aac(6')-Ib(11) translation. AAC(6')-Ib(11) had Leu118 and Ser119 as opposed to Gln and Leu or Gln and Ser, respectively, which were observed in all previously described enzymes of this type. We have evaluated the effect of Leu or Gln at position 118 by site-directed mutagenesis of aac(6')-Ib(11) and two other acetyltransferase gene variants, aac(6')-Ib(7) and -Ib(8), which naturally encode Gln118. Our results show that the combination of Leu118 and Ser119 confers an extended-spectrum aminoglycoside resistance, with the MICs of all aminoglycosides in clinical use, including gentamicin, being two to eight times higher for strains with Leu118 and Ser119 than for those with Gln118 and Ser119.
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Affiliation(s)
- Isabelle Casin
- Service de Microbiologie, Hôpital Saint-Louis, INSERM EMI-U 0004-LRMA, Université Paris VI, France.
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Thungapathra M, Sinha KK, Chaudhuri SR, Garg P, Ramamurthy T, Nair GB, Ghosh A. Occurrence of antibiotic resistance gene cassettes aac(6')-Ib, dfrA5, dfrA12, and ereA2 in class I integrons in non-O1, non-O139 Vibrio cholerae strains in India. Antimicrob Agents Chemother 2002; 46:2948-55. [PMID: 12183252 PMCID: PMC395331 DOI: 10.1128/aac.46.9.2948-2955.2002] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular mechanisms of multidrug resistance in Vibrio cholerae belonging to non-O1, non-O139 serogroups isolated during 1997 to 1998 in Calcutta, India, were investigated. Out of the 94 strains examined, 22 strains were found to have class I integrons. The gene cassettes identified were dfrA1, dfrA15, dfrA5, and dfrA12 for trimethoprim; aac(6')-Ib for amikacin and tobramycin; aadA1 and aadA2 for streptomycin and spectinomycin; and ereA2 for erythromycin resistance. To our knowledge, this is the first report of the presence of dfrA5, dfrA12, aac(6')-Ib, and ereA2 cassettes in class I integrons of V. cholerae. Forty-three of 94 strains also had plasmids, and out of these, 14 contained both class I integrons and plasmids. Pulsed-field gel electrophoresis followed by Southern hybridization revealed that in the 14 plasmid-bearing strains, class I integrons resided either on chromosomes, on plasmids, or on both. Our results indicated that besides class I integrons and plasmids, a conjugative transposon element, SXT, possibly contributed to the multiple antibiotic resistance.
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