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Harmer CJ, Nelson MJ, Lebreton F, Lertsethtakarn P, McGann PT, Hall RM. Distribution and expression of the aac(6')-Im (aacA16) aminoglycoside resistance gene. J Antimicrob Chemother 2024:dkae136. [PMID: 38742708 DOI: 10.1093/jac/dkae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND The aac(6')-Im (aacA16) amikacin, netilmicin and tobramycin resistance gene cassette had been circulating globally undetected for many years in a sublineage of Acinetobacter baumannii global clone 2. OBJECTIVES To identify sources for the aac(6')-Im fragment found in A. baumannii. METHODS MinION long-read sequencing and Unicycler hybrid assemblies were used to determine the genetic context of the aac(6')-Im gene. Quantitative reverse transcriptase PCR was used to measure expression. RESULTS Among >60 000 non-Acinetobacter draft genomes in the MRSN collection, the aac(6')-Im gene was detected in Pseudomonas putida and Enterobacter hormaechei isolates recovered from patients in Thailand between 2016 and 2019. Genomes of multiply resistant P. putida MRSN365855 and E. hormaechei MRSN791417 were completed. The class 1 integron containing the aac(6')-Im cassette was in the chromosome in MRSN365855, and in an HI2 plasmid in MRSN791417. However, MRSN791417 was amikacin susceptible and the gene was not expressed due to loss of the Pc promoter of the integron. Further examples of aac(6')-Im in plasmids from or the chromosome of various Gram-negative species were found in the GenBank nucleotide database. The aac(6')-Im context in integrons in pMRSN791417-8 and a Klebsiella plasmid pAMR200031 shared similarities with the aac(6')-Im region of AbGRI2-Im islands in A. baumannii. In other cases, the cassette array including the aac(6')-Im cassette was different. CONCLUSIONS The aac(6')-Im gene is widespread, being found so far in several different species and in several different gene cassette arrays. The lack of amikacin resistance in E. hormaechei highlights the importance of correlating resistance gene content and antibiotic resistance phenotype.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Messiah J Nelson
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Francois Lebreton
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Paphavee Lertsethtakarn
- Bacterial and Parasitic Diseases Department, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Patrick T McGann
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
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Luo X, Dong F, Dai P, Xu M, Yu L, Hu D, Feng J, Zhang J, Jing Y. Coexistence of blaKPC-2 and blaNDM-1 in one IncHI5 plasmid confers transferable carbapenem resistance from a clinical isolate of Klebsiella michiganensis in China. J Glob Antimicrob Resist 2023; 35:104-109. [PMID: 37714378 DOI: 10.1016/j.jgar.2023.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/23/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023] Open
Abstract
OBJECTIVES This study firstly identified an IncHI5 plasmid pK254-KPC_NDM co-carrying two different class carbapenemase genes blaKPC-2 and blaNDM-1 in Klebsiella michiganensis K254. METHODS The strain K254 was sequenced by high-throughput genome sequencing. A detailed genomic and phenotypic characterization of pK254-KPC_NDM was performed. RESULTS pK254-KPC_NDM displayed the conserve IncHI5 backbone and carried a resistant accessory region: Tn1696-related transposon Tn7414 containing blaKPC-2 and blaNDM-1. A sequence comparison was applied to a collection of four Tn1696-related transposons (Tn7414-Tn7417) harbouring carbapenemase genes. For all these four transposons, the blaNDM-1 was carried by Tn125 derivatives within three different mobile genetic elements. Tn7414 further acquired another carbapenemase gene, blaKPC-2, because of the integration of the local blaKPC-2 genetic environment from Tn6296, resulting in the high-level carbapenem resistance of K. michiganensis K254. The conjugal transfer and plasmid stability experiments confirmed that pK254-KPC_NDM could be transferred intercellularly and keep the stable vertical inheritance in different bacteria, which would contribute to the further dissemination of multiple carbapenemase genes and enhance the adaption and survival of K. michiganensis under complex and diverse antimicrobial selection pressures. CONCLUSION This study was the first to report the K. michiganensis isolate coharbouring blaKPC-2 and blaNDM-1 in the Tn1696-related transposon in IncHI5 plasmid. The emergence of novel transposons simultaneously carrying multiple carbapenemase genes might contribute to the further dissemination of high-level carbapenem resistance in the isolates of the hospital settings and pose new challenges for the treatment of nosocomial infection.
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Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Fang Dong
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Piaopiao Dai
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Mengqiao Xu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Jiao Feng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, China
| | - Ying Jing
- Department of Clinical Laboratory Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China.
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Izdebski R, Biedrzycka M, Urbanowicz P, Żabicka D, Gniadkowski M. Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp., Poland. Emerg Infect Dis 2023; 29:1618-1626. [PMID: 37486192 PMCID: PMC10370858 DOI: 10.3201/eid2908.230199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
We sequenced all nonduplicate 934 VIM/IMP carbapenemase-producing Enterobacterales (CPE) reported in Poland during 2006-2019 and found ≈40% of the isolates (n = 375) were Enterobacter spp. During the study period, incidence of those bacteria gradually grew in nearly the entire country. The major factor affecting the increase was clonal spread of several E. hormaechei lineages responsible for multiregional and interregional outbreaks (≈64% of all isolates), representing mainly the pandemic sequence type (ST) 90 or the internationally rare ST89 and ST121 clones. Three main VIM-encoding integron types efficiently disseminated across the clone variants (subclones) with various molecular platforms. Those variants were predominantly Pseudomonas aeruginosa-derived In238-like elements, present with IncHI2+HI2A, IncFII+FIA, IncFIB, or IncN3 plasmids, or chromosomal genomic islands in 30 Enterobacter STs. Another prevalent type, found in 34 STs, were In916-like elements, spreading in Europe recently with a lineage of IncA-like plasmids.
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Wang J, Dong X, Wang F, Jiang J, Zhao Y, Gu J, Xu J, Mao X, Tu B. Molecular Characteristics and Genetic Analysis of Extensively Drug-Resistant Isolates with different Tn3 Mobile Genetic Elements. Curr Microbiol 2023; 80:246. [PMID: 37335402 DOI: 10.1007/s00284-023-03340-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/22/2023] [Indexed: 06/21/2023]
Abstract
Extensively drug-resistant (XDR) bacteria are the main caues for causing clinical infectious diseases. Our aim was to distinguish the present molecular epidemiological situation of XDR Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli isolates recovered from local hospitals in Changzhou. Antibiotic susceptibility and phenotypic analysis, multilocus sequence typing and Pulsed Field Gel Electrophoresis were performed to trace these isolates. Resistant phenotype and gene analysis from 29 XDR strains demonstrated that they mainly included TEM, CTX-M-1/2, OXA-48, and KPC products. A. baumannii strains belonged to sequence type (ST) ST224, and carrying the blaCTX-M-2/TEM gene. The quinolone genes aac(6')-ib-cr and qnrB were carrying only in A. baumannii and E.coli. Three (2.3%) of these strains were found to contain the blaNDM-1 or blaNDM-5 gene. A new genotype of K. pneumoniae was found as ST2639. Epidemic characteristics of the XDR clones showed that antibiotic resistance genes distributed unevenly in different wards in Changzhou's local hospitals. With the sequencing of blaNDM carrying isolates, the plasmids often carrying a highly conservative Tn3-relavent mobile genetic element. The especially coupled insert sequence ISKox3 may be a distinctive resistance gene transfer loci. The genotypic diversity variation of XDRs suggested that tracking and isolating the sources of antibiotic resistance especially MBL-encoding genes such as blaNDM-will help manage the risk of infection by these XDRs.
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Affiliation(s)
- Jiazhen Wang
- School of Public Health, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xin Dong
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Fengming Wang
- School of Public Health, Xuzhou Medical University, Xuzhou, 221004, China
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Jinyi Jiang
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Ying Zhao
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Jingyue Gu
- School of Public Health, Xuzhou Medical University, Xuzhou, 221004, China
| | - Jian Xu
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Xujian Mao
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Bowen Tu
- School of Public Health, Xuzhou Medical University, Xuzhou, 221004, China.
- Pathogenic Biological Laboratory, Changzhou Disease Control and Prevention Centre, Changzhou Medical Centre, Nanjing Medical University, Changzhou, 213000, Jiangsu, China.
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Unravelling complex transposable elements surrounding bla GES-16 in a Pseudomonas aeruginosa ExoU strain. J Glob Antimicrob Resist 2022; 30:143-147. [PMID: 35447384 DOI: 10.1016/j.jgar.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES We characterised the complex surrounding regions of blaGES-16 in a Pseudomonas aeruginosa exoU+ strain (P-10.226) in Brazil. METHODS Species identification was performed by MALDI-TOF MS, and the antimicrobial susceptibility profile was determined by broth microdilution based on European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. The whole genome sequencing (WGS) of P-10.226 strain was performed using both short-read paired-end sequencing on the Illumina MiSeq platform as well as the long-read Oxford Nanopore MinION. RESULTS WGS analysis showed that P-10.226 carried blaGES-16, which was found as a gene cassette inserted into a novel class I integron, In1992 (aadB-blaOXA-56-blaGES-16-aadB-aadA6c), whose 3'-CS was truncated by a nested transposable element, IS5564::ISPa157. The structure was even more complex since IS6100-ΔIS6100 structure and a TnAs2-like harbouring the operon merRTPADE was found downstream In1992. Fragments of TnAs3 harbouring 25-bp imperfect inverted repeats were identified bordering the intl1 of In1992 and also flanking IS6100-ΔIS6100, which might be genetic marks of its previous presence in the genome. Interestingly, In1992 also shows a distinct cassette array from In581 (blaGES-16-dfrA22-aacA27-aadA1), which was previously reported in Serratia marcescens strains recovered in Brazil. Finally, exoU gene, which encodes a potent cytotoxin of type III secretion systems (T3SS) effector proteins from P. aeruginosa and is associated to severe infections, was also detected. CONCLUSION We described the novel In1992 carrying blaGES-16 surrounded by complex transposition events in a XDR P. aeruginosa strain. The identification of many sets of direct repeats adjacent to TnAs3 fragments indicates a major past of transposition events that shaped the current genetic environment of In1992.
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Li S, Jiang X, Li C, Ju Y, Yue L, Chen F, Hu L, Wang J, Hu X, Tuohetaerbaike B, Wen H, Zhang W, Zhou D, Yin Z, Chen F. A blaSIM-1 and mcr-9.2 harboring Klebsiella michiganensis strain reported and genomic characteristics of Klebsiella michiganensis. Front Cell Infect Microbiol 2022; 12:973901. [PMID: 36093205 PMCID: PMC9448873 DOI: 10.3389/fcimb.2022.973901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
As a newly emerging Klebsiella pathogen, more and more Klebsiella michiganensis drug resistant strains have been reported in recent years, which posed serious threats to public health. Here we first reported a multidrug-resistant K. michiganensis strain 12084 with two blaSIM-1 and one mcr-9.2 genes isolated from the sputum specimen of a patient in the Second Affiliated Hospital of Zhejiang University School of Medicine and analyzed its genetic basis and drug-resistance phenotypes. Genetic analysis showed that this strain harbored three different incompatibility groups (IncHI2, IncHI5, and IncFIIpKPHS2:IncFIB-4.1) of plasmids (p12084-HI2, p12084-HI5, and p12084-FII). A total of 26 drug-resistance genes belonging to 12 classes of antibiotics were identified, most of which (24) were located on two plasmids (p12084-HI2 and p12084-HI5). Interestingly, two blaSIM-1 genes were identified to locate on p12084-HI2 and p12084-HI5, respectively, both of which were embedded in In630, indicating their genetic homogeny. It was noting that one blaSIM-1 gene was situated in a novel unit transposon (referred to as Tn6733) on the p12084-HI5 plasmid. We also discovered an mcr-9.2 gene on the p12084-HI2 plasmid. To the best of our knowledge, this is the first report of a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain. We then investigated the population structure/classification, and antibiotic resistance for all 275 availably global K. michiganensis genomes. Population structure revealed that K. michiganensis could be divided into two main clades (Clade 1 and Clade 2); the most popular ST29 was located in Clade 1, while other common STs (such as ST50, ST27, and ST43) were located in Clade 2. Drug-resistance analysis showed 25.5% of the K. michiganensis strains (70/275) harboring at least one carbapenemase gene, indicating severe drug resistance of K. michiganensis beyond our imagination; this is a dangerous trend and should be closely monitored, especially for ST27 K. michiganensis with the most drug-resistant genes among all the STs. Overall, we reported a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain, and further revealed the population structure/classification, and drug-resistance of K. michiganensis, which provided an important framework, reference, and improved understanding of K. michiganensis.
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Affiliation(s)
- Shuangshuang Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyuan Jiang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Cuidan Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Yingjiao Ju
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liya Yue
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Xin Hu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Bahetibieke Tuohetaerbaike
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Dongsheng Zhou
- 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
- *Correspondence: Zhe Yin, ; Fei Chen,
| | - Fei Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Zhe Yin, ; Fei Chen,
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Selvaraj GK, Wang H, Zhang Y, Tian Z, Chai W, Lu H. Class 1 In-Tn5393c array contributed to antibiotic resistance of non-pathogenic Pseudoxanthomonas mexicana isolated from a wastewater bioreactor treating streptomycin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153537. [PMID: 35101502 DOI: 10.1016/j.scitotenv.2022.153537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The emergence of antibiotic resistance in retort to environmental pollutants during wastewater treatment still remains elusive. Here, we first to investigate the emergence of antibiotic resistance in an environmental non-pathogenic bacterium, Pseudoxanthomonas mexicana isolated from a lab-scale bioreactor treating wastewater containing streptomycin. The molecular mechanism of antibiotic resistance development was evaluated in its genomic, transcriptional, and proteomic levels. The streptomycin resistant (SR) strain showed strong resistance to streptomycin (MIC > 600 μg/mL) as well to sulfamethoxazole, ampicillin, and kanamycin (≥250 μg/mL). A 13.4 kb class-1-integron array consisting of a new arrangement of gene cassette (IS6100-sul1-aadA2-catB3-aacA1-2-aadB-int1-IS256-int) linked with Tn5393c transposon was identified in the SR strain, which has only been reported in clinical pathogens so far. iTRAQ-LC-MS/MS proteomics revealed 22 up-regulated proteins in the SR strain growing under 100 mg L-1 streptomycin, involving antibiotic resistance, toxin production, stress response, and ribosomal protein synthesis. At the mRNA level, elevated expressions of ARGs (strA, strB, and aadB) and 30S-ribosomal protein genes (rpsA and rpsU) were observed in the SR strain. The results highlighted the genomic plasticity and multifaceted regulatory mechanism employed by P. mexicana in adaptation to high-level streptomycin during biological wastewater treatment.
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Affiliation(s)
- Ganesh-Kumar Selvaraj
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India
| | - Hanqing Wang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenbo Chai
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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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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Luo X, Zhang J, Yuan M, Mou S, Xu M, Hu D, Ma Q, Sun L, Li P, Song Z, Yu L, Mu K. Epidemiology of Klebsiella michiganensis Carrying Multidrug-Resistant IncHI5 Plasmids in the Southeast Coastal Area of China. Infect Drug Resist 2022; 15:1831-1843. [PMID: 35444429 PMCID: PMC9013925 DOI: 10.2147/idr.s358839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/26/2022] [Indexed: 12/18/2022] Open
Abstract
Purpose This study aimed to explore the genomic characterization of multidrug-resistant IncHI5-carrying Klebsiella michiganensis strains and detailed genomic dissection of the IncHI5 plasmids. Materials and Methods Through whole-genome sequencing, the IncHI5 plasmid pK92-qnrS was obtained from a single clinical K. michiganensis isolate K92. All complete genomes of K. michiganensis strains from the Genome database of NCBI were collected and used to construct a maximum likelihood (ML) phylogenetic tree. The epidemiology and geographic distribution of all the K. michiganensis strains were conducted. An extensive comparison of the seven IncHI5 plasmids of K. michiganensis (one from this study, six from GenBank) was applied. Results This study revealed that all K. michiganensis strains carrying IncHI5 plasmids from different clonal groups were located in the southeast coastal area of China. The backbone regions of IncHI5 plasmids were composed of replicon (repHI5B and repFIB), partition (parABC), and conjugal transfer (tra1/tra2). The main accessory resistant regions of IncHI5 could be divided into two categories, Tn1696-related region and Tn6535-related region. These seven IncHI5 plasmids carried multiple drug-resistance genes which were all mediated by the mobile genetic elements (MGEs). Conclusion Data presented here help to provide an overall in-depth understanding of epidemiology and geographic distribution of IncHI5-carrying K. michiganensis and the structure and evolutionary history of IncHI5 plasmids.
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Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Min Yuan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Sihua Mou
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Mengqiao Xu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Qinfei Ma
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Lingfen Sun
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Piaopiao Li
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Zhiwei Song
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
- Lianhua Yu, Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China, Email
| | - Kai Mu
- Beijing Institute of Radiation Medicine, Beijing, 100850, People’s Republic of China
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People’s Republic of China
- Correspondence: Kai Mu, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People’s Republic of China, Tel +86-010-66874794, Email
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10
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Xu Y, Jing Y, Hu L, Cheng Q, Gao H, Zhang Z, Yang H, Zhao Y, Zhou D, Yin Z, Dai E. IncFIB-4.1 and IncFIB-4.2 Single-Replicon Plasmids: Small Backbones with Large Accessory Regions. Infect Drug Resist 2022; 15:1191-1203. [PMID: 35345473 PMCID: PMC8957301 DOI: 10.2147/idr.s332949] [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: 08/09/2021] [Accepted: 02/09/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To establish a typing scheme for IncFIB replicon and to dissect genomic features of IncFIB-4.1/4.2 single-replicon plasmids. Methods A total of 146 representative fully sequenced IncFIB-replicon-containing plasmids were selected to construct a phylogenetic tree of repBIncFIB sequences. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids from China were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank to dissect their genomic diversity. Results In this study, a repB sequence-based scheme was proposed for grouping IncFIB replicon into seven primary types and further into 70 subtypes. A collection of nine IncFIB-4.1/4.2 single-replicon plasmids were fully sequenced here and compared with the first sequenced IncFIB-4.1/4.2 single-replicon plasmids from GenBank. These 11 plasmids had small backbones and shared only three key backbone markers repB together with its iterons, parABC, and stbD. Each plasmid contained one large accessory region (LAR) inserted into the backbone, and these 11 LARs had significantly distinct profiles of mobile genetic elements (MGEs) and resistance/metabolism gene loci. Antibiotic resistance regions (ARRs; the antibiotic resistance gene-containing genetic elements) were found in seven of these 11 LARs. Besides resistance genes, ARRs carried unit or composite transposons, integrons, and putative resistance units. IncFIB-4.1/4.2 single-replicon plasmids were important vectors of drug resistance genes. This was the first report of three novel MGEs: In1776, Tn6755, and Tn6857. Conclusion Data presented here provided a deeper insight into diversity and evolution of IncFIB replicon and IncFIB-4.1/4.2 single-replicon plasmids.
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Affiliation(s)
- Yanan Xu
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050011, 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
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Qiaoxiang Cheng
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050011, People’s Republic of China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei, 050021, People’s Republic of China
| | - Zhi Zhang
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei, 050021, People’s Republic of China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, 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
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Erhei Dai
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, Hebei, 050011, People’s Republic of China
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei, 050021, People’s Republic of China
- Correspondence: Erhei Dai; Zhe Yin, Tel +86-311-85814612; +86-10-66948557, Email ;
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11
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Jing Y, Yin Z, Wang P, Guan J, Chen F, Wang L, Li X, Mu X, Zhou D. A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes. Microbiol Spectr 2022; 10:e0265021. [PMID: 35196820 PMCID: PMC8865565 DOI: 10.1128/spectrum.02650-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 11/20/2022] Open
Abstract
In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures. IMPORTANCE This study presents a comprehensive genomic epidemiology analysis on global sequenced Morganella isolates. First, a genome sequence-based species classification scheme for Morganella is established with a higher resolution and accuracy than those of the conventional scheme. Second, the prevalence of accessory genetic elements (AGEs) and associated antimicrobial resistance genes (ARGs) among Morganella isolates is disclosed based on genome sequences. Finally, a detailed sequence comparison of eight groups of 23 AGEs (including 19 Morganella chromosomal AGEs) reveals that Morganella chromosomes have evolved to acquire diverse AGEs harboring different profiles of ARGs and that some of these AGEs harbor large accessory modules that exhibit complex mosaic structures and contain a large number of ARGs. Data presented here provide a deeper understanding of the classification and evolution of Morganella species and also those of ARG-containing AGEs in Morganella at the genomic scale.
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Affiliation(s)
- Ying Jing
- 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
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiayao Guan
- 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
| | - Lingling Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaofei Mu
- 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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12
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Jadeja NB, Worrich A. From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches. Environ Microbiol 2022; 24:3290-3306. [PMID: 35172395 DOI: 10.1111/1462-2920.15927] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.
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Affiliation(s)
- Niti B Jadeja
- Ashoka Trust for Research in Ecology and the Environment, PO, Royal Enclave, Srirampura, Jakkur, Bengaluru, Karnataka, 560064, India
| | - Anja Worrich
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstr. 15, Leipzig, 04318, Germany
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13
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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14
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Imported One-Day-Old Chicks as Trojan Horses for Multidrug-Resistant Priority Pathogens Harboring mcr-9, rmtG and Extended-Spectrum β-Lactamase Genes. Appl Environ Microbiol 2021; 88:e0167521. [PMID: 34731047 DOI: 10.1128/aem.01675-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving intensive animal production systems. In this study, we have performed a microbiological and molecular investigation of priority pathogens carrying transferable resistance genes to critical antimicrobials in one-day-old chickens imported from Brazil to Uruguay. Bacterial identification was performed by MALDI-TOF mass spectrometry and antibiotic susceptibility was determined by Sensititre. Antimicrobial resistance genes were sought by polymerase chain reaction and clonality was assessed by PFGE. Four multidrug-resistant (MDR) representative strains were sequenced by Illumina and/or Oxford Nanopore Technologies. Twenty-eight MDR isolates identified as Escherichia coli (n= 14), Enterobacter cloacae (n= 11) and Klebsiella pneumoniae (n= 3). While resistance to oxyiminocephalosporins was due to blaCTX-M-2, blaCTX-M-8, blaCTX-M-15, blaCTX-M-55 and blaCMY-2, plasmid-mediated quinolone resistance was associated with qnrB19, qnrE1, and qnrB2 genes. Finally, resistance to aminoglycosides and fosfomycin was due to the presence of 16S rRNA methyltransferase rmtG and fosA-type genes, respectively. Short and long-read genome sequencing of E. cloacae ODC-Eclo3 strain revealed the presence of IncQ/rmtG (pUR-EC3.1, 7400-pb), IncHI2A/mcr-9.1/blaCTX-M-2 [pUR-EC3.2, ST16 (pMLST), 408,436-bp] and IncN2/qnrB19/aacC3/aph(3'')-Ib (pUR-EC3.3) resistance plasmids. Strikingly, the blaCTX-M-2 gene was carried by a novel Tn1696-like composite transposon designated Tn7337. In summary, we report that imported one-day-old chicks can act as Trojan horses for the hidden spread of WHO critical priority MDR pathogens harboring mcr-9, rmtG and extended-spectrum β-lactamase genes in poultry farms, which is a critical issue within a One Health perspective. Importance section Antimicrobial resistance is considered a significant problem for global health, including within the concept of "One Health", therefore, the food chain is a link that connects human and animal health directly. In this work, we searched for microorganisms resistant to antibiotics considered critical for human health in intestinal microbiota of one-day-old baby chicks imported to Uruguay from Brazil. We described antibiotic-resistant genes to antibiotics named as to watch or reserve for the WHO, such as rmtG or mcr9.1, which confers resistance to all the aminoglycosides and colistin, respectively, among others genes, and their presence in new mobile genetic elements that favor its dissemination. The sustained entry of these microorganisms evades the sanitary measures implemented by the countries and production establishments to reduce the selection of resistant microorganisms. These silently imported resistant microorganisms could explain a considerable part of the antimicrobial resistance problems found in the production stages of the system.
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15
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Abe R, Oyama F, Akeda Y, Nozaki M, Hatachi T, Okamoto Y, Yoshida H, Hamaguchi S, Tomono K, Matsumoto Y, Motooka D, Iida T, Hamada S. Hospital-wide outbreaks of carbapenem-resistant Enterobacteriaceae horizontally spread through a clonal plasmid harbouring blaIMP-1 in children's hospitals in Japan. J Antimicrob Chemother 2021; 76:3314-3317. [PMID: 34477841 DOI: 10.1093/jac/dkab303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Ryuichiro Abe
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Anaesthesiology and Intensive Care Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Fumiya Oyama
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yukihiro Akeda
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan.,National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatoshi Nozaki
- Department of Neonatal Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Takeshi Hatachi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yuya Okamoto
- Department of Laboratory Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Hisao Yoshida
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeto Hamaguchi
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kazunori Tomono
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tetsuya Iida
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shigeyuki Hamada
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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16
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Rajabal V, Taner F, Sanlidag T, Suer K, Guler E, Sayan M, Petrovski S. Genetic characterisation of antibiotic resistance transposons Tn6608 and Tn6609 isolated from clinical Pseudomonas strains in Cyprus. J Glob Antimicrob Resist 2021; 26:330-334. [PMID: 34363995 DOI: 10.1016/j.jgar.2021.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES Antibiotic therapy for Pseudomonas infections is becoming increasingly difficult. In this study, the transposons from two multidrug-resistant (MDR) clinical Pseudomonas strains containing related transposons responsible for giving rise to resistance determinants were characterised. METHODS Two MDR clinical Pseudomonas isolates were obtained from a medical facility in Cyprus. The strains were identified as Pseudomonas putida C54 and Pseudomonas aeruginosa C69. DNA was extracted from both strains and was sequenced. Transposons were identified, annotated and compared with DNA sequences in GenBank. RESULTS Two related nested transposons, here named Tn6608 (from P. putida C54) and Tn6609 (from P. aeruginosa C69), were characterised. The transposons are built on an ancestral Tn1403 base element (here named Tn1403A) that contains only the transposition module (tnpA and tnpR) and the associated cargo gene module (orfA, orfB, orfC and orfD) flanked by a 38-bp inverted repeat. The nested transposons identified in this study have evolved via acquisition of multiple transposons, adding multiple resistance genes to an ancestral transposon that originally lacked any resistance determinants. CONCLUSION Transposons related to Tn6608 and Tn6609 have evolved and are globally disseminated. Of particular interest is that most of these nested transposons are located within the same site in a genomic island, providing alternative avenues for dissemination.
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Affiliation(s)
- Vaheesan Rajabal
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Ferdiye Taner
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia; Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Nicosia, Cyprus
| | - Tamer Sanlidag
- DESAM Research Institute, Near East University, Nicosia, Cyprus
| | - Kaya Suer
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Emrah Guler
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Murat Sayan
- DESAM Research Institute, Near East University, Nicosia, Cyprus; Faculty of Medicine, Clinical Laboratory, PCR Unit, Kocaeli University, Kocaeli, Turkey
| | - Steve Petrovski
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia.
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17
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Shi Y, Zhang Y, Wu X, Zhang H, Yang M, Tian Z. Potential dissemination mechanism of the tetC gene in Aeromonas media from the aerobic biofilm reactor under oxytetracycline stresses. J Environ Sci (China) 2021; 105:90-99. [PMID: 34130843 DOI: 10.1016/j.jes.2020.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The tetC gene has been found to be one of the most widely distributed tetracycline resistance (tet) genes in various environmental niches, but the detailed dissemination mechanisms are still largely unknown. In the present study, 11 tetC-containing Aeromonas media strains were isolated from an aerobic biofilm reactor under oxytetracycline stresses, and the genome of one strain was sequenced using the PacBio RSII sequencing approach to reveal the genetic environment of tetC. The tetC gene was carried by an IS26 composite transposon, named Tn6434. The tetC-carrying Tn6434 structure was detected in all of the A. media strains either in a novel plasmid pAeme2 (n=9) or other DNA molecules (n=2) by PCR screening. The NCBI database searching result shows that this structure was also present in the plasmids or chromosomes of other 13 genera, indicating the transferability of Tn6434. Inverse PCR and sequencing confirmed that Tn6434 can form a circular intermediate and is able to incorporate into a preexisting IS26 element, suggesting that Tn6434 might be responsible for the dissemination of tetC between different DNA molecules. This study will be helpful in uncovering the spread mechanism of tet genes in water environments.
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Affiliation(s)
- Yanhong Shi
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Xiangyang Wu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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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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19
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Papa-Ezdra R, Cordeiro NF, Di Pilato V, Chiarelli A, Pallecchi L, Garcia-Fulgueiras V, Vignoli R. Description of novel resistance islands harbouring bla CTX-M-2 in IncC type 2 plasmids. J Glob Antimicrob Resist 2021; 26:37-41. [PMID: 34020071 DOI: 10.1016/j.jgar.2021.03.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/29/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES We sequenced two IncA/C plasmids harbouring blaCTX-M-2 in Klebsiella pneumoniae clinical isolates and compared their antibiotic resistance islands. METHODS Transconjugants were obtained from two clinical K. pneumoniae isolates harbouring blaCTX-M-2. Plasmid DNA from transconjugants underwent short-read whole-genome sequencing, reads were assembled, and gaps were closed by PCR and sequencing. Determination of plasmid replicons, antibiotic resistance genes, identification and characterisation of insertion sequence (IS) elements, and comparison with publicly available plasmid sequences were performed. RESULTS blaCTX-M-2 was located in a complex class 1 integron In35::ISCR1::blaCTX-M-2, inserted in two different transposons designated Tn7057 and Tn7058, that reside in the resistance islands of plasmids pUR-KP0923 and pUR-KP1025, respectively. The general modules of both transposons were In35::ISCR1::blaCTX-M-2-Tn1000-like-Tn2*-ISKpn11-12-13 variable module-ΔTn21. In Tn7057 there was ΔIS10R-catA2 associated with an additional ISKpn13. Both plasmids belonged to IncC type 2 and ST3. pUR-KP0923 was 167 138 bp in length and had a 37 926-bp resistance island at position 4 (RI-4). Plasmid pUR-KP1025 was 168 128 bp with a RI-4 of 36 222 bp. CONCLUSION This report describes the molecular nature of two transposons (Tn7057 and Tn7058) harbouring blaCTX-M-2 that reside in IncC type 2 ST3 plasmids. These transposons mediate resistance to oxyimino-cephalosporins, gentamicin and, in the case of Tn7057, chloramphenicol. CTX-M-2 is an important extended-spectrum β-lactamase (ESBL) to South American epidemiology. It is remarkable that despite being only two plasmid sequences, the information revealed here could contribute to a better understanding of the resistance islands from IncC type 2 plasmids.
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Affiliation(s)
- R Papa-Ezdra
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - N F Cordeiro
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - V Di Pilato
- Department of Surgical Sciences & Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - A Chiarelli
- EERA Unit 'Ecology and Evolution of Antibiotic Resistance', Institut Pasteur - Assistance Publique/Hôpitaux de Paris - University Paris-Saclay, Paris, France
| | - L Pallecchi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - V Garcia-Fulgueiras
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - R Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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20
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Varani A, He S, Siguier P, Ross K, Chandler M. The IS6 family, a clinically important group of insertion sequences including IS26. Mob DNA 2021; 12:11. [PMID: 33757578 PMCID: PMC7986276 DOI: 10.1186/s13100-021-00239-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
The IS6 family of bacterial and archaeal insertion sequences, first identified in the early 1980s, has proved to be instrumental in the rearrangement and spread of multiple antibiotic resistance. Two IS, IS26 (found in many enterobacterial clinical isolates as components of both chromosome and plasmids) and IS257 (identified in the plasmids and chromosomes of gram-positive bacteria), have received particular attention for their clinical impact. Although few biochemical data are available concerning the transposition mechanism of these elements, genetic studies have provided some interesting observations suggesting that members of the family might transpose using an unexpected mechanism. In this review, we present an overview of the family, the distribution and phylogenetic relationships of its members, their impact on their host genomes and analyse available data concerning the particular transposition pathways they may use. We also provide a mechanistic model that explains the recent observations on one of the IS6 family transposition pathways: targeted cointegrate formation between replicons.
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Affiliation(s)
- Alessandro Varani
- School of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil
| | - Susu He
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Patricia Siguier
- Centre de Biologie Intégrative-Université Paul SABATIER, CNRS - Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100 - bât. CNRS-IBCG, Toulouse, France
| | - Karen Ross
- Protein Information Resource, Department of Biochem., Mol. and Cell. Biol, Georgetown University Medical Center, Washington, DC, USA
| | - Michael Chandler
- Department of Biochem., Mol. and Cell. Biol, Georgetown University Medical Center, Washington, DC, USA.
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21
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Yu T, Yang H, Li J, Chen F, Hu L, Jing Y, Luo X, Yin Z, Zou M, Zhou D. Novel Chromosome-Borne Accessory Genetic Elements Carrying Multiple Antibiotic Resistance Genes in Pseudomonas aeruginosa. Front Cell Infect Microbiol 2021; 11:638087. [PMID: 33816340 PMCID: PMC8012812 DOI: 10.3389/fcimb.2021.638087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is noted for its intrinsic antibiotic resistance and capacity of acquiring additional resistance genes. In this study, the genomes of nine clinical P. aeruginosa isolates were fully sequenced. An extensive genetic comparison was applied to 18 P. aeruginosa accessory genetic elements (AGEs; 13 of them were sequenced in this study and located within P. aeruginosa chromosomes) that were divided into four groups: five related integrative and conjugative elements (ICEs), four related integrative and mobilizable elements (IMEs), five related unit transposons, and two related IMEs and their two derivatives. At least 45 resistance genes, involved in resistance to 10 different categories of antibiotics and heavy metals, were identified from these 18 AGEs. A total of 10 β-lactamase genes were identified from 10 AGEs sequenced herein, and nine of them were captured within class 1 integrons, which were further integrated into ICEs and IMEs with intercellular mobility, and also unit transposons with intracellular mobility. Through this study, we identified for the first time 20 novel MGEs, including four ICEs Tn6584, Tn6585, Tn6586, and Tn6587; three IMEs Tn6853, Tn6854, and Tn6878; five unit transposons Tn6846, Tn6847, Tn6848, Tn6849, and Tn6883; and eight integrons In1795, In1778, In1820, In1784, In1775, In1774, In1789, and In1799. This was also the first report of two resistance gene variants blaCARB-53 and catB3s, and a novel ST3405 isolate of P. aeruginosa. The data presented here denoted that complex transposition and homologous recombination promoted the assembly and integration of AGEs with mosaic structures into P. aeruginosa chromosomes.
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Affiliation(s)
- Ting Yu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- 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
| | - 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
| | - Mingxiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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22
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Singh NS, Singhal N, Kumar M, Virdi JS. High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk. Front Microbiol 2021; 12:621564. [PMID: 33633708 PMCID: PMC7899961 DOI: 10.3389/fmicb.2021.621564] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/05/2021] [Indexed: 11/16/2022] Open
Abstract
Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of blaCTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, blaTEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), blaCTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where blaCTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of blaCTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of blaCTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.
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Affiliation(s)
- Nambram Somendro Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi, India.,Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
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23
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Sarwar A, Ahmad I, Amin A, Saleem MA. Paper currency harbours antibiotic-resistant coliform bacteria and integron integrase. J Appl Microbiol 2020; 130:1721-1729. [PMID: 32966644 DOI: 10.1111/jam.14856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/07/2020] [Accepted: 09/13/2020] [Indexed: 01/16/2023]
Abstract
AIMS This study was designed to analyse the prevalence of class 1 and class 2 integron integrase genes among antibiotic-resistant coliform bacteria isolated from paper currency circulating in Pakistan. METHODS AND RESULTS A total of 500 individual currency notes were collected from different food vending sites at Lahore, Pakistan. Bacterial population were identified by biochemical and PCR techniques. Antimicrobial susceptibility testing was performed by disc diffusion assay. The highest bacterial population on currency was found from street vendors and butcher shops. Escherichia coli was found to be the most prevalent coliform bacteria followed by Klebsiella sp. and Enterobacter sp. PCR amplification of antimicrobial resistance gene showed the presence of ampC, blaTEM , blaNDM-1 , qnrA, tet(A) and tet(B) genes among coliform isolates. A total of 47 integron integrase bearing strains of coliform bacteria were analysed. Sequence analysis showed the presence of dfrA1-aadA1, dfrA1, dfrA5, dfrA7, aadA1, aadA4 cassette arrays in class 1 integron and dfrA1-sat2-aadA1 in class 2 integrase genes. CONCLUSION Circulating currency was heavily contaminated with antimicrobial-resistant coliform bacteria bearing class 1 and class 2 integron integrase genes. SIGNIFICANCE AND IMPACT OF THE STUDY This study describes a potential threat of severe bacterial infections due to improper hand hygiene and community sanitation when dealing with the currency notes.
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Affiliation(s)
- A Sarwar
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - I Ahmad
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - A Amin
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - M A Saleem
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
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24
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Cummins ML, Hamidian M, Djordjevic SP. Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae. Microorganisms 2020; 8:microorganisms8020161. [PMID: 31979280 PMCID: PMC7074787 DOI: 10.3390/microorganisms8020161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022] Open
Abstract
Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that plays an important role in the capture and spread of multiple drug resistance. To date, SGI1 has been found in clinical isolates of Salmonella enterica serovars, Proteus mirabilis, Morganella morganii, Acinetobacter baumannii, Providencia stuartii, Enterobacter spp, and recently in Escherichia coli. SGI1 preferentially targets the 3´-end of trmE, a conserved gene found in the Enterobacteriaceae and among members of the Gammaproteobacteria. It is, therefore, hypothesised that SGI1 and SGI1-related elements (SGI1-REs) may have been acquired by diverse bacterial genera. Here, Bitsliced Genomic Signature Indexes (BIGSI) was used to screen the NCBI Sequence Read Archive (SRA) for putative SGI1-REs in Gammaproteobacteria. Novel SGI-REs were identified in diverse genera including Cronobacter spp, Klebsiella spp, and Vibrio spp and in two additional isolates of Escherichia coli. An extensively drug-resistant human clonal lineage of Klebsiella pneumoniae carrying an SGI1-RE in the United Kingdom and an SGI1-RE that lacks a class 1 integron were also identified. These findings provide insight into the origins of this diverse family of clinically important genomic islands and expand the knowledge of the potential host range of SGI1-REs within the Gammaproteobacteria.
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Affiliation(s)
- Max Laurence Cummins
- The ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; (M.L.C.); (M.H.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Mohammad Hamidian
- The ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; (M.L.C.); (M.H.)
| | - Steven Philip Djordjevic
- The ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; (M.L.C.); (M.H.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
- Correspondence:
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25
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Botelho J, Lood C, Partridge SR, van Noort V, Lavigne R, Grosso F, Peixe L. Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain. Emerg Microbes Infect 2019; 8:1186-1194. [PMID: 31381486 PMCID: PMC6713103 DOI: 10.1080/22221751.2019.1648182] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Horizontal transfer of plasmids plays a pivotal role in dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Plasmid sequencing is thus paramount for accurate epidemiological tracking in hospitals and routine surveillance. Combining Nanopore and Illumina sequencing allowed full assembly of a carbapenemase-encoding megaplasmid carried by multidrug-resistant clinical isolate FFUP_PS_41. Average nucleotide identity analyses revealed that FFUP_PS_41 belongs to the recently proposed new species Pseudomonas shirazica, related to the P. putida phylogenetic group. FFUP_PS_41 harbours a 498,516-bp megaplasmid (pJBCL41) with limited similarity to publicly-available plasmids. pJBCL41 contains genes predicted to encode replication, conjugation, partitioning and maintenance functions and heavy metal resistance. The |aacA7|blaVIM-2|aacA4| cassette array (resistance to carbapenems and aminoglycosides) is located within a class 1 integron that is a defective Tn402 derivative. This transposon lies within a 50,273-bp region bound by Tn3-family 38-bp inverted repeats and flanked by 5-bp direct repeats (DR) that composes additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach allowed full resolution of a carbapenemase-encoding megaplasmid from P. shirazica. Identification of novel megaplasmids sheds new light on the evolutionary effects of gene transfer and the selective forces driving antibiotic resistance.
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Affiliation(s)
- João Botelho
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
| | - Cédric Lood
- b Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven , Leuven , Belgium.,c Laboratory of Gene Technology, Department of Biosystems, KU Leuven , Leuven , Belgium
| | - Sally R Partridge
- d Centre for Microbiology and Infectious Diseases, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital , Sydney , Australia
| | - Vera van Noort
- b Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven , Leuven , Belgium.,e Institute of Biology, Leiden University , Leiden , The Netherlands
| | - Rob Lavigne
- c Laboratory of Gene Technology, Department of Biosystems, KU Leuven , Leuven , Belgium
| | - Filipa Grosso
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
| | - Luísa Peixe
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
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26
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Wang F, Wang D, Hou W, Jin Q, Feng J, Zhou D. Evolutionary Diversity of Prophage DNA in Klebsiella pneumoniae Chromosomes. Front Microbiol 2019; 10:2840. [PMID: 31866991 PMCID: PMC6908951 DOI: 10.3389/fmicb.2019.02840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
Mobile gene elements play an important role in the continuous evolution of the prophage DNA of bacteria, promoting the emergence of new gene structures. This study explored the evolution of four strains of Klebsiella pneumoniae harboring prophages, 19051, 721005, 911021, and 675920, and 16 genomes of K. pneumoniae from GenBank. The results revealed a wide range of genetic variation in the prophage DNA inserted into the sap sites of K. pneumoniae chromosomes. From analysis and comparison of the sequences of the 20 prophage DNAs determined from the four strains and the 16 GenBank genomes of K. pneumoniae using high-throughput sequencing and antimicrobial susceptibility tests, we identified a novel transposon, Tn6556. We also identified at least nine large genetic structures with massive genetic acquisitions or losses and five hotspot sites showing a tendency to undergo insertion of gene elements such as IS1T, IS1R, IS26, ISKpn26, ISKpn28, Tn6556, MDR, and In27-related regions as variable regions; however, the only highly conserved core genes were int and umuCD among the 20 prophage DNAs. These findings provide important insights into the evolutionary diversity of bacteriophage DNA contained in K. pneumoniae.
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Affiliation(s)
- Fengling Wang
- Department of Infectious Disease, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Dongguo Wang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Wei Hou
- Department of Infectious Disease, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Qian Jin
- Department of Infectious Disease, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Jiao Feng
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Cheng Q, Jiang X, Xu Y, Hu L, Luo W, Yin Z, Gao H, Yang W, Yang H, Zhao Y, Zhao X, Zhou D, Dai E. Type 1, 2, and 1/2-Hybrid IncC Plasmids From China. Front Microbiol 2019; 10:2508. [PMID: 31803147 PMCID: PMC6872532 DOI: 10.3389/fmicb.2019.02508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/18/2019] [Indexed: 11/13/2022] Open
Abstract
A collection of 11 IncC plasmids from China were fully sequenced herein and compared with reference plasmids pR148 and pR55. These 13 plasmids could be assigned into three different subgroups: type 1, type 2, and type 1/2 hybrid. Type 1/2-hybrid plasmids most likely emerged from homologous recombination between type 1 and type 2 plasmids. Different IncC plasmids had evolved to acquire quite different profiles of accessory modules and thus different collections of resistance genes. The accessory resistance modules included not only the bla CMY-carrying region, the ARI-A island, and the ARI-B island, but also various additional kinds of resistance islands such as the bla CTX-M-carrying regions and the MDR regions. Insertion of accessory modules was sometimes accompanied by deletion, inversion, and translocation of surrounding backbone regions. pR148 and pR55 were confirmed to have the most complete backbones for type 1 and type 2, respectively. This was the first report of a bla IMP- 8-carrying IncC plasmid, and that of three novel mobile elements: a Tn1696-derived unit transposon Tn6395, a class 2 integron In2-76, and an insertion sequence ISEcl10.
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Affiliation(s)
- Qiaoxiang Cheng
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanan Xu
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, China.,Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenbo 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
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Wenhui Yang
- 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
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaodong Zhao
- 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
| | - Erhei Dai
- Department of Clinical Laboratory Medicine, Hebei Medical University, Shijiazhuang, China.,Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
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Harmer CJ, Hall RM. The Complete Nucleotide Sequence of pZM3, a 1970 FIA:FIB:FII Plasmid Carrying Antibiotic Resistance and Virulence Determinants. Microb Drug Resist 2019; 26:438-446. [PMID: 31718432 DOI: 10.1089/mdr.2019.0248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The multiresistance plasmid, pZM3, from a 1970 Salmonella enterica serovar Wien isolate from Algeria represents the multiresistance FIme-type plasmids conferring resistance to ampicillin, chloramphenicol, kanamycin, neomycin, sulfonamides, streptomycin, spectinomycin, tetracycline, and mercuric ions circulating in the Middle East in the 1970s. pZM3 was sequenced to determine the relationship between IS1936, the IS26-like insertion sequence it carries, and IS26. IS1936 is identical to IS26. pZM3 is a 166.8-kb plasmid with three replicons typed as FIA-1, FIB-1, and FII-1, consistent with other FIme plasmids. However, Tn3, containing the blaTEM-1a ampicillin resistance gene, disrupts the FII repA gene. pZM3 also contains an IS1-flanked virulence region, including the sit and aerobactin operons, shared with many other FIB-1 virulence plasmids. The remaining resistance genes are located in a 44.7-kb complex resistance island that includes the Tn21-like transposon, Tn1935, identified previously. Relative to Tn21, Tn1935 includes an additional gene cassette, oxa1, and Tn4352 in tniA. Tn1935 is in the same Tn2670 context as Tn21 in NR1, and identity to NR1 extends beyond the IS1 flanking the catA1 gene. On the other side, IS1-mediated events have brought in a Tn10 remnant and inverted part of it, highlighting the role of IS1 in resistance region evolution. The backbone of pZM3 was found to be almost identical to that of pRSB225, recovered in Germany in 2013, and their resistance islands are in the same position. The pRSB225 resistance island has evolved in situ from the pZM3 configuration through an insertion, a replacement, and an inversion.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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Yin Z, Hu L, Cheng Q, Jiang X, Xu Y, Yang W, Yang H, Zhao Y, Gao B, Wang J, Dai E, Zhou D. First Report of Coexistence of Three Different MDR Plasmids, and That of Occurrence of IMP-Encoding Plasmid in Leclercia adecarboxylata. Front Microbiol 2019; 10:2468. [PMID: 31749779 PMCID: PMC6848029 DOI: 10.3389/fmicb.2019.02468] [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: 06/16/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
Three different MDR plasmids p16005813A, p16005813B, and p16005813C, which carried a total of 18 non-redundant resistance genes or gene loci, were identified in a single clinical isolate of Leclercia adecarboxylata. The p16005813A backbone showed very low levels of identity to all DNA sequences available in public databases and carried a repA gene that could not assigned into any of known incompatibility groups. The IncFII-family p16005813B and pECAZ161_KPC had essentially identical backbones. p16005813C belonged to an IncR single-replicon plasmid. p16005813A, p16005813B, and p16005813C harbored three different novel MDR regions as their sole accessory modules. The MDR region of p16005813B manifested as Tn6505, which was generated from insertion of blaIMP–8-carrying In655 instead of In4 into the Tn1696 backbone. Other key antibiotic resistance elements included Tn2, IS26–mph(A)–mrx–mphR(A)–IS6100 unit, chrA region, In27, and aacC2–tmrB region in the MDR region of p16005813A, and ΔTn9 carrying catA1, In609, and IS26–tetA(C)–tetR(C)–IS26 unit in the MDR region of p16005813C. This was the first report of coexistence of three different MDR plasmids, and that of occurrence of IMP-encoding plasmid and blaIMP–8 gene in L. adecarboxylata.
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Affiliation(s)
- Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qiaoxiang Cheng
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yanan Xu
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Wenhui Yang
- 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
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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30
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Dickinson AW, Power A, Hansen MG, Brandt KK, Piliposian G, Appleby P, O'Neill PA, Jones RT, Sierocinski P, Koskella B, Vos M. Heavy metal pollution and co-selection for antibiotic resistance: A microbial palaeontology approach. ENVIRONMENT INTERNATIONAL 2019; 132:105117. [PMID: 31473413 DOI: 10.1016/j.envint.2019.105117] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Frequent and persistent heavy metal pollution has profound effects on the composition and activity of microbial communities. Heavy metals select for metal resistance but can also co-select for resistance to antibiotics, which is a global health concern. We here document metal concentration, metal resistance and antibiotic resistance along a sediment archive from a pond in the North West of the United Kingdom covering over a century of anthropogenic pollution. We specifically focus on zinc, as it is a ubiquitous and toxic metal contaminant known to co-select for antibiotic resistance, to assess the impact of temporal variation in heavy metal pollution on microbial community diversity and to quantify the selection effects of differential heavy metal exposure on antibiotic resistance. Zinc concentration and bioavailability was found to vary over the core, likely reflecting increased industrialisation around the middle of the 20th century. Zinc concentration had a significant effect on bacterial community composition, as revealed by a positive correlation between the level of zinc tolerance in culturable bacteria and zinc concentration. The proportion of zinc resistant isolates was also positively correlated with resistance to three clinically relevant antibiotics (oxacillin, cefotaxime and trimethoprim). The abundance of the class 1 integron-integrase gene, intI1, marker for anthropogenic pollutants correlated with the prevalence of zinc- and cefotaxime resistance but not with oxacillin and trimethoprim resistance. Our microbial palaeontology approach reveals that metal-contaminated sediments from depths that pre-date the use of antibiotics were enriched in antibiotic resistant bacteria, demonstrating the pervasive effects of metal-antibiotic co-selection in the environment.
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Affiliation(s)
- A W Dickinson
- College of Life and Environmental Science, University of Exeter, Penryn, UK; UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
| | - A Power
- Biocatalysis Centre, University of Exeter, Exeter, UK
| | - M G Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - K K Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - G Piliposian
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | - P Appleby
- Department of Mathematical Sciences, University of Liverpool, Liverpool, UK
| | - P A O'Neill
- Welcome Trust Biomedical Informatics Hub, Geoffrey Pope Building, University of Exeter, Exeter, UK
| | - R T Jones
- School of Geography, College of Life and Environmental Sciences, University of Exeter, Amory Building, Rennes Drive, Exeter, UK
| | - P Sierocinski
- College of Life and Environmental Science, University of Exeter, Penryn, UK
| | - B Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - M Vos
- European Centre for Environment and Human Health, College of Medicine and Health, University of Exeter, Penryn, UK
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31
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Zhan Z, Hu L, Jiang X, Zeng L, Feng J, Wu W, Chen W, Yang H, Yang W, Gao B, Yin Z, Zhou D. Plasmid and chromosomal integration of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp. J Antimicrob Chemother 2019; 73:3005-3015. [PMID: 30351436 DOI: 10.1093/jac/dky288] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Objectives To provide detailed genetic characterization of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp. Methods P. aeruginosa 60512, K. pneumoniae 447, P. aeruginosa 12939 and Enterobacter sp. A1137 were subjected to genome sequencing. The complete nucleotide sequences of two plasmids (p60512-IMP from the 60512 isolate and p447-IMP from the 447 isolate) and two chromosomes (the 12939 and A1137 isolates) were determined, then a genomic comparison of p60512-IMP, p447-IMP and four novel blaIMP-carrying transposons (Tn6394, Tn6375, Tn6411 and Tn6397) with related sequences was performed. Transferability of the blaIMP gene and bacterial antimicrobial susceptibility were tested. Results Tn6394 and Tn6375 were located in p60512-IMP and p447-IMP, respectively, while Tn6411 and Tn6397 were integrated into the 12939 and A1137 chromosomes, respectively. Tn6394 was an ISPa17-based transposition unit that harboured the integron In992 (carrying blaIMP-1). In73 (carrying blaIMP-8), In73 and In992, together with the ISEcp1:IS1R-blaCTX-M-14-IS903D unit, the macAB-tolC region and the truncated aacC2-tmrB region, respectively, were integrated into the prototype transposons Tn1722, Tn1696 and Tn7, respectively, generating the Tn3-family unit transposons, Tn6375 and Tn6378, and the Tn7-family unit transposon Tn6411, respectively. Tn6397 was a large integrative and conjugative element carrying Tn6378. Conclusions Complex events of transposition and homologous recombination have occurred during the original formation and further plasmid and chromosomal integration of these four transposons, promoting accumulation and spread of antimicrobial resistance genes.
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Affiliation(s)
- Zhe Zhan
- Anhui Medical University, Hefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 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
| | - Lijun Zeng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Weili Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bo Gao
- 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
| | - Dongsheng Zhou
- Anhui Medical University, Hefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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32
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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33
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Dahanayake PS, Hossain S, Wickramanayake MVKS, Heo GJ. Antibiotic and heavy metal resistance genes in Aeromonas spp. isolated from marketed Manila Clam (Ruditapes philippinarum) in Korea. J Appl Microbiol 2019; 127:941-952. [PMID: 31211903 DOI: 10.1111/jam.14355] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 11/29/2022]
Abstract
AIMS Manila clam (Ruditapes philippinarum) is one of the most popular seafood in Korea, owing to their unique taste and nutritional value. This study aimed to disclose the antibiotic and heavy metal resistance characteristics of Aeromonas spp. isolated from marketed Manila clam in Korea. METHODS AND RESULTS A total of 36 Aeromonas spp. strains were isolated and subjected to two tests: an antibiotic disk diffusion test to determine their resistance to antibiotics, and a broth dilution test to determine their resistance to heavy metals. PCR-based amplification was performed to detect the resistance genes. A high level of resistance to ampicillin (100%) and cephalothin (89%) was observed, while 42, 39, 36 and 36% of the isolates were resistant to oxytetracycline, imipenem, nalidixic acid and tetracycline respectively. In addition, among the tested heavy metals, cadmium (Cd) recorded the highest resistance rate (61%), followed by chromium (Cr) (50%), lead (Pb) (47%) and copper (Cu) (37%). However, mercury (Hg) resistance was not observed. PCRs revealed the occurrence of blaTEM , blaSHV , blaCTX-M , qnrS, tetB, tetE, aac(6')-Ib, strA-strB and intI1 genes among 100, 31, 31, 78, 78, 89, 25, 50 and 72% of the isolates respectively. Moreover, heavy metal resistance genes, copA, merA and czcA were detected in 25, 47 and 61% of the isolates respectively. CONCLUSIONS The results suggest the importance of multi-drug and heavy metal-resistant aeromonads in Manila clam to assess the consumer safety and public health. SIGNIFICANCE AND IMPACT OF THE STUDY This study is the first to elaborate on the importance of multi-drug and heavy metal-resistant aeromonads in Manila clam. Particularly, the presence of extended-spectrum-β-lactamase genes and other antibiotic resistance genes intensifies the possible health risks and may complicate therapeutic treatments upon infection, while heavy metal resistance suggests possible heavy metal exposure.
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Affiliation(s)
- P S Dahanayake
- Veterinary Medical Center, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - S Hossain
- Veterinary Medical Center, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - M V K S Wickramanayake
- Veterinary Medical Center, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
| | - G-J Heo
- Veterinary Medical Center, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Korea
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34
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Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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35
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Zheng Z, Li R, Ye L, Wai-Chi Chan E, Xia X, Chen S. Genetic Characterization of bla CTX-M-55 -Bearing Plasmids Harbored by Food-Borne Cephalosporin-Resistant Vibrio parahaemolyticus Strains in China. Front Microbiol 2019; 10:1338. [PMID: 31275270 PMCID: PMC6591265 DOI: 10.3389/fmicb.2019.01338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 11/24/2022] Open
Abstract
This study aims to investigate and compare the complete nucleotide sequences of the multidrug resistance plasmids pVb0267 and pVb0499, which were recovered from foodborne Vibrio parahaemolyticus isolates, and analyze the genetic environment of blaCTX–M–55 to provide insight into the dissemination mechanisms of this resistance element. Analysis of the sequences of plasmids pVb0267 (166,467 bp) and pVb0499 (192,739 bp) revealed that the backbones of these two plasmids exhibited a high degree of similarity with pR148, a recognized type 1a IncC plasmid recovered from Aeromonas hydrophila (99% identity). The resistance genes, found in both plasmids, included qacH, aadB, arr2, blaOXA–10, aadA1, sul1, tet(A), and blaCTX–M–55, which were mostly arranged in a specific region designated ARI-A. Plasmid pVb0499 was found to possess a larger size of ARI-A than pVb0267, which lacked a mer determination region, a qnr A segment, an aacC3 gene and several mobility-encoding genes. Comparative analysis of resistance island (RI) of these plasmids and others revealed the potential evolution route of these RI sequences. In conclusion, plasmids harboring the blaCTX–M–55 gene has been recovered in Vibrio parahaemolyticus strains of food origin. It is alarming to find that IncC plasmids harboring resistance islands are disseminating in aquatic bacterial strains. The continuous evolution of resistance genes in conjugative plasmid in aquatic bacteria could be due to bacterial adaption to aquaculture environment, where antibiotics were increasingly used.
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Affiliation(s)
- Zhiwei Zheng
- College of Food Science and Engineering, Northwest A&F University, Yangling, China.,Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China
| | - Ruichao Li
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Lianwei Ye
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Xiaodong Xia
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Sheng Chen
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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36
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Jing Y, Jiang X, Yin Z, Hu L, Zhang Y, Yang W, Yang H, Gao B, Zhao Y, Zhou D, Wang C, Luo Y. Genomic diversification of IncR plasmids from China. J Glob Antimicrob Resist 2019; 19:358-364. [PMID: 31216492 DOI: 10.1016/j.jgar.2019.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/02/2019] [Accepted: 06/10/2019] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES The aim of this study was to perform a detailed genomic characterisation of IncR plasmids from China. METHODS Three IncR plasmids (p13190-tetA, p02085-tetA and p30860-tetA) from clinical isolates ofKlebsiella pneumoniae, Citrobacter freundii and Enterobacter cloacae, respectively, were fully sequenced using high-throughput genome sequencing and were compared with five previously sequenced IncR plasmids (pHN84KPC, pSH-01, pK245, pKPC_P16 and pKPC-LK30) from China. RESULTS The eight IncR plasmids from China possessed conserved IncR backbones composed of repB, parAB, umuCD, retA and resD. Resistance accessory modules integrated into the IncR backbones included multidrug resistance (MDR) regions in p30860-tetA, p02085-tetA, p13190-tetA and pK245, blaKPC-2 regions in pHN84KPC, pKPC-LK30 and pKPC_P16, and the ΔTn1721-sil region in pSH-01. These resistance accessory modules were inserted at a site between retA and vagD, resulting in loss of the backbone genes vagCD in some of the plasmids. The resistance accessory modules differed dramatically from one another and carried distinct profiles of resistance markers. In particular, all of p13190-tetA, p02085-tetA, p30860-tetA, pHN84KPC, pSH-01 and pK245 carried tetracycline resistance tet gene modules, and the carbapenemase gene blaKPC-2 was identified in pHN84KPC, pKPC-LK30 and pKPC_P16. In addition, one or more regions responsible for plasmid replication and/or maintenance were found in some of the resistance accessory modules, facilitating stable replication of corresponding IncR plasmids at steady-state copy numbers. CONCLUSIONS This detailed comparative genomics analysis of IncR plasmids from China provides a deeper insight into the diversification and evolution of IncR plasmids.
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Affiliation(s)
- Ying Jing
- Medical Laboratory Center, General Hospital of People's Liberation Army, Beijing 100085, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China.
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Ying Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Chengbin Wang
- Medical Laboratory Center, General Hospital of People's Liberation Army, Beijing 100085, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, China.
| | - Yanping Luo
- Medical Laboratory Center, General Hospital of People's Liberation Army, Beijing 100085, China.
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Partridge SR, Tsafnat G. Automated annotation of mobile antibiotic resistance in Gram-negative bacteria: the Multiple Antibiotic Resistance Annotator (MARA) and database. J Antimicrob Chemother 2019; 73:883-890. [PMID: 29373760 DOI: 10.1093/jac/dkx513] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/08/2017] [Indexed: 01/26/2023] Open
Abstract
Background Multiresistance in Gram-negative bacteria is often due to acquisition of several different antibiotic resistance genes, each associated with a different mobile genetic element, that tend to cluster together in complex conglomerations. Accurate, consistent annotation of resistance genes, the boundaries and fragments of mobile elements, and signatures of insertion, such as DR, facilitates comparative analysis of complex multiresistance regions and plasmids to better understand their evolution and how resistance genes spread. Objectives To extend the Repository of Antibiotic resistance Cassettes (RAC) web site, which includes a database of 'features', and the Attacca automatic DNA annotation system, to encompass additional resistance genes and all types of associated mobile elements. Methods Antibiotic resistance genes and mobile elements were added to RAC, from existing registries where possible. Attacca grammars were extended to accommodate the expanded database, to allow overlapping features to be annotated and to identify and annotate features such as composite transposons and DR. Results The Multiple Antibiotic Resistance Annotator (MARA) database includes antibiotic resistance genes and selected mobile elements from Gram-negative bacteria, distinguishing important variants. Sequences can be submitted to the MARA web site for annotation. A list of positions and orientations of annotated features, indicating those that are truncated, DR and potential composite transposons is provided for each sequence, as well as a diagram showing annotated features approximately to scale. Conclusions The MARA web site (http://mara.spokade.com) provides a comprehensive database for mobile antibiotic resistance in Gram-negative bacteria and accurately annotates resistance genes and associated mobile elements in submitted sequences to facilitate comparative analysis.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital, Sydney, Australia
| | - Guy Tsafnat
- Centre for Health Informatics, Australian Institute of Health Innovation, Macquarie University, Sydney, Australia.,Spokade Pty Ltd, Sydney, Australia
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Liu Y, Zhang H, Zhang X, Jiang N, Zhang Z, Zhang J, Zhu B, Wang G, Zhao K, Zhou Y. Characterization of an NDM-19-producing Klebsiella pneumoniae strain harboring 2 resistance plasmids from China. Diagn Microbiol Infect Dis 2019; 93:355-361. [DOI: 10.1016/j.diagmicrobio.2018.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023]
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Liang Q, Jiang X, Hu L, Yin Z, Gao B, Zhao Y, Yang W, Yang H, Tong Y, Li W, Jiang L, Zhou D. Sequencing and Genomic Diversity Analysis of IncHI5 Plasmids. Front Microbiol 2019; 9:3318. [PMID: 30692976 PMCID: PMC6339943 DOI: 10.3389/fmicb.2018.03318] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/20/2018] [Indexed: 12/05/2022] Open
Abstract
IncHI plasmids could be divided into five different subgroups IncHI1–5. In this study, the complete nucleotide sequences of seven blaIMP- or blaVIM-carrying IncHI5 plasmids from Klebsiella pneumoniae, K. quasipneumoniae, and K. variicola were determined and compared in detail with all the other four available sequenced IncHI5 plasmids. These plasmids carried conserved IncHI5 backbones composed of repHI5B and a repFIB-like gene (replication), parABC (partition), and tra1 (conjugal transfer). Integration of a number of accessory modules, through horizontal gene transfer, at various sites of IncHI5 backbones resulted in various deletions of surrounding backbone regions and thus considerable diversification of IncHI5 backbones. Among the accessory modules were three kinds of resistance accessory modules, namely Tn10 and two antibiotic resistance islands designated ARI-A and ARI-B. These two islands, inserted at two different fixed sites (one island was at one site and the other was at a different site) of IncHI5 backbones, were derived from the prototype Tn3-family transposons Tn1696 and Tn6535, respectively, and could be further discriminated as various intact transposons and transposon-like structures. The ARI-A or ARI-B islands from different IncHI5 plasmids carried distinct profiles of antimicrobial resistance markers and associated mobile elements, and complex events of transposition and homologous recombination accounted for assembly of these islands. The carbapenemase genes blaIMP-4, blaIMP-38 and blaVIM-1 were identified within various class 1 integrons from ARI-A or ARI-B of the seven plasmids sequenced in this study. Data presented here would provide a deeper insight into diversification and evolution history of IncHI5 plasmids.
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Affiliation(s)
- Quanhui Liang
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Clinical Laboratory, The First People's Hospital of Foshan, Foshan, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- 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
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Weixuan Li
- Department of Clinical Laboratory, The First People's Hospital of Foshan, Foshan, China
| | - Lingxiao Jiang
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Hamidian M, Hall RM. The AbaR antibiotic resistance islands found in Acinetobacter baumannii global clone 1 - Structure, origin and evolution. Drug Resist Updat 2018; 41:26-39. [PMID: 30472242 DOI: 10.1016/j.drup.2018.10.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/15/2018] [Accepted: 10/30/2018] [Indexed: 11/28/2022]
Abstract
In multiply resistant Acinetobacter baumannii, complex transposons located in the chromosomal comM gene carry antibiotic and heavy metal resistance determinants. For one type, known collectively as AbaR, the ancestral form, AbaR0, entered a member of global clone 1 (GC1) in the mid 1970s and continued to evolve in situ forming many variants. In AbaR0, antibiotic and mercuric ion resistance genes are located between copies of a cadmium-zinc resistance transposon, Tn6018, and this composite transposon is in a class III transposon, Tn6019, carrying arsenate/arsenite resistance genes and five tni transposition genes. The antibiotic resistance genes in the AbaR0 and derived AbaR3 configurations are aphA1b, blaTEM, catA1, sul1, tetA(A), and cassette-associated aacC1 and aadA1 genes. These genes are in a specific arrangement of fragments from well-known transposons, e.g. Tn1, Tn1721, Tn1696 and Tn2670, that arose in an IncM1 plasmid. All known GC1 lineage 1 isolates carry AbaR0 or AbaR3, which arose around 1990, or a variant derived from one of them. Variants arose via deletions caused by one of three internal IS26s, by recombination between duplicate copies of sul1 or Tn6018, or by gene cassette addition or replacement. A few GC2 isolates also carry an AbaR island with different cassette-associated genes, aacA4 and oxa20.
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Affiliation(s)
- Mohammad Hamidian
- School of Molecular and Microbial Biosciences, The University of Sydney, NSW 2006, Australia; The ithree institute, University of Technology Sydney, Ultimo 2007, NSW, Australia
| | - Ruth M Hall
- School of Molecular and Microbial Biosciences, The University of Sydney, NSW 2006, Australia.
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1101] [Impact Index Per Article: 183.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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Wiggins AG, LaVoie SP, Wireman J, Summers AO. Thinking outside the (pill) box: Does toxic metal exposure thwart antibiotic stewardship best practices? Plasmid 2018; 99:68-71. [DOI: 10.1016/j.plasmid.2018.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 01/03/2023]
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Babakhani S, Oloomi M. Transposons: the agents of antibiotic resistance in bacteria. J Basic Microbiol 2018; 58:905-917. [PMID: 30113080 DOI: 10.1002/jobm.201800204] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/08/2018] [Accepted: 07/31/2018] [Indexed: 12/29/2022]
Abstract
Transposons are a group of mobile genetic elements that are defined as a DNA sequence. Transposons can jump into different places of the genome; for this reason, they are called jumping genes. However, some transposons are always kept at the insertion site in the genome. Most transposons are inactivated and as a result, cannot move. Transposons are divided into two main groups: retrotransposons (class І) and DNA transposons (class ІІ). Retrotransposons are often found in eukaryotes. DNA transposons can be found in both eukaryotes and prokaryotes. The bacterial transposons belong to the DNA transposons and the Tn family, which are usually the carrier of additional genes for antibiotic resistance. Transposons can transfer from a plasmid to other plasmids or from a DNA chromosome to plasmid and vice versa that cause the transmission of antibiotic resistance genes in bacteria. The treatment of bacterial infectious diseases is difficult because of existing antibiotic resistance that part of this antibiotic resistance is caused by transposons. Bacterial infectious diseases are responsible for the increasing rise in world mortality rate. In this review, transposons and their roles have been studied in bacterial antibiotic resistance, in detail.
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Affiliation(s)
- Sajad Babakhani
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mana Oloomi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
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Mindlin SZ, Petrova MA. On the Origin and Distribution of Antibiotic Resistance: Permafrost Bacteria Studies. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2018. [DOI: 10.3103/s0891416817040048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Botelho J, Grosso F, Quinteira S, Mabrouk A, Peixe L. The complete nucleotide sequence of an IncP-2 megaplasmid unveils a mosaic architecture comprising a putative novel blaVIM-2-harbouring transposon in Pseudomonas aeruginosa. J Antimicrob Chemother 2018; 72:2225-2229. [PMID: 28505370 DOI: 10.1093/jac/dkx143] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/19/2017] [Indexed: 01/01/2023] Open
Abstract
Objectives In Pseudomonas aeruginosa , bla VIM-2 has been mostly associated with a chromosomal location and rarely with a plasmid backbone. Until now, only three complete bla VIM-2 -carrying plasmid sequences have been described in this species. Here we explore the modular structure of pJB37, the first bla VIM-2 -carrying megaplasmid described in P. aeruginosa . Methods The complete nucleotide sequence of plasmid pJB37 was determined with an Illumina HiSeq, with de novo assembly by SPAdes, annotation by RAST and searching for antimicrobial resistance genes and virulence factors. Conjugation assays were conducted. Results Megaplasmid pJB37 (464 804 bp long and GC content of 57.2%) comprised: an IncP-2 repA-oriV-parAB region; a conjugative transfer region ( traF , traG , virD2 and trbBCDEJLFGI genes); Tn 6356 , a new putative bla VIM-2 -carrying transposon; heavy metal (mercury and tellurite) resistance operons; and an arsenal of virulence genes. Plasmid pJB37 was transferable by conjugation to a spontaneous rifampicin-resistant mutant of P. aeruginosa PAO1. Here, a bla VIM-2 -harbouring In58 integron was associated with a new complex transposable structure, herein named Tn 6356 , suggesting that In58 was most likely acquired by insertion of this element. Conclusions The mosaic arrangement exhibited by the pJB37 IncP-2 megaplasmid, which highlights the vast assembly potential of distinct genetic elements in a Pseudomonas widespread plasmid platform, gives new insights into bacterial adaptation and evolution.
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Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Sandra Quinteira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO/UP)/InBio Laboratório Associado, Vairão, Portugal.,Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Porto, Portugal.,CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
| | - Aymen Mabrouk
- Laboratories UR12ES02 - The National Bone Marrow Transplant Centre, Tunis, Tunisia.,University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisia
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Ma L, Yin Z, Zhang D, Zhan Z, Wang Q, Duan X, Gao H, Liang Q, Zhao Y, Feng J, Zhao Y, Tong Y, Dai E, Zhou D. Comparative genomics of type 1 IncC plasmids from China. Future Microbiol 2017; 12:1511-1522. [PMID: 29140102 DOI: 10.2217/fmb-2017-0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study dealt with genomic characterization of type 1 IncC resistance plasmids, capable of spreading across taxonomic borders, from China. Materials & methods: p112298-tetA was sequenced and compared with type 1 IncC reference plasmid pR148 and two available sequenced type 1 IncC plasmids pHS36-NDM and pVAS3-1 from China. Results: These plasmids contained one or more exogenous resistance islands, which included the ARI-A islands, the ARI-B islands, the ISEcp1-blaCMY units and the bla KPC-2 region and were inserted at various sites in the IncC backbone and thus represented three distinct lineages. Conclusion: Complex rearrangement and homologous recombination events have occurred during evolution of p112298-tetA, making it significantly differ modularly from the other three plasmids with respect to both plasmid backbone and exogenous resistance regions.
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Affiliation(s)
- Lizhi Ma
- Department of Emergency Medicine, General Hospital of Chinese People's Armed Police Forces, Beijing 100039, China
| | - Zhe Yin
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Defu Zhang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Zhe Zhan
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Qian Wang
- Department of Emergency Medicine, General Hospital of Chinese People's Armed Police Forces, Beijing 100039, China
| | - Xiongbo Duan
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Quanhui Liang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yuzong Zhao
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Jiao Feng
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yachao Zhao
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
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Shi L, Liang Q, Zhan Z, Feng J, Zhao Y, Chen Y, Huang M, Tong Y, Wu W, Chen W, Li X, Yin Z, Wang J, Zhou D. Co-occurrence of 3 different resistance plasmids in a multi-drug resistant Cronobacter sakazakii isolate causing neonatal infections. Virulence 2017; 9:110-120. [PMID: 28771073 PMCID: PMC5955447 DOI: 10.1080/21505594.2017.1356537] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Cronobacter sakazakii 505108 was isolated from a sputum specimen of a neonate with severe pneumonia. C. sakazakii 505108 co-harbors 3 resistance plasmids of the IncHI2, IncX3, and IncFIB incomparability groups, respectively. These 3 plasmids have acquired several accessory modules, which carry an extremely large number of resistance genes, especially including those involved in resistance to carbapenems, aminoglycoside, tetracyclines, and phenicols and sulphonamide/trimethoprim. These plasmid-borne antibiotic resistance genes were associated with insertion sequences, integrons, and transposons, indicating that the assembly and mobilization of the corresponding accessory modules with complex chimera structures are facilitated by transposition and/or homologous recombination. This is the first report of fully sequence plasmids in clinical Cronobacter, which provides a deeper insight into plasmid-mediated multi-drug resistance in Cronobacter from hospital settings.
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Affiliation(s)
- Lining Shi
- a Institute of Medical Laboratory Sciences, Jinling Hospital, School of Medicine, Nanjing University , Nanjing , China
| | - Quanhui Liang
- b Department of Clinical Laboratory , The First People's Hospital of Foshan , Foshan , China
| | - Zhe Zhan
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Jiao Feng
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Yachao Zhao
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Yong Chen
- a Institute of Medical Laboratory Sciences, Jinling Hospital, School of Medicine, Nanjing University , Nanjing , China
| | - Mei Huang
- a Institute of Medical Laboratory Sciences, Jinling Hospital, School of Medicine, Nanjing University , Nanjing , China
| | - Yigang Tong
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Weili Wu
- d Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , China
| | - Weijun Chen
- d Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , China
| | - Xiaojun Li
- a Institute of Medical Laboratory Sciences, Jinling Hospital, School of Medicine, Nanjing University , Nanjing , China
| | - Zhe Yin
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Jinglin Wang
- b Department of Clinical Laboratory , The First People's Hospital of Foshan , Foshan , China
| | - Dongsheng Zhou
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing , China
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Genomic characterization of novel IncFII-type multidrug resistant plasmids p0716-KPC and p12181-KPC from Klebsiella pneumoniae. Sci Rep 2017; 7:5830. [PMID: 28725038 PMCID: PMC5517477 DOI: 10.1038/s41598-017-06283-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022] Open
Abstract
This study aimed to genetically characterize two fully-sequenced novel IncFII-type multidrug resistant (MDR) plasmids, p0716-KPC and p12181-KPC, recovered from two different clinical Klebsiella pneumoniae isolates. p0716-KPC and p12181-KPC had a very similar genomic content. The backbones of p0716-KPC/p12181-KPC contained two different replicons (belonging to a novel IncFII subtype and the Rep_3 family), the IncFIIK and IncFIIY maintenance regions, and conjugal transfer gene sets from IncFIIK-type plasmids and unknown origins. p0716-KPC and p12181-KPC carried similar three accessory resistance regions, namely ΔTn6209, a MDR region, and the blaKPC-2 region. Resistance genes blaKPC-2, mph(A), strAB, aacC2, qacEΔ1, sul1, sul2, and dfrA25, which are associated with transposons, integrons, and insertion sequence-based mobile units, were located in these accessory regions. p0716-KPC carried two additional resistance genes: aphA1a and blaTEM-1. Together, our analyses showed that p0716-KPC and p12181-KPC belong to a novel IncFII subtype and display a complex chimeric nature, and that the carbapenem resistance gene blaKPC-2 coexists with a lot of additional resistance genes on these two plasmids.
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Presence of VIM-Positive Pseudomonas Species in Chickens and Their Surrounding Environment. Antimicrob Agents Chemother 2017; 61:AAC.00167-17. [PMID: 28438943 DOI: 10.1128/aac.00167-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/14/2017] [Indexed: 12/19/2022] Open
Abstract
Metallo-β-lactamase gene blaVIM was identified on the chromosome of four Pseudomonas sp. isolates from a chicken farm, including one Pseudomonas aeruginosa isolate from a swallow (Yanornis martini), one Pseudomonas putida isolate from a fly, and two P. putida isolates from chickens. The four isolates shared two variants of blaVIM-carrying genomic contexts that resemble the corresponding regions of clinical metallo-β-lactamase-producing Pseudomonas spp. Our study suggests that the surveillance of carbapenemase-producing bacteria in livestock and their surrounding environment is urgently needed.
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Liang Q, Yin Z, Zhao Y, Liang L, Feng J, Zhan Z, Wang H, Song Y, Tong Y, Wu W, Chen W, Wang J, Jiang L, Zhou D. Sequencing and comparative genomics analysis of the IncHI2 plasmids pT5282-mphA and p112298-catA and the IncHI5 plasmid pYNKP001-dfrA. Int J Antimicrob Agents 2017; 49:709-718. [DOI: 10.1016/j.ijantimicag.2017.01.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/09/2016] [Accepted: 01/22/2017] [Indexed: 01/16/2023]
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