201
|
In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World. mSphere 2019; 4:4/2/e00040-19. [PMID: 30944210 PMCID: PMC6449604 DOI: 10.1128/msphere.00040-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE. Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis strains derived from various environmental settings and human infections from different geographic regions around the world from 1950s to the present. Putative integrative and conjugative elements (ICEs) were identified in 31/36 (86.1%) strains in the study. A total of 52 putative ICEs (including eight degenerated elements lacking integrases) were identified and categorized into three types based on the architecture of the conjugation module and the phylogeny of the relaxase, coupling protein, TraG, and TraJ protein sequences. The type II and III ICEs were found to integrate adjacent to tRNA genes, while type I ICEs integrate into intergenic regions or into a gene. The ICEs carry various cargo genes, including transcription regulator genes and genes conferring antibiotic resistance. The adaptive immune CRISPR-Cas system was found in nine strains, including five strains in which CRISPR-Cas machinery and ICEs coexist at different locations on the same chromosome. One ICE-derived spacer was present in the CRISPR locus in one strain. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in E. anophelis differ in architecture and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. The categorization of ICEs will facilitate further investigations of the impact of ICE on virulence, genome epidemiology, and adaptive genomics of E. anophelis. IMPORTANCEElizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE.
Collapse
|
202
|
Vivant AL, Boutin C, Prost-Boucle S, Papias S, Ziebal C, Pourcher AM. Fate of two strains of extended-spectrum beta-lactamase producing Escherichia coli in constructed wetland microcosm sediments: survival and change in antibiotic resistance profiles. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:1550-1560. [PMID: 31169513 DOI: 10.2166/wst.2019.153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Free water surface constructed wetlands (FWS CW) are efficient technologies to limit the transfer of antibiotic resistant bacteria (ARB) originating from urban effluents into the aquatic environment. However, the decrease in ARB from inflow to outflow through the FWS CW may be explained by their transfer from the water body to the sediment. To investigate the behavior of ARB in the sediment of a FWS CW, we inoculated three microcosms with two strains of extended-spectrum beta-lactamase producing Escherichia coli (ESBL E. coli) belonging to two genotypes. Microcosms were composed of two sediments collected at two locations of an FWS CW from which the strains were isolated. Phragmites were planted in one of the microcosms. The survival curves of the two strains were close regardless of the genotype and the type of sediment. After a rapid decline, both strains were able to survive at low level in the sediments for 50 days. Their fate was not affected by the presence of phragmites. Changes in the bla content and antibiotic resistance of the inoculated strains were observed after three weeks of incubation, indicating that FWS CW sediments are favorable environments for spread of antibiotic resistance genes and for the acquisition of new antibiotic resistance.
Collapse
Affiliation(s)
- Anne-Laure Vivant
- Irstea, UR OPAALE, 17 Avenue de Cucillé-CS 64427, F-35044 Rennes, France and Univ Bretagne Loire, CS 54417, 35044 Rennes, France E-mail:
| | - Catherine Boutin
- Irstea, UR REVERSAAL, 5 rue de la Doua, CS 20244, F-69625, Villeurbanne, France
| | | | - Sandrine Papias
- Irstea, UR REVERSAAL, 5 rue de la Doua, CS 20244, F-69625, Villeurbanne, France
| | - Christine Ziebal
- Irstea, UR OPAALE, 17 Avenue de Cucillé-CS 64427, F-35044 Rennes, France and Univ Bretagne Loire, CS 54417, 35044 Rennes, France E-mail:
| | - Anne-Marie Pourcher
- Irstea, UR OPAALE, 17 Avenue de Cucillé-CS 64427, F-35044 Rennes, France and Univ Bretagne Loire, CS 54417, 35044 Rennes, France E-mail:
| |
Collapse
|
203
|
Abstract
Proteus mirabilis, a Gram-negative rod-shaped bacterium most noted for its swarming motility and urease activity, frequently causes catheter-associated urinary tract infections (CAUTIs) that are often polymicrobial. These infections may be accompanied by urolithiasis, the development of bladder or kidney stones due to alkalinization of urine from urease-catalyzed urea hydrolysis. Adherence of the bacterium to epithelial and catheter surfaces is mediated by 17 different fimbriae, most notably MR/P fimbriae. Repressors of motility are often encoded by these fimbrial operons. Motility is mediated by flagella encoded on a single contiguous 54-kb chromosomal sequence. On agar plates, P. mirabilis undergoes a morphological conversion to a filamentous swarmer cell expressing hundreds of flagella. When swarms from different strains meet, a line of demarcation, a "Dienes line," develops due to the killing action of each strain's type VI secretion system. During infection, histological damage is caused by cytotoxins including hemolysin and a variety of proteases, some autotransported. The pathogenesis of infection, including assessment of individual genes or global screens for virulence or fitness factors has been assessed in murine models of ascending urinary tract infections or CAUTIs using both single-species and polymicrobial models. Global gene expression studies performed in culture and in the murine model have revealed the unique metabolism of this bacterium. Vaccines, using MR/P fimbria and its adhesin, MrpH, have been shown to be efficacious in the murine model. A comprehensive review of factors associated with urinary tract infection is presented, encompassing both historical perspectives and current advances.
Collapse
|
204
|
Wang M, Gao H, Lin N, Zhang Y, Huang N, Walker ED, Ming D, Chen S, Hu S. The antibiotic resistance and pathogenicity of a multidrug-resistant Elizabethkingia anophelis isolate. Microbiologyopen 2019; 8:e804. [PMID: 30891912 PMCID: PMC6854844 DOI: 10.1002/mbo3.804] [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: 11/30/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
Elizabethkingia anophelis 12012‐2 PRCM was isolated from a patient with multiple organ dysfunction syndrome and lower respiratory tract infection in China. Minimum inhibitory concentration (MIC) analysis demonstrated that it was resistant to 20 antibiotics including trimethoprim/sulfamethoxazole and ciprofloxacin, which were effective for the elimination of other Elizabethkingia infections. To investigate multidrug resistance and pathogenicity mechanisms, we analyzed genome features of 12012‐2 PRCM and compared them to the other Elizabethkingia species. The draft genome size was 4.02 Mb with a GC content of 32%, comparable to that of other E. anophelis strains. Phylogenetic analysis showed that E. anophelis 12012‐2 PRCM formed a sister group with E. anophelis 502, distinct from clades formed by other clinical and environmental E. anophelis isolates. E. anophelis 12012‐2 PRCM contained multiple copies of β‐lactamase genes as well as genes predicted to function in antimicrobial efflux. It also contained 92 genes that were potentially involved in virulence, disease, and defense, and were associated with resistance and pathogenicity. Comparative genomic analysis showed high homology among three clinical and two environmental E. anophelis strains having a variety of similar antibiotic resistance and virulence factor genes, and similar genomic structure. Applications of this analysis will contribute to understanding the antibiotic resistance and pathogenic mechanisms of E. anophelis infections, which will assist in the management of infections as it increases in prevalence.
Collapse
Affiliation(s)
- Mingxi Wang
- Yun Leung Laboratory for Molecular Diagnostics, School of Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Hongzhi Gao
- Clinical Center for Molecular Diagnosis and Therapy, Fujian Medical University 2nd Affiliated Hospital, Quanzhou, Fujian, China
| | - Nanfei Lin
- Clinical Center for Molecular Diagnosis and Therapy, Fujian Medical University 2nd Affiliated Hospital, Quanzhou, Fujian, China
| | - Yaping Zhang
- Department of Pulmonary and Critical Care Medicine, Fujian Medical University 2nd Affiliated Hospital, Quanzhou, Fujian, China
| | - Nan Huang
- Quanzhou Medical College, Quanzhou, Fujian, China
| | - Edward D Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Desong Ming
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Fujian, China
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Shaohua Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
205
|
Li J, Tai C, Deng Z, Zhong W, He Y, Ou HY. VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Brief Bioinform 2019; 19:566-574. [PMID: 28077405 DOI: 10.1093/bib/bbw141] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Indexed: 11/13/2022] Open
Abstract
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile.
Collapse
Affiliation(s)
- Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Cui Tai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Yongqun He
- Department of microbiology and immunology research, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Hong-Yu Ou
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
206
|
Li Y, Li L, Kromann S, Chen M, Shi L, Meng H. Antibiotic Resistance of Lactobacillus spp. and Streptococcus thermophilus Isolated from Chinese Fermented Milk Products. Foodborne Pathog Dis 2019; 16:221-228. [DOI: 10.1089/fpd.2018.2516] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yiming Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Lili Li
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Sofie Kromann
- Department of Veterinary Disease Biology, Faculty Health and Medicine, University of Copenhagen, Frederiksberg Copenhagen, Denmark
| | - Miaorui Chen
- Xiamen Hongyi Testing Co., Ltd., Xiamen, Fujian, China
| | - Lei Shi
- Research Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Guangzhou, China
| |
Collapse
|
207
|
Palmer M, Venter SN, Coetzee MP, Steenkamp ET. Prokaryotic species are sui generis evolutionary units. Syst Appl Microbiol 2019; 42:145-158. [DOI: 10.1016/j.syapm.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 12/25/2022]
|
208
|
Abstract
Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
Collapse
Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
- Corresponding author: E-mail:
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
| |
Collapse
|
209
|
Parra B, Tortella GR, Cuozzo S, Martínez M. Negative effect of copper nanoparticles on the conjugation frequency of conjugative catabolic plasmids. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 169:662-668. [PMID: 30496999 DOI: 10.1016/j.ecoenv.2018.11.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 06/09/2023]
Abstract
Due to their antimicrobial properties, copper nanoparticles (CuNPs) have been proposed to be used in agriculture for pest control. Pesticides removal is mainly done by microorganisms, whose genes usually are found in conjugative catabolic plasmids (CCP). The aim of this work was to evaluate if CuNPs at subinhibitory concentrations modify the conjugation frequency (CF) of two CCP (pJP4 and pADP1). CuNPs were characterized by scanning electron microscopy with an X-ray detector, dynamic light scattering and X-ray diffraction. Mating assays were done in LB broth supplemented with CuNPs (10, 20, 50 and 100 µg mL-1) or equivalent concentrations of CuSO4. Interestingly, we observed that in LB, Cu+2 release from CuNPs is fast as evaluated by atomic absorption spectrophotometry. Donor and recipient strains were able to grow in all copper concentrations assayed, but CF of mating pairs was reduced to 10% in the presence of copper at 20 or 50 µg Cu mL-1 compared to control. Thus, our results indicated that both copper forms, CuNPs or CuSO4, negatively affected the transfer of catabolic plasmids by conjugation. Since dissemination of degradative genes by conjugation contribute to degradation of pesticides by microorganisms, this work improves our understanding of the risks of using copper in agriculture soils, which could affect the biodegradative potential of microbial communities.
Collapse
Affiliation(s)
- Boris Parra
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Gonzalo R Tortella
- Departamento de Ingeniería Química, Universidad de la Frontera, Temuco, Chile; Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Universidad de la Frontera, Temuco, Chile; Planta de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina
| | - Sergio Cuozzo
- Planta de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina
| | - Miguel Martínez
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
210
|
Coyne MJ, Comstock LE. Type VI Secretion Systems and the Gut Microbiota. Microbiol Spectr 2019; 7:10.1128/microbiolspec.PSIB-0009-2018. [PMID: 30825301 PMCID: PMC6404974 DOI: 10.1128/microbiolspec.psib-0009-2018] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Indexed: 12/14/2022] Open
Abstract
The human colonic microbiota is a dense ecosystem comprised of numerous microbes, including bacteria, phage, fungi, archaea, and protozoa, that compete for nutrients and space. Studies are beginning to reveal the antagonistic mechanisms that gut bacteria use to compete with other members of this ecosystem. In the healthy human colon, the majority of the Gram-negative bacteria are of the order Bacteroidales. Proteobacteria, such as Escherichia coli, are numerically fewer but confer important properties to the host, such as colonization resistance. Several enteric pathogens use type VI secretion systems (T6SSs) to antagonize symbiotic gut E. coli, facilitating colonization and disease progression. T6SS loci are also widely distributed in human gut Bacteroidales, which includes three predominant genera: Bacteroides, Parabacteroides, and Prevotella. There are three distinct genetic architectures of T6SS loci among the gut Bacteroidales, termed GA1, GA2, and GA3. GA1 and GA2 T6SS loci are contained on integrative and conjugative elements and are the first T6SS loci shown to be readily transferred in the human gut between numerous species and families of Bacteroidales. In contrast, the GA3 T6SSs are present exclusively in Bacteroides fragilis. There are divergent regions in all three T6SS GAs that contain genes encoding effector and immunity proteins, many of which function by unknown mechanisms. To date, only the GA3 T6SSs have been shown to antagonize bacteria, and they target nearly all gut Bacteroidales species analyzed. This review delves more deeply into properties of the T6SSs of these human gut bacteria and the ecological outcomes of their synthesis in vivo.
Collapse
Affiliation(s)
- Michael J Coyne
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
211
|
Flores-Ríos R, Moya-Beltrán A, Pareja-Barrueto C, Arenas-Salinas M, Valenzuela S, Orellana O, Quatrini R. The Type IV Secretion System of ICE Afe1: Formation of a Conjugative Pilus in Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:30. [PMID: 30804894 PMCID: PMC6370655 DOI: 10.3389/fmicb.2019.00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/09/2019] [Indexed: 01/10/2023] Open
Abstract
The dispersal of mobile genetic elements and their gene cargo relies on type IV secretion systems (T4SS). In this work the ICEAfe1 Tra-type T4SS nanomachine, encoded in the publicly available genome of Acidithiobacillus ferrooxidans ATCC 23270TY, was characterized in terms of its organization, conservation, expression and mating bridge formation. Twenty-one conjugative genes grouped in four genetic clusters encode the ICEAfe1 T4SS, containing all the indispensable functions for the formation and stabilization of the pili and for DNA processing. The clusters' organization resembles that of other mobile genetic elements (such as plasmids and integrative and conjugative elements-ICEs). Sequence conservation, genetic organization and distribution of the tra system in the genomes of other sequenced Acidithiobacillus spp. suggests that the ICEAfe1 T4SS could mediate the lateral gene transfer between related bacteria. All ICEAfe1 T4SS genes are transcriptionally active and expressed from four independent operons. The transcriptional levels of selected marker genes increase in response to Mitomycin C treatment, a DNA damage elicitor that has acknowledged stimulatory effects on excision rates and gene expression of other ICEs, including ICEAfe1. Using a tailor-made pilin-antiserum against ICEAfe1 T4SS TraA pilin and epifluorescence microscopy, the presence of the conjugative pili on the cell surface of A. ferrooxidans could be demonstrated. Additionally, immunodetection assays, by immunogold, allowed the identification of pili-like extracellular structures. Together, the results obtained in this work demonstrate that the ICEAfe1 T4SS is phylogenetically conserved within the taxon, is expressed at mRNA and protein levels in vivo in the A. ferrooxidans type strain, and produces a pili-like structure of extracellular and intercellular localization in this model acidophile, supporting its functionality. Additional efforts will be required to prove conjugation of the ICEAfe1 or parts of this element through the cognate T4SS.
Collapse
Affiliation(s)
- Rodrigo Flores-Ríos
- Fundación Ciencia y Vida, Santiago, Chile.,Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia y Vida, Santiago, Chile.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | | | - Mauricio Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | | | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| |
Collapse
|
212
|
Husain F, Tang K, Veeranagouda Y, Boente R, Patrick S, Blakely G, Wexler HM. Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation. Microb Genom 2019; 3. [PMID: 29208130 PMCID: PMC5729914 DOI: 10.1099/mgen.0.000136] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems. Conjugative transposon-like genes within a transferred segment and within a putative integrative conjugative element (ICE5) ~45 kb downstream from the transferred segment both encode proteins that may be involved in the observed transfer. These data indicate that chromosomal transfer is a driver of antigenic diversity and nutrient adaptation in Bacteroides that (1) contributes to the dissemination of the extensive B. fragilis pan-genome, (2) allows rapid adaptation to a changing environment and (3) can confer pathogenic characteristics to host symbionts.
Collapse
Affiliation(s)
- Fasahath Husain
- Brentwood Biomedical Research Institute, Los Angeles, CA, USA
| | | | | | | | | | | | - Hannah M. Wexler
- Research, GLAVAHCS, 11301 Wilshire Blvd., 691/151J Bldg. 115, Room 312, Los Angeles, CA, USA
- *Correspondence: Hannah M. Wexler,
| |
Collapse
|
213
|
Bag S, Ghosh TS, Banerjee S, Mehta O, Verma J, Dayal M, Desigamani A, Kumar P, Saha B, Kedia S, Ahuja V, Ramamurthy T, Das B. Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota. MICROBIAL ECOLOGY 2019; 77:546-557. [PMID: 30009332 DOI: 10.1007/s00248-018-1228-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.
Collapse
Affiliation(s)
- Satyabrata Bag
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Tarini Shankar Ghosh
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Sayantan Banerjee
- Division of Infectious Diseases, Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ojasvi Mehta
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Jyoti Verma
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Mayanka Dayal
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Anbumani Desigamani
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Pawan Kumar
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Bipasa Saha
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Thandavarayan Ramamurthy
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO Box #04, Faridabad, Haryana, 121001, India.
| |
Collapse
|
214
|
Shi Y, Tian Z, Leclercq SO, Zhang H, Yang M, Zhang Y. Genetic characterization and potential molecular dissemination mechanism of tet(31) gene in Aeromonas caviae from an oxytetracycline wastewater treatment system. J Environ Sci (China) 2019; 76:259-266. [PMID: 30528016 DOI: 10.1016/j.jes.2018.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 06/09/2023]
Abstract
Recently, the rarely reported tet(31) tetracycline resistance determinant was commonly found in Aeromonas salmonicida, Gallibacterium anatis, and Oblitimonas alkaliphila isolated from farming animals and related environment. However, its distribution in other bacteria and potential molecular dissemination mechanism in environment are still unknown. The purpose of this study was to investigate the potential mechanism underlying dissemination of tet(31) by analysing the tet(31)-carrying fragments in A. caviae strains isolated from an aerobic biofilm reactor treating oxytetracycline bearing wastewater. Twenty-three A. caviae strains were screened for the tet(31) gene by polymerase chain reaction (PCR). Three strains (two harbouring tet(31), one not) were subjected to whole genome sequencing using the PacBio RSII platform. Seventeen A. caviae strains carried the tet(31) gene and exhibited high resistance levels to oxytetracycline with minimum inhibitory concentrations (MICs) ranging from 256 to 512 mg/L. tet(31) was comprised of the transposon Tn6432 on the chromosome of A. caviae, and Tn6432 was also found in 15 additional tet(31)-positive A. caviae isolates by PCR. More important, Tn6432 was located on an integrative conjugative element (ICE)-like element, which could mediate the dissemination of the tet(31)-carrying transposon Tn6432 between bacteria. Comparative analysis demonstrated that Tn6432 homologs with the structure ISCR2-∆phzF-tetR(31)-tet(31)-∆glmM-sul2 were also carried by A. salmonicida, G. anatis, and O. alkaliphila, suggesting that this transposon can be transferred between species and even genera. This work provides the first report on the identification of the tet(31) gene in A. caviae, and will be helpful in exploring the dissemination mechanisms of tet(31) in water environment.
Collapse
Affiliation(s)
- Yanhong Shi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sébastien Olivier Leclercq
- INRA, UMR1282 Infectiology and Public Health, F-37380 Nouzilly, France; François Rabelais University, UMR1282 Infectiology and Public Health, F-37000 Tours, France
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
215
|
Pan Z, Liu J, Zhang Y, Chen S, Ma J, Dong W, Wu Z, Yao H. A novel integrative conjugative element mediates transfer of multi-drug resistance between Streptococcus suis strains of different serotypes. Vet Microbiol 2019; 229:110-116. [DOI: 10.1016/j.vetmic.2018.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022]
|
216
|
Faucher M, Nouvel LX, Dordet-Frisoni E, Sagné E, Baranowski E, Hygonenq MC, Marenda MS, Tardy F, Citti C. Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer. PLoS Genet 2019; 15:e1007910. [PMID: 30668569 PMCID: PMC6358093 DOI: 10.1371/journal.pgen.1007910] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/01/2019] [Accepted: 12/19/2018] [Indexed: 11/18/2022] Open
Abstract
Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes (ca. 0.5 to 2.0 Mb) and their limited metabolic pathways. This view was recently challenged by the discovery of conjugative exchanges of large chromosomal fragments that equally affected all parts of the chromosome via an unconventional mechanism, so that the whole mycoplasma genome is potentially mobile. By combining next generation sequencing to classical mating and evolutionary experiments, the current study further explored the contribution and impact of this phenomenon on mycoplasma evolution and adaptation using the fluoroquinolone enrofloxacin (Enro), for selective pressure and the ruminant pathogen Mycoplasma agalactiae, as a model organism. For this purpose, we generated isogenic lineages that displayed different combination of spontaneous mutations in Enro target genes (gyrA, gyrB, parC and parE) in association to gradual level of resistance to Enro. We then tested whether these mutations can be acquired by a susceptible population via conjugative chromosomal transfer knowing that, in our model organism, the 4 target genes are scattered in three distinct and distant loci. Our data show that under antibiotic selective pressure, the time scale of the mutational pathway leading to high-level of Enro resistance can be readily compressed into a single conjugative step, in which several EnroR alleles were transferred from resistant to susceptible mycoplasma cells. In addition to acting as an accelerator for antimicrobial dissemination, mycoplasma chromosomal transfer reshuffled genomes beyond expectations and created a mosaic of resistant sub-populations with unpredicted and unrelated features. Our findings provide insights into the process that may drive evolution and adaptability of several pathogenic Mycoplasma spp. via an unconventional conjugative mechanism.
Collapse
Affiliation(s)
- Marion Faucher
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | | | | | - Eveline Sagné
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | | | | | - Marc-Serge Marenda
- Asia-Pacific Centre for Animal Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Florence Tardy
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | - Christine Citti
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- * E-mail: (LXN); (CC)
| |
Collapse
|
217
|
Blesa A, Sánchez M, Sacristán-Horcajada E, González-de la Fuente S, Peiró R, Berenguer J. Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp. Microorganisms 2019; 7:microorganisms7010025. [PMID: 30669685 PMCID: PMC6352166 DOI: 10.3390/microorganisms7010025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 11/28/2022] Open
Abstract
A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.
Collapse
Affiliation(s)
- Alba Blesa
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain.
| | - Mercedes Sánchez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Eva Sacristán-Horcajada
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Sandra González-de la Fuente
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Ramón Peiró
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (CBMSO), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| |
Collapse
|
218
|
Botelho J, Roberts AP, León-Sampedro R, Grosso F, Peixe L. Carbapenemases on the move: it's good to be on ICEs. Mob DNA 2018; 9:37. [PMID: 30574213 PMCID: PMC6299553 DOI: 10.1186/s13100-018-0141-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022] Open
Abstract
Background The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored. Results Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encoding genes (CEGs). Most CEGs of the MPFG class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons were located within Tn3-like and composite transposons. Conserved attachment site could be predicted for the MPFG class ICEs. MPFT class ICEs carried the CEGs within composite transposons which were not associated with integrons. Conclusions The data presented here provides a global snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciated contribution of these elements to the evolution and dissemination of antibiotic resistance on P. aeruginosa. Electronic supplementary material The online version of this article (10.1186/s13100-018-0141-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- João Botelho
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Adam P Roberts
- 2Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.,3Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ricardo León-Sampedro
- 4Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Filipa Grosso
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Luísa Peixe
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| |
Collapse
|
219
|
Fu L, Wang S, Zhang Z, Yan X, Yang X, Zhang L, Li Y, Wang G, Zhao K, Zhou Y. Co-carrying of KPC-2, NDM-5, CTX-M-3 and CTX-M-65 in three plasmids with serotype O89: H10 Escherichia coli strain belonging to the ST2 clone in China. Microb Pathog 2018; 128:1-6. [PMID: 30576714 DOI: 10.1016/j.micpath.2018.12.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 01/09/2023]
Abstract
Carbapenem-resistant Enterobacteriaceae strains as a new serious threat for the public health have been increasingly reported worldwide. In this study, one multi-resistant Escherichia coli strain ZSH6 which co-carried blaKPC-2, blaNDM-5 and blaCTX-M, was isolated from human blood sample. By using plasmid conjugation experiments, ZSH6 was found to harbor three plasmids carrying the blaNDM-5 gene, the blaKPC-2 and blaCTX-M gene, respectively. Whole-genome sequencing of ZSH6 yielded 122 scaffolds of chromosomal DNA and three circular plasmids including pZSH6-blaKPC-2 (46,319 bp), pZSH6-blaNDM-5 (46,161bp) and pZSH6-blaCTX-M (184,723). The isolate was classified to Sequence Type 2 and to the O89: H10 serotype. The results of genome analyses revealed that ZSH6 carried three virulence factors (capU, gad and iss) and twenty resistance genes [blaKPC-2blaNDM-5, blaCTX-M-3, blaCTX-M-65, blaTEM-1, floR, tet(A), tet(B), dfrA17, aadA5, sul1, mdf(A), mph(A), erm(B), aph(3')-Ia, aph(3')-Ib, aph(4)-Ia, aph(6)-Id, aac(3)-Iva, aac(3)-IId]. Therefore, the co-existence of such a large number of resistance genes in multiple plasmids making ZSH6 highly resistant to almost all kinds of commonly used antibiotics, and brings a serious challenge for resistance control and clinical treatment of infections caused by this bacterium.
Collapse
Affiliation(s)
- Li Fu
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China; Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Shanmei Wang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China; The People's Hospital of Henan Province, Zhengzhou, 450000, Henan, China
| | - Zhikun Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Xiangjing Yan
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Xingyou Yang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Luhua Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Ying Li
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Guangxi Wang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, 610052, Sichuan, China.
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, China.
| |
Collapse
|
220
|
Rehman MA, Yin X, Zaheer R, Goji N, Amoako KK, McAllister T, Pritchard J, Topp E, Diarra MS. Genotypes and Phenotypes of Enterococci Isolated From Broiler Chickens. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00083] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
|
221
|
Abstract
The genus Streptococcus includes Gram-positive organisms shaped in cocci and organized in chains. They are commensals, pathogens, and opportunistic pathogens for humans and animals. Most Streptococcus species of veterinary relevance have a specific ecological niche, such as S. uberis, which is almost exclusively an environmental pathogen causing bovine mastitis. In contrast, S. suis can be considered as a true zoonotic pathogen, causing specific diseases in humans after contact with infected animals or derived food products. Finally, Streptococcus species such as S. agalactiae can be sporadically zoonotic, even though they are pathogens of both humans and animals independently. For clarification, a short taxonomical overview will be given here to highlight the diversity of streptococci that infect animals. Several families of antibiotics are used to treat animals for streptococcal infections. First-line treatments are penicillins (alone or in combination with aminoglycosides), macrolides and lincosamides, fluoroquinolones, and tetracyclines. Because of the selecting role of antibiotics, resistance phenotypes have been reported in streptococci isolated from animals worldwide. Globally, the dynamic of resistance acquisition in streptococci is slower than what is experienced in Enterobacteriaceae, probably due to the much more limited horizontal spread of resistance genes. Nonetheless, transposons or integrative and conjugative elements can disseminate resistance determinants among streptococci. Besides providing key elements on the prevalence of resistance in streptococci from animals, this article will also largely consider the mechanisms and molecular epidemiology of the major types of resistance to antimicrobials encountered in the most important streptococcal species in veterinary medicine.
Collapse
|
222
|
Gillings M, Westoby M, Ghaly T. Pollutants That Replicate: Xenogenetic DNAs. Trends Microbiol 2018; 26:975-977. [DOI: 10.1016/j.tim.2018.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 01/12/2023]
|
223
|
Gong L, Yu P, Zheng H, Gu W, He W, Tang Y, Wang Y, Dong Y, Peng X, She Q, Xie L, Chen L. Comparative genomics for non-O1/O139 Vibrio cholerae isolates recovered from the Yangtze River Estuary versus V. cholerae representative isolates from serogroup O1. Mol Genet Genomics 2018; 294:417-430. [PMID: 30488322 DOI: 10.1007/s00438-018-1514-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/13/2018] [Indexed: 01/03/2023]
Abstract
Vibriocholerae, which is autochthonous to estuaries worldwide, can cause human cholera that is still pandemic in developing countries. A number of V. cholerae isolates of clinical and environmental origin worldwide have been subjected to genome sequencing to address their phylogenesis and bacterial pathogenesis, however, little genome information is available for V. cholerae isolates derived from estuaries, particularly in China. In this study, we determined the complete genome sequence of V. cholerae CHN108B (non-O1/O139 serogroup) isolated from the Yangtze River Estuary, China and performed comparative genome analysis between CHN108B and other eight representative V. cholerae isolates. The 4,168,545-bp V. cholerae CHN108B genome (47.2% G+C) consists of two circular chromosomes with 3,691 predicted protein-encoding genes. It has 110 strain-specific genes, the highest number among the eight representative V. cholerae whole genomes from serogroup O1: there are seven clinical isolates linked to cholera pandemics (1937-2010) and one environmental isolate from Brazil. Various mobile genetic elements (such as insertion sequences, prophages, integrative and conjugative elements, and super-integrons) were identified in the nine V. cholerae genomes of clinical and environmental origin, indicating that the bacterium undergoes extensive genetic recombination via lateral gene transfer. Comparative genomics also revealed different virulence and antimicrobial resistance gene patterns among the V. cholerae isolates, suggesting some potential virulence factors and the rising development of resistance among pathogenic V. cholerae. Additionally, draft genome sequences of multiple V. cholerae isolates recovered from the Yangtze River Estuary were also determined, and comparative genomics revealed many genes involved in specific metabolism pathways, which are likely shaped by the unique estuary environment. These results provide additional evidence of V. cholerae genome plasticity and will facilitate better understanding of the genome evolution and pathogenesis of this severe water-borne pathogen worldwide.
Collapse
Affiliation(s)
- Li Gong
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Pan Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
| | - Wenyi Gu
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, People's Republic of China
| | - Wei He
- Shanghai Hanyu Bio-lab, Shanghai, People's Republic of China
| | - Yadong Tang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Yaping Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Yue Dong
- University of Oklahoma, Norman, USA
| | - Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Qunxin She
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai, People's Republic of China.
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China.
| |
Collapse
|
224
|
Waskito LA, Yih-Wu J, Yamaoka Y. The role of integrating conjugative elements in Helicobacter pylori: a review. J Biomed Sci 2018; 25:86. [PMID: 30497458 PMCID: PMC6264033 DOI: 10.1186/s12929-018-0489-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/16/2018] [Indexed: 12/15/2022] Open
Abstract
The genome of Helicobacter pylori contains many putative genes, including a genetic region known as the Integrating Conjugative Elements of H. pylori type four secretion system (ICEHptfs). This genetic regions were originally termed as "plasticity zones/regions" due to the great genetic diversity between the original two H. pylori whole genome sequences. Upon analysis of additional genome sequences, the regions were reported to be extremely common within the genome of H. pylori. Moreover, these regions were also considered conserved rather than genetically plastic and were believed to act as mobile genetic elements transferred via conjugation. Although ICEHptfs(s) are highly conserved, these regions display great allele diversity, especially on ICEHptfs4, with three different subtypes: ICEHptfs4a, 4b, and 4c. ICEHptfs were also reported to contain a novel type 4 secretion system (T4SS) with both epidemiological and in vitro infection model studies highlighting that this novel T4SS functions primarily as a virulence factor. However, there is currently no information regarding the structure, the genes responsible for forming the T4SS, and the interaction between this T4SS and other virulence genes. Unlike the cag pathogenicity island (PAI), which contains CagA, a gene found to be essential for H. pylori virulence, these novel T4SSs have not yet been reported to contain genes that contribute significant effects to the entire system. This notion prompted the hypothesis that these novel T4SSs may have different mechanisms involving cag PAI.
Collapse
Affiliation(s)
- Langgeng Agung Waskito
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu City, Oita, Japan.,Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Jeng Yih-Wu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu City, Oita, Japan. .,Department of Medicine, Gastroenterology Section, Baylor College of Medicine, Houston, TX, USA. .,Global Oita Medical Advanced Research Center for Health, Yufu City, Oita, Japan.
| |
Collapse
|
225
|
Intensive targeting of regulatory competence genes by transposable elements in streptococci. Mol Genet Genomics 2018; 294:531-548. [DOI: 10.1007/s00438-018-1507-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/21/2018] [Indexed: 10/27/2022]
|
226
|
Gillis A, Fayad N, Makart L, Bolotin A, Sorokin A, Kallassy M, Mahillon J. Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensis. FEMS Microbiol Rev 2018; 42:829-856. [PMID: 30203090 PMCID: PMC6199540 DOI: 10.1093/femsre/fuy034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Bacillus thuringiensis is a well-known biopesticide that has been used for more than 80 years. This spore-forming bacterium belongs to the group of Bacillus cereus that also includes, among others, emetic and diarrheic pathotypes of B. cereus, the animal pathogen Bacillus anthracis and the psychrotolerant Bacillus weihenstephanensis. Bacillus thuringiensis is rather unique since it has adapted its lifestyle as an efficient pathogen of specific insect larvae. One of the peculiarities of B. thuringiensis strains is the extent of their extrachromosomal pool, with strains harbouring more than 10 distinct plasmid molecules. Among the numerous serovars of B. thuringiensis, 'israelensis' is certainly emblematic since its host spectrum is apparently restricted to dipteran insects like mosquitoes and black flies, vectors of human and animal diseases such as malaria, yellow fever, or river blindness. In this review, the putative role of the mobile gene pool of B. thuringiensis serovar israelensis in its pathogenicity and dedicated lifestyle is reviewed, with specific emphasis on the nature, diversity, and potential mobility of its constituents. Variations among the few related strains of B. thuringiensis serovar israelensis will also be reported and discussed in the scope of this specialised insect pathogen, whose lifestyle in the environment remains largely unknown.
Collapse
Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Nancy Fayad
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
- Laboratory of Biodiversity and Functional Genomics (BGF), Faculty of Sciences, Université Saint-Joseph, 1107 2050 Beirut, Lebanon
| | - Lionel Makart
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Alexander Bolotin
- UMR1319 Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Alexei Sorokin
- UMR1319 Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Mireille Kallassy
- Laboratory of Biodiversity and Functional Genomics (BGF), Faculty of Sciences, Université Saint-Joseph, 1107 2050 Beirut, Lebanon
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| |
Collapse
|
227
|
Yadav M, Rathore JS. TAome analysis of type-II toxin-antitoxin system from Xenorhabdus nematophila. Comput Biol Chem 2018; 76:293-301. [DOI: 10.1016/j.compbiolchem.2018.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/23/2018] [Accepted: 07/07/2018] [Indexed: 12/23/2022]
|
228
|
Sun D. Pull in and Push Out: Mechanisms of Horizontal Gene Transfer in Bacteria. Front Microbiol 2018; 9:2154. [PMID: 30237794 PMCID: PMC6135910 DOI: 10.3389/fmicb.2018.02154] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/22/2018] [Indexed: 01/06/2023] Open
Abstract
Horizontal gene transfer (HGT) plays an important role in bacterial evolution. It is well accepted that DNA is pulled/pushed into recipient cells by conserved membrane-associated DNA transport systems, which allow the entry of only single-stranded DNA (ssDNA). However, recent studies have uncovered a new type of natural bacterial transformation in which double-stranded DNA (dsDNA) is taken up into the cytoplasm, thus complementing the existing methods of DNA transfer among bacteria. Regulated by the stationary-phase regulators RpoS and cAMP receptor protein (CRP), Escherichia coli establishes competence for natural transformation with dsDNA, which occurs in agar plates. To pass across the outer membrane, a putative channel, which may compete for the substrate with the porin OmpA, may mediate the transfer of exogenous dsDNA into the cell. To pass across the inner membrane, dsDNA may be bound to the periplasmic protein YdcS, which delivers it into the inner membrane channel formed by YdcV. The discovery of cell-to-cell contact-dependent plasmid transformation implies the presence of additional mechanism(s) of transformation. This review will summarize the current knowledge about mechanisms of HGT with an emphasis on recent progresses regarding non-canonical mechanisms of natural transformation. Fully understanding the mechanisms of HGT will provide a foundation for monitoring and controlling multidrug resistance.
Collapse
Affiliation(s)
- Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| |
Collapse
|
229
|
Begum J, Mir NA, Dev K, Khan IA. Dynamics of antibiotic resistance with special reference to Shiga toxin-producing Escherichia coli infections. J Appl Microbiol 2018; 125:1228-1237. [PMID: 29957827 DOI: 10.1111/jam.14034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 11/26/2022]
Abstract
The discovery of antibiotics was paralleled by the evolution of antibiotic resistance which is probably the best example of contemporary evolution in action. The selection pressure, imposed by indiscriminate use of antibiotics, has changed the scale, mode and tempo of antibiotic resistance evolution. The presence of multidrug resistance, wide range of adaptability features and the infectivity make antibiotic resistance of Shiga toxin-producing Escherichia coli (STEC) more dangerous. The characterization, prevalence and the virulence factors of STEC have been profusely reported, whereas, the antibiotic resistance has been largely ignored because the antibiotic use in STEC infections is controversial. Thus, the current review has focussed on the source, evolution, persistence, mechanism, dissemination and control of antibiotic resistance viz-a-viz the STEC infections. The resistance development occurs by the inactivation of antibiotics, regulating the membrane permeability, modification of natural antibiotic targets or the use of efflux pumps against antibiotics. And, the dissemination of resistance genes occurs vertically by DNA replication and horizontally by conjugation, transduction and transformation. The prevention of development and dissemination of antibiotic resistance needs international public health bodies to rationalize the antibiotic use, prevent the flux of antibiotics into the environment, develop the rapid diagnostics tests, undertake proper surveillance of antibiotic resistance, promote the research on antibiotic resistance prevention, promote the research and development of novel alternative antibiotics, and encourage the widespread social awareness campaigns against the inappropriate antibiotic usage.
Collapse
Affiliation(s)
- J Begum
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, GBPUAT, Panthnagar, Udham Singh Nagar, Uttarakhand, India
| | - N A Mir
- ICAR- Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - K Dev
- ICAR- Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - I A Khan
- ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| |
Collapse
|
230
|
Molenda O, Tang S, Lomheim L, Gautam VK, Lemak S, Yakunin AF, Maxwell KL, Edwards EA. Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes. ISME JOURNAL 2018; 13:24-38. [PMID: 30104577 DOI: 10.1038/s41396-018-0254-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 01/12/2023]
Abstract
Dehalococcoides mccartyi are obligate organohalide-respiring bacteria that play an important detoxifying role in the environment. They have small genomes (~1.4 Mb) with a core region interrupted by two high plasticity regions (HPRs) containing dozens of genes encoding reductive dehalogenases involved in organohalide respiration. The genomes of eight new strains of D. mccartyi were closed from metagenomic data from a related set of enrichment cultures, bringing the total number of genomes to 24. Two of the newly sequenced strains and three previously sequenced strains contain CRISPR-Cas systems. These D. mccartyi CRISPR-Cas systems were found to primarily target prophages and genomic islands. The genomic islands were identified either as integrated into D. mccartyi genomes or as circular extrachromosomal elements. We observed active circularization of the integrated genomic island containing vcrABC operon encoding the dehalogenase (VcrA) responsible for the transformation of vinyl chloride to non-toxic ethene. We interrogated archived DNA from established enrichment cultures and found that the CRISPR array acquired three new spacers in 11 years. These data provide a glimpse into dynamic processes operating on the genomes distinct to D. mccartyi strains found in enrichment cultures and provide the first insights into possible mechanisms of lateral DNA exchange in D. mccartyi.
Collapse
Affiliation(s)
- Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Vasu K Gautam
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada. .,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
231
|
Chen Y, Hammer EE, Richards VP. Phylogenetic signature of lateral exchange of genes for antibiotic production and resistance among bacteria highlights a pattern of global transmission of pathogens between humans and livestock. Mol Phylogenet Evol 2018; 125:255-264. [DOI: 10.1016/j.ympev.2018.03.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 01/08/2023]
|
232
|
Li Y, Li Y, Fernandez Crespo R, Leanse LG, Langford PR, Bossé JT. Characterization of the Actinobacillus pleuropneumoniae SXT-related integrative and conjugative element ICEApl2 and analysis of the encoded FloR protein: hydrophobic residues in transmembrane domains contribute dynamically to florfenicol and chloramphenicol efflux. J Antimicrob Chemother 2018; 73:57-65. [PMID: 29029160 PMCID: PMC5890775 DOI: 10.1093/jac/dkx342] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/23/2017] [Indexed: 11/29/2022] Open
Abstract
Objectives To characterize ICEApl2, an SXT-related integrative and conjugative element (ICE) found in a clinical isolate of the porcine pathogen Actinobacillus pleuropneumoniae, and analyse the functional nature of the encoded FloR. Methods ICEApl2 was identified in the genome of A. pleuropneumoniae MIDG3553. Functional analysis was done using conjugal transfer experiments. MIDG3553 was tested for susceptibility to the antimicrobials for which resistance genes are present in ICEApl2. Lack of florfenicol/chloramphenicol resistance conferred by the encoded FloR protein was investigated by cloning and site-directed mutagenesis experiments in Escherichia coli. Results ICEApl2 is 92660 bp and contains 89 genes. Comparative sequence analysis indicated that ICEApl2 is a member of the SXT/R391 ICE family. Conjugation experiments showed that, although ICEApl2 is capable of excision from the chromosome, it is not self-transmissible. ICEApl2 encodes the antimicrobial resistance genes floR, strAB, sul2 and dfrA1, and MIDG3553 is resistant to streptomycin, sulfisoxazole and trimethoprim, but not florfenicol or chloramphenicol. Cloning and site-directed mutagenesis of the floR gene revealed the importance of the nature of the hydrophobic amino acid residues at positions 160 and 228 in FloR for determining resistance to florfenicol and chloramphenicol. Conclusions Our results indicate that the nature of hydrophobic residues at positions 160 and 228 of FloR contribute dynamically to specific efflux of florfenicol and chloramphenicol, although some differences in resistance levels may depend on the bacterial host species. This is also, to our knowledge, the first description of an SXT/R391 ICE in A. pleuropneumoniae or any member of the Pasteurellaceae.
Collapse
Affiliation(s)
- Yinghui Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK.,Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Roberto Fernandez Crespo
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Leon G Leanse
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| |
Collapse
|
233
|
Botelho J, Grosso F, Peixe L. Unravelling the genome of a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235 reveals an integrative conjugative element housing a blaGES-6 carbapenemase. J Antimicrob Chemother 2018; 73:77-83. [PMID: 29029083 DOI: 10.1093/jac/dkx337] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022] Open
Abstract
Objectives In Pseudomonas aeruginosa, the blaGES-6 carbapenemase gene was previously associated with an In1076 class I integron. Here, we conducted a genome-based analysis and explored the genetic platform associated with the mobility of this gene. Methods WGS of a blaGES-6-harbouring P. aeruginosa isolate (FFUP_PS_690) was performed with Illumina HiSeq, de novo assembly was performed using SPAdes and subsequent bioinformatic analysis was performed concerning antibiotic resistance genes, virulence features and mobile genetic elements. Results The FFUP_PS_690 isolate belongs to the ST235 high-risk clone and houses a novel integrative conjugative element (ICE), hereby named ICEPae690. This clc-like ICE comprises the blaGES-6-harbouring In1076 integron and specific modules. An ExoU island A variant was also identified. Conclusions The presence of a 'hitch-hiking' blaGES-6-harbouring In1076 integron in an ICE and an exoU-carrying genomic island highlight the potential spread of these elements through conjugation and/or clonal expansion of the ST235 lineage.
Collapse
Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| |
Collapse
|
234
|
Obi CC, Vayla S, de Gannes V, Berres ME, Walker J, Pavelec D, Hyman J, Hickey WJ. The Integrative Conjugative Element clc (ICEclc) of Pseudomonas aeruginosa JB2. Front Microbiol 2018; 9:1532. [PMID: 30050515 PMCID: PMC6050381 DOI: 10.3389/fmicb.2018.01532] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022] Open
Abstract
Integrative conjugative elements (ICE) are a diverse group of chromosomally integrated, self-transmissible mobile genetic elements (MGE) that are active in shaping the functions of bacteria and bacterial communities. Each type of ICE carries a characteristic set of core genes encoding functions essential for maintenance and self-transmission, and cargo genes that endow on hosts phenotypes beneficial for niche adaptation. An important area to which ICE can contribute beneficial functions is the biodegradation of xenobiotic compounds. In the biodegradation realm, the best-characterized ICE is ICEclc, which carries cargo genes encoding for ortho-cleavage of chlorocatechols (clc genes) and aminophenol metabolism (amn genes). The element was originally identified in the 3-chlorobenzoate-degrader Pseudomonas knackmussii B13, and the closest relative is a nearly identical element in Burkholderia xenovorans LB400 (designated ICEclc-B13 and ICEclc-LB400, respectively). In the present report, genome sequencing of the o-chlorobenzoate degrader Pseudomonas aeruginosa JB2 was used to identify a new member of the ICEclc family, ICEclc-JB2. The cargo of ICEclc-JB2 differs from that of ICEclc-B13 and ICEclc-LB400 in consisting of a unique combination of genes that encode for the utilization of o-halobenzoates and o-hydroxybenzoate as growth substrates (ohb genes and hyb genes, respectively) and which are duplicated in a tandem repeat. Also, ICEclc-JB2 lacks an operon of regulatory genes (tciR-marR-mfsR) that is present in the other two ICEclc, and which controls excision from the host. Thus, the mechanisms regulating intracellular behavior of ICEclc-JB2 may differ from that of its close relatives. The entire tandem repeat in ICEclc-JB2 can excise independently from the element in a process apparently involving transposases/insertion sequence associated with the repeats. Excision of the repeats removes important niche adaptation genes from ICEclc-JB2, rendering it less beneficial to the host. However, the reduced version of ICEclc-JB2 could now acquire new genes that might be beneficial to a future host and, consequently, to the survival of ICEclc-JB2. Collectively, the present identification and characterization of ICEclc-JB2 provides insights into roles of MGE in bacterial niche adaptation and the evolution of catabolic pathways for biodegradation of xenobiotic compounds.
Collapse
Affiliation(s)
- Chioma C Obi
- Department of Biological Sciences, Bells University of Technology, Ota, Nigeria
| | - Shivangi Vayla
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Vidya de Gannes
- Department of Food Production, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Mark E Berres
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jason Walker
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Derek Pavelec
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Joshua Hyman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - William J Hickey
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
235
|
de Santis B, Stockhofe N, Wal JM, Weesendorp E, Lallès JP, van Dijk J, Kok E, De Giacomo M, Einspanier R, Onori R, Brera C, Bikker P, van der Meulen J, Kleter G. Case studies on genetically modified organisms (GMOs): Potential risk scenarios and associated health indicators. Food Chem Toxicol 2018; 117:36-65. [DOI: 10.1016/j.fct.2017.08.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/03/2017] [Accepted: 08/22/2017] [Indexed: 01/07/2023]
|
236
|
ICEAplChn1, a novel SXT/R391 integrative conjugative element (ICE), carrying multiple antibiotic resistance genes in Actinobacillus pleuropneumoniae. Vet Microbiol 2018; 220:18-23. [DOI: 10.1016/j.vetmic.2018.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 11/18/2022]
|
237
|
Beker M, Rose S, Lykkebo CA, Douthwaite S. Integrative and Conjugative Elements (ICEs) in Pasteurellaceae Species and Their Detection by Multiplex PCR. Front Microbiol 2018; 9:1329. [PMID: 29997583 PMCID: PMC6028734 DOI: 10.3389/fmicb.2018.01329] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/30/2018] [Indexed: 11/13/2022] Open
Abstract
Strains of the Pasteurellaceae bacteria Pasteurella multocida and Mannheimia haemolytica are major etiological agents of bovine respiratory disease (BRD). Treatment of BRD with antimicrobials is becoming more challenging due to the increasing occurrence of resistance in infecting strains. In Pasteurellaceae strains exhibiting resistance to multiple antimicrobials including aminoglycosides, beta-lactams, macrolides and sulfonamides, the resistance determinants are often chromosomally encoded within integrative and conjugative elements (ICEs). To gain a more comprehensive picture of ICE structures, we sequenced the genomes of six strains of P. multocida and four strains of M. haemolytica; all strains were independent isolates and eight of them were multiple-resistant. ICE sequences varied in size from 49 to 79 kb, and were comprised of an array of conserved genes within a core region and varieties of resistance genes within accessory regions. These latter regions mainly account for the variation in the overall ICE sizes. From the sequence data, we developed a multiplex PCR assay targeting four conserved core genes required for integration and maintenance of ICE structures. Application of this assay on 75 isolates of P. multocida and M. haemolytica reveals how the presence and structures of ICEs are related to their antibiotic resistance phenotypes. The assay is also applicable to other members of the Pasteurellaceae family including Histophilus somni and indicates how clustering and dissemination of the resistance genes came about.
Collapse
Affiliation(s)
- Michal Beker
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Simon Rose
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Claus A Lykkebo
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Stephen Douthwaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
238
|
Abstract
Vibrio is a genus of ubiquitous heterotrophic bacteria found in aquatic environments. Although they are a small percentage of the bacteria in these environments, vibrios can predominate during blooms. Vibrios also play important roles in the degradation of polymeric substances, such as chitin, and in other biogeochemical processes. Vibrios can be found as free-living bacteria, attached to particles, or associated with other organisms in a mutualistic, commensal, or pathogenic relationship. This review focuses on vibrio ecology and genome plasticity, which confers an ability to adapt to new niches and is driven, at least in part, by horizontal gene transfer (HGT). The extent of HGT and its role in pathogen emergence are discussed based on genomic studies of environmental and pathogenic vibrios, mobile genetically encoded virulence factors, and mechanistic studies on the different modes of HGT.
Collapse
Affiliation(s)
- Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, F-29280 Plouzané, France.,Laboratoire de Biologie Intégrative des Modèles Marins, Station Biologique de Roscoff, CNRS UMR 8227, UPMC Paris 06, Sorbonne Universités, F-29688 Roscoff CEDEX, France;
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland;
| |
Collapse
|
239
|
Acquisition of resistance to carbapenem and macrolide-mediated quorum sensing inhibition by Pseudomonas aeruginosa via ICE Tn4371 6385. Commun Biol 2018; 1:57. [PMID: 30271939 PMCID: PMC6123621 DOI: 10.1038/s42003-018-0064-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/03/2018] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa can cause life-threatening infections in immunocompromised patients. The first-line agents to treat P. aeruginosa infections are carbapenems. However, the emergence of carbapenem-resistant P. aeruginosa strains greatly compromised the effectiveness of carbapenem treatment, which makes the surveillance on their spreading and transmission important. Here we characterized the full-length genomes of two carbapenem-resistant P. aeruginosa clinical isolates that are capable of producing New Delhi metallo-β-lactamase-1 (NDM-1). We show that blaNDM-1 is carried by a novel integrative and conjugative element (ICE) ICETn43716385, which also carries the macrolide resistance gene msr(E) and the florfenicol resistance gene floR. By exogenously expressing msr(E) in P. aeruginosa laboratory strains, we show that Msr(E) can abolish azithromycin-mediated quorum sensing inhibition in vitro and anti-Pseudomonas effect in vivo. We conclude that ICEs are important in transmitting carbapenem resistance, and that anti-virulence treatment of P. aeruginosa infections using sub-inhibitory concentrations of macrolides can be challenged by horizontal gene transfer. Yichen Ding et al. identify a novel integrative and conjugative element that confers Pseudomonas aeruginosa with resistance to carbapenem, the last-resort drug for susceptable Gram-negative bacterial infections. This study also shows how antivirulence treatment for P. aeruginosainfections can be challenged by horizontal gene transfer.
Collapse
|
240
|
Hall JPJ, Brockhurst MA, Harrison E. Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0424. [PMID: 29061896 DOI: 10.1098/rstb.2016.0424] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2017] [Indexed: 12/26/2022] Open
Abstract
In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
Collapse
Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ellie Harrison
- P3 Institute, Department of Animal and Plant Sciences, Arthur Willis Environment Centre, University of Sheffield, 1 Maxfield Avenue, Sheffield S10 1AE, UK
| |
Collapse
|
241
|
Fang Y, Wang Y, Li Z, Liu Z, Li X, Diao B, Kan B, Wang D. Distribution and Genetic Characteristics of SXT/R391 Integrative Conjugative Elements in Shewanella spp. From China. Front Microbiol 2018; 9:920. [PMID: 29867831 PMCID: PMC5958206 DOI: 10.3389/fmicb.2018.00920] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/20/2018] [Indexed: 01/31/2023] Open
Abstract
The genus Shewanella consists of facultatively anaerobic Gram-negative bacteria, which are regarded as potential agents of food contamination and opportunistic human pathogens. Information about the distribution and genetic characteristics of SXT/R391 integrative conjugative elements (ICEs) in Shewanella species is limited. Here, 91 Shewanella strains collected from diverse samples in China were studied for the presence of SXT/R391 ICEs. Three positive strains, classified as Shewanella upenei, were obtained from patients and water from a local mill. In light of their close clonal relationships and high sequence similarity, a representative ICE was selected and designated ICESupCHN110003. The BLASTn searches against GenBank showed that ICEVchBan5 was most closely related to ICESupCHN110003, with the coverage of 76% and identity of 99%. The phylogenetic tree of concatenated core genes demonstrated that ICESupCHN110003 formed a distinct branch outside the cluster comprising ICEValA056-1, ICEPmiCHN2410, and ICEPmiChn1. Comparison of the genetic structures revealed that ICESupCHN110003 encoded uncommon genes in hotspots, such as specific type III restriction-modification system, conferring adaptive functions to the host. Based on the low coverage in the sequence analysis, independent clade in the phylogenetic tree, and unique inserted fragments in hotspots, ICESupCHN110003 represented a novel SXT/R391 element, which widened the list of ICEs. Furthermore, the antibiotic resistance genes floR, strA, strB, and sul2 in ICESupCHN110003 and resistance to multiple drugs of the positive isolates were detected. A cross-species transfer capability of the SXT/R391 ICEs was also discovered. In summary, it is necessary to reinforce continuous surveillance of SXT/R391 ICEs in the genus Shewanella.
Collapse
Affiliation(s)
- Yujie Fang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yonglu Wang
- Ma'anshan Center for Disease Control and Prevention, Ma'anshan, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zongdong Liu
- Laizhou Center for Disease Control and Prevention, Laizhou, China
| | - Xinyue Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Duochun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
242
|
Zeaiter Z, Mapelli F, Crotti E, Borin S. Methods for the genetic manipulation of marine bacteria. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
243
|
Chu HY, Sprouffske K, Wagner A. Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing. BMC Evol Biol 2018; 18:54. [PMID: 29673327 PMCID: PMC5909237 DOI: 10.1186/s12862-018-1164-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/22/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors. RESULTS At the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination. CONCLUSIONS To our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.
Collapse
Affiliation(s)
- Hoi Yee Chu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Kathleen Sprouffske
- The Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, 1015 Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, 1015 Lausanne, Switzerland
- Santa Fe Institute, Santa Fe, New Mexico USA
| |
Collapse
|
244
|
Olsen I, Chen T, Tribble GD. Genetic exchange and reassignment in Porphyromonas gingivalis. J Oral Microbiol 2018; 10:1457373. [PMID: 29686783 PMCID: PMC5907639 DOI: 10.1080/20002297.2018.1457373] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/19/2018] [Indexed: 12/30/2022] Open
Abstract
Porphyromonas gingivalis is considered a keystone pathogen in adult periodontitis but has also been associated with systemic diseases. It has a myriad of virulence factors that differ between strains. Genetic exchange and intracellular genome rearrangements may be responsible for the variability in the virulence of P. gingivalis. The present review discusses how the exchange of alleles can convert this bacterium from commensalistic to pathogenic and potentially shapes the host-microbe environment from homeostasis to dysbiosis. It is likely that genotypes of P. gingivalis with increased pathogenic adaptations may spread in the human population with features acquired from a common pool of alleles. The exact molecular mechanisms that trigger this exchange are so far unknown but they may be elicited by environmental pressure.
Collapse
Affiliation(s)
- Ingar Olsen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Tsute Chen
- Department of Microbiology, Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Gena D Tribble
- Department of Periodontics and Dental Hygiene, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| |
Collapse
|
245
|
Safety assessment and functional properties of four enterococci strains isolated from regional Argentinean cheese. Int J Food Microbiol 2018; 277:1-9. [PMID: 29669304 DOI: 10.1016/j.ijfoodmicro.2018.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/07/2018] [Accepted: 04/07/2018] [Indexed: 01/22/2023]
Abstract
The members of the Enterococcus genus are widely distributed in nature. Its strains have been extensively reported to be present in plant surfaces, soil, water and food. In an attempt to assess their potential application in food industry, four Enterococcus faecium group-strains recently isolated from Argentinean regional cheese products were evaluated using a combination of whole genome analyses and in vivo assays. In order to identify these microorganisms at species level, in silico analyses using their newly reported sequences were conducted. The average nucleotide identity (ANI), in silico DNA-DNA hybridization, and phylogenomic trees constructed using core genome data allowed IQ110, GM70 and GM75 strains to be classified as E. faecium while IQ23 strain was identified as E. durans. Besides their common origin, the strains showed differences in their genetic structure and mobile genetic element content. Furthermore, it was possible to determine the absence or presence of specific features related to growth in milk, cheese ripening, probiotic capability and gut adaptation including sugar, amino acid, and peptides utilization, flavor compound production, bile salt tolerance as well as biogenic amine production. Remarkably, all strains encoded for peptide permeases, maltose utilization, bile salt tolerance, diacetyl and tyramine production genes. On the other hand, some variability was observed regarding citrate and lactose utilization, esterase, and cell wall-associated proteinase. In addition, while strains were predicted to be non-human pathogens by the in silico inspection of pathogenicity and virulence factors, only the GM70 strain proved to be non-virulent in Galleria mellonella model. In conclusion, we propose that, in order to improve the rational selection of strains for industrial applications, a holistic approach involving a comparative genomic analysis of positive and negative features as well as in vivo evaluation of virulence behavior should be performed.
Collapse
|
246
|
Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. Sci Rep 2018; 8:5550. [PMID: 29615803 PMCID: PMC5882942 DOI: 10.1038/s41598-018-23858-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Integrative and conjugative elements (ICEs) comprise ubiquitous large mobile regions in prokaryotic chromosomes that transmit vertically to daughter cells and transfer horizontally to distantly related lineages. Their evolutionary success originates in maximized combined ICE-host fitness trade-offs, but how the ICE impacts on the host metabolism and physiology is poorly understood. Here we investigate global changes in the host genetic network and physiology of Pseudomonas putida with or without an integrated ICEclc, a model ICE widely distributed in proteobacterial genomes. Genome-wide gene expression differences were analyzed by RNA-seq using exponentially growing or stationary phase-restimulated cultures on 3-chlorobenzoate, an aromatic compound metabolizable thanks to specific ICEclc-located genes. We found that the presence of ICEclc imposes a variety of changes in global pathways such as cell cycle and amino acid metabolism, which were more numerous in stationary-restimulated than exponential phase cells. Unexpectedly, ICEclc stimulates cellular motility and leads to more rapid growth on 3-chlorobenzoate than cells carrying only the integrated clc genes. ICEclc also concomitantly activates the P. putida Pspu28-prophage, but this in itself did not provoke measurable fitness effects. ICEclc thus interferes in a number of cellular pathways, inducing both direct benefits as well as indirect costs in P. putida.
Collapse
|
247
|
Haskett TL, Terpolilli JJ, Ramachandran VK, Verdonk CJ, Poole PS, O’Hara GW, Ramsay JP. Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements. PLoS Genet 2018; 14:e1007292. [PMID: 29565971 PMCID: PMC5882170 DOI: 10.1371/journal.pgen.1007292] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/03/2018] [Accepted: 03/06/2018] [Indexed: 12/14/2022] Open
Abstract
Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases–or recombination directionality factors—RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a “master controller” of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer. Bacteria evolve and adapt quickly through the horizontal transfer of DNA. A major mechanism facilitating this transfer is conjugation. Conjugative DNA elements that integrate into the chromosome are termed ‘Integrative and Conjugative Elements’ (ICE). We recently discovered a unique form of ICE that undergoes a complex series of recombination events with the host chromosome to split itself into three separate parts. This tripartite ICE must also precisely order its recombination when leaving the current host to avoid splitting the host chromosome and the ICE into non-viable parts. In this work, we show that the tripartite ICEs use chemical cell-cell communication to stimulate recombination and that recombination events are specifically ordered through cascaded transcriptional activation of small DNA-binding proteins called recombination directionality factors. Despite the inherent complexity of tripartite ICEs this work exposes a surprisingly simple system to stimulate their precise and ordered molecular assembly prior to horizontal transfer.
Collapse
Affiliation(s)
- Timothy L. Haskett
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
- * E-mail:
| | - Jason J. Terpolilli
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | | | - Callum J. Verdonk
- School of Pharmacy and Biomedical Sciences and the Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Phillip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Graham W. O’Hara
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Joshua P. Ramsay
- School of Pharmacy and Biomedical Sciences and the Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| |
Collapse
|
248
|
Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell 2018; 173:208-220.e20. [PMID: 29551265 PMCID: PMC5871717 DOI: 10.1016/j.cell.2018.02.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/08/2018] [Accepted: 02/12/2018] [Indexed: 12/28/2022]
Abstract
Conjugative transposition drives the emergence of multidrug resistance in diverse bacterial pathogens, yet the mechanisms are poorly characterized. The Tn1549 conjugative transposon propagates resistance to the antibiotic vancomycin used for severe drug-resistant infections. Here, we present four high-resolution structures of the conserved Y-transposase of Tn1549 complexed with circular transposon DNA intermediates. The structures reveal individual transposition steps and explain how specific DNA distortion and cleavage mechanisms enable DNA strand exchange with an absolute minimum homology requirement. This appears to uniquely allow Tn916-like conjugative transposons to bypass DNA homology and insert into diverse genomic sites, expanding gene transfer. We further uncover a structural regulatory mechanism that prevents premature cleavage of the transposon DNA before a suitable target DNA is found and generate a peptide antagonist that interferes with the transposase-DNA structure to block transposition. Our results reveal mechanistic principles of conjugative transposition that could help control the spread of antibiotic resistance genes. Antibiotic resistance-carrying conjugative transposon integrase structure revealed DNA distortion and special cleavage site allow insertion into diverse genomic sites Key structural features are conserved among numerous conjugative transposons Structures uncover auto-inhibition, allowing transposition antagonist design
Collapse
Affiliation(s)
- Anna Rubio-Cosials
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Eike C Schulz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Hamburg Outstation, European Molecular Biology Laboratory, 22603 Hamburg, Germany
| | - Lotte Lambertsen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Georgy Smyshlyaev
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Carlos Rojas-Cordova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Kristoffer Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Ezgi Karaca
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey
| | - Aleksandra Bebel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
| |
Collapse
|
249
|
Staphylococcal Osteomyelitis: Disease Progression, Treatment Challenges, and Future Directions. Clin Microbiol Rev 2018; 31:31/2/e00084-17. [PMID: 29444953 DOI: 10.1128/cmr.00084-17] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Osteomyelitis is an inflammatory bone disease that is caused by an infecting microorganism and leads to progressive bone destruction and loss. The most common causative species are the usually commensal staphylococci, with Staphylococcus aureus and Staphylococcus epidermidis responsible for the majority of cases. Staphylococcal infections are becoming an increasing global concern, partially due to the resistance mechanisms developed by staphylococci to evade the host immune system and antibiotic treatment. In addition to the ability of staphylococci to withstand treatment, surgical intervention in an effort to remove necrotic and infected bone further exacerbates patient impairment. Despite the advances in current health care, osteomyelitis is now a major clinical challenge, with recurrent and persistent infections occurring in approximately 40% of patients. This review aims to provide information about staphylococcus-induced bone infection, covering the clinical presentation and diagnosis of osteomyelitis, pathophysiology and complications of osteomyelitis, and future avenues that are being explored to treat osteomyelitis.
Collapse
|
250
|
Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik. Proteins 2018; 86:268. [PMID: 30338965 PMCID: PMC5094899 DOI: 10.1002/prot.24679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The above article from the Proteins: Structure, Function, and Bioinformatics, published online on 1 September 2014 in Wiley Online Library as Accepted Article (http://onlinelibrary.wiley.com/doi/10.1002/prot.24679/full), has been retracted by agreement between William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik, the Editor‐in‐Chief, Bertrand E. Garcia‐Moreno, and Wiley Periodicals, Inc. The retraction has been agreed because submission was made without agreement from co‐author Adam Godzik.
Collapse
|