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Aihara M, Gotoh Y, Shirahama S, Matsushima Y, Uchiumi T, Kang D, Hayashi T. Generation and maintenance of the circularized multimeric IS26-associated translocatable unit encoding multidrug resistance. Commun Biol 2024; 7:597. [PMID: 38762617 PMCID: PMC11102541 DOI: 10.1038/s42003-024-06312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 05/08/2024] [Indexed: 05/20/2024] Open
Abstract
In gram-negative bacteria, IS26 often exists in multidrug resistance (MDR) regions, forming a pseudocompound transposon (PCTn) that can be tandemly amplified. It also generates a circular intermediate called the "translocatable unit (TU)", but the TU has been detected only by PCR. Here, we demonstrate that in a Klebsiella pneumoniae MDR clone, mono- and multimeric forms of the TU were generated from the PCTn in a preexisting MDR plasmid where the inserted form of the TU was also tandemly amplified. The two modes of amplification were reproduced by culturing the original clone under antimicrobial selection pressure, and the amplified state was maintained in the absence of antibiotics. Mono- and multimeric forms of the circularized TU were generated in a RecA-dependent manner from the tandemly amplified TU, which can be generated in RecA-dependent and independent manners. These findings provide novel insights into the dynamic processes of genome amplification in bacteria.
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Affiliation(s)
- Masamune Aihara
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan.
- Department of Health Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Saki Shirahama
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Yuichi Matsushima
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Uchiumi
- Department of Health Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Kashiigaoka Rehabilitation Hospital, Fukuoka, Japan
- Department of Medical Laboratory Science, Faculty of Health Sciences, Junshin Gakuen University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Yescas-Zazueta V, Rocha-Gracia RDC, González-Bonilla CR, Ayala-Zavala JF, Enciso-Martínez Y, Carreón-León EA, González Corona BA, Valencia D, Ballesteros-Monrreal MG, Barrios-Villa E. Resistance phenotype and virulence potential of Leclercia adecarboxylata strains isolated from different sources. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001457. [PMID: 38661713 PMCID: PMC11084626 DOI: 10.1099/mic.0.001457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to β-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50 % of the strains; bla TEM was the most prevalent BLEE gene (70 %), while the quinolone qnrB gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.
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Affiliation(s)
- Viviana Yescas-Zazueta
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Rosa del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
| | - Cesar R. González-Bonilla
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
| | - J. Fernando Ayala-Zavala
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C., 83304 Hermosillo, Mexico
| | - Yessica Enciso-Martínez
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C., 83304 Hermosillo, Mexico
| | - Eder A. Carreón-León
- Laboratorio de Análisis Clínicos de la Universidad Autónoma de Chihuahua, Av. Universidad S/N, Circuito Universitario Campus 1, 31310 Chihuahua, Mexico
| | - Brigitte A. González Corona
- Laboratorio de Análisis Clínicos de la Universidad Autónoma de Chihuahua, Av. Universidad S/N, Circuito Universitario Campus 1, 31310 Chihuahua, Mexico
| | - Dora Valencia
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Manuel G. Ballesteros-Monrreal
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Edwin Barrios-Villa
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
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Harmer CJ, Hall RM. IS 26 and the IS 26 family: versatile resistance gene movers and genome reorganizers. Microbiol Mol Biol Rev 2024:e0011922. [PMID: 38436262 DOI: 10.1128/mmbr.00119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Abstract
SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Sobkowiak A, Scherff N, Schuler F, Bletz S, Mellmann A, Schwierzeck V, van Almsick V. Plasmid-encoded gene duplications of extended-spectrum β-lactamases in clinical bacterial isolates. Front Cell Infect Microbiol 2024; 14:1343858. [PMID: 38469349 PMCID: PMC10925753 DOI: 10.3389/fcimb.2024.1343858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction The emergence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is an urgent and alarming One Health problem. This study aimed to investigate duplications of plasmid-encoded ESBL genes and their impact on antimicrobial resistance (AMR) phenotypes in clinical and screening isolates. Methods Multi-drug-resistant bacteria from hospitalized patients were collected during routine clinical surveillance from January 2022 to June 2023, and their antimicrobial susceptibility patterns were determined. Genotypes were extracted from long-read whole-genome sequencing data. Furthermore, plasmids and other mobile genetic elements associated with ESBL genes were characterized, and the ESBL genes were correlated to ceftazidime minimal inhibitory concentration (MIC). Results In total, we identified four cases of plasmid-encoded ESBL gene duplications that match four genetically similar plasmids during the 18-month surveillance period: five Escherichia coli and three Klebsiella pneumoniae isolates. As the ESBL genes were part of transposable elements, the surrounding sequence regions were duplicated as well. In-depth analysis revealed insertion sequence (IS)-mediated transposition mechanisms. Isolates with duplicated ESBL genes exhibited a higher MIC for ceftazidime in comparison to isolates with a single gene copy (3-256 vs. 1.5-32 mg/L, respectively). Conclusion ESBL gene duplications led to an increased phenotypic resistance against ceftazidime. Our data suggest that ESBL gene duplications by an IS-mediated transposition are a relevant mechanism for how AMR develops in the clinical setting and is part of the microevolution of plasmids.
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Affiliation(s)
- Annika Sobkowiak
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
| | - Natalie Scherff
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Franziska Schuler
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan Bletz
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Vera Schwierzeck
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Vincent van Almsick
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
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Wang L, Zhu M, Yan C, Zhang Y, He X, Wu L, Xu J, Lu J, Bao Q, Hu Y, Xu T, Liang J. Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China. Front Microbiol 2023; 14:985102. [PMID: 36950157 PMCID: PMC10026359 DOI: 10.3389/fmicb.2023.985102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Background The emergence of highly drug-resistant K. pneumoniae, has become a major public health challenge. In this work, we aim to investigate the diversity of species and sequence types (STs) of clinical Klebsiella isolates and to characterize the prevalence and structure of class 1 integrons. Methods Based on the whole genome sequencing, species identification was performed by 16S rRNA gene homology and average nucleotide identity (ANI) analysis. STs were determined in accordance with the international MLST schemes for K. pneumoniae and K. variicola. Integron characterization and comparative genomic analysis were performed using various bioinformatic tools. Results Species identification showed that the 167 isolates belonged to four species: K. pneumoniae, K. variicola subsp. variicola, K. quasipneumoniae and K. aerogenes. Thirty-six known and 5 novel STs were identified in K. pneumoniae, and 10 novel STs were identified in K. variicola subsp. variicola. Class 1 integrons were found in 57.49% (96/167) of the isolates, and a total of 169 resistance gene cassettes encoding 19 types of resistance genes, including carbapenem resistance gene (bla IPM-4) and class D β-lactamases gene (bla OXA-1 and bla OXA-10), were identified. Among the 17 complete genomes, 29 class 1 integrons from 12 groups were found, only 1 group was encoded on chromosomes. Interestingly, one plasmid (pKP167-261) carrying two copies of approximately 19-kb IS26-Int1 complex resistance region that contains an integron and a multidrug resistance gene fragment. Conclusion The results of this work demonstrated that the species and STs of the clinical Klebsiella isolates were more complex by the whole genome sequence analysis than by the traditional laboratory methods. Finding of the new structure of MGEs related to the resistance genes indicates the great importance of deeply exploring the molecular mechanisms of bacterial multidrug resistance.
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Affiliation(s)
- Lan Wang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Chunxia Yan
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Yanfang Zhang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Xuying He
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Lin Wu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Jiefeng Xu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Qiyu Bao
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yunliang Hu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
- *Correspondence: Teng Xu,
| | - Jialei Liang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Jialei Liang,
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Harmer CJ, Lebreton F, Stam J, McGann PT, Hall RM. Mechanisms of IS 26-Mediated Amplification of the aphA1 Gene Leading to Tobramycin Resistance in an Acinetobacter baumannii Isolate. Microbiol Spectr 2022; 10:e0228722. [PMID: 36073931 PMCID: PMC9602291 DOI: 10.1128/spectrum.02287-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/19/2022] [Indexed: 01/04/2023] Open
Abstract
Enhanced levels of resistance to antibiotics arising from amplification of an antibiotic resistance gene that impact therapeutic options are increasingly observed. Amplification can also disclose novel phenotypes leading to treatment failure. However, the mechanism is poorly understood. Here, the route to amplification of the aphA1 kanamycin and neomycin resistance gene during tobramycin treatment of an Acinetobacter baumannii clinical isolate, leading to tobramycin resistance and treatment failure, was investigated. In the tobramycin-susceptible parent isolate, MRSN56, a single copy of aphA1 is present in the pseudocompound transposon PTn6020, bounded by directly oriented copies of IS26. For two clinical resistant isolates, new long-read sequence data were combined with available short-read data to complete the genomes. Comparison to the completed genome of MRSN56 revealed that, in both cases, IS26 had generated a circular translocatable unit (TU) containing PTn6020 and additional adjacent DNA. In one case, this TU was reincorporated into the second product generated by the deletion that formed the TU via the targeted conservative route and amplified about 7 times. In the second case, the TU was incorporated at a new location via the copy-in route and amplified about 65 times. Experimental amplification ex vivo by subjecting MRSN56 to tobramycin selection pressure yielded different TUs, which were incorporated at either the original location or a new location and amplified many times. The outcomes suggest that when IS26 is involved, amplification occurs via rolling circle replication of a newly formed TU coupled to the IS26-mediated TU formation or reincorporation step. IMPORTANCE Heteroresistance, a significant issue that is known to impact antibiotic treatment outcomes, is caused by the presence of spontaneously arising cells with elevated levels of resistance to therapeutically important antibiotics in a population of susceptible cells. Gene amplification is one well-documented cause of heteroresistance, but precisely how extensive amplification occurs is not understood. Here, we establish the case for the direct involvement of IS26 activity in the amplification of the aphA1 gene to disclose resistance to tobramycin. The aphA1 gene is usually found associated with IS26 in Gram-negative pathogens and is commonly found in extensively resistant Acinetobacter baumannii strains. IS26 and related IS cause adjacent deletions, forming a nonreplicating circular molecule known as a translocatable unit (TU), and amplification via a rolling circle mechanism appears to be coupled to either IS26-mediated TU formation or reincorporation. Related IS found in Gram-positive pathogens may play a similar role.
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Affiliation(s)
- Christopher J. Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Francois Lebreton
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jason Stam
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Patrick T. McGann
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ruth M. Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Méndez-Moreno E, Caporal-Hernandez L, Mendez-Pfeiffer PA, Enciso-Martinez Y, De la Rosa López R, Valencia D, Arenas-Hernández MMP, Ballesteros-Monrreal MG, Barrios-Villa E. Characterization of Diarreaghenic Escherichia coli Strains Isolated from Healthy Donors, including a Triple Hybrid Strain. Antibiotics (Basel) 2022; 11:833. [PMID: 35884087 PMCID: PMC9312309 DOI: 10.3390/antibiotics11070833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 12/10/2022] Open
Abstract
Escherichia coli is a well-recognized inhabitant of the animal and human gut. Its presence represents an essential component of the microbiome. There are six pathogenic variants of E. coli associated with diarrheal processes, known as pathotypes. These harbor genetic determinants that allow them to be classified as such. In this work, we report the presence of diarrheagenic pathotypes of E. coli strains isolated from healthy donors. Ninety E. coli strains were analyzed, of which forty-six (51%) harbored virulence markers specifics for diarrheagenic pathotypes, including four hybrids (one of them with genetic determinants of three DEC pathotypes). We also identified phylogenetic groups with a higher prevalence of B2 (45.6%) and A (17.8%). In addition, resistance to sulfonamides (100%), and aminoglycosides (100%) was found in 100% of the strains, with a lower prevalence of resistance to cefotaxime (13.3%), ceftriaxone (12.2%), fosfomycin (10%), and meropenem (0%). All analyzed strains were classified as multidrug resistant. Virulence genes were also investigated, which led us to propose three new virotypes. Among the virulence traits observed, the ability to form biofilms stands out, which was superior to that of the E. coli and Staphylococcus aureus strains used as positive controls.
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Affiliation(s)
- Evelyn Méndez-Moreno
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Liliana Caporal-Hernandez
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Pablo A. Mendez-Pfeiffer
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Yessica Enciso-Martinez
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Rafael De la Rosa López
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Dora Valencia
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Margarita M. P. Arenas-Hernández
- Posgrado en Microbiología, Centro de Investigación en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla CP 72570, Pue, Mexico;
| | - Manuel G. Ballesteros-Monrreal
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Edwin Barrios-Villa
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
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Castanheira M, Simner PJ, Bradford PA. Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection. JAC Antimicrob Resist 2021; 3:dlab092. [PMID: 34286272 PMCID: PMC8284625 DOI: 10.1093/jacamr/dlab092] [Citation(s) in RCA: 218] [Impact Index Per Article: 72.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.
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Varani A, He S, Siguier P, Ross K, Chandler M. The IS6 family, a clinically important group of insertion sequences including IS26. Mob DNA 2021; 12:11. [PMID: 33757578 PMCID: PMC7986276 DOI: 10.1186/s13100-021-00239-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
The IS6 family of bacterial and archaeal insertion sequences, first identified in the early 1980s, has proved to be instrumental in the rearrangement and spread of multiple antibiotic resistance. Two IS, IS26 (found in many enterobacterial clinical isolates as components of both chromosome and plasmids) and IS257 (identified in the plasmids and chromosomes of gram-positive bacteria), have received particular attention for their clinical impact. Although few biochemical data are available concerning the transposition mechanism of these elements, genetic studies have provided some interesting observations suggesting that members of the family might transpose using an unexpected mechanism. In this review, we present an overview of the family, the distribution and phylogenetic relationships of its members, their impact on their host genomes and analyse available data concerning the particular transposition pathways they may use. We also provide a mechanistic model that explains the recent observations on one of the IS6 family transposition pathways: targeted cointegrate formation between replicons.
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Affiliation(s)
- Alessandro Varani
- School of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil
| | - Susu He
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Patricia Siguier
- Centre de Biologie Intégrative-Université Paul SABATIER, CNRS - Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100 - bât. CNRS-IBCG, Toulouse, France
| | - Karen Ross
- Protein Information Resource, Department of Biochem., Mol. and Cell. Biol, Georgetown University Medical Center, Washington, DC, USA
| | - Michael Chandler
- Department of Biochem., Mol. and Cell. Biol, Georgetown University Medical Center, Washington, DC, USA.
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10
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Harmer CJ, Pong CH, Hall RM. Structures bounded by directly-oriented members of the IS26 family are pseudo-compound transposons. Plasmid 2020; 111:102530. [DOI: 10.1016/j.plasmid.2020.102530] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022]
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11
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Chen CM, Yu WL, Huang M, Liu JJ, Chen IC, Chen HF, Wu LT. Characterization of IS26-composite transposons and multidrug resistance in conjugative plasmids from Enterobacter cloacae. Microbiol Immunol 2016. [PMID: 26223152 DOI: 10.1111/1348-0421.12289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SHV-12 is the most widespread resistance determinant of Enterobacter cloacae in Taiwan; however, blaSHV-12 has rarely been mobilized. Six multidrug-resistant E. cloacae isolates were collected. After conjugal transfer, plasmid profiling and analysis of incompatibility groups was performed to characterize the genetic context of blaSHV-12 -containing fragments. The presence of mobile genetic elements was demonstrated by PCR, cloning, sequencing and bioinformatics analyses. Four different β-lactamase genes (blaTEM-1 , blaSHV-12 , blaCTX-M-3 and/or blaCTX-M-14 ) were observed in the conjugative plasmids belonging to the IncHI2 (n = 4), IncI1 or IncP incompatibility groups. The IS26-blaSHV-12 -IS26 locus was located in five different genetic environments. A novel structural organization of a class 1 integron with the aac(6')-IIc cassette truncated by IS26 was identified in one isolate. Thus, blaSHV-12 was obtained from different plasmids through IS26-mediated homologous recombination. IS26 plays a vital role in the distribution of mobile resistance elements between different plasmids found in multidrug-resistant E. cloacae isolates.
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Affiliation(s)
- Chih-Ming Chen
- Division of Infectious Disease, Department of Internal Medicine, Tungs' Taichung Metro Harbor Hospital, Taichung
| | - Wen-Liang Yu
- Departments of Medical Research.,Intensive Care Medicine, Chi-Mei Medical Center, Yungkang City, Tainan.,Department of Medicine, Taipei Medical University, Taipei
| | - Mei Huang
- Division of Infectious Disease, Chang Bing Show Chwan Memorial Hospital, Changhua County
| | - Jau-Jin Liu
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
| | - I-Chien Chen
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
| | - Huei-Fen Chen
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
| | - Lii-Tzu Wu
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
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12
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Preston KE, Hitchcock SA, Aziz AY, Tine JA. The complete nucleotide sequence of the multi-drug resistance-encoding IncL/M plasmid pACM1. Plasmid 2014; 76:54-65. [PMID: 25291385 DOI: 10.1016/j.plasmid.2014.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/20/2014] [Accepted: 08/29/2014] [Indexed: 11/25/2022]
Abstract
The 89,977 bp nucleotide sequence of pACM1, isolated from a 1993 outbreak strain of cephalosporin-resistant Klebsiella oxytoca, has been completed and assigned GenBank accession number KJ541681. The plasmid has a single 31,842 bp mosaic multi-drug resistance-encoding (MDR) region comprising the mer resistance module of Tn1696, two integrons with a total of seven cassettes, one complete copy each of IS1R and IS26, and the bla(SHV-5)-carrying Tn2003 (with defective IS26 termini), all within a Tn1721-like element inserted into the mucB gene of the IncL/M plasmid backbone. The Tn1721-Tn1696 combination resembles sequence found in the chromosomal MDR islands of some Acinetobacter baumannii isolates. Among the completely sequenced IncL/M resistance plasmids, the Tn1721-based MDR region is unique, but data from older studies suggest that this type of plasmid was widespread in the 1990s. Since resistance gene dosage is affected by plasmid copy number (PCN), we used a relatively simple new "efficiency-corrected" qPCR assay to measure the PCN of pACM1. There are approximately three copies per chromosome in an Escherichia coli DH5α host, and two in the original Klebsiella oxytoca isolate. We could not find similar PCN data for other medically important plasmids for comparison. The study of this plasmid property and its effect on resistance levels should be facilitated in the future by the availability of qPCR instruments and complete genome sequences.
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Affiliation(s)
- Karen E Preston
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA.
| | - Sandra A Hitchcock
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA; Hudson Valley Community College, 80 Vandenburgh Ave., Troy, NY 12180, USA
| | - Abdullah Y Aziz
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA; Hudson Valley Community College, 80 Vandenburgh Ave., Troy, NY 12180, USA
| | - John A Tine
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA
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13
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Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum β-lactamase from an Escherichia coli strain. Antimicrob Agents Chemother 2014; 58:6550-7. [PMID: 25136025 DOI: 10.1128/aac.03183-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
P1 bacteriophages lysogenize bacteria as independent plasmid-like elements. We describe here a P1-like bacteriophage, RCS47, carrying a blaSHV-2 gene, isolated from a clinical strain of Escherichia coli from phylogroup B1, and we report the prevalence of P1-like prophages in natural E. coli isolates. We found that 70% of the sequence of RCS47, a 115-kb circular molecule, was common to the reference P1 bacteriophage under GenBank accession no. AF234172.1, with the shared sequences being 99% identical. RCS47 had acquired two main foreign DNA fragments: a 9,636-bp fragment mobilized by two IS26 elements containing a blaSHV-2 gene, and an 8,544-bp fragment mobilized by two IS5 elements containing an operon encoding a dimethyl sulfoxide reductase. The reference P1 prophage plasmid replication gene belonged to the IncY incompatibility group, whereas that of RCS47 was from an unknown group. The lytic capacity of RCS47 and blaSHV-2 gene transduction, through the lysogenization of RCS47 in the recipient E. coli strains, were not demonstrated. The prevalence of P1-like prophages in various animal and human E. coli strain collections, as determined by the PCR detection of repL, the lytic replication gene, was 12.6%. No differences in the prevalences of these prophages were found between extended-spectrum β-lactamase (ESBL)-producing and non-ESBL-producing strains (P = 0.69), but this prevalence was lower in phylogroup B2 than in the other phylogroups (P = 0.008), suggesting epistatic interactions between P1 family phages and the genetic background of E. coli strains. P1-like phages are part of the mobile elements that carry antibiotic resistance. The high prevalence of P1-like prophages suggests their role may be underestimated.
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14
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Elliott KT, Cuff LE, Neidle EL. Copy number change: evolving views on gene amplification. Future Microbiol 2014; 8:887-99. [PMID: 23841635 DOI: 10.2217/fmb.13.53] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The rapid pace of genomic sequence analysis is increasing the awareness of intrinsically dynamic genetic landscapes. Gene duplication and amplification (GDA) contribute to adaptation and evolution by allowing DNA regions to expand and contract in an accordion-like fashion. This process affects diverse aspects of bacterial infection, including antibiotic resistance and host-pathogen interactions. In this review, microbial GDA is discussed, primarily using recent bacterial examples that demonstrate medical and evolutionary consequences. Interplay between GDA and horizontal gene transfer further impact evolutionary trajectories. Complementing the discovery of gene duplication in clinical and environmental settings, experimental evolution provides a powerful method to document genetic change over time. New methods for GDA detection highlight both its importance and its potential application for genetic engineering, synthetic biology and biotechnology.
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Affiliation(s)
- Kathryn T Elliott
- Biology Department, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA.
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15
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Zienkiewicz M, Kern-Zdanowicz I, Carattoli A, Gniadkowski M, Cegłowski P. Tandem multiplication of the IS26-flanked amplicon with the bla(SHV-5) gene within plasmid p1658/97. FEMS Microbiol Lett 2013; 341:27-36. [PMID: 23330672 DOI: 10.1111/1574-6968.12084] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/04/2013] [Accepted: 01/11/2013] [Indexed: 11/28/2022] Open
Abstract
The IncF plasmid p1658/97 (c. 125 kb) from Escherichia coli isolates recovered during a clonal outbreak in a hospital in Warsaw, Poland, in 1997 contains the extended-spectrum β-lactamase (ESBL) gene bla(SHV-5), originated from the Klebsiella pneumoniae chromosome. A region containing the bla(SHV-5) gene is flanked by two IS26 copies and its copy number multiplies spontaneously within p1658/97 and RecA-deficient E. coli strains. Here, we demonstrate that the amplified IS26-bla(SHV-5) units were arranged in tandems, containing up to more than 10 units, which could raise ceftazidime MICs for host strains from 4 μg mL(-1) to more than 128 μg mL(-1). Successive deletions within p1658/97, located outside the amplifiable module and encompassing even as little as c. 15% of the plasmid, blocked the amplification. Moreover, the complementing re-introduction of the deleted fragments in trans did not restore the process. Similarly, insertions of a 1-kb DNA fragment into the amplicon inhibited its self-multiplication ability. The module was able to transmit into another IS26-containing plasmid by recombination. The results prompted us to speculate that local DNA structure, especially favorable in p1658/97, might have been responsible for the IS26-bla(SHV-5) multiplication ability.
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Affiliation(s)
- Maksymilian Zienkiewicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of Polish Academy of Sciences, Warsaw, Poland.
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16
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Silva-Sanchez J, Garza-Ramos JU, Reyna-Flores F, Sánchez-Perez A, Rojas-Moreno T, Andrade-Almaraz V, Pastrana J, Castro-Romero JI, Vinuesa P, Barrios H, Cervantes C. Extended-spectrum β-Lactamase-Producing Enterobacteriaceae Causing Nosocomial Infections in Mexico. A Retrospective and Multicenter Study. Arch Med Res 2011; 42:156-62. [DOI: 10.1016/j.arcmed.2011.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 02/09/2011] [Indexed: 11/29/2022]
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17
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Garza-González E, Mendoza Ibarra SI, Llaca-Díaz JM, Gonzalez GM. Molecular characterization and antimicrobial susceptibility of extended-spectrum {beta}-lactamase-producing Enterobacteriaceae isolates at a tertiary-care centre in Monterrey, Mexico. J Med Microbiol 2010; 60:84-90. [PMID: 20930052 DOI: 10.1099/jmm.0.022970-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our objective was to analyse phenotypic and genetic data of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae, Enterobacter cloacae, Escherichia coli and Serratia marcescens that cause infections in our hospital. Over a 3 year period, 342 randomly selected clinical Enterobacteriaceae isolates were tested for ESBL production and evaluated for the presence of the β-lactamase genes bla(SHV), bla(TEM,) bla(CTX-M) and bla(TLA-1). The antibiotic susceptibilities of these isolates were also determined, and the clonality of the isolates was assessed by PFGE. Based on our analyses, 33/92 (35.9 %) K. pneumoniae, 31/87 (35.6 %) Enterobacter cloacae, 24/80 (30 %) E. coli and 17/83 (20.5 %) S. marcescens were identified as ESBL producers. The presence of TEM, SHV or CTX ESBL types was detected in 99/105 (94 %) of the isolates. TLA-1 was not detected in any of the 105 isolates. The dominant ESBL types were bla(SHV-5) (n=33), bla(SHV12) (n=31) and bla(CTX-M-15) (n=30). The predominant ESBL identified in E. coli and Enterobacter cloacae isolates was CTX-M-15, whereas in K. pneumoniae and S. marcescens the predominant types were SHV-12 and SHV-5, respectively. PFGE genotyping revealed two main genetic patterns in the K. pneumoniae isolates, types SHV-12 and TEM-1+SHV-5. An outbreak caused by Enterobacter cloacae SHV-5+CTX-M-15 was detected. In contrast, most ESBL-producing isolates of E. coli and S. marcescens did not have similar PFGE banding patterns and thus were not genetically similar. Enterobacteriaceae are a concern in our hospital, especially K. pneumoniae and Enterobacter cloacae. Our results confirm that the CTX-M-15 ESBL type has spread rapidly in the hospital, and thus requires careful monitoring.
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Affiliation(s)
- Elvira Garza-González
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Sandra Iveth Mendoza Ibarra
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Jorge M Llaca-Díaz
- Hospital Universitario 'Dr José Eleuterio González', Universidad Autónoma de Nuevo León, Monterrey, Nuevo Leon, Mexico
| | - Gloria M Gonzalez
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
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18
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A novel IS26 structure surrounds bla
CTX-M genes in different plasmids from German clinical Escherichia coli isolates. J Med Microbiol 2010; 59:580-587. [DOI: 10.1099/jmm.0.016188-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This report focuses on the molecular characterization of 22 extended-spectrum β-lactamase-producing Escherichia coli isolates collected in a German university hospital during a period of 9 months in 2006. Relationship analysis of clinical isolates was done via PFGE, multilocus sequence typing, plasmid profiling and additionally PCR for bla
ESBL detection and determination of phylogroups. After conjugal transfer, plasmid isolation and subsequent PCR for bla
ESBL detection and determination of incompatibility groups were performed. Using one-primer walking, up to 3600 bp upstream and downstream of different bla
CTX-M genes could be sequenced. β-Lactamases found were TEM-1 (n=14), SHV-5 (n=1) and a wide variety of CTX-M types (n=21), i.e. CTX-M-15 (n=12), CTX-M-1 (n=4), CTX-M-14 (n=2), CTX-M-9 (n=1), CTX-M-3 (n=1) and one new type, CTX-M-65 (n=1). In 18 isolates, bla
ESBL genes were located on conjugative plasmids of sizes between 40 and 180 kbp belonging to incompatibility groups FII (n=9), N (n=5) and I1 (n=4). bla
CTX-M was found to be associated with the common elements ISEcp1, IS26 and IS903-D, but with unusual spacer sequences for ISEcp1 in two isolates. These insertion sequences, connected to bla
CTX-M as well as other genes, were located between two IS26 elements in a configuration that has not yet been described. The results reveal the emergence of bla
ESBL, predominantly bla
CTX-M, located on different plasmids harboured by genotypically different E. coli strains. The identical gene arrangement in the bla
CTX-M neighbourhood in plasmids of different incompatibility groups indicates a main role of IS26 in distribution of mobile resistance elements between different plasmids.
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