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Peng K, Li Y, Wang Q, Yang P, Wang Z, Li R. Integrative conjugative elements mediate the high prevalence of tmexCD3-toprJ1b in Proteus spp. of animal source. mSystems 2023; 8:e0042923. [PMID: 37707055 PMCID: PMC10654056 DOI: 10.1128/msystems.00429-23] [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: 04/29/2023] [Accepted: 07/23/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE The emergence and spread of tmexCD-toprJ have greatly weakened the function of tigecycline. Although studies have demonstrated the significance of Proteus as carriers for tmexCD-toprJ, the epidemic mechanism and characteristics of tmexCD-toprJ in Proteus remain unclear. Herein, we deciphered that the umuC gene in VRIII of SXT/R391 ICEs was a hotspot for the integration of tmexCD3-toprJ1b-bearing mobile genetic elements by genomic analysis. The mobilization and dissemination of tmexCD3-toprJ1b in Proteus were mediated by highly prevalent ICEs. Furthermore, the co-occurrence of tmexCD3-toprJ1b-bearing ICEs with other chromosomally encoded multidrug resistance gene islands warned that the chromosomes of Proteus are significant reservoirs of ARGs. Overall, our results provide significant insights for the prevention and control of tmexCD3-toprJ1b in Proteus.
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Affiliation(s)
- Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yangfan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Pengbin Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
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2
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Cerbino GN, Traglia GM, Ayala Nuñez T, Parmeciano Di Noto G, Ramírez MS, Centrón D, Iriarte A, Quiroga C. Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages. Front Microbiol 2023; 14:1124225. [PMID: 36925471 PMCID: PMC10011109 DOI: 10.3389/fmicb.2023.1124225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.
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Affiliation(s)
- Gabriela N Cerbino
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - German M Traglia
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Teolincacihuatl Ayala Nuñez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, Fullerton, CA, United States
| | - Daniela Centrón
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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3
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Yu K, Huang Z, Xiao Y, Wang D. Shewanella infection in humans: Epidemiology, clinical features and pathogenicity. Virulence 2022; 13:1515-1532. [PMID: 36065099 PMCID: PMC9481105 DOI: 10.1080/21505594.2022.2117831] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The genus Shewanella consists of Gram-negative proteobacteria that are ubiquitously distributed in environment. As the members of this genus have rapidly increased within the past decade, several species have become emerging pathogens worldwide, attracting the attention of the medical community. These species are also associated with severe community- and hospital-acquired infections. Patients infected with Shewanella spp. had experiences of occupational or recreational exposure; meanwhile, the process of infection is complex and the pathogenicity is influenced by a variety of factors. Here, an exhaustive internet-based literature search was carried out in PUBMED using terms “Achromobacter putrefaciens,” “Pseudomonas putrefaciens,” “Alteromonas putrefaciens” and “Shewanella” to search literatures published between 1978 and June 2022. We provided a comprehensive review on the epidemiology, clinical features and pathogenicity of Shewanella, which will contribute a better understanding of its clinical aetiology, and facilitate the timely diagnosis and effective treatment of Shewanella infection for clinicians and public health professionals.
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Affiliation(s)
- Keyi Yu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Zhenzhou Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Yue Xiao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
| | - Duochun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.,Center for Human Pathogenic Culture Collection, China CDC, Beijing, China
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4
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Sugimoto Y, Kadoya A, Suzuki S. An Integrative and Conjugative Element (ICE) Found in Shewanella halifaxensis Isolated from Marine Fish Intestine May Connect Genetic Materials between Human and Marine Environments. Microbes Environ 2022; 37. [PMID: 36058879 PMCID: PMC9530723 DOI: 10.1264/jsme2.me22038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Integrative and conjugative elements (ICEs) play a role in the horizontal transfer of antibiotic resistance genes (ARGs). We herein report an ICE from Shewanella halifaxensis isolated from fish intestine with a similar structure to both a clinical bacterial ICE and marine bacterial plasmid. The ICE was designated ICEShaJpn1, a member of the SXT/R391 family of ICEs (SRIs). ICEShaJpn1 has a common core structure with SRIs of clinical and fish origins and an ARG cassette with the pAQU1 plasmid of Photobacterium damselae subsp. damselae, suggesting that the common core of SRIs is widely distributed and ARG cassettes are collected from regional bacteria.
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Affiliation(s)
- Yuta Sugimoto
- Center for Marine Environmental Studies, Ehime University
| | - Aya Kadoya
- Center for Marine Environmental Studies, Ehime University
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University.,Graduate School of Science and Engineering, Ehime University
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Guan J, Bao C, Wang P, Jing Y, Wang L, Li X, Mu X, Li B, Zhou D, Guo X, Yin Z. Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia. Infect Drug Resist 2022; 15:2253-2270. [PMID: 35510160 PMCID: PMC9058013 DOI: 10.2147/idr.s354934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose The aim of this study was to gain a deeper genomics and bioinformatics understanding of diversification of accessory genetic elements (AGEs) in Providencia. Methods Herein, the complete genome sequences of five Providencia isolates from China were determined, and seven AGEs were identified from the chromosomes. Detailed genetic dissection and sequence comparison were applied to these seven AGEs, together with additional 10 chromosomal ones from GenBank (nine of them came from Providencia). Results These 17 AGEs were divided into four groups: Tn6512 and its six derivatives, Tn6872 and its two derivatives, Tn6875 and its one derivative, and Tn7 and its four derivatives. These AGEs display high-level diversification in modular structures that had complex mosaic natures, and particularly different multidrug resistance (MDR) regions were presented in these AGEs. At least 52 drug resistance genes, involved in resistance to 15 different categories of antimicrobials and heavy metal, were found in 15 of these 17 AGEs. Conclusion Integration of these AGEs into the Providencia chromosomes would contribute to the accumulation and distribution of drug resistance genes and enhance the ability of Providencia isolates to survive under drug selection pressure.
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Affiliation(s)
- Jiayao Guan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
| | - Chunmei Bao
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Lingling Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Boan Li
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xuejun Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
- Xuejun Guo, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China, Tel +86-431-86985931, Email
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
- Correspondence: Zhe Yin, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China, Tel +86-10-66948557, Email
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6
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McDonald JP, Quiros DR, Vaisman A, Mendez AR, Reyelt J, Schmidt M, Gonzalez M, Woodgate R. CroS R391 , an ortholog of the λ Cro repressor, plays a major role in suppressing polV R391 -dependent mutagenesis. Mol Microbiol 2021; 116:877-889. [PMID: 34184328 PMCID: PMC8460599 DOI: 10.1111/mmi.14777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/26/2022]
Abstract
When subcloned into low-copy-number expression vectors, rumAB, encoding polVR391 (RumA'2 B), is best characterized as a potent mutator giving rise to high levels of spontaneous mutagenesis in vivo. This is in dramatic contrast to the poorly mutable phenotype when polVR391 is expressed from the native 88.5 kb R391, suggesting that R391 expresses cis-acting factors that suppress the expression and/or the activity of polVR391 . Indeed, we recently discovered that SetRR391 , an ortholog of λ cI repressor, is a transcriptional repressor of rumAB. Here, we report that CroSR391 , an ortholog of λ Cro, also serves as a potent transcriptional repressor of rumAB. Levels of RumA are dependent upon an interplay between SetRR391 and CroSR391 , with the greatest reduction of RumA protein levels observed in the absence of SetRR391 and the presence of CroSR391 . Under these conditions, CroSR391 completely abolishes the high levels of mutagenesis promoted by polVR391 expressed from low-copy-number plasmids. Furthermore, deletion of croSR391 on the native R391 results in a dramatic increase in mutagenesis, indicating that CroSR391 plays a major role in suppressing polVR391 mutagenesis in vivo. Inactivating mutations in CroSR391 therefore have the distinct possibility of increasing cellular mutagenesis that could lead to the evolution of antibiotic resistance of pathogenic bacteria harboring R391.
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Affiliation(s)
- John P. McDonald
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Dominic R. Quiros
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Alexandra Vaisman
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | | | - Jan Reyelt
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
- Present address:
AGC Biologics GmbHHeidelbergGermany
| | - Marlen Schmidt
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
| | | | - Roger Woodgate
- Laboratory of Genomic IntegrityNational Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
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7
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Zheng Z, Ye L, Li R, Chen S. Whole-genome sequencing of strains of Vibrio spp. from China reveals different genetic contexts of blaCTX-M-14 among diverse lineages. J Antimicrob Chemother 2021; 76:950-956. [PMID: 33394022 DOI: 10.1093/jac/dkaa545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/04/2020] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES To investigate the prevalence and genetic contexts of the blaCTX-M-14 gene harboured by foodborne isolates of Vibrio spp. in China. METHODS A total of 1856 Vibrio spp. isolates collected from raw meat and shrimp samples in Guangdong Province of China were screened for blaCTX-M-14 by PCR. The blaCTX-M-14-positive isolates were characterized by MIC, PFGE, MLST, conjugation, S1-PFGE and Southern blotting and WGS using Illumina and Nanopore platforms. RESULTS A total of 35 (1.9%) Vibrio isolates were positive for blaCTX-M-14, including 33 Vibrio parahaemolyticus strains and two Vibrio alginolyticus strains. MLST showed that most of the blaCTX-M-14-bearing isolates could be assigned into two major STs, with ST163 being more prevalent (n = 23), followed by ST180 (n = 6). Whole-genome analysis of these 35 isolates revealed that the blaCTX-M-14 gene was associated with ISEcp1 in the upstream region, of which 32 blaCTX-M-14 genes were located in the same loci of chromosome I, 1 blaCTX-M-14 gene was located in a novel chromosomal integrative conjugative element (ICE) belonging to the SXT/R391 family and 2 blaCTX-M-14 genes were located in the same type of plasmid, which belonged to the IncP-1 group. Conjugation experiments showed that only the plasmid-borne blaCTX-M-14 gene could be transferred to the recipient strain Escherichia coli J53. CONCLUSIONS The emergence of the novel ICE and IncP-1 plasmids has contributed to the variable genetic contexts of blaCTX-M-14 among strains of Vibrio spp. and facilitated the horizontal transfer of such genes between Vibrio spp. and other zoonotic pathogens, resulting in a rapid increase in the prevalence of blaCTX-M-14-bearing bacterial pathogens worldwide.
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Affiliation(s)
- Zhiwei Zheng
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, P. R. China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
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8
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Luo X, Yin Z, Zeng L, Hu L, Jiang X, Jing Y, Chen F, Wang D, Song Y, Yang H, Zhou D. Chromosomal Integration of Huge and Complex bla NDM-Carrying Genetic Elements in Enterobacteriaceae. Front Cell Infect Microbiol 2021; 11:690799. [PMID: 34211858 PMCID: PMC8239412 DOI: 10.3389/fcimb.2021.690799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, a detailed genetic dissection of the huge and complex blaNDM-carrying genetic elements and their related mobile genetic elements was performed in Enterobacteriaceae. An extensive comparison was applied to 12 chromosomal genetic elements, including six sequenced in this study and the other six from GenBank. These 12 genetic elements were divided into five groups: a novel IME Tn6588; two related IMEs Tn6523 (SGI1) and Tn6589; four related ICEs Tn6512 (R391), Tn6575 (ICEPvuChnBC22), Tn6576, and Tn6577; Tn7 and its derivatives Tn6726 and 40.7-kb Tn7-related element; and two related IMEs Tn6591 (GIsul2) and Tn6590. At least 51 resistance genes, involved in resistance to 18 different categories of antibiotics and heavy metals, were found in these 12 genetic elements. Notably, Tn6576 carried another ICE Tn6582. In particular, the six blaNDM-carrying genetic elements Tn6588, Tn6589, Tn6575, Tn6576, Tn6726, and 40.7-kb Tn7-related element contained large accessory multidrug resistance (MDR) regions, each of which had a very complex mosaic structure that comprised intact or residual mobile genetic elements including insertion sequences, unit or composite transposons, integrons, and putative resistance units. Core blaNDM genetic environments manifested as four different Tn125 derivatives and, notably, two or more copies of relevant Tn125 derivatives were found in each of Tn6576, Tn6588, Tn6589, and 40.7-kb Tn7-related element. The huge and complex blaNDM-carrying genetic elements were assembled from complex transposition and homolog recombination. Firstly identified were eight novel mobile elements, including three ICEs Tn6576, Tn6577, and Tn6582, two IMEs, Tn6588 and Tn6589, two composite transposons Tn6580a and Tn6580b, and one integron In1718.
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Affiliation(s)
- Xinhua Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lijun Zeng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,The Fifth Medical Center, Chinese Peoples Liberation Army General Hospital, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongguo Wang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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9
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Botelho J, Mourão J, Roberts AP, Peixe L. Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. Microb Genom 2020; 6:mgen000424. [PMID: 32841111 PMCID: PMC7660259 DOI: 10.1099/mgen.0.000424] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/02/2020] [Indexed: 12/24/2022] Open
Abstract
Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.
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Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Present address: Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
| | - Joana Mourão
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology, Coimbra, Portugal
- University of Coimbra, Center for Neuroscience and Cell Biology, Coimbra, Portugal
- University of Coimbra, Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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10
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Spotlight on a novel bactericidal mechanism and a novel SXT/R391-like integrative and conjugative element, carrying multiple antibiotic resistance genes, in Pseudoalteromonas flavipulchra strain CDM8. Microbiol Res 2020; 242:126598. [PMID: 33039801 DOI: 10.1016/j.micres.2020.126598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022]
Abstract
Many Pseudoalteromonas strains can produce bioactive compounds with antimicrobial activities. This study focused on a probiotic candidate P.flavipulchra CDM8 to reveal its novel antibacterial mechanism and risks for antibiotic resistance dissemination. Strain CDM8 could form floating biofilm, displayed strikingly broad antibacterial activities against multiple Vibrio and Bacillus species, and decreased the competitor's concentration in their co-cultures in the microtiter plate tests. It could also form vesicle/pilus-like structures on the outer surface, which were indicated to participate in the bactericidal activity and represent a novel antibacterial mechanism of CDM8, according to the scanning electron microscopic observation. However, CDM8 displayed multi-antibiotic resistance, conferred by the multidrug resistance regions in hotspot 4 and variable region III of a novel SXT/R391-like integrative and conjugative element (ICEPflCDM8). Summing up, our results provided a better understanding of the bactericidal mechanism of P. flavipulchra and highlighted the role of SXT/R391-like ICEs in conferring multidrug resistance phenotype of probiotic P. flavipulchra candidates.
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Zago V, Veschetti L, Patuzzo C, Malerba G, Lleo MM. Resistome, Mobilome and Virulome Analysis of Shewanella algae and Vibrio spp. Strains Isolated in Italian Aquaculture Centers. Microorganisms 2020; 8:microorganisms8040572. [PMID: 32326629 PMCID: PMC7232470 DOI: 10.3390/microorganisms8040572] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/02/2020] [Accepted: 04/13/2020] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial resistance is a major public health concern restricted not only to healthcare settings but also to veterinary and environmental ones. In this study, we analyzed, by whole genome sequencing (WGS) the resistome, mobilome and virulome of 12 multidrug-resistant (MDR) marine strains belonging to Shewanellaceae and Vibrionaceae families collected at aquaculture centers in Italy. The results evidenced the presence of several resistance mechanisms including enzyme and efflux pump systems conferring resistance to beta-lactams, quinolones, tetracyclines, macrolides, polymyxins, chloramphenicol, fosfomycin, erythromycin, detergents and heavy metals. Mobilome analysis did not find circular elements but class I integrons, integrative and conjugative element (ICE) associated modules, prophages and different insertion sequence (IS) family transposases. These mobile genetic elements (MGEs) are usually present in other aquatic bacteria but also in Enterobacteriaceae suggesting their transferability among autochthonous and allochthonous bacteria of the resilient microbiota. Regarding the presence of virulence factors, hemolytic activity was detected both in the Shewanella algae and in Vibrio spp. strains. To conclude, these data indicate the role as a reservoir of resistance and virulence genes in the environment of the aquatic microbiota present in the examined Italian fish farms that potentially might be transferred to bacteria of medical interest.
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Affiliation(s)
- Vanessa Zago
- Department of Diagnostics and Public Health, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy;
| | - Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy; (L.V.); (C.P.); (G.M.)
| | - Maria M. Lleo
- Department of Diagnostics and Public Health, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy;
- Correspondence: ; Tel.: +39-045-802-7194
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Ryan MP, Slattery S, Pembroke JT. A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements. Genes (Basel) 2019; 10:genes10121048. [PMID: 31888308 PMCID: PMC6947025 DOI: 10.3390/genes10121048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (E. coli) isolate K802 (which contains the ICEpMERPH) was carried out using Illumina sequencing technology. ICEpMERPH has a size of 110 Kb and 112 putative open reading frames (ORFs). The “hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences, and heavy metal resistance genes that encoded resistance to mercury, as previously reported, but also surprisingly to arsenate. A novel arsenate resistance system was identified in hotspot 4 of the element, unrelated to other SXT/R391 elements. This arsenate resistance system was potentially linked to two genes: orf69, encoding an organoarsenical efflux major facilitator superfamily (MFS) transporter-like protein related to ArsJ, and orf70, encoding nicotinamide adenine dinucleotide (NAD)-dependent glyceraldehyde-3-phosphate dehydrogenase. Phenotypic analysis using isogenic strains of Escherichia coli strain AB1157 with and without the ICEpMERPH revealed resistance to low levels of arsenate in the range of 1–5 mM. This novel, low-level resistance may have an important adaptive function in polluted environments, which often contain low levels of arsenate contamination. A bioinformatic analysis on the novel determinant and the phylogeny of ICEpMERPH was presented.
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Pu C, Yu Y, Diao J, Gong X, Li J, Sun Y. Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:262-269. [PMID: 31229823 DOI: 10.1016/j.scitotenv.2019.06.081] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
The main avenue in which antibiotic resistance enters soils is through the application of livestock manure. However, whether antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) persist and spread to vegetables with the application of manure and manure products is still unclear. This study assessed seven kinds of cultured ARB, 221 ARGs subtypes and three transposon genes in the vegetable production chain (from manure to biocompost, soils and vegetables). Results showed that at least 80% of ARB, ARGs and transposon genes were removed after aerobic composting. However, aerobic composting did not reduce the diversity of ARGs in pig and chicken manure. A total of 19 ARGs subtypes still persisted during aerobic composting. Compared to the temperature-thermophilic stage, the number of bacteria resistant to erythromycin, the relative abundance of ARGs and IS613 increased 1.7-4.9 times at the temperature-decreasing stage. Direct application of biocompost introduced 11 ARGs subtypes to pakchoi, but these ARGs did not present in biocompost-amended soil. A transposon gene tnpA was also detected in the biocompost-amended soil, but surprisingly was found in the control vegetable. This demonstrated that the transposon gene is intrinsic in pakchoi. Bacterial community analysis and network analysis revealed that a specific genus Terrisporobacter carrying tetO, tetW ermB and tnpA persisted in the vegetable production chain, which may generate a potential risk in the following production. Our study illuminates the persistence and spreading of antibiotic resistance in the vegetable production chain which could help manage the ecological risks arising from antibiotic resistance in manure sources.
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Affiliation(s)
- Chengjun Pu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Yao Yu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Jianxiong Diao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Gong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Ji Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Ying Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China.
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Genome Sequence of Colistin-Resistant Bacteremic Shewanella algae Carrying the Beta-Lactamase Gene bla OXA-55. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2019; 2019:3840563. [PMID: 31281553 PMCID: PMC6590586 DOI: 10.1155/2019/3840563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/06/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022]
Abstract
Shewanella algae is an emerging pathogen widely distributed in aquatic environment. Bacteremia is a major manifestation of S. algae infections, and there are increasing reports of antibiotic-resistant strains. However, little is known about the genomic characteristics of human bacteremic S. algae. Here, we report the results of the whole-genome sequencing of colistin-resistant S. algae TYL, a blood isolate. Chromosome-encoded pmrC associated with colistin resistance and blaOXA-55 gene intrinsic to S. algae was identified. Continuous surveillance for the emergence of S. algae is needed.
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ICE SXT vs. ICESh95: Co-existence of Integrative and Conjugative Elements and Competition for a New Host. Sci Rep 2019; 9:8045. [PMID: 31142760 PMCID: PMC6541609 DOI: 10.1038/s41598-019-44312-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/15/2019] [Indexed: 01/15/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that contribute to horizontal gene transfer. The aim of this work was to study different types of ICEs in clinical isolates of the emergent pathogen Shewanella spp., to compare their transfer efficiency and their ability to integrate a new host. Here we show that 3 out of 10 clinical isolates contained an ICE. Two of these elements were similar to ICEs from the SXT/R391 family and the other one was similar to ICESh95, a hybrid platform. Mating assays showed that these elements co-exist for several generations in the same host. Furthermore, transfer rates and competition assays between ICESh95 and ICESh392, an SXT-like element, suggest that the latter has evolved into a well-oiled machine that efficiently spread to different bacteria. Our results provide strong evidence of the role that ICEs play in the dissemination of genetic traits in nature and the implications that they have in the global threat of antimicrobial resistance.
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Seoane P, Tapia-Paniagua ST, Bautista R, Alcaide E, Esteve C, Martínez-Manzanares E, Balebona MC, Claros MG, Moriñigo MA. TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11. PeerJ 2019; 7:e6526. [PMID: 30842906 PMCID: PMC6397758 DOI: 10.7717/peerj.6526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/26/2019] [Indexed: 11/20/2022] Open
Abstract
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.
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Affiliation(s)
- Pedro Seoane
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain
| | | | - Rocío Bautista
- Andalusian Platform for Bioinformatics, Universidad de Málaga, Málaga, Spain
| | - Elena Alcaide
- Department of Microbiology and Ecology, Universidad de Valencia, Valencia, Spain
| | - Consuelo Esteve
- Department of Microbiology and Ecology, Universidad de Valencia, Valencia, Spain
| | | | | | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain
- Andalusian Platform for Bioinformatics, Universidad de Málaga, Málaga, Spain
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