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Zhang Z, Kuang D, Xu X, Zhan Z, Ren H, Shi C. Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China. Int J Food Microbiol 2024; 417:110708. [PMID: 38653121 DOI: 10.1016/j.ijfoodmicro.2024.110708] [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: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024]
Abstract
Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.
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Affiliation(s)
- Zengfeng Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dai Kuang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; National Health Commission (NHC) Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, China
| | - Xuebin Xu
- Laboratory of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200050, China
| | - Zeqiang Zhan
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Ren
- Xianyang Center for Food and Drug Control, Shaanxi, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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Saha M, Pragasam AK, Kumari S, Verma J, Das B, Bhadra RK. Genomic and functional insights into antibiotic resistance genes floR and strA linked with the SXT element of Vibrio cholerae non-O1/non-O139. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001424. [PMID: 38180462 PMCID: PMC10866021 DOI: 10.1099/mic.0.001424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024]
Abstract
The emergence and spread of antibiotic-resistant bacterial pathogens are a critical public health concern across the globe. Mobile genetic elements (MGEs) play an important role in the horizontal acquisition of antimicrobial resistance genes (ARGs) in bacteria. In this study, we have decoded the whole genome sequences of multidrug-resistant Vibrio cholerae clinical isolates carrying the ARG-linked SXT, an integrative and conjugative element, in their large chromosomes. As in others, the SXT element has been found integrated into the 5'-end of the prfC gene (which encodes peptide chain release factor 3 involved in translational regulation) on the large chromosome of V. cholerae non-O1/non-O139 strains. Further, we demonstrate the functionality of SXT-linked floR and strAB genes, which confer resistance to chloramphenicol and streptomycin, respectively. The floR gene-encoded protein FloR belongs to the major facilitator superfamily efflux transporter containing 12 transmembrane domains (TMDs). Deletion analysis confirmed that even a single TMD of FloR is critical for the export function of chloramphenicol. The floR gene has two putative promoters, P1 and P2. Sequential deletions reveal that P2 is responsible for the expression of the floR. Deletion analysis of the N- and/or C-terminal coding regions of strA established their importance for conferring resistance against streptomycin. Interestingly, qPCR analysis of the floR and strA genes indicated that both of the genes are constitutively expressed in V. cholerae cells. Further, whole genome-based global phylogeography confirmed the presence of the integrative and conjugative element SXT in non-O1/non-O139 strains despite being non-multidrug resistant by lacking antimicrobial resistance (AMR) gene cassettes, which needs monitoring.
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Affiliation(s)
- Mousumi Saha
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology (CSIR), Kolkata-700032, India
| | - Agila Kumari Pragasam
- Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Shashi Kumari
- Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Jyoti Verma
- Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Bhabatosh Das
- Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Rupak K. Bhadra
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology (CSIR), Kolkata-700032, India
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Mevada V, Patel R, Dudhagara P, Chaudhari R, Vohra M, Khan V, J. H. Shyu D, Chen YY, Zala D. Whole Genome Sequencing and Pan-Genomic Analysis of Multidrug-Resistant Vibrio cholerae VC01 Isolated from a Clinical Sample. Microorganisms 2023; 11:2030. [PMID: 37630590 PMCID: PMC10457874 DOI: 10.3390/microorganisms11082030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Cholera, a disease caused by the Vibrio cholerae bacteria, threatens public health worldwide. The organism mentioned above has a significant historical record of being identified as a prominent aquatic environmental pollutant capable of adapting its phenotypic and genotypic traits to react to host patients effectively. This study aims to elucidate the heterogeneity of the sporadic clinical strain of V. cholerae VC01 among patients residing in Silvasa. The study involved conducting whole-genome sequencing of the isolate obtained from patients exhibiting symptoms, including those not commonly observed in clinical practice. The strain was initially identified through a combination of biochemical analysis, microscopy, and 16s rRNA-based identification, followed by type strain-based identification. The investigation demonstrated the existence of various genetic alterations and resistance profiles against multiple drugs, particularly chloramphenicol (catB9), florfenicol (floR), oxytetracycline (tet(34)), sulfonamide (sul2), and Trimethoprim (dfrA1). The pan-genomic analysis indicated that 1099 distinct clusters were detected within the genome sequences of recent isolates worldwide. The present study helps to establish a correlation between the mutation and the coexistence of antimicrobial resistance toward current treatment.
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Affiliation(s)
- Vishal Mevada
- DNA Division, Directorate of Forensic Science, Gandhinagar 382007, India;
| | - Rajesh Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India;
| | - Pravin Dudhagara
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India;
| | - Rajesh Chaudhari
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad 382424, India;
| | - Mustafa Vohra
- Directorate of Medical & Health Services, UT of Dadra & Nagar Haveli and Daman & Diu, Silvassa 396230, India; (M.V.); (V.K.)
| | - Vikram Khan
- Directorate of Medical & Health Services, UT of Dadra & Nagar Haveli and Daman & Diu, Silvassa 396230, India; (M.V.); (V.K.)
| | - Douglas J. H. Shyu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan;
| | - Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi City 600, Taiwan;
| | - Dolatsinh Zala
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad 382424, India;
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Pons MC, Praud K, Da Re S, Cloeckaert A, Doublet B. Conjugative IncC Plasmid Entry Triggers the SOS Response and Promotes Effective Transfer of the Integrative Antibiotic Resistance Element SGI1. Microbiol Spectr 2023; 11:e0220122. [PMID: 36472437 PMCID: PMC9927553 DOI: 10.1128/spectrum.02201-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
The broad-host-range IncC plasmid family and the integrative mobilizable Salmonella genomic island 1 (SGI1) and its derivatives enable the spread of medically important antibiotic resistance genes among Gram-negative pathogens. Although several aspects of the complex functional interactions between IncC plasmids and SGI1 have been recently deciphered regarding their conjugative transfer and incompatibility, the biological signal resulting in the hijacking of the conjugative plasmid by the integrative mobilizable element remains unknown. Here, we demonstrate that the conjugative entry of IncC/IncA plasmids is detected at an early stage by SGI1 through the transient activation of the SOS response, which induces the expression of the SGI1 master activators SgaDC, shown to play a crucial role in the complex biology between SGI1 and IncC plasmids. Besides, we developed an original tripartite conjugation approach to directly monitor SGI1 mobilization in a time-dependent manner following conjugative entry of IncC plasmids. Finally, we propose an updated biological model of the conjugative mobilization of the chromosomal resistance element SGI1 by IncC plasmids. IMPORTANCE Antimicrobial resistance has become a major public health issue, particularly with the increase of multidrug resistance (MDR) in both animal and human pathogenic bacteria and with the emergence of resistance to medically important antibiotics. The spread between bacteria of successful mobile genetic elements, such as conjugative plasmids and integrative elements conferring multidrug resistance, is the main driving force in the dissemination of acquired antibiotic resistances among Gram-negative bacteria. Broad-host-range IncC plasmids and their integrative mobilizable SGI1 counterparts contribute to the spread of critically important resistance genes (e.g., extended-spectrum β-lactamases [ESBLs] and carbapenemases). A better knowledge of the complex biology of these broad-host-range mobile elements will help us to understand the dissemination of antimicrobial resistance genes that occurred across Gammaproteobacteria borders.
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Affiliation(s)
| | - Karine Praud
- INRAE, Université de Tours, ISP, Nouzilly, France
| | - Sandra Da Re
- INSERM, Université de Limoges, CHU de Limoges, RESINFIT, Limoges, France
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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Luo Y, Ye J, Payne M, Hu D, Jiang J, Lan R. Genomic Epidemiology of Vibrio cholerae O139, Zhejiang Province, China, 1994-2018. Emerg Infect Dis 2022; 28:2253-2260. [PMID: 36285907 PMCID: PMC9622232 DOI: 10.3201/eid2811.212066] [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] [Indexed: 08/30/2023] Open
Abstract
Cholera caused by Vibrio cholerae O139 was first reported in Bangladesh and India in 1992. To determine the genomic epidemiology and origins of O139 in China, we sequenced 104 O139 isolates collected from Zhejiang Province, China, during 1994-2018 and compared them with 57 O139 genomes from other countries in Asia. Most Zhejiang isolates fell into 3 clusters (C1-C3), which probably originated in India (C1) and Thailand (C2 and C3) during the early 1990s. Different clusters harbored different antimicrobial resistance genes and IncA/C plasmids. The integrative and conjugative elements carried by Zhejiang isolates were of a new type, differing from ICEVchInd4 and SXTMO10 by single-nucleotide polymorphisms and presence of genes. Quinolone resistance-conferring mutations S85L in parC and S83I in gyrA occurred in 71.2% of the Zhejiang isolates. The ctxB copy number differed among the 3 clusters. Our findings provided new insights for prevention and control of O139 cholera .
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Affiliation(s)
- Yun Luo
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China (Y. Luo, J. Ye, J. Jiang)
- University of New South Wales, Sydney, New South Wales, Australia (Y. Luo, M. Payne, D. Hu, R. Lan)
- Key Laboratory of Vaccine, Hangzhou (J. Jiang)
| | - Julian Ye
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China (Y. Luo, J. Ye, J. Jiang)
- University of New South Wales, Sydney, New South Wales, Australia (Y. Luo, M. Payne, D. Hu, R. Lan)
- Key Laboratory of Vaccine, Hangzhou (J. Jiang)
| | - Michael Payne
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China (Y. Luo, J. Ye, J. Jiang)
- University of New South Wales, Sydney, New South Wales, Australia (Y. Luo, M. Payne, D. Hu, R. Lan)
- Key Laboratory of Vaccine, Hangzhou (J. Jiang)
| | - Dalong Hu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China (Y. Luo, J. Ye, J. Jiang)
- University of New South Wales, Sydney, New South Wales, Australia (Y. Luo, M. Payne, D. Hu, R. Lan)
- Key Laboratory of Vaccine, Hangzhou (J. Jiang)
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Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis. PLoS One 2022; 17:e0271627. [PMID: 35917316 PMCID: PMC9345347 DOI: 10.1371/journal.pone.0271627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
The exchange of antimicrobial resistance (AMR) genes between aquaculture and terrestrial microbial populations has emerged as a serious public health concern. However, the nature of the mobile genetic elements in marine bacteria is poorly documented. To gain insight into the genetic mechanisms underlying AMR gene transfer from marine bacteria, we mated a multidrug-resistant Vibrio alfacsensis strain with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains. Sequence analysis revealed a conjugative multidrug resistance plasmid in the donor strain, which was integrated into the chromosome of the recipient. The plasmid backbone in the transconjugant chromosome was flanked by two copies of a 7.1 kb unclassifiable integrative element harboring a β-lactamase gene. The 7.1 kb element and the previously reported element Tn6283 share four coding sequences, two of which encode the catalytic R-H-R-Y motif of tyrosine recombinases. Polymerase chain reaction and sequencing experiments revealed that these elements generate a circular copy of one specific strand without leaving an empty site on the donor molecule, in contrast to the movement of integron gene cassettes or ICE/IMEs discovered to date. These elements are termed SEs (strand-biased circularizing integrative elements): SE-6945 (the 7.1 kb element) and SE-6283 (Tn6283). The copy number and location of SE-6945 in the chromosome affected the antibiotic resistance levels of the transconjugants. SEs were identified in the genomes of other Vibrio species. Overall, these results suggest that SEs are involved in the spread of AMR genes among marine bacteria.
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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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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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Bioinformatic and experimental characterization of SEN1998: a conserved gene carried by the Enterobacteriaceae-associated ROD21-like family of genomic islands. Sci Rep 2022; 12:2435. [PMID: 35165310 PMCID: PMC8844411 DOI: 10.1038/s41598-022-06183-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Genomic islands (GIs) are horizontally transferred elements that shape bacterial genomes and contributes to the adaptation to different environments. Some GIs encode an integrase and a recombination directionality factor (RDF), which are the molecular GI-encoded machinery that promotes the island excision from the chromosome, the first step for the spread of GIs by horizontal transfer. Although less studied, this process can also play a role in the virulence of bacterial pathogens. While the excision of GIs is thought to be similar to that observed in bacteriophages, this mechanism has been only studied in a few families of islands. Here, we aimed to gain a better understanding of the factors involved in the excision of ROD21 a pathogenicity island of the food-borne pathogen Salmonella enterica serovar Enteritidis and the most studied member of the recently described Enterobacteriaceae-associated ROD21-like family of GIs. Using bioinformatic and experimental approaches, we characterized the conserved gene SEN1998, showing that it encodes a protein with the features of an RDF that binds to the regulatory regions involved in the excision of ROD21. While deletion or overexpression of SEN1998 did not alter the expression of the integrase-encoding gene SEN1970, a slight but significant trend was observed in the excision of the island. Surprisingly, we found that the expression of both genes, SEN1998 and SEN1970, were negatively correlated to the excision of ROD21 which showed a growth phase-dependent pattern. Our findings contribute to the growing body of knowledge regarding the excision of GIs, providing insights about ROD21 and the recently described EARL family of genomic islands.
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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: 66] [Impact Index Per Article: 22.0] [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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Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Wood AJ, Paterson S, Brockhurst MA. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19:e3001225. [PMID: 34644303 PMCID: PMC8544851 DOI: 10.1371/journal.pbio.3001225] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/25/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.
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Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C. T. Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Katie J. Muddiman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - A. Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Steve Paterson
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Michael A. Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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Durand R, Deschênes F, Burrus V. Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids. PLoS Genet 2021; 17:e1009669. [PMID: 34415925 PMCID: PMC8409611 DOI: 10.1371/journal.pgen.1009669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/01/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella Genomic Island 1 (SGI1) and its variants are significant contributors to the spread of antibiotic resistance among Gammaproteobacteria. All known SGI1 variants integrate at the 3’ end of trmE, a gene coding for a tRNA modification enzyme. SGI1 variants are mobilized specifically by conjugative plasmids of the incompatibility groups A and C (IncA and IncC). Using a comparative genomics approach based on genes conserved among members of the SGI1 group, we identified diverse integrative elements distantly related to SGI1 in several species of Vibrio, Aeromonas, Salmonella, Pokkaliibacter, and Escherichia. Unlike SGI1, these elements target two alternative chromosomal loci, the 5’ end of dusA and the 3’ end of yicC. Although they share many features with SGI1, they lack antibiotic resistance genes and carry alternative integration/excision modules. Functional characterization of IMEVchUSA3, a dusA-specific integrative element, revealed promoters that respond to AcaCD, the master activator of IncC plasmid transfer genes. Quantitative PCR and mating assays confirmed that IMEVchUSA3 excises from the chromosome and is mobilized by an IncC helper plasmid from Vibrio cholerae to Escherichia coli. IMEVchUSA3 encodes the AcaC homolog SgaC that associates with AcaD to form a hybrid activator complex AcaD/SgaC essential for its excision and mobilization. We identified the dusA-specific recombination directionality factor RdfN required for the integrase-mediated excision of dusA-specific elements from the chromosome. Like xis in SGI1, rdfN is under the control of an AcaCD-responsive promoter. Although the integration of IMEVchUSA3 disrupts dusA, it provides a new promoter sequence and restores the reading frame of dusA for proper expression of the tRNA-dihydrouridine synthase A. Phylogenetic analysis of the conserved proteins encoded by SGI1-like elements targeting dusA, yicC, and trmE gives a fresh perspective on the possible origin of SGI1 and its variants. We identified integrative elements distantly related to Salmonella Genomic Island 1 (SGI1), a key vector of antibiotic resistance genes in Gammaproteobacteria. SGI1 and its variants reside at the 3’ end of trmE, share a large, highly conserved core of genes, and carry a complex integron that confers multidrug resistance phenotypes to their hosts. Unlike members of the SGI1 group, these novel genomic islands target the 5’ end dusA or the 3’ end of yicC, lack multidrug resistance genes, and seem much more diverse. We showed here that, like SGI1, these elements are mobilized by conjugative plasmids of the IncC group. Based on comparative genomics and functional analyses, we propose a hypothetical model of the evolution of SGI1 and its siblings from the progenitor of IncA and IncC conjugative plasmids via an intermediate dusA-specific integrative element through gene losses and gain of alternative integration/excision modules.
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Affiliation(s)
- Romain Durand
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Florence Deschênes
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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Durand R, Huguet KT, Rivard N, Carraro N, Rodrigue S, Burrus V. Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids. Nucleic Acids Res 2021; 49:7807-7824. [PMID: 33834206 PMCID: PMC8373056 DOI: 10.1093/nar/gkab204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/26/2022] Open
Abstract
IncC conjugative plasmids and the multiple variants of Salmonella Genomic Island 1 (SGI1) are two functionally interacting families of mobile genetic elements commonly associated with multidrug resistance in the Gammaproteobacteria. SGI1 and its siblings are specifically mobilised in trans by IncC conjugative plasmids. Conjugative transfer of IncC plasmids is activated by the plasmid-encoded master activator AcaCD. SGI1 carries five AcaCD-responsive promoters that drive the expression of genes involved in its excision, replication, and mobilisation. SGI1 encodes an AcaCD homologue, the transcriptional activator complex SgaCD (also known as FlhDCSGI1) that seems to recognise and activate the same SGI1 promoters. Here, we investigated the relevance of SgaCD in SGI1's lifecycle. Mating assays revealed the requirement for SgaCD and its IncC-encoded counterpart AcaCD in the mobilisation of SGI1. An integrative approach combining ChIP-exo, Cappable-seq, and RNA-seq confirmed that SgaCD activates each of the 18 AcaCD-responsive promoters driving the expression of the plasmid transfer functions. A comprehensive analysis of the activity of the complete set of AcaCD-responsive promoters of SGI1 and the helper IncC plasmid was performed through reporter assays. qPCR and flow cytometry assays revealed that SgaCD is essential to elicit the excision and replication of SGI1 and destabilise the helper IncC plasmid.
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Affiliation(s)
- Romain Durand
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Kévin T Huguet
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Nicolas Rivard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Nicolas Carraro
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Vincent Burrus
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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De R. Mobile Genetic Elements of Vibrio cholerae and the Evolution of Its Antimicrobial Resistance. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.691604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Vibrio cholerae (VC) is the causative agent of the severe dehydrating diarrheal disease cholera. The primary treatment for cholera is oral rehydration therapy (ORT). However, in case of moderate to severe dehydration, antibiotics are administered to reduce morbidity. Due to the emergence of multidrug resistant (MDR) strains of VC routinely used antibiotics fail to be effective in cholera patients. Antimicrobial resistance (AMR) is encoded in the genome of bacteria and is usually acquired from other organisms cohabiting in the environment or in the gut with which it interacts in the gut or environmental niche. The antimicrobial resistance genes (ARGs) are usually borne on mobile genetic elements (MGEs) like plasmids, transposons, integrons and SXT constin. Horizontal gene transfer (HGT) helps in the exchange of ARGs among bacteria leading to dissemination of AMR. In VC the acquisition and loss of AMR to many antibiotics have been found to be a dynamic process. This review describes the different AMR determinants and mechanisms of resistance that have been discovered in VC. These ARGs borne usually on MGEs have been recovered from isolates associated with past and present epidemics worldwide. These are responsible for resistance of VC to common antibiotics and are periodically lost and gained contributing to its genetic evolution. These resistance markers can be routinely used for AMR surveillance in VC. The review also presents a precise perspective on the importance of the gut microbiome in the emergence of MDR VC and concludes that the gut microbiome is a potential source of molecular markers and networks which can be manipulated for the interception of AMR in the future.
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Chen Y, Zhang Z, Zhang H, Luo H, Li Z. Characteristics of soil bacterial and fungal communities on interval seawater covering Linchang Island, China. Arch Microbiol 2021; 203:2453-2461. [PMID: 33666689 DOI: 10.1007/s00203-021-02268-9] [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: 08/01/2020] [Revised: 12/03/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022]
Abstract
Characterization of microbial communities is important for understanding the soil biodiversity distribution affected by environmental factors. Here, we combined high-throughput sequencing of 16S rDNA and ITS to investigate the composition of bacterial and fungal communities in interval seawater covering Linchang Island, China. We compared the microbial communities in the soil of three sample points from the southern part to the northern part. No difference was observed in microbial abundance, richness and diversity in those three different locations. In addition, weighted and unweighted UniFrac distances revealed that three soil samples could not be separated from each other, even if the LCNS sample had significantly lower organic matter (OM), sodium and sulfate contents than the LCSS and LCMS samples. This result indicated that the microbial community of the soil may be influenced more strongly by interval seawater than by soil chemical characteristics. The bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes were the four most abundant phyla in all samples, accounting for 83.22% of the microbial community. Escherichia-Shigella and Vibrio were abundant in the samples and accounted for 1.17% and 0.27%, respectively. Fungal structure, phylogenetic diversity, richness, and bacterial structure had a significant negative relationship with Vibrio abundance. In addition, Vibrio showed negative correlations with the genera Simiduia, Microbulbifer and Haliangium. The results reveal that the re-shaped microbiome and introduced typical microbes could be strategies for inhibiting Vibrio in the soil of Linchang Island.
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Affiliation(s)
- Yonggan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean UniversityMinistry of Education, Sanya, 572022, China.,Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China.,College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Zhenhua Zhang
- Key Laboratory of Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, 210042, China.
| | - Haonan Zhang
- Key Laboratory of Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, 210042, China
| | - Hongwei Luo
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Zhen Li
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, China
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18
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Antibiotic Resistance in Vibrio cholerae: Mechanistic Insights from IncC Plasmid-Mediated Dissemination of a Novel Family of Genomic Islands Inserted at trmE. mSphere 2020; 5:5/4/e00748-20. [PMID: 32848007 PMCID: PMC7449626 DOI: 10.1128/msphere.00748-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing association of the etiological agent of cholera, Vibrio cholerae serogroup O1 and O139, with multiple antibiotic resistance threatens to deprive health practitioners of this effective tool. Drug resistance in cholera results mainly from acquisition of mobile genetic elements. Genomic islands conferring multidrug resistance and mobilizable by IncC conjugative plasmids were reported to circulate in non-O1/non-O139 V. cholerae clinical strains isolated from the 2010 Haitian cholera outbreak. As these genomic islands can be transmitted to pandemic V. cholerae serogroups, their mechanism of transmission needed to be investigated. Our research revealed plasmid- and genomic island-encoded factors required for the resistance island excision, mobilization, and integration, as well as regulation of these functions. The discovery of related genomic islands carrying diverse phage resistance genes but lacking antibiotic resistance-conferring genes in a wide range of marine dwelling bacteria suggests that these elements are ancient and recently acquired drug resistance genes. Cholera remains a formidable disease, and reports of multidrug-resistant strains of the causative agent Vibrio cholerae have become common during the last 3 decades. The pervasiveness of resistance determinants has largely been ascribed to mobile genetic elements, including SXT/R391 integrative conjugative elements, IncC plasmids, and genomic islands (GIs). Conjugative transfer of IncC plasmids is activated by the master activator AcaCD whose regulatory network extends to chromosomally integrated GIs. MGIVchHai6 is a multidrug resistance GI integrated at the 3′ end of trmE (mnmE or thdF) in chromosome 1 of non-O1/non-O139 V. cholerae clinical isolates from the 2010 Haitian cholera outbreak. In the presence of an IncC plasmid expressing AcaCD, MGIVchHai6 excises from the chromosome and transfers at high frequency. Herein, the mechanism of mobilization of MGIVchHai6 GIs by IncC plasmids was dissected. Our results show that AcaCD drives expression of GI-borne genes, including xis and mobIM, involved in excision and mobilization. A 49-bp fragment upstream of mobIM was found to serve as the minimal origin of transfer (oriT) of MGIVchHai6. The direction of transfer initiated at oriT was determined using IncC plasmid-driven mobilization of chromosomal markers via MGIVchHai6. In addition, IncC plasmid-encoded factors, including the relaxase TraI, were found to be required for GI transfer. Finally, in silico exploration of Gammaproteobacteria genomes identified 47 novel related and potentially AcaCD-responsive GIs in 13 different genera. Despite sharing conserved features, these GIs integrate at trmE, yicC, or dusA and carry a diverse cargo of genes involved in phage resistance. IMPORTANCE The increasing association of the etiological agent of cholera, Vibrio cholerae serogroup O1 and O139, with multiple antibiotic resistance threatens to deprive health practitioners of this effective tool. Drug resistance in cholera results mainly from acquisition of mobile genetic elements. Genomic islands conferring multidrug resistance and mobilizable by IncC conjugative plasmids were reported to circulate in non-O1/non-O139 V. cholerae clinical strains isolated from the 2010 Haitian cholera outbreak. As these genomic islands can be transmitted to pandemic V. cholerae serogroups, their mechanism of transmission needed to be investigated. Our research revealed plasmid- and genomic island-encoded factors required for the resistance island excision, mobilization, and integration, as well as regulation of these functions. The discovery of related genomic islands carrying diverse phage resistance genes but lacking antibiotic resistance-conferring genes in a wide range of marine dwelling bacteria suggests that these elements are ancient and recently acquired drug resistance genes.
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Huguet KT, Rivard N, Garneau D, Palanee J, Burrus V. Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss. PLoS Genet 2020; 16:e1008965. [PMID: 32760058 PMCID: PMC7433901 DOI: 10.1371/journal.pgen.1008965] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/18/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
The mobilizable resistance island Salmonella genomic island 1 (SGI1) is specifically mobilized by IncA and IncC conjugative plasmids. SGI1, its variants and IncC plasmids propagate multidrug resistance in pathogenic enterobacteria such as Salmonella enterica serovars and Proteus mirabilis. SGI1 modifies and uses the conjugation apparatus encoded by the helper IncC plasmid, thus enhancing its own propagation. Remarkably, although SGI1 needs a coresident IncC plasmid to excise from the chromosome and transfer to a new host, these elements have been reported to be incompatible. Here, the stability of SGI1 and its helper IncC plasmid, each expressing a different fluorescent reporter protein, was monitored using fluorescence-activated cell sorting (FACS). Without selective pressure, 95% of the cells segregated into two subpopulations containing either SGI1 or the helper plasmid. Furthermore, FACS analysis revealed a high level of SGI1-specific fluorescence in IncC+ cells, suggesting that SGI1 undergoes active replication in the presence of the helper plasmid. SGI1 replication was confirmed by quantitative PCR assays, and extraction and restriction of its plasmid form. Deletion of genes involved in SGI1 excision from the chromosome allowed a stable coexistence of SGI1 with its helper plasmid without selective pressure. In addition, deletion of S003 (rep) or of a downstream putative iteron-based origin of replication, while allowing SGI1 excision, abolished its replication, alleviated the incompatibility with the helper plasmid and enabled its cotransfer to a new host. Like SGI1 excision functions, rep expression was found to be controlled by AcaCD, the master activator of IncC plasmid transfer. Transient SGI1 replication seems to be a key feature of the life cycle of this family of genomic islands. Sequence database analysis revealed that SGI1 variants encode either a replication initiator protein with a RepA_C domain, or an alternative replication protein with N-terminal replicase and primase C terminal 1 domains. The Salmonella genomic island 1 (SGI1) and its variants propagate multidrug resistance in several species of human and animal pathogens with the help of IncA and IncC conjugative plasmids that are absolutely required for SGI1 dissemination. These helper plasmids are known to trigger the excision of SGI1 from the chromosome. Here, we found that IncC plasmids also trigger the replication of the excised, circular form of SGI1 by enabling the expression of an SGI1-borne replication initiator gene. In return, high-copy replication of SGI1 interferes with the persistence of the IncC plasmid and prevents its cotransfer into a recipient cell, thereby allowing integration and stabilization of SGI1 into the chromosome of the new host. This finding is important to better understand the complex interactions between SGI1-like elements and their helper plasmids that lead to widespread and highly efficient propagation of multidrug resistance genes to a broad range of human and animal pathogens.
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Affiliation(s)
- Kévin T. Huguet
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Nicolas Rivard
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Daniel Garneau
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jason Palanee
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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Antibiotic Susceptibility Testing (AST) Reports: A Basis for Environmental/Epidemiological Surveillance and Infection Control Amongst Environmental Vibrio cholerae. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17165685. [PMID: 32781601 PMCID: PMC7460427 DOI: 10.3390/ijerph17165685] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
Distribution, investigation, surveillance and control (DISC) of cholera outbreaks in endemic/non-endemic regions has been a concerted approach towards the management of the causal pathogen. Relevant organization, government, health systems and the public have implemented several steps towards controlling the menace, yet pathogen continues to occur with diverse phenotypes/genotypes of high clinical and epidemiological relevance. The study determines antibiotic susceptibility/resistance pattern of Vibrio cholerae isolates retrieved from six domestic water sources between March and August 2018. Serological and molecular typing methods (polymerase chain reaction or PCR) were used to confirm the isolates identity. Antibiotic susceptibility testing was conducted using six commonly employed antibiotics of V. cholerae according to the recommendation of Clinical Laboratory Standard and European Committee for Antimicrobial Susceptibility Testing with other relevant antibiotics of investigative epidemiology and infection control, employing both disc diffusion test and PCR gene detection. Samples presumptive counts ranged between 1.10 to 7.91 log10 CFU/mL. Amongst the 759 presumptive isolates retrieved, sixty-one were confirmed as V. cholerae which were further serogrouped as Non-O1/Non-O139 V. cholerae. Various V. cholerae resistant phenotypes/genoytypes were detected vis: carbapenemase (CR-Vc; 31.1%/5.3%). New Delhi Metallobetalactamase (NDM-1-Vc; 23.0%/42.5%), extended spectrum betalactamase (ESBL-Vc; 42.6%/blaTEM:86,7%), chloramphenicol resistance (62.3%/Flor: 46.2%}, tetracycline resistance (70.5%/46.7%), AmpC resistance (21.0 (34.4%/56.7%)) and various other resistant genotypes/phenotypes. It was observed that more than 50% of the confirmed V. cholerae isolates possess resistance to two or more antibiotic classes/groups with multiple antibiotic resistance index (MARI) ranging from 0.031 to 0.5. This observation provides necessary information and updates for surveillance, planning and implementation of control strategies for cholera. It would also encourage decision making, formulation of policy by the government and cholera control authorities.
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Morita D, Takahashi E, Morita M, Ohnishi M, Mizuno T, Miyoshi SI, Dutta D, Ramamurthy T, Chowdhury G, Mukhopadhyay AK, Okamoto K. Genomic characterization of antibiotic resistance-encoding genes in clinical isolates of Vibrio cholerae non-O1/non-O139 strains from Kolkata, India: generation of novel types of genomic islands containing plural antibiotic resistance genes. Microbiol Immunol 2020; 64:435-444. [PMID: 32222116 DOI: 10.1111/1348-0421.12790] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/02/2020] [Accepted: 03/22/2020] [Indexed: 11/30/2022]
Abstract
Non-O1/non-O139 nontoxigenic Vibrio cholerae associated with cholera-like diarrhea has been reported in Kolkata, India. However, the property involved in the pathogenicity of these strains has remained unclear. The character of 25 non-O1/non-O139 nontoxigenic V. cholerae isolated during 8 years from 2007 to 2014 in Kolkata was examined. Determination of the serogroup showed that the serogroups O6, O10, O35, O36, O39, and O70 were represented by two strains in each serogroup, and the remaining isolates belonged to different serogroups. To clarify the character of antibiotic resistance of these isolates, an antibiotic resistance test and the gene analysis were performed. According to antimicrobial drug susceptibility testing, 13 strains were classified as drug resistant. Among them, 10 strains were quinolone resistant and 6 of the 13 strains were resistant to more than three antibiotics. To define the genetic background of the antibiotic character of these strains, whole-genome sequences of these strains were determined. From the analysis of these sequences, it becomes clear that all quinolone resistance isolates have mutations in quinolone resistance-determining regions. Further research on the genome sequence showed that four strains possess Class 1 integrons in their genomes, and that three of the four integrons are found to be located in their genomic islands. These genomic islands are novel types. This indicates that various integrons containing drug resistance genes are spreading among V. cholerae non-O1/non-O139 strains through the action of newly generated genomic islands.
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Affiliation(s)
- Daichi Morita
- Collaborative Research Center of Okayama University for Infectious Diseases in India, Okayama University, Kolkata, India
| | - Eizo Takahashi
- Collaborative Research Center of Okayama University for Infectious Diseases in India, Okayama University, Kolkata, India
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tamaki Mizuno
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Devarati Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Thandavarayan Ramamurthy
- Center for Human Microbial Ecology, Translational Health Science and Technology Institute, Faridabad, India
| | - Goutam Chowdhury
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Keinosuke Okamoto
- Collaborative Research Center of Okayama University for Infectious Diseases in India, Okayama University, Kolkata, India
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22
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Arteaga M, Velasco J, Rodriguez S, Vidal M, Arellano C, Silva F, Carreño LJ, Vidal R, Montero DA. Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. Microb Genom 2020; 6:e000340. [PMID: 32100707 PMCID: PMC7200058 DOI: 10.1099/mgen.0.000340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Vibrio cholerae is a human pathogen, which is transmitted by the consumption of contaminated food or water. V. cholerae strains belonging to the serogroups O1 and O139 can cause cholera outbreaks and epidemics, a severe life-threatening diarrheal disease. In contrast, serogroups other than O1 and O139, denominated as non-O1/non-O139, have been mainly associated with sporadic cases of moderate or mild diarrhea, bacteremia and wound infections. Here we investigated the virulence determinants and phylogenetic origin of a non-O1/non-O139 V. cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. We found that this outbreak strain lacks the classical virulence genes harboured by O1 and O139 strains, including the cholera toxin (CT) and the toxin-coregulated pilus (TCP). However, this strain carries genomic islands (GIs) encoding Type III and Type VI secretion systems (T3SS/T6SS) and antibiotic resistance genes. Moreover, we found these GIs are wide distributed among several lineages of non-O1/non-O139 strains. Our results suggest that the acquisition of these GIs may enhance the virulence of non-O1/non-O139 strains that lack the CT and TCP-encoding genes. Our results highlight the pathogenic potential of these V. cholerae strains.
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Affiliation(s)
- Mónica Arteaga
- Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Juliana Velasco
- Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Shelly Rodriguez
- Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Maricel Vidal
- Laboratorio de Salud Pública Ambiental y Laboral, Secretaría Regional Ministerial de Salud Región Metropolitana, Santiago, Chile
| | - Carolina Arellano
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Francisco Silva
- Servicio de Laboratorio Clínico, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Leandro J. Carreño
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - David A. Montero
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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23
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Eduardo-Correia B, Morales-Filloy H, Abad JP. Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players. Front Microbiol 2020; 10:3071. [PMID: 31998281 PMCID: PMC6965355 DOI: 10.3389/fmicb.2019.03071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Bacterial resistance to antibiotics is an ever-increasing phenomenon that, besides clinical settings, is generally assumed to be prevalent in environmental soils and waters. The analysis of bacteria resistant to each one of 11 antibiotics in waters and sediments of the Huelva’s estuary, a multi-contaminated environment, showed high levels of bacteria resistant mainly to Tm, among others. To further gain knowledge on the fate of multi-drug resistance (MDR) in environmental bacteria, 579 ampicillin-resistant bacteria were isolated tested for resistance to 10 antibiotics. 92.7% of the isolates were resistant to four or more antibiotic classes, indicating a high level of multi-resistance. 143 resistance profiles were found. The isolates with different MDR profiles and/or colony morphologies were phylogenetically ascribed based on 16S rDNA to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, including 48 genera. Putative intrinsic resistance was detected in different phylogenetic groups including genera Altererythrobacter, Bacillus, Brevundimonas, Erythrobacter, Mesonia, Ochrobactrum, and Ponticaulis. Correlation of the presence of pairs of the non-intrinsic-resistances in phylogenetic groups based on the kappa index (κ) highlighted the co-habitation of some of the tested pairs at different phylogenetic levels. Maximum correlation (κ = 1.000) was found for pairs CzR/TcR in Betaproteobacteria, and CcR/TcR and EmR/SmR in Sphingobacteriia at the class level, while at the genus level, was found for CcR/TcR and NxR/TmR in Mesonia, CzR/TmR and EmR/KmR in Paenibacillus, and CcR/EmR and RpR/TcR in Pseudomonas. These results could suggest the existence of intra-class and intra-genus-transmissible genetic elements containing determinants for both members of each pair. Network analysis based on κ values higher than 0.4 indicated the sharing of paired resistances among several genera, many of them centered on the Paenibacillus node and raising the hypothesis of inter-genera transmission of resistances interconnected through members of this genus. This is the first time that a possible hotspot of resistance interchange in a particular environment may have been detected, opening up the possibility that one, or a few, bacterial members of the community could be important promoters of antibiotic resistance (AR) dissemination in this environment’s bacterial population. Further studies using the available isolates will likely give insights of the possible mechanisms and genetic elements involved.
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Affiliation(s)
- Benedito Eduardo-Correia
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - Héctor Morales-Filloy
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - José P Abad
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
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24
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Narendrakumar L, Gupta SS, Johnson JB, Ramamurthy T, Thomas S. Molecular Adaptations and Antibiotic Resistance inVibrio cholerae: A Communal Challenge. Microb Drug Resist 2019; 25:1012-1022. [DOI: 10.1089/mdr.2018.0354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Lekshmi Narendrakumar
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Kerala, India
- Research Scholar, University of Kerala, Kerala, India
| | | | - John B. Johnson
- Viral Disease Biology, Rajiv Gandhi Centre for Biotechnology, Kerala, India
| | | | - Sabu Thomas
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Kerala, India
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25
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Kaushik M, Kumar S, Kapoor RK, Gulati P. Integrons and antibiotic resistance genes in water-borne pathogens: threat detection and risk assessment. J Med Microbiol 2019; 68:679-692. [DOI: 10.1099/jmm.0.000972] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Megha Kaushik
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Sanjay Kumar
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Rajeev Kr. Kapoor
- Enzyme Biotechnology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
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26
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Entry Exclusion of Conjugative Plasmids of the IncA, IncC, and Related Untyped Incompatibility Groups. J Bacteriol 2019; 201:JB.00731-18. [PMID: 30858294 DOI: 10.1128/jb.00731-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
Conjugative plasmids of incompatibility group C (IncC), formerly known as A/C2, disseminate antibiotic resistance genes globally in diverse pathogenic species of Gammaproteobacteria. Salmonella genomic island 1 (SGI1) can be mobilized by IncC plasmids and was recently shown to reshape the conjugative type IV secretion system (T4SS) encoded by these plasmids to evade entry exclusion. Entry exclusion blocks DNA translocation between cells containing identical or highly similar plasmids. Here, we report that the protein encoded by the entry exclusion gene of IncC plasmids (eexC) mediates entry exclusion in recipient cells through recognition of the IncC-encoded TraGC protein in donor cells. Phylogenetic analyses based on EexC and TraGC homologs predicted the existence of at least three different exclusion groups among IncC-related conjugative plasmids. Mating assays using Eex proteins encoded by representative IncC and IncA (former A/C1) and related untyped plasmids confirmed these predictions and showed that the IncC and IncA plasmids belong to the C exclusion group, thereby explaining their apparent incompatibility despite their compatible replicons. Representatives of the two other exclusion groups (D and E) are untyped conjugative plasmids found in Aeromonas sp. Finally, we determined through domain swapping that the carboxyl terminus of the EexC and EexE proteins controls the specificity of these exclusion groups. Together, these results unravel the role of entry exclusion in the apparent incompatibility between IncA and IncC plasmids while shedding light on the importance of the TraG subunit substitution used by SGI1 to evade entry exclusion.IMPORTANCE IncA and IncC conjugative plasmids drive antibiotic resistance dissemination among several pathogenic species of Gammaproteobacteria due to the diversity of drug resistance genes that they carry and their ability to mobilize antibiotic resistance-conferring genomic islands such as SGI1 of Salmonella enterica While historically grouped as "IncA/C," IncA and IncC replicons were recently confirmed to be compatible and to abolish each other's entry into the cell in which they reside during conjugative transfer. The significance of our study is in identifying an entry exclusion system that is shared by IncA and IncC plasmids. It impedes DNA transfer to recipient cells bearing a plasmid of either incompatibility group. The entry exclusion protein of this system is unrelated to any other known entry exclusion proteins.
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27
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Kiss J, Szabó M, Hegyi A, Douard G, Praud K, Nagy I, Olasz F, Cloeckaert A, Doublet B. Identification and Characterization of oriT and Two Mobilization Genes Required for Conjugative Transfer of Salmonella Genomic Island 1. Front Microbiol 2019; 10:457. [PMID: 30894848 PMCID: PMC6414798 DOI: 10.3389/fmicb.2019.00457] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/20/2019] [Indexed: 11/13/2022] Open
Abstract
The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resistance to critically important antibiotics among enteric bacteria. Even though many aspects of SGI1 mobilization by IncA and IncC plasmids have been explored, the basic transfer elements such as oriT and self-encoded mobilization proteins remain undiscovered. Here we describe the mobilization region of SGI1 that is well conserved throughout the family and carries the oriT SGI1 and two genes, mpsA and mpsB (originally annotated as S020 and S019, respectively) that are essential for the conjugative transfer of SGI1. OriT SGI1, which is located in the vicinity of the two mobilization genes proved to be a 125-bp GC-rich sequence with several important inverted repeat motifs. The mobilization proteins MpsA and MpsB are expressed from a bicistronic mRNA, although MpsB can be produced from its own mRNA as well. The protein structure predictions imply that MpsA belongs to the lambda tyrosine recombinase family, while MpsB resembles the N-terminal core DNA binding domains of these enzymes. The results suggest that MpsA may act as an atypical relaxase, which needs MpsB for SGI1 transfer. Although the helper plasmid-encoded relaxase proved not to be essential for SGI1 transfer, it appeared to be important to achieve the high transfer rate of the island observed with the IncA/IncC-SGI1 system.
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Affiliation(s)
- János Kiss
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Mónika Szabó
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Anna Hegyi
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary.,ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - Gregory Douard
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - Karine Praud
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - István Nagy
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Ferenc Olasz
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllõ, Hungary
| | - Axel Cloeckaert
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
| | - Benoît Doublet
- ISP, Institut National de la Recherche Agronomique, Université de Tours, UMR 1282, Nouzilly, France
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28
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Juhas M. Genomic Islands and the Evolution of Multidrug-Resistant Bacteria. HORIZONTAL GENE TRANSFER 2019:143-153. [DOI: 10.1007/978-3-030-21862-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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29
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Abstract
Enterococcus faecium has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCCmec This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of rlmH and encoded large serine recombinases ccrAB similar to SCCmec Horizontal transfer of an ECC element termed ECC::cat containing a knock-in cat chloramphenicol resistance determinant occurred in the presence of a conjugative rep pLG1 plasmid. We determined the ECC::cat insertion site in the 3' region of rlmH in the E. faecium recipient by long-read sequencing. ECC::cat also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC::cat and the conjugative plasmid. The ccrABEnt genes were found in 69 of 516 E. faecium genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by attR and attL sites of approximately 50 bp. The attECC sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare E. faecium genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in E. faecium IMPORTANCE Enterococcus faecium is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid E. faecium in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, ccrAB Ent, large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci.
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30
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Cholera: an overview with reference to the Yemen epidemic. Front Med 2018; 13:213-228. [DOI: 10.1007/s11684-018-0631-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/18/2017] [Indexed: 12/12/2022]
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31
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Ceccarelli D, Garriss G, Choi SY, Hasan NA, Stepanauskas R, Pop M, Huq A, Colwell RR. Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139. Front Microbiol 2017; 8:2283. [PMID: 29218035 PMCID: PMC5703827 DOI: 10.3389/fmicb.2017.02283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022] Open
Abstract
We report the complete sequence of two novel plasmids, pSDH-1 and pSDH-2, isolated from clinical Vibrio cholerae non-O1/non-O139 during the early phase of the 2010 Haitian cholera epidemic. Plasmids were revealed by employing single-cell genomics and their genome content suggests self-mobilization and, for pSDH-2, a toxin-antitoxin (TA) system for plasmid stabilization was identified. The putative origin of replication of pSDH-2 was mapped suggesting it replicates following the ColE1 model of plasmid replication. pSDH-1 and pSDH-2 were widespread among environmental V. cholerae non-O1/non-O139 with variable prevalence in four Haitian Departments. pSDH-2 was the most common element, either alone or with pSDH-1. The two plasmids detection adds to the composite scenario of mobile genetic elements (MGEs) observed in V. cholerae in Haiti. The role these small cryptic plasmids circulating in Vibrio spp. play in bacterial fitness or pathogenicity merits further investigation.
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Affiliation(s)
- Daniela Ceccarelli
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Geneviève Garriss
- Department of Microbiology, Cell Biology and Tumor Biology, Karolinska Institutet, Stockholm, Sweden
| | - Seon Y Choi
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,CosmosID Inc., Rockville, MD, United States
| | - Nur A Hasan
- CosmosID Inc., Rockville, MD, United States.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | | | - Mihai Pop
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States
| | - Anwar Huq
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,Maryland Institute of Applied Environmental Health, University of Maryland, College Park, MD, United States
| | - Rita R Colwell
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.,CosmosID Inc., Rockville, MD, United States.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States.,Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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32
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The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems. Genes (Basel) 2017; 8:genes8110337. [PMID: 29165361 PMCID: PMC5704250 DOI: 10.3390/genes8110337] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.
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33
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Burks DJ, Norris S, Kauffman KM, Joy A, Arevalo P, Azad RK, Wildschutte H. Environmental vibrios represent a source of antagonistic compounds that inhibit pathogenic Vibrio cholerae and Vibrio parahaemolyticus strains. Microbiologyopen 2017; 6:e00504. [PMID: 28857444 PMCID: PMC5635165 DOI: 10.1002/mbo3.504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/05/2017] [Accepted: 05/16/2017] [Indexed: 12/16/2022] Open
Abstract
With the overuse of antibiotics, many pathogens including Vibrio cholerae and Vibrio parahaemolyticus have evolved multidrug resistance making treatment more difficult. While understanding the mechanisms that underlie pathogenesis is crucial, knowledge of bacterial interactions of V. cholerae and V. parahaemolyticus could provide insight to their susceptibility outside of the human host. Based on previous work showing competition among environmental strains, we predict that marine-derived bacteria should inhibit Vibrio pathogens and may be a source of unique antibiotic compounds. We tested a collection of 3,456 environmental Vibrio isolates from diverse habitats against a panel of V. cholerae and V. parahaemolyticus, and identified 102 strains that inhibited the growth of these pathogens. Phylogenetic analysis revealed that 40 pathogen-inhibiting strains were unique at the hsp60 gene sequence while 62 of the isolates were identical suggesting clonal groups. Genomic comparisons of ten strains revealed diversity even between clonal isolates and were identified as being closely related to known Vibrio crassostreae, Vibrio splendidus, and Vibrio tasmaniensis strains. Further analysis revealed multiple biosynthetic gene clusters within all sequenced genomes that encoded secondary metabolites with potential antagonistic activity. Thus, environmental vibrios represent a source of compounds that inhibit Vibrio pathogens.
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Affiliation(s)
- David J. Burks
- Department of Biological SciencesUniversity of North TexasDentonTexas
| | - Stephen Norris
- Department of Biological SciencesBowling Green State UniversityBowling GreenOhio
| | - Kathryn M. Kauffman
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Abigail Joy
- Department of Biological SciencesBowling Green State UniversityBowling GreenOhio
| | - Philip Arevalo
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Rajeev K. Azad
- Department of Biological SciencesUniversity of North TexasDentonTexas
- Department of MathematicsUniversity of North TexasDentonTexas
| | - Hans Wildschutte
- Department of Biological SciencesBowling Green State UniversityBowling GreenOhio
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34
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Baron S, Larvor E, Chevalier S, Jouy E, Kempf I, Granier SA, Lesne J. Antimicrobial Susceptibility among Urban Wastewater and Wild Shellfish Isolates of Non-O1/Non-O139 Vibrio cholerae from La Rance Estuary (Brittany, France). Front Microbiol 2017; 8:1637. [PMID: 28955305 PMCID: PMC5601046 DOI: 10.3389/fmicb.2017.01637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/11/2017] [Indexed: 12/26/2022] Open
Abstract
The early 2000s marked the end of the Golden age of the antibiotics and the beginning of the awareness on the potential threat to human health due to the dissemination of antimicrobial resistance. As a base-line study, we investigated the antimicrobial susceptibility of 99 strains of non-O1/non-O139 Vibrio cholerae isolated from wastewater and shellfish in 2000/2001 within La Rance estuary (Brittany, France). All isolates were susceptible to amoxicillin-clavulanic acid, cefotaxime, imipenem, chloramphenicol, nalidixic acid, ciprofloxacin, norfloxacin, amikacin, gentamicin, tetracycline, doxycycline, trimethoprim-sulfamethoxazole, and erythromycin. The only resistances were to streptomycin, sulfonamides and ampicillin: 54.6% of the isolates had acquired resistance to at least one antimicrobial agent among them and only six isolates from cockles were multidrug resistant. On the basis of the distribution of a limited selection of resistance associated genes, our study shows that V. cholerae can constitute an environmental reservoir for these genes. However, none of our isolates harbored integron. This result casts doubt on the capacity of non-O1/non-O139 V. cholerae to acquire resistance-associated genes in such context, and on its potential role of indicator of the dissemination of antimicrobial resistance in the aquatic environment.
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Affiliation(s)
- Sandrine Baron
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Emeline Larvor
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Séverine Chevalier
- Bretagne-Loire UniversityRennes, France.,Ecole des Hautes Etudes en Santé Publique, Laboratoire d'Etude et de Recherche en Environnement et Santé, Institut de Recherche en Santé, Environnement et Travail, UMR 1085Rennes, France
| | - Eric Jouy
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Isabelle Kempf
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Sophie A Granier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Paris-Est UniversityMaisons-Alfort, France
| | - Jean Lesne
- Bretagne-Loire UniversityRennes, France.,Ecole des Hautes Etudes en Santé Publique, Laboratoire d'Etude et de Recherche en Environnement et Santé, Institut de Recherche en Santé, Environnement et Travail, UMR 1085Rennes, France
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35
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Tran F, Boedicker JQ. Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer. Sci Rep 2017; 7:8813. [PMID: 28821711 PMCID: PMC5562762 DOI: 10.1038/s41598-017-07447-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/27/2017] [Indexed: 12/22/2022] Open
Abstract
Most bacteria release extracellular vesicles (EVs). Recent studies have found these vesicles are capable of gene delivery, however the consequences of vesicle-mediated transfer on the patterns and rates of gene flow within microbial communities remains unclear. Previous studies have not determined the impact of both the genetic cargo and the donor and recipient species on the rate of vesicle-mediated gene exchange. This report examines the potential for EVs as a mechanism of gene transfer within heterogeneous microbial populations. EVs were harvested from three species of Gram-negative microbes carrying different plasmids. The dynamics of gene transfer into recipient species was measured. This study demonstrates that vesicles enable gene exchange between five species of Gram-negative bacteria, and that the identity of the genetic cargo, donor strain, and recipient strain all influence gene transfer rates. Each species released and acquired vesicles containing genetic material to a variable degree, and the transfer rate did not correlate with the relatedness of the donor and recipient species. The results suggest that EVs may be a general mechanism to exchange non-specialized genetic cargo between bacterial species.
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Affiliation(s)
- Frances Tran
- University of Southern California, Department of Biological Sciences, Seaver Science Center (SSC) 212, 920 Bloom Walk, Los Angeles, CA, 90089, USA
| | - James Q Boedicker
- University of Southern California, Department of Biological Sciences, Seaver Science Center (SSC) 212, 920 Bloom Walk, Los Angeles, CA, 90089, USA.
- University of Southern California, Department of Physics and Astronomy, Seaver Science Center (SSC) 212, 920 Bloom Walk, Los Angeles, CA, 90089, USA.
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Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR. The hidden life of integrative and conjugative elements. FEMS Microbiol Rev 2017; 41:512-537. [PMID: 28369623 PMCID: PMC5812530 DOI: 10.1093/femsre/fux008] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE 'fitness'). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells.
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Affiliation(s)
- François Delavat
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8566, Japan
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Nicolas Pradervand
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
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Bañuelos-Vazquez LA, Torres Tejerizo G, Brom S. Regulation of conjugative transfer of plasmids and integrative conjugative elements. Plasmid 2017; 91:82-89. [DOI: 10.1016/j.plasmid.2017.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 10/25/2022]
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Mala W, Faksri K, Samerpitak K, Yordpratum U, Kaewkes W, Tattawasart U, Chomvarin C. Antimicrobial resistance and genetic diversity of the SXT element in Vibrio cholerae from clinical and environmental water samples in northeastern Thailand. INFECTION GENETICS AND EVOLUTION 2017; 52:89-95. [PMID: 28412524 DOI: 10.1016/j.meegid.2017.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 04/04/2017] [Accepted: 04/11/2017] [Indexed: 11/26/2022]
Abstract
Multidrug resistance in V. cholerae has been increasing around the world including northeastern Thailand. The aquatic environment is a reservoir of V. cholerae and might be an important source of resistant strains. The aims of this study were to investigate the phylogenetic relationships of intSXT gene sequences from 31 clinical and 14 environmental V. cholerae O1 and non-O1/non-O139 isolates and 11 sequences amplified directly from environmental water samples. We also amplified class 1 integrons, the SXT elements (targeting the intSXT gene) and antimicrobial resistance genes directly from water samples. Phylogenetic analysis displayed two major distinct clusters (clusters 1 and 2). Most V. cholerae O1 (19/20, 95%) and non-O1/non-O139 isolates (8/11, 72.7%) from clinical sources, and all sequences obtained directly from water samples, belonged to cluster 1. Cluster 2 mostly comprised environmental non-O1/non-O139 isolates (10/12, 83.3%). We successfully amplified the SXT elements directly from17.5% of water samples. Associated resistance genes were also amplified as follows: sul2 (41.3% of water samples), dfrA1 (60%), dfr18 (33.8%), strB (70%) and tetA (2.5%). Class 1 integrons were not found in water samples, indicating that the SXT element was the major contributor of multidrug resistance determinants in this region. The SXT element and antimicrobial resistance genes could be transferred from clinical V. cholerae O1 to environmental V. cholerae non-O1/non-O139 was demonstrated by conjugation experiment. These findings indicate that there may have been cross dissemination and horizontal gene transfer (HGT) of the SXT element harbored by V. cholerae O1 and non-O1/non-O139 strains isolated from clinical and environmental water sources. Environmental water might be an important source of antimicrobial resistance genes in V. cholerae in this region. Direct detection of antimicrobial resistance genes in water samples can be used for monitoring the spread of such genes in the ecosystem.
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Affiliation(s)
- Wanida Mala
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Kittipan Samerpitak
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Umaporn Yordpratum
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Wanlop Kaewkes
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Unchalee Tattawasart
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand.
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Carraro N, Rivard N, Burrus V, Ceccarelli D. Mobilizable genomic islands, different strategies for the dissemination of multidrug resistance and other adaptive traits. Mob Genet Elements 2017; 7:1-6. [PMID: 28439449 PMCID: PMC5397120 DOI: 10.1080/2159256x.2017.1304193] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 02/15/2017] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
Mobile genetic elements are near ubiquitous DNA segments that revealed a surprising variety of strategies for their propagation among prokaryotes and between eukaryotes. In bacteria, conjugative elements were shown to be key drivers of evolution and adaptation by efficiently disseminating genes involved in pathogenicity, symbiosis, metabolic pathways, and antibiotic resistance. Conjugative plasmids of the incompatibility groups A and C (A/C) are important vehicles for the dissemination of antibiotic resistance and the consequent global emergence and spread of multi-resistant pathogenic bacteria. Beyond their own mobility, A/C plasmids were also shown to drive the mobility of unrelated non-autonomous mobilizable genomic islands, which may also confer further advantageous traits. In this commentary, we summarize the current knowledge on different classes of A/C-dependent mobilizable genomic islands and we discuss other DNA hitchhikers and their implication in bacterial evolution. Furthermore, we glimpse at the complex genetic network linking autonomous and non-autonomous mobile genetic elements, and at the associated flow of genetic information between bacteria.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada.,Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Rivard
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
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40
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Salmonella genomic island 1 (SGI1) reshapes the mating apparatus of IncC conjugative plasmids to promote self-propagation. PLoS Genet 2017; 13:e1006705. [PMID: 28355215 PMCID: PMC5389848 DOI: 10.1371/journal.pgen.1006705] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/12/2017] [Accepted: 03/20/2017] [Indexed: 11/20/2022] Open
Abstract
IncC conjugative plasmids and Salmonella genomic island 1 (SGI1) and relatives are frequently associated with multidrug resistance of clinical isolates of pathogenic Enterobacteriaceae. SGI1 is specifically mobilized in trans by IncA and IncC plasmids (commonly referred to as A/C plasmids) following its excision from the chromosome, an event triggered by the transcriptional activator complex AcaCD encoded by these helper plasmids. Although SGI1 is not self-transmissible, it carries three genes, traNS, traHS and traGS, coding for distant homologs of the predicted mating pore subunits TraNC, TraHC and TraGC, respectively, encoded by A/C plasmids. Here we investigated the regulation of traNS and traHGS and the role of these three genes in the transmissibility of SGI1. Transcriptional fusion of the promoter sequences of traNS and traHGS to the reporter gene lacZ confirmed that expression of these genes is inducible by AcaCD. Mating experiments using combinations of deletion mutants of SGI1 and the helper IncC plasmid pVCR94 revealed complex interactions between these two mobile genetic elements. Whereas traNC and traHGC are essential for IncC plasmid transfer, SGI1 could rescue null mutants of each individual gene revealing that TraNS, TraHS and TraGS are functional proteins. Complementation assays of individual traC and traS mutants showed that not only do TraNS/HS/GS replace TraNC/HC/GC in the mating pore encoded by IncC plasmids but also that traGS and traHS are both required for SGI1 optimal transfer. In fact, remodeling of the IncC-encoded mating pore by SGI1 was found to be essential to enhance transfer rate of SGI1 over the helper plasmid. Furthermore, traGS was found to be crucial to allow DNA transfer between cells bearing IncC helper plasmids, thereby suggesting that by remodeling the mating pore SGI1 disables an IncC-encoded entry exclusion mechanism. Hence traS genes facilitate the invasion by SGI1 of cell populations bearing IncC plasmids. Acquisition and dissemination of multidrug resistance genes among Enterobacteriaceae is in part driven by IncA and IncC (A/C) conjugative plasmids and Salmonella genomic island 1 (SGI1). Although unrelated, SGI1 relies on the self-transmissible A/C plasmids to disseminate within bacterial populations. The mechanisms allowing SGI1 to hijack the mating apparatus synthesized by A/C plasmids have not been previously established. Here, we show that IncC plasmids trigger the expression of three SGI1-borne genes that code for functional mating pore subunits distantly related to those encoded by the IncC helper plasmids. Our results indicate that these subunits alter the mating pore encoded by IncC plasmids to ensure optimal transfer of SGI1 and promote SGI1 dissemination in cell populations harboring IncC plasmids. Apart from SGI1 and relatives, documented mobilizable genomic islands are not known to code for mating pore components, possibly because of redundancy with those encoded by helper conjugative elements. Instead they usually code for mobilization proteins such as a relaxase and auxiliary factors involved in DNA recognition, processing and docking to the mating pore encoded by their helper conjugative element. From an ecological and epidemiological perspective, the strategy used by SGI1 likely confers a strong competitive advantage to SGI1 over IncC plasmids in clinical settings and could account for the high prevalence of SGI1 and relatives in multidrug-resistant Salmonella enterica and Proteus mirabilis.
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Ceccarelli D, Alam M, Huq A, Colwell RR. Reduced Susceptibility to Extended-Spectrum β-Lactams in Vibrio cholerae Isolated in Bangladesh. Front Public Health 2016; 4:231. [PMID: 27803895 PMCID: PMC5067765 DOI: 10.3389/fpubh.2016.00231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/04/2016] [Indexed: 11/21/2022] Open
Abstract
β-lactams are antibiotic molecules able to inhibit cell wall biosynthesis. Among other mechanisms, resistance in Gram-negative bacteria is mostly associated with production of β-lactamase enzymes able to bind and hydrolyze the β-lactam ring. Extended-spectrum β-lactamases extend this ability also to third- and fourth-generation cephalosporins, as well as to carbapenems and monobactams. Vibrio cholerae is the causative agent of epidemic cholera and a public health burden for developing countries like Bangladesh. Although appropriate oral or intravenous rehydration is the therapy of choice for cholera, severe infections and V. cholerae-associated septicemia are treated with antimicrobial drugs, including doxycycline, erythromycin, azithromycin, ciprofloxacin, and/or third-generation cephalosporins. In the years after the introduction of antibiotics in clinical practice, V. cholerae developed resistance to commonly used drugs worldwide mostly through gene acquisition via horizontal gene transfer. Reduced susceptibility of V. cholerae to third-generation cephalosporins has been occasionally documented. However, carbapenemase-producing V. cholerae has been reported at higher rates than resistance to extended-spectrum β-lactams, mainly associated with blaNDM-1 emergence and successful plasmid dissemination. Recent findings suggest limited β-lactam resistance is present in V. cholerae O1 isolates collected during ecological and epidemiological surveillance in Bangladesh. However, a trend to intermediate-susceptibility insurgence was observed. Horizontal gene transfer of β-lactam resistance from enteric pathogens to environmental microorganisms should not be underrated, given the ability of V. cholerae to acquire new genetic information.
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Affiliation(s)
- Daniela Ceccarelli
- Maryland Pathogen Research Institute, University of Maryland , College Park, MD , USA
| | - Munirul Alam
- International Center for Diarrheal Disease Research, Bangladesh (icddr,b) , Dhaka , Bangladesh
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA; Maryland Institute for Applied Environmental Health, University of Maryland, College Park, MD, USA
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA; Maryland Institute for Applied Environmental Health, University of Maryland, College Park, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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