scholarly journals CRISPR-Cas Loci of Yersinia pseudotuberculosis Strains with Different Genetic Determinants

2020 ◽  
Vol 19 (2) ◽  
pp. 31-39
Author(s):  
N. P. Peretolchina ◽  
V. T. Klimov ◽  
E. A. Voskresenskaya ◽  
G. I. Kokorina ◽  
E. A. Bogumilchik ◽  
...  
Keyword(s):  
Clinical Manifestation ◽  
Horizontal Transfer ◽  
Yersinia Pseudotuberculosis ◽  
Mobile Genetic Elements ◽  
Severe Form ◽  
Virulence Determinants ◽  
Genetic Determinants ◽  
Genetic Elements ◽  
Serotype O ◽  
Specific Virulence

Relevance. Yersinia pseudotuberculosis is a causative agent of pseudotuberculosis, a disease with polymorphism of clinical manifestation that is determined by the presence of specific virulence determinants: plasmid pVM82, pathogenicity islands HPI and YAPI, and superantigen YPM. Occurrence of new determinants depends on horizontal transfer of mobile genetic elements, hence, systems regulating horizontal transfer participate in evolution of pathogenic species. CRISPR-Cas is and adaptive protection system of prokaryotes against mobile genetic elements. Aim. The study analyzed an interaction between CRISPR-loci of Y. pseudotuberculosis and virulence determinants. Results. 86% of strains includes three CRISPR-loci: YP1, YP2, and YP3. Length of locus YP3 mostly depends on presence of virulence determinants in strains of Y. pseudotuberculosis serotype O:1b. Strains with virulence genes are able to cause a severe form of pseudotuberculosis and have longer locus than strains without determinants. Conclusion. Therefore, CRIPSRCas system of Y. pseudotuberculosis may participate in formation of a certain strain genotype that defines clinical manifestation of pseudotuberculosis.

scholarly journals CRISPR-Cas Loci of Yersinia pseudotuberculosis Strains with Different Genetic Determinants

2020 ◽  
Vol 19 (2) ◽  
pp. 31-39
Author(s):  
N. P. Peretolchina ◽  
V. T. Klimov ◽  
E. A. Voskresenskaya ◽  
G. I. Kokorina ◽  
E. A. Bogumilchik ◽  
...  
Keyword(s):  
Clinical Manifestation ◽  
Horizontal Transfer ◽  
Yersinia Pseudotuberculosis ◽  
Mobile Genetic Elements ◽  
Severe Form ◽  
Virulence Determinants ◽  
Genetic Determinants ◽  
Genetic Elements ◽  
Serotype O ◽  
Specific Virulence

Relevance. Yersinia pseudotuberculosis is a causative agent of pseudotuberculosis, a disease with polymorphism of clinical manifestation that is determined by the presence of specific virulence determinants: plasmid pVM82, pathogenicity islands HPI and YAPI, and superantigen YPM. Occurrence of new determinants depends on horizontal transfer of mobile genetic elements, hence, systems regulating horizontal transfer participate in evolution of pathogenic species. CRISPR-Cas is and adaptive protection system of prokaryotes against mobile genetic elements. Aim. The study analyzed an interaction between CRISPR-loci of Y. pseudotuberculosis and virulence determinants. Results. 86% of strains includes three CRISPR-loci: YP1, YP2, and YP3. Length of locus YP3 mostly depends on presence of virulence determinants in strains of Y. pseudotuberculosis serotype O:1b. Strains with virulence genes are able to cause a severe form of pseudotuberculosis and have longer locus than strains without determinants. Conclusion. Therefore, CRIPSRCas system of Y. pseudotuberculosis may participate in formation of a certain strain genotype that defines clinical manifestation of pseudotuberculosis.

scholarly journals In situ detection of horizontal transfer of mobile genetic elements

2002 ◽  
Vol 42 (2) ◽  
pp. 261-268 ◽  
Author(s):  
Janus A.J. Haagensen ◽  
S.K. Hansen ◽  
T. Johansen ◽  
S. Molin
Keyword(s):  
Horizontal Transfer ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
In Situ Detection

scholarly journals ICEEc2, a New Integrative and Conjugative Element Belonging to the pKLC102/PAGI-2 Family, Identified in Escherichia coli Strain BEN374

2010 ◽  
Vol 192 (19) ◽  
pp. 5026-5036 ◽  
Author(s):  
David Roche ◽  
Maud Fléchard ◽  
Nathalie Lallier ◽  
Maryline Répérant ◽  
Annie Brée ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Yersinia Pseudotuberculosis ◽  
Trna Gene ◽  
Mobile Genetic Elements ◽  
Wide Distribution ◽  
Coli Strain ◽  
Host Chromosome ◽  
E Coli ◽  
Genetic Elements ◽  
Integrative And Conjugative Element

ABSTRACT The diversity of the Escherichia coli species is in part due to the large number of mobile genetic elements that are exchanged between strains. We report here the identification of a new integrative and conjugative element (ICE) of the pKLC102/PAGI-2 family located downstream of the tRNA gene pheU in the E. coli strain BEN374. Indeed, this new region, which we called ICEEc2, can be transferred by conjugation from strain BEN374 to the E. coli strain C600. We were also able to transfer this region into a Salmonella enterica serovar Typhimurium strain and into a Yersinia pseudotuberculosis strain. This transfer was then followed by the integration of ICEEc2 into the host chromosome downstream of a phe tRNA gene. Our data indicated that this transfer involved a set of three genes encoding DNA mobility enzymes and a type IV pilus encoded by genes present on ICEEc2. Given the wide distribution of members of this family, these mobile genetic elements are likely to play an important role in the diversification of bacteria.

scholarly journals Swine liquid manure: a hotspot of mobile genetic elements and antibiotic resistance genes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fengxia Yang ◽  
Bingjun Han ◽  
Yanru Gu ◽  
Keqiang Zhang
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Horizontal Transfer ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Full Scale ◽  
Liquid Manure ◽  
Piggery Wastewater ◽  
Genetic Elements ◽  
Swine Farms

Abstract The overuse or abuse of antibiotics as veterinary medicine and growth promoters accelerates antibiotic resistance, creating a serious threat to public health in the world. Swine liquid manure as an important reservoir of antibiotic resistance genes (ARGs) has received much attention, but little information is known regarding the occurrence, persistence and fate of ARGs-associated mobile genetic elements (MGEs) in swine farms, especially their change patterns and removal in full-scale piggery wastewater treatment systems (PWWTSs). In this study, we searched the presence and distribution of MGEs and associated ARGs in swine farms, and addressed their fate and seasonal variation in full-scale PWWTSs by real-time quantitative PCR (qPCR). Our results revealed class 1 integrons, class 2 integrons and conjugative plasmids were prevalent in pig feces and piggery wastewater. A clear pattern of these MGE levels in swine liquid manure was also observed, i.e., intI1 > intI2 > traA (p < 0.01), and their absolute abundances in winter were all higher than that in summer with 0.07–2.23 logs. Notably, MGEs and ARGs prevailed through various treatment units of PWWTSs, and considerable levels of them were present in the treated effluent discharged from swine farms (up to 101–107 copies/mL for MGEs and 103–108 copies/mL for ARGs). There were significant correlations between most ARG abundance and MGE levels (p < 0.05), such as tetQ and traA (r = 0.775), sul1 and intI1 (r = 0.847), qnrS and inI2 (r = 0.859), suggesting the potential of ARGs—horizontal transfer. Thus the high prevalence and enrichment of MGEs and ARGs occurred in pig feces and piggery wastewater, also implicating that swine liquid manure could be a hotspot for horizontal transfer of ARGs.

scholarly journals Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis

2011 ◽  
Vol 1 (1) ◽  
pp. 17 ◽  
Author(s):  
Susanna KP Lau ◽  
Gilman KM Wong ◽  
Alan KL Tsang ◽  
Jade LL Teng ◽  
Rachel YY Fan ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Mobile Genetic Elements ◽  
Virulence Determinants ◽  
Genome Wide Analysis ◽  
Genetic Elements ◽  
Genome Wide ◽  
A Genome ◽  
Laribacter Hongkongensis

scholarly journals The Superantigen Gene ypm Is Located in an Unstable Chromosomal Locus of Yersinia pseudotuberculosis

2002 ◽  
Vol 184 (16) ◽  
pp. 4489-4499 ◽  
Author(s):  
Christophe Carnoy ◽  
Stephanie Floquet ◽  
Michael Marceau ◽  
Florent Sebbane ◽  
Stephanie Haentjens-Herwegh ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Yersinia Pseudotuberculosis ◽  
Gc Content ◽  
Mobile Genetic Elements ◽  
Open Reading Frames ◽  
Chromosomal Locus ◽  
Genetic Elements ◽  
Encoding Genes ◽  
Reading Frames

ABSTRACT Yersinia pseudotuberculosis produces YPM (Y. pseudotuberculosis-derived mitogen), a superantigenic toxin that exacerbates the virulence of the bacterium in vivo. To date, three alleles of the superantigen gene (ypmA, ypmB, and ypmC) have been described. These genes are not found in all Y. pseudotuberculosis strains and have a low GC content, suggesting their location on mobile genetic elements. To elucidate this question, the genetic environment of the superantigen-encoding genes was characterized and 11 open reading frames (ORFs) were defined. Sequence analysis revealed that the ypm genes were not associated with plasmids, phages, transposons, or pathogenicity islands and that the superantigen genes were always located in the chromosome between ORF3 and ORF4. Nonsuperantigenic strains exhibited the same genetic organization of the locus but lacked the ypm gene between ORF3 and ORF4. A new insertion sequence, designated IS1398, which displays features of the Tn3 family, was characterized downstream of the ypmA and ypmC genes. A 13.3-kb region containing the ypm genes was not found in the genome of Y. pestis (CO92 and KIM 5 strains). We experimentally induced deletion of the ypm gene from a superantigen-expressing Y. pseudotuberculosis: using the association of aph(3′)-IIIa and sacB genes, we demonstrated that when these reporter genes were present in the ypm locus, deletion of these genes was about 250 times more frequent than when they were located in another region of the Y. pseudotuberculosis chromosome. These results indicate that unlike other superantigenic toxin genes, the Yersinia ypm genes are not associated with mobile genetic elements but are inserted in an unstable locus of the genome.

scholarly journals Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp inKlebsiella pneumoniaepopulations

2017 ◽  
Author(s):  
Margaret M. C. Lam ◽  
Ryan R. Wick ◽  
Kelly L. Wyres ◽  
Claire L. Gorrie ◽  
Louise M. Judd ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Population Genomics ◽  
Bacterial Species ◽  
Critical Role ◽  
Mobile Element ◽  
Mobile Genetic Elements ◽  
Virulence Determinants ◽  
Genome Sequences ◽  
Genetic Elements ◽  
Resistant Strains

ABSTRACTMobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key accessory genes that associate with a bacteria’s ability to cause disease. MGEs carrying antimicrobial resistance (AMR) and/or virulence determinants are common in opportunistic pathogenKlebsiella pneumoniae, which are a leading cause of highly drug-resistant infections in hospitals. Well-characterised virulence determinants inK. pneumoniaeinclude the polyketide synthesis lociybtandclb(also known aspks), encoding the iron-scavenging siderophore yersiniabactin and genotoxin colibactin respectively. These loci are located within an MGE called ICEKp, which is the most common virulence-associated MGE ofK. pneumoniae,providing a mechanism for these virulence factors to spread within the population.Here we apply population genomics to investigate the prevalence, evolution and mobility ofybtandclbinK. pneumoniaepopulations through comparative analysis of 2,498 whole genome sequences. Theybtlocus was detected in 40% ofK. pneumoniaegenomes, particularly amongst those associated with invasive infections. We identified 17 distinctybtlineages and 3clblineages, each associated with one of 14 different structural variants of ICEKp. Comparison with the wider Enterobacteriaceae population showed occasional ICEKpacquisition by other members. Theclblocus was present in 14% of allK. pneumoniaeand 38.4% ofybt+ genomes. Hundreds of independent ICEKpintegration events were detected affecting hundreds of phylogenetically distinctK. pneumoniaelineages, including ≥19 in the globally-disseminated carbapenem-resistant clone CG258. A novel plasmid-encoded form ofybtwas also identified, representing a new mechanism forybtdispersal inK. pneumoniaepopulations. These data show that MGEs carryingybtandclbcirculate freely in theK. pneumoniaepopulation, including among multidrug-resistant strains, and should be considered a target for genomic surveillance along with AMR determinants.AUTHOR SUMMARYKlebsiella pneumoniaeinfections are becoming increasingly difficult to treat with antibiotics. SomeK. pneumoniaestrains also carry extra genes that allow them to synthesise yersiniabactin, an iron-scavenging molecule, which enhances their ability to cause disease. These genes are located on a genetic element that can easily transfer between strains. Here, we screened 2498K. pneumoniaegenome sequences and found substantial diversity in the yersiniabactin genes and the associated genetic elements, including a novel mechanism of transfer, and detected hundreds of distinct yersiniabactin acquisition events betweenK. pneumoniaestrains. We show that these yersiniabactin mobile genetic elements are specifically adapted to theK. pneumoniaepopulation but also occasionally acquired by other bacterial members belonging to the Enterobacteriaceae family such asE. coli.These insights into the movement and genetics of yersiniabactin genes allow tracking of the evolution and spread of yersiniabactin in globalK. pneumoniaepopulations and monitoring for acquisition of yersiniabactin in antibiotic-resistant strains.

scholarly journals Evolution of a 72-Kilobase Cointegrant, Conjugative Multiresistance Plasmid in Community-Associated Methicillin-Resistant Staphylococcus aureus Isolates from the Early 1990s

2019 ◽  
Vol 63 (11) ◽  
Author(s):  
Karina Yui Eto ◽  
Neville Firth ◽  
Amy M. Davis ◽  
Stephen M. Kwong ◽  
Marcelina Krysiak ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Resistance Genes ◽  
Tetracycline Resistance ◽  
Mobile Genetic Elements ◽  
Conjugative Plasmid ◽  
Penicillin Resistance ◽  
Virulence Determinants ◽  
Methicillin Resistant ◽  
Content Type ◽  
Genetic Elements

ABSTRACT Horizontal transfer of plasmids encoding antimicrobial resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s, the first CA-MRSA strain isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline, and penicillin resistance genes on plasmid pWBG753 (∼30 kb). WA-5 and pWBG753 appeared only briefly in WA; however, fusidic acid resistance plasmids related to pWBG753 were also present in the first European CA-MRSA isolates at the time. Here, we characterize a 72-kb conjugative plasmid, pWBG731, present in multiresistant WA-5-like clones from the same period. pWBG731 was a cointegrant formed from pWBG753 and a pWBG749 family conjugative plasmid. pWBG731 carried mupirocin, trimethoprim, cadmium, and penicillin resistance genes. The stepwise evolution of pWBG731 likely occurred through the combined actions of IS257, IS257-dependent miniature inverted-repeat transposable elements (MITEs), and the BinL resolution system of the β-lactamase transposon Tn552. An evolutionarily intermediate ∼42-kb nonconjugative plasmid, pWBG715, possessed the same resistance genes as pWBG731 but retained an integrated copy of the small tetracycline resistance plasmid pT181. IS257 likely facilitated the replacement of pT181 with conjugation genes on pWBG731, thus enabling autonomous transfer. Like conjugative plasmid pWBG749, pWBG731 also mobilized nonconjugative plasmids carrying oriT mimics. It seems likely that pWBG731 represents the product of multiple recombination events between the WA-5 pWBG753 plasmid and other mobile genetic elements present in indigenous community-associated methicillin-sensitive S. aureus (CA-MSSA) isolates. The molecular evolution of pWBG731 saliently illustrates how diverse mobile genetic elements can together facilitate rapid accrual and horizontal dissemination of multiresistance in S. aureus CA-MRSA.

scholarly journals Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Suzanne Humphrey ◽  
Alfred Fillol-Salom ◽  
Nuria Quiles-Puchalt ◽  
Rodrigo Ibarra-Chávez ◽  
Andreas F. Haag ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Mobile Genetic Elements ◽  
Transfer Rates ◽  
High Frequencies ◽  
Genetic Elements ◽  
Chromosomal Genes ◽  
Definition Of ◽  
Generalized Transduction

AbstractIt is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.

scholarly journals Comprehensive analysis of mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

2017 ◽  
Author(s):  
Xiaofang Jiang ◽  
Andrew Brantley Hall ◽  
Ramnik J. Xavier ◽  
Eric Alm
Keyword(s):  
Antibiotic Resistance ◽  
Human Health ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Horizontal Transfer ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Comprehensive Analysis ◽  
Gene Pools ◽  
Genetic Elements

AbstractMobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method called Split Read Insertion Detection (SRID) that enables the identification of the exact mobilizable unit of MGEs. Leveraging the SRID method, we curated a database of 5600 putative MGEs encompassing seven MGE classes called ImmeDB (Intestinal microbiome mobile element database) (https://immedb.mit.edu/). We observed that many MGEs carry genes that confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Additionally, we observed that horizontal transfer of MGEs is extensive within phyla but rare across phyla. Taken together, our findings support a phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future fundamental and translational studies on the gut microbiome and MGE communities.

Sign in / Sign up

Export Citation Format

Share Document