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Marí-Almirall M, Ferrando N, Fernández MJ, Cosgaya C, Viñes J, Rubio E, Cuscó A, Muñoz L, Pellice M, Vergara A, Campo I, Rodríguez-Serna L, Santana G, Del Río A, Francino O, Ciruela P, Ballester F, Marco F, Martínez JA, Soriano Á, Pitart C, Vila J, Roca I. Clonal Spread and Intra- and Inter-Species Plasmid Dissemination Associated With Klebsiella pneumoniae Carbapenemase-Producing Enterobacterales During a Hospital Outbreak in Barcelona, Spain. Front Microbiol 2021; 12:781127. [PMID: 34867923 PMCID: PMC8637019 DOI: 10.3389/fmicb.2021.781127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023] Open
Abstract
Objectives: The study aimed to characterize the clonal spread of resistant bacteria and dissemination of resistance plasmids among carbapenem-resistant Enterobacterales at a tertiary hospital in Catalonia, Spain. Methods: Isolates were recovered from surveillance rectal swabs and diagnostic samples. Species identification was by matrix-assisted laser desorption ionization-time time of flight mass spectrometry (MALDI-TOF MS). Molecular typing was performed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Antimicrobial susceptibility was assessed by gradient-diffusion and carriage of bla genes was detected by PCR. Plasmid typing, conjugation assays, S1-PFGE studies and long-read sequencing were used to characterize resistance plasmids. Results: From July 2018 to February 2019, 125 Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacterales were recovered from 101 inpatients from surveillance (74.4%) or clinical samples (25.6%), in a tertiary hospital in Barcelona. Clonality studies identified a major clone of Klebsiella pneumoniae belonging to sequence type ST15 and additional isolates of K. pneumoniae, Escherichia coli and Enterobacter sp. from different STs. All isolates but one carried the bla KPC-2 allelic variant. The bla KPC-2 gene was located in an IncFIIk plasmid of circa 106 Kb in a non-classical Tn4401 element designated NTEKPC-pMC-2-1. Whole-genome sequencing revealed different rearrangements of the 106 Kb plasmid while the NTEKPC-pMC-2-1 module was highly conserved. Conclusion: We report a hospital outbreak caused by the clonal dissemination of KPC-producing ST15 K. pneumoniae but also the intra- and inter-species transmission of the bla KPC-2 gene associated with plasmid conjugation and/or transposon dissemination. To our knowledge, this is the first report of an outbreak caused by KPC-producing Enterobacterales isolated from human patients in Catalonia and highlights the relevance of surveillance studies in the early detection and control of antibiotic resistant high-risk clones.
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Affiliation(s)
- Marta Marí-Almirall
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Núria Ferrando
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Mariana José Fernández
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Clara Cosgaya
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Viñes
- Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Barcelona, Spain
- Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisa Rubio
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Anna Cuscó
- Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Muñoz
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Martina Pellice
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Irene Campo
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Laura Rodríguez-Serna
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Gemina Santana
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Ana Del Río
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pilar Ciruela
- Public Health Agency of Catalonia (ASPCAT), Generalitat de Catalunya, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Frederic Ballester
- Hospital Universitari Sant Joan de Reus-Laboratori de Referència del Camp de Tarragona i de les Terres de l’Ebre, Reus, Spain
| | - Francesc Marco
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - José Antonio Martínez
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Álex Soriano
- Department of Infectious Diseases, Hospital Clínic–Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Pitart
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Roca
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
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Burgess SA, Aplin J, Biggs PJ, Breckell G, Benschop J, Fayaz A, Toombs-Ruane LJ, Midwinter AC. Characterisation of AmpC and extended-spectrum beta-lactamase producing E. coli from New Zealand dairy farms. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.104998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Law A, Solano O, Brown CJ, Hunter SS, Fagnan M, Top EM, Stalder T. Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria. Front Microbiol 2021; 12:606409. [PMID: 33967971 PMCID: PMC8098119 DOI: 10.3389/fmicb.2021.606409] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022] Open
Abstract
Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.
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Affiliation(s)
- Aaron Law
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Olubunmi Solano
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Celeste J. Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Samuel S. Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
- UC-Davis Genome Center, Davis, CA, United States
| | - Matt Fagnan
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Eva M. Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
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Detection of a New Resistance-Mediating Plasmid Chimera in a blaOXA-48-Positive Klebsiella pneumoniae Strain at a German University Hospital. Microorganisms 2021; 9:microorganisms9040720. [PMID: 33807212 PMCID: PMC8066831 DOI: 10.3390/microorganisms9040720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
Mobile genetic elements, such as plasmids, facilitate the spread of antibiotic resistance genes in Enterobacterales. In line with this, we investigated the plasmid-resistome of seven blaOXA-48 gene-carrying Klebsiella pneumoniae isolates, which were isolated between 2013 and 2014 at the University Medical Center in Göttingen, Germany. All isolates were subjected to complete genome sequencing including the reconstruction of entire plasmid sequences. In addition, phenotypic resistance testing was conducted. The seven isolates comprised both disease-associated isolates and colonizers isolated from five patients. They fell into two clusters of three sequence type (ST)101 and two ST11 isolates, respectively; and ST15 and ST23 singletons. The seven isolates harbored various plasmids of the incompatibility (Inc) groups IncF, IncL/M, IncN, IncR, and a novel plasmid chimera. All blaOXA-48 genes were encoded on the IncL/M plasmids. Of note, distinct phenotypical resistance patterns associated with different sets of resistance genes encoded by IncL/M and IncR plasmids were observed among isolates of the ST101 cluster in spite of high phylogenetic relatedness of the bacterial chromosomes, suggesting nosocomial transmission. This highlights the importance of plasmid uptake and plasmid recombination events for the fast generation of resistance variability after clonal transmission. In conclusion, this study contributes a piece in the puzzle of molecular epidemiology of resistance gene-carrying plasmids in K. pneumoniae in Germany.
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Fu Y, Xu X, Zhang L, Xiong Z, Ma Y, Wei Y, Chen Z, Bai J, Liao M, Zhang J. Fourth Generation Cephalosporin Resistance Among Salmonella enterica Serovar Enteritidis Isolates in Shanghai, China Conferred by bla CTX-M-55 Harboring Plasmids. Front Microbiol 2020; 11:910. [PMID: 32477310 PMCID: PMC7242564 DOI: 10.3389/fmicb.2020.00910] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/17/2020] [Indexed: 02/04/2023] Open
Abstract
In this study, we investigated the pattern of antimicrobial resistance in Salmonella enterica serotype Enteritidis isolates in Shanghai, China from 2005 to 2014. We found the first isolates with resistance to the fourth-generation cephalosporin cefepime starting in 2010. Furthermore, we analyzed the epidemic characteristics and mechanisms of underlying cefepime resistance in S. Enteritidis isolates found from 2010. In total, 38 of 2,914 (1.30%) isolates were identified as cefepime-resistant S. Enteritidis (CRSE) isolates by Kirby-Bauer disk diffusion. Two isolates were from animal derived food sources; 36 isolates were from fecal samples of human patients with salmonellosis. Antimicrobial susceptibility testing using the agar dilution method revealed that all CRSE isolates showed additional resistances at least to ceftazidime, cefotaxime, and ampicillin. Additionally, pulsed-field gel electrophoresis (PFGE) profiles indicated that 89.47% of CRSE isolates also displayed similar PFGE patterns. Five types of β-lactamase genes, bla CTX-M (100.00%, 38/38), bla SHV (65.79%, 25/38), bla TEM (52.63%, 20/38), bla ACC (18.42%, 7/38), and bla PSE (5.26%, 2/38) were detected by PCR and sequencing. Among bla CTX-M genes, bla CTX-M-55 was the dominant type (84.21%, 32/38). Conjugation and transformation experiments along with plasmid replicon typing revealed that bla CTX-M-55 was located on plasmids of various replicon types with sizes ranging from 76.8 to 138.9 kb. Plasmid sequence analysis also showed that the bla CTX-M-55 gene was mobilized mainly by the ISEcp1-bla CTX-M-55-ORF477 transposition unit and had its own ISEcp1-based promoter, which accelerated the expression and transmission of bla CTX-M-55. Analysis of whole genome sequences (Illumina) of one selected transformant SH12G706-C showed high similarity of the bla CTX-M-55 carrying plasmid with the IncI1 plasmid backbone p628-CTX-M of Klebsiella pneumoniae detected in 2010 in China. The present study demonstrated that the bla CTX-M-55 gene mobilized by ISEcp1- bla CTX-M-55-ORF477 was the main feature shared by CRSE isolates and seems to play an important role for transmission of cefepime resistance. The number of CRSE isolates is rising annually, and the strong dissemination ability of ISEcp1-bla CTX-M-55-ORF477-harboring plasmids among different species represents an important threat to the therapeutic effectiveness of cefepime.
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Affiliation(s)
- Ying Fu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Lina Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhiying Xiong
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yeben Ma
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yihuan Wei
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhengquan Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jie Bai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangdong Laboratory for Lingnan Modern Agriculture, Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson’s disease. Neurosci Lett 2019; 696:93-98. [DOI: 10.1016/j.neulet.2018.12.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/11/2018] [Accepted: 12/15/2018] [Indexed: 12/15/2022]
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Lu J, Zhang J, Xu L, Liu Y, Li P, Zhu T, Cheng C, Lu S, Xu T, Yi H, Li K, Zhou W, Li P, Ni L, Bao Q. Spread of the florfenicol resistance floR gene among clinical Klebsiella pneumoniae isolates in China. Antimicrob Resist Infect Control 2018; 7:127. [PMID: 30410748 PMCID: PMC6211440 DOI: 10.1186/s13756-018-0415-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 09/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Florfenicol is a derivative of chloramphenicol that is used only for the treatment of animal diseases. A key resistance gene for florfenicol, floR, can spread among bacteria of the same and different species or genera through horizontal gene transfer. To analyze the potential transmission of resistance genes between animal and human pathogens, we investigated floR in Klebsiella pneumoniae isolates from patient samples. floR in human pathogens may originate from animal pathogens and would reflect the risk to human health of using antimicrobial agents in animals. Methods PCR was used to identify floR-positive strains. The floR genes were cloned, and the minimum inhibitory concentrations (MICs) were determined to assess the relative resistance levels of the genes and strains. Sequencing and comparative genomics methods were used to analyze floR gene-related sequence structure as well as the molecular mechanism of resistance dissemination. Results Of the strains evaluated, 20.42% (67/328) were resistant to florfenicol, and 86.96% (20/23) of the floR-positive strains demonstrated high resistance to florfenicol with MICs ≥512 μg/mL. Conjugation experiments showed that transferrable plasmids carried the floR gene in three isolates. Sequencing analysis of a plasmid approximately 125 kb in size (pKP18-125) indicated that the floR gene was flanked by multiple copies of mobile genetic elements. Comparative genomics analysis of a 9-kb transposon-like fragment of pKP18-125 showed that an approximately 2-kb sequence encoding lysR-floR-virD2 was conserved in the majority (79.01%, 83/105) of floR sequences collected from NCBI nucleotide database. Interestingly, the most similar sequence was a 7-kb fragment of plasmid pEC012 from an Escherichia coli strain isolated from a chicken. Conclusions Identified on a transferable plasmid in the human pathogen K. pneumoniae, the floR gene may be disseminated through horizontal gene transfer from animal pathogens. Studies on the molecular mechanism of resistance gene dissemination in different bacterial species of animal origin could provide useful information for preventing or controlling the spread of resistance between animal and human pathogens.
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Affiliation(s)
- Junwan Lu
- School of Medicine and Health, Lishui University, Lishui, 323000 China
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Jinfang Zhang
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Lei Xu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Yabo Liu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Pingping Li
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Tingyuan Zhu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Cong Cheng
- School of Medicine and Health, Lishui University, Lishui, 323000 China
| | - Shunfei Lu
- School of Medicine and Health, Lishui University, Lishui, 323000 China
| | - Teng Xu
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Huiguang Yi
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Kewei Li
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Wu Zhou
- School of Medicine and Health, Lishui University, Lishui, 323000 China
| | - Peizhen Li
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
| | - Liyan Ni
- The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325035 China
| | - Qiyu Bao
- School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, 325035 China
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Lam MMC, Wyres KL, Judd LM, Wick RR, Jenney A, Brisse S, Holt KE. Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome Med 2018; 10:77. [PMID: 30371343 PMCID: PMC6205773 DOI: 10.1186/s13073-018-0587-5] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/12/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a recognised agent of multidrug-resistant (MDR) healthcare-associated infections; however, individual strains vary in their virulence potential due to the presence of mobile accessory genes. In particular, gene clusters encoding the biosynthesis of siderophores aerobactin (iuc) and salmochelin (iro) are associated with invasive disease and are common amongst hypervirulent K. pneumoniae clones that cause severe community-associated infections such as liver abscess and pneumonia. Concerningly, iuc has also been reported in MDR strains in the hospital setting, where it was associated with increased mortality, highlighting the need to understand, detect and track the mobility of these virulence loci in the K. pneumoniae population. METHODS Here, we examined the genetic diversity, distribution and mobilisation of iuc and iro loci amongst 2503 K. pneumoniae genomes using comparative genomics approaches and developed tools for tracking them via genomic surveillance. RESULTS Iro and iuc were detected at low prevalence (< 10%). Considerable genetic diversity was observed, resolving into five iro and six iuc lineages that show distinct patterns of mobilisation and dissemination in the K. pneumoniae population. The major burden of iuc and iro amongst the genomes analysed was due to two linked lineages (iuc1/iro1 74% and iuc2/iro2 14%), each carried by a distinct non-self-transmissible IncFIBK virulence plasmid type that we designate KpVP-1 and KpVP-2. These dominant types also carry hypermucoidy (rmpA) determinants and include all previously described virulence plasmids of K. pneumoniae. The other iuc and iro lineages were associated with diverse plasmids, including some carrying IncFII conjugative transfer regions and some imported from Escherichia coli; the exceptions were iro3 (mobilised by ICEKp1) and iuc4 (fixed in the chromosome of K. pneumoniae subspecies rhinoscleromatis). Iro/iuc mobile genetic elements (MGEs) appear to be stably maintained at high frequency within known hypervirulent strains (ST23, ST86, etc.) but were also detected at low prevalence in others such as MDR strain ST258. CONCLUSIONS Iuc and iro are mobilised in K. pneumoniae via a limited number of MGEs. This study provides a framework for identifying and tracking these important virulence loci, which will be important for genomic surveillance efforts including monitoring for the emergence of hypervirulent MDR K. pneumoniae strains.
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Affiliation(s)
- Margaret M C Lam
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Louise M Judd
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Adam Jenney
- Department of Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, Victoria, 3004, Australia
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, 75015, Paris, France
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
- London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
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Hawkey PM. The 2017 Garrod Lecture: Genes, guts and globalization. J Antimicrob Chemother 2018; 73:2589-2600. [PMID: 30085107 DOI: 10.1093/jac/dky277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The widespread use of antibacterial drugs over the last 70 years has brought immense benefits to human health at the price of increasing drug inefficacy. Antibacterial agents have a strong selective effect in both favouring resistant strains and allowing particular species and families of bacteria to prosper, especially in the healthcare setting. Whilst important Gram-positive bacterial pathogens such as Staphylococcus aureus and Streptococcus pneumoniae caused concern over the last 20 years because of the spread of antibiotic-resistant strains, Enterobacteriaceae have become the biggest challenge. They have very efficient mechanisms for genetic exchange, as illustrated by the emergence and rapid spread of CTX-M β-lactamases and the carbapenemases. The unique epidemiology of Enterobacteriaceae, with substantial numbers colonizing the mammalian gut and subsequent release into and spread in the environment, presents a significant threat to human health because of the high levels of exposure for the whole community. The use of antimicrobials in agriculture combined with global movements of people, animals and food, arising from worldwide industrialization, generates a diversity and level of resistance not seen previously. Control will require globally coordinated interventions similar to those needed to ameliorate climate change.
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Affiliation(s)
- Peter M Hawkey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK.,Department of Microbiology, Queen Elizabeth Hospital, University Hospitals Birmingham Foundation Trust, Birmingham, UK
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Hernandez-Flores JL, Pérez JC, Gutiérrez CS, Hernández AC, Alonso GS, Hernández SP, Gómez SR, Fernández F, Loske AM, Guillén JC. pMEX01, a 70kb plasmid isolated from Escherichia coli that confers resistance to multiple β-lactam antibiotics. Braz J Microbiol 2018; 49:569-574. [PMID: 29449172 PMCID: PMC6066732 DOI: 10.1016/j.bjm.2017.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/27/2017] [Accepted: 11/07/2017] [Indexed: 11/25/2022] Open
Abstract
Multidrug-resistant microorganisms are of great concern to public health. Genetic mobile elements, such as plasmids, are among the most relevant mechanisms by which bacteria achieve this resistance. We obtained an Escherichia coli strain CM6, isolated from cattle presenting severe diarrheic symptoms in the State of Querétaro, Mexico. It was found to contain a 70 kb plasmid (pMEX01) with a high similarity to the pHK01-like plasmids that were previously identified and described in Hong Kong. Analysis of the pMEX01 sequence revealed the presence of a blaCTX-M-14 gene, which is responsible for conferring resistance to multiple β-lactam antibiotics. Several genes putatively involved in the conjugative transfer were also identified on the plasmid. The strain CM6 is of high epidemiological concern because it not only displays resistance to multiple β-lactam antibiotics but also to other kinds of antibiotics.
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Affiliation(s)
- Jose Luis Hernandez-Flores
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Departamento de Ingeniería Genética, Irapuato, Guanajuato, Mexico
| | | | | | | | - Gerardo Soto Alonso
- Universidad Autónoma de Querétaro, Facultad de Ciencias Naturales, Querétaro, Mexico
| | | | | | - Francisco Fernández
- Universidad Nacional Autónoma de México, Centro de Física Aplicada y Tecnología Avanzada, Querétaro, Mexico
| | - Achim M Loske
- Universidad Nacional Autónoma de México, Centro de Física Aplicada y Tecnología Avanzada, Querétaro, Mexico.
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11
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Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev 2018; 41:252-275. [PMID: 28521338 DOI: 10.1093/femsre/fux013] [Citation(s) in RCA: 638] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/28/2017] [Indexed: 01/15/2023] Open
Abstract
Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen affecting humans and a major source for hospital infections associated with high morbidity and mortality due to limited treatment options. We summarize the wide resistome of this pathogen, which encompasses plentiful chromosomal and plasmid-encoded antibiotic resistance genes (ARGs). Under antibiotic selective pressure, K. pneumoniae continuously accumulates ARGs, by de novo mutations, and via acquisition of plasmids and transferable genetic elements, leading to extremely drug resistant (XDR) strains harboring a 'super resistome'. In the last two decades, numerous high-risk (HiR) MDR and XDR K. pneumoniae sequence types have emerged showing superior ability to cause multicontinent outbreaks, and continuous global dissemination. The data highlight the complex evolution of MDR and XDR K. pneumoniae, involving transfer and spread of ARGs, and epidemic plasmids in highly disseminating successful clones. With the worldwide catastrophe of antibiotic resistance and the urgent need to identify the main pathogens that pose a threat on the future of infectious diseases, further studies are warranted to determine the epidemic traits and plasmid acquisition in K. pneumoniae. There is a need for future genomic and translational studies to decipher specific targets in HiR clones to design targeted prevention and treatment.
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Affiliation(s)
- Shiri Navon-Venezia
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Kira Kondratyeva
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Alessandra Carattoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
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12
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Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK. The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host growth and motility. FEMS Microbiol Ecol 2017; 93:3940222. [DOI: 10.1093/femsec/fix090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/07/2017] [Indexed: 01/24/2023] Open
Affiliation(s)
- Xinlei Jiang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Xuan Liu
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Carmen O. K. Law
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Ya Wang
- Department of Microbiology, University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region
| | - Wai U Lo
- Department of Microbiology, University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region
| | - Xing Weng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Ting Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - P. L. Ho
- Department of Microbiology, University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region
| | - Terrence C. K. Lau
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
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13
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Ying J, Wu S, Zhang K, Wang Z, Zhu W, Zhu M, Zhang Y, Cheng C, Wang H, Tou H, Zhu C, Li P, Ying J, Xu T, Yi H, Li J, Ni L, Xu Z, Bao Q, Lu J. Comparative genomics analysis of pKF3-94 in Klebsiella pneumoniae reveals plasmid compatibility and horizontal gene transfer. Front Microbiol 2015; 6:831. [PMID: 26347723 PMCID: PMC4539522 DOI: 10.3389/fmicb.2015.00831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 07/28/2015] [Indexed: 11/18/2022] Open
Abstract
In order to get insights into plasmid evolution and the dissemination of multidrug resistance, we performed extensive comparative genomics analyses of the Klebsiella pneumoniae plasmid pKF3-94 and some of its related plasmids. pKF3-94 is one of three plasmids isolated from the K. pneumoniae strain KF3. Of the 144 putative genes it harbors, 69 can be functionally assigned to be involved in transfer conjugation, transfer leading, antimicrobial resistance, transposon function, and plasmid replication. Comparison of plasmid replicon sequence types revealed that pKF3-94 carries two replicons that are distinct from those carried on the two sibling K. pneumonia plasmids pKF3-70 and pKF3-140, thereby allowing pKF3-94 to coexist with these latter plasmids in the same host cell. Comparative genomics analyses further showed that pKF3-94 is more similar to plasmids pK1HV and pC15-k, which were isolated from different K. pneumonia strains, than to pKF3-70 and pKF3-140. Interestingly, pK1HV contains a unique 49 kb region rich in mobile genetic elements and drug resistance genes, while pKF3-94 and pC15-k share a 15 kb homology region partitioned into a region rich in drug resistance genes and one containing a replicon. It is conceivable, therefore, that pK1HV and pC15-k have both arisen from a common pKF3-94-like plasmid. The comparisons lend further support for the role horizontal gene transfer plays in genome evolution and in the dissemination of genetic elements including drug resistance genes.
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Affiliation(s)
- Jianchao Ying
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Songquan Wu
- School of Medicine, Lishui College Lishui, China
| | - Kaibo Zhang
- School of Medicine, Lishui College Lishui, China
| | - Ziqiang Wang
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Wen Zhu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Mei Zhu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Ying Zhang
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Cong Cheng
- School of Medicine, Lishui College Lishui, China
| | - Huifeng Wang
- National Institute of Biological Sciences Beijing, China
| | - Huifen Tou
- Wenzhou Center for Disease Control and Prevention Wenzhou, China
| | - Chuanxin Zhu
- Wenzhou Center for Disease Control and Prevention Wenzhou, China
| | - Peizhen Li
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Jun Ying
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Teng Xu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Huiguang Yi
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Jinsong Li
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Liyan Ni
- The Second Affiliated Hospital, Wenzhou Medical University Wenzhou, China
| | - Zuyuan Xu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Qiyu Bao
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Junwan Lu
- School of Medicine, Lishui College Lishui, China
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14
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Soto-Alonso G, Cruz-Medina J, Caballero-Pérez J, Arvizu-Hernández I, Ávalos-Esparza L, Cruz-Hernández A, Romero-Gómez S, Rodríguez A, Pastrana-Martínez X, Fernández F, Loske A, Campos-Guillén J. Isolation of a conjugative F-like plasmid from a multidrug-resistant Escherichia coli strain CM6 using tandem shock wave-mediated transformation. J Microbiol Methods 2015; 114:1-8. [DOI: 10.1016/j.mimet.2015.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 04/20/2015] [Indexed: 10/23/2022]
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Abstract
ABSTRACT
Plasmids confer genetic information that benefits the bacterial cells containing them. In pathogenic bacteria, plasmids often harbor virulence determinants that enhance the pathogenicity of the bacterium. The ability to acquire iron in environments where it is limited, for instance the eukaryotic host, is a critical factor for bacterial growth. To acquire iron, bacteria have evolved specific iron uptake mechanisms. These systems are often chromosomally encoded, while those that are plasmid-encoded are rare. Two main plasmid types, ColV and pJM1, have been shown to harbor determinants that increase virulence by providing the cell with essential iron for growth. It is clear that these two plasmid groups evolved independently from each other since they do not share similarities either in the plasmid backbones or in the iron uptake systems they harbor. The siderophores aerobactin and salmochelin that are found on ColV plasmids fall in the hydroxamate and catechol group, respectively, whereas both functional groups are present in the anguibactin siderophore, the only iron uptake system found on pJM1-type plasmids. Besides siderophore-mediated iron uptake, ColV plasmids carry additional genes involved in iron metabolism. These systems include ABC transporters, hemolysins, and a hemoglobin protease. ColV- and pJM1-like plasmids have been shown to confer virulence to their bacterial host, and this trait can be completely ascribed to their encoded iron uptake systems.
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Characterization of Klebsiella sp. strain 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates. Antimicrob Agents Chemother 2014; 58:1879-88. [PMID: 24395222 DOI: 10.1128/aac.01605-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A unique Klebsiella species strain, 10982, was cultured from a perianal swab specimen obtained from a patient in the University of Maryland Medical Center intensive care unit. Klebsiella sp. 10982 possesses a large IncA/C multidrug resistance plasmid encoding a novel FOX AmpC β-lactamase designated FOX-10. A novel variant of the LEN β-lactamase was also identified. Genome sequencing and bioinformatic analysis demonstrated that this isolate contains genes associated with nitrogen fixation, allantoin metabolism, and citrate fermentation. These three gene regions are typically present in either Klebsiella pneumoniae clinical isolates or Klebsiella nitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis of Klebsiella sp. 10982 and sequenced Klebsiella genomes demonstrated that Klebsiella sp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes and K. pneumoniae clinical isolates. Metabolic features identified in the genome of Klebsiella sp. 10982 distinguish this isolate from other Klebsiella clinical isolates. These features include the nitrogen fixation (nif) gene cluster, which is typically present in endophytic Klebsiella isolates and is absent from Klebsiella clinical isolates. Additionally, the Klebsiella sp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily in K. pneumoniae isolates from liver abscesses. Comparative genomic analysis of Klebsiella sp. 10982 demonstrated that this organism has acquired genes conferring new metabolic strategies and novel antibiotic resistance alleles, both of which may enhance its ability to colonize the human body.
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17
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Brolund A, Franzén O, Melefors O, Tegmark-Wisell K, Sandegren L. Plasmidome-analysis of ESBL-producing escherichia coli using conventional typing and high-throughput sequencing. PLoS One 2013; 8:e65793. [PMID: 23785449 PMCID: PMC3681856 DOI: 10.1371/journal.pone.0065793] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/02/2013] [Indexed: 12/17/2022] Open
Abstract
Infections caused by Extended spectrum β-lactamase (ESBL)-producing E. coli are an emerging global problem, threatening the effectiveness of the extensively used β-lactam antibiotics. ESBL dissemination is facilitated by plasmids, transposons, and other mobile elements. We have characterized the plasmid content of ESBL-producing E. coli from human urinary tract infections. Ten diverse isolates were selected; they had unrelated pulsed-field gel electrophoresis (PFGE) types (<90% similarity), were from geographically dispersed locations and had diverging antibiotic resistance profiles. Three isolates belonged to the globally disseminated sequence type ST131. ESBL-genes of the CTX-M-1 and CTX-M-9 phylogroups were identified in all ten isolates. The plasmid content (plasmidome) of each strain was analyzed using a combination of molecular methods and high-throughput sequencing. Hidden Markov Model-based analysis of unassembled sequencing reads was used to analyze the genetic diversity of the plasmid samples and to detect resistance genes. Each isolate contained between two and eight distinct plasmids, and at least 22 large plasmids were identified overall. The plasmids were variants of pUTI89, pKF3-70, pEK499, pKF3-140, pKF3-70, p1ESCUM, pEK204, pHK17a, p083CORR, R64, pLF82, pSFO157, and R721. In addition, small cryptic high copy-number plasmids were frequent, containing one to seven open reading frames per plasmid. Three clustered groups of such small cryptic plasmids could be distinguished based on sequence similarity. Extrachromosomal prophages were found in three isolates. Two of them resembled the E. coli P1 phage and one was previously unknown. The present study confirms plasmid multiplicity in multi-resistant E. coli. We conclude that high-throughput sequencing successfully provides information on the extrachromosomal gene content and can be used to generate a genetic fingerprint of possible use in epidemiology. This could be a valuable tool for tracing plasmids in outbreaks.
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Affiliation(s)
- Alma Brolund
- Swedish Institute for Communicable Disease Control, Solna, Sweden.
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18
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Bai J, Liu Q, Yang Y, Wang J, Yang Y, Li J, Li P, Li X, Xi Y, Ying J, Ren P, Yang L, Ni L, Wu J, Bao Q, Zhou T. Insights into the evolution of gene organization and multidrug resistance from Klebsiella pneumoniae plasmid pKF3-140. Gene 2013; 519:60-6. [PMID: 23402892 DOI: 10.1016/j.gene.2013.01.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 12/20/2012] [Accepted: 01/27/2013] [Indexed: 01/02/2023]
Abstract
Plasmid-mediated transfer of drug-resistance genes among various bacterial species is considered one of the most important mechanisms for the spread of multidrug resistance. To gain insights into the evolution of gene organization and antimicrobial resistance in clinical bacterial samples, a complete plasmid genome of Klebsiella pneumoniae pKF3-140 is determined, which has a circular chromosome of 147,416bp in length. Among the 203 predicted genes, 142 have function assignment and about 50 appear to be involved in plasmid replication, maintenance, conjugative transfer, iron acquisition and transport, and drug resistance. Extensive comparative genomic analyses revealed that pKF3-140 exhibits a rather low sequence similarity and structural conservation with other reported K. pneumoniae plasmids. In contrast, the overall organization of pKF3-140 is highly similar to Escherichia coli plasmids p1ESCUM and pUTI89, which indicates the possibility that K. pneumoniae pKF3-140 may have a potential origin in E. coli. Meanwhile, interestingly, several drug resistant genes show high similarity to the plasmid pU302L in Salmonella enterica serovar Typhimurium U302 strain G8430 and the plasmid pK245 in K. pneumoniae. This mosaic pattern of sequence similarities suggests that pKF3-140 might have arisen from E. coli and acquired the resistance genes from a variety of enteric bacteria and underscores the importance of a further understanding of horizontal gene transfer among enteric bacteria.
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Affiliation(s)
- Jie Bai
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, and The First Affiliated Hospital of Wenzhou Medical College, Wenzhou 325000, China
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The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant's on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates. Plasmid 2012; 69:127-37. [PMID: 23212116 DOI: 10.1016/j.plasmid.2012.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/12/2012] [Accepted: 11/18/2012] [Indexed: 11/22/2022]
Abstract
The IncF antibiotic resistance and virulence plasmid pRSB225, isolated from an unknown bacterium released with the purified wastewater from a municipal sewage treatment plant into the environment has been analysed at the genomic level by pyrosequencing. The 164,550bp plasmid comprises 210 coding sequences (cds). It is composed of three replicons (RepFIA, RepFIB, and RepFII) and encodes further plasmid-specific functions for stable maintenance and inheritance and conjugative plasmid transfer. The plasmid is self-transmissible and shows a narrow host range limited to the family Enterobacteriaceae. The accessory modules of the plasmid mainly comprise genes conferring resistance to ampicillin (bla(TEM-1b)), chloramphenicol (catA1), erythromycin (mphA), kanamycin and neomycin (aphA1), streptomycin (strAB), sulphonamides (sul2), tetracycline (tetA(B)) and trimethoprim (dfrA14), as well as mercuric ions (mer genes). In addition, putative virulence-associated genes coding for iron uptake (iutA/iucABCD, sitABCD, and a putative high-affinity Fe²⁺ uptake system) and for a toxin/antitoxin system (vagCD) were identified on the plasmid. All antibiotic and heavy metal resistance genes are located either on class 1 (Tn10-remnant, Tn4352B) and class 2 transposons (Tn2-remnant, Tn21, Tn402-remnant) or a class 1 integron, whereas almost all putative virulence genes are associated with IS elements (IS1, IS26), indicating that transposition and/or recombination events were responsible for acquisition of the accessory pRSB225 modules. Particular modules of plasmid pRSB225 are related to corresponding segments of different virulence plasmids harboured by pathogenic Escherichia coli strains. Moreover, pRSB225 modules were also detected in entero-aggregative-haemorrhagic E. coli (EAHEC) draft genome sequences suggesting that IncF plasmids related to pRSB225 mediated gene transfer into pathogenic E. coli derivatives.
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20
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Xu T, Ying J, Yao X, Song Y, Ma P, Bao B, Jiang W, Wu X, Tou H, Li P, Ren P, Fei J, Yang L, Liu Q, Xu Z, Zhou T, Ni L, Bao Q. Identification and characterization of two novel bla(KLUC) resistance genes through large-scale resistance plasmids sequencing. PLoS One 2012; 7:e47197. [PMID: 23056610 PMCID: PMC3467222 DOI: 10.1371/journal.pone.0047197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 09/10/2012] [Indexed: 11/18/2022] Open
Abstract
Plasmids are important antibiotic resistance determinant carriers that can disseminate various drug resistance genes among species or genera. By using a high throughput sequencing approach, two groups of plasmids of Escherichia coli (named E1 and E2, each consisting of 160 clinical E. coli strains isolated from different periods of time) were sequenced and analyzed. A total of 20 million reads were obtained and mapped onto the known resistance gene sequences. As a result, a total of 9 classes, including 36 types of antibiotic resistant genes, were identified. Among these genes, 25 and 27 single nucleotide polymorphisms (SNPs) appeared, of which 9 and 12 SNPs are nonsynonymous substitutions in the E1 and E2 samples. It is interesting to find that a novel genotype of blaKLUC, whose close relatives, blaKLUC-1 and blaKLUC-2, have been previously reported as carried on the Kluyvera cryocrescens chromosome and Enterobacter cloacae plasmid, was identified. It shares 99% and 98% amino acid identities with Kluc-1 and Kluc-2, respectively. Further PCR screening of 608 Enterobacteriaceae family isolates yielded a second variant (named blaKLUC-4). It was interesting to find that Kluc-3 showed resistance to several cephalosporins including cefotaxime, whereas blaKLUC-4 did not show any resistance to the antibiotics tested. This may be due to a positively charged residue, Arg, replaced by a neutral residue, Leu, at position 167, which is located within an omega-loop. This work represents large-scale studies on resistance gene distribution, diversification and genetic variation in pooled multi-drug resistance plasmids, and provides insight into the use of high throughput sequencing technology for microbial resistance gene detection.
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Affiliation(s)
- Teng Xu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
- The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot, Inner Mongolia Autonomous Region, People’s Republic of China
| | - Jun Ying
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Xiaoding Yao
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Yulong Song
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Ping Ma
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Bokan Bao
- College of Biological Science, Agricultural University of China, Beijing, People’s Republic of China
| | - Weiyan Jiang
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Xinmei Wu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Huifen Tou
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Peizhen Li
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Ping Ren
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Jingxian Fei
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Lei Yang
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Qi Liu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Zuyuan Xu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Tieli Zhou
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
| | - Liyan Ni
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
- * E-mail: (LN); (QB)
| | - Qiyu Bao
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, Zhejiang, People’s Republic of China
- * E-mail: (LN); (QB)
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Ho P, Lo W, Yeung M, Li Z, Chan J, Chow K, Yam W, Tong AH, Bao JY, Lin C, Lok S, Chiu SS. Dissemination of pHK01-like incompatibility group IncFII plasmids encoding CTX-M-14 in Escherichia coli from human and animal sources. Vet Microbiol 2012; 158:172-9. [DOI: 10.1016/j.vetmic.2012.02.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 02/01/2012] [Accepted: 02/06/2012] [Indexed: 11/30/2022]
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22
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Ho PL, Yeung MK, Lo WU, Tse H, Li Z, Lai EL, Chow KH, To KK, Yam WC. Predominance of pHK01-like incompatibility group FII plasmids encoding CTX-M-14 among extended-spectrum beta-lactamase–producing Escherichia coli in Hong Kong, 1996–2008. Diagn Microbiol Infect Dis 2012; 73:182-6. [DOI: 10.1016/j.diagmicrobio.2012.03.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/30/2011] [Accepted: 03/15/2012] [Indexed: 10/28/2022]
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23
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Tamminen M, Virta M, Fani R, Fondi M. Large-scale analysis of plasmid relationships through gene-sharing networks. Mol Biol Evol 2011; 29:1225-40. [PMID: 22130968 DOI: 10.1093/molbev/msr292] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Plasmids are vessels of genetic exchange in microbial communities. They are known to transfer between different host organisms and acquire diverse genetic elements from chromosomes and/or other plasmids. Therefore, they constitute an important element in microbial evolution by rapidly disseminating various genetic properties among different communities. A paradigmatic example of this is the dissemination of antibiotic resistance (AR) genes that has resulted in the emergence of multiresistant pathogenic bacterial strains. To globally analyze the evolutionary dynamics of plasmids, we built a large graph in which 2,343 plasmids (nodes) are connected according to the proteins shared by each other. The analysis of this gene-sharing network revealed an overall coherence between network clustering and the phylogenetic classes of the corresponding microorganisms, likely resulting from genetic barriers to horizontal gene transfer between distant phylogenetic groups. Habitat was not a crucial factor in clustering as plasmids from organisms inhabiting different environments were often found embedded in the same cluster. Analyses of network metrics revealed a statistically significant correlation between plasmid mobility and their centrality within the network, providing support to the observation that mobile plasmids are particularly important in spreading genes in microbial communities. Finally, our study reveals an extensive (and previously undescribed) sharing of AR genes between Actinobacteria and Gammaproteobacteria, suggesting that the former might represent an important reservoir of AR genes for the latter.
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Affiliation(s)
- Manu Tamminen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
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F33:A-:B- and F2:A-:B- plasmids mediate dissemination of rmtB-blaCTX-M-9 group genes and rmtB-qepA in Enterobacteriaceae isolates from pets in China. Antimicrob Agents Chemother 2011; 55:4926-9. [PMID: 21788459 DOI: 10.1128/aac.00133-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study investigated the prevalence of 16S rRNA methylase genes in 267 Enterobacteriaceae isolates collected from pets. The rmtB gene was detected in 69 isolates, most of which were clonally unrelated. The coexistence of the rmtB gene with the bla(CTX-M-9) group genes and/or qepA within the same IncFII replicons was commonly detected. The two dominant types of IncF plasmids, F2:A-:B-, carrying rmtB-qepA, and F33:A-:B-, carrying the rmtB-bla(CTX-M-9) group genes (and especially bla(CTX-M-65)), shared restriction patterns within each incompatibility group.
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25
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Peng C, Zong Z. Sequence type 38 Escherichia coli carrying bla(CTX-M-14). J Med Microbiol 2011; 60:694-695. [PMID: 21292855 DOI: 10.1099/jmm.0.028316-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Chunhong Peng
- Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, PR China.,Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, PR China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, PR China
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26
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Curiao T, Morosini MI, Ruiz-Garbajosa P, Robustillo A, Baquero F, Coque TM, Canton R. Emergence of blaKPC-3-Tn4401a associated with a pKPN3/4-like plasmid within ST384 and ST388 Klebsiella pneumoniae clones in Spain. J Antimicrob Chemother 2010; 65:1608-14. [DOI: 10.1093/jac/dkq174] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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