scholarly journals Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in Klebsiella pneumoniae

2020 ◽  
Author(s):  
Camilo Berríos-Pastén ◽  
Rodolfo Acevedo ◽  
Patricio Arros ◽  
Macarena A. Varas ◽  
Kelly L. Wyres ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Integration Site ◽  
Phylogenetic Analyses ◽  
Bacterial Genome ◽  
Mobile Genetic Elements ◽  
Genomic Islands ◽  
Genomic Context ◽  
Genetic Elements ◽  
Genes Encoding ◽  
Integration Sites

ABSTRACTThe evolution of traits including antibiotic resistance, virulence, and increased fitness in Klebsiella pneumoniae and related species has been linked to the acquisition of mobile genetic elements through horizontal transfer. Among them, genomic islands (GIs) preferentially integrating at genes encoding tRNAs and the tmRNA (t(m)DNAs) would be significant in promoting chromosomal diversity. Here, we studied the whole set of t(m)DNAs present in 66 Klebsiella chromosomes, investigating their usage as integration sites and the properties of the integrated GIs. A total of 5,624 t(m)DNAs were classified based on their sequence conservation, genomic context, and prevalence. 161 different GIs and prophages were found at these sites, hosting 3,540 gene families including various related to virulence and drug resistance. Phylogenetic analyses supported the acquisition of several of these elements through horizontal gene transfer, likely mediated by a highly diverse set of encoded integrases targeting specific t(m)DNAs and sublocations inside them. Only a subset of the t(m)DNAs had integrated GIs and even identical tDNA copies showed dissimilar usage frequencies, suggesting that the genomic context would influence the integration site selection. This usage bias, likely towards avoiding disruption of polycistronic transcriptional units, would be conserved across Gammaproteobacteria. The systematic comparison of the t(m)DNAs across different strains allowed us to discover an unprecedented number of K. pneumoniae GIs and prophages and to raise important questions and clues regarding the fundamental properties of t(m)DNAs as targets for the integration of mobile genetic elements and drivers of bacterial genome evolution and pathogen emergence.

scholarly journals Accessory Genomes Drive Independent Spread of Carbapenem-Resistant Klebsiella pneumoniae Clonal Groups 258 and 307

2021 ◽  
Author(s):  
William C Shropshire ◽  
An Q Dinh ◽  
Michelle Earley ◽  
Lauren Komarow ◽  
Diana Panesso ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Klebsiella Pneumoniae ◽  
Large City ◽  
Mobile Genetic Elements ◽  
Divergent Evolution ◽  
Genetic Elements ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Long Read ◽  
Inverse Probability Weighted

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKp) are urgent public health threats. Worldwide dissemination of CRKp has been largely attributed to the clonal group (CG) 258. However, recent evidence indicates the global emergence of a CRKp CG307 lineage. Houston, Texas is the first large city in the US with co-circulation of both CRKp CG307 and CG258. We sought to characterize the genomic and clinical factors contributing to the parallel endemic spread of CG258 and CG307. Methods: CRKp isolates were collected as part of the prospective, Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacterales 2 (CRACKLE-2) study. Hybrid short-read and long-read genome assemblies were generated from 119 CRKp isolates (95 originated from Houston hospitals). A comprehensive characterization of phylogenies, gene transfer, and plasmid content with pan-genome analysis were performed on all CRKp isolates. Plasmid mating experiments were performed with CG307 and CG258 isolates of interest. An inverse-probability weighted Desirability of Ordinal Outcome Ranking (DOOR) analysis was conducted to determine if patients infected/colonized with CG307 had differences in overall clinical outcomes from patients infected/colonized with CG258. Results: Dissection of the accessory genomes suggested independent evolution and limited horizontal gene transfer between CG307 and CG258 lineages. CG307 contained a diverse repertoire of mobile genetic elements harboring carbapenemases, which were shared with other non-CG258 K. pneumoniae isolates. Three unique clades of Houston CG307 isolates contained a diverse repertoire of mobile genetic elements harboring carbapenemases and clustered distinctly from other global CG307 isolates. CG307 were often isolated from the urine of hospitalized patients, likely serving as important reservoirs for genes encoding carbapenemases and extended-spectrum beta-lactamases. The DOOR probability estimate (64%; 95% CI: 48, 79) of our Houston-based cohort suggested that there was a general trend for patients infected/colonized with CG307 to have more favorable outcomes than patients infected/colonized with CG258. Conclusions: Our findings suggest parallel co-circulation of high-risk lineages with potentially divergent evolution. CG307 is widely circulating CRKp clone in the Houston region with the potential to transfer major resistance determinants to other non-CG258 CRKp lineages. Our findings provide major insights into the mechanism of epidemic spread of CRKp.

scholarly journals Rapidly disseminating blaOXA-232 carrying Klebsiella pneumoniae belonging to ST231 in India: multiple and varied mobile genetic elements

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Chaitra Shankar ◽  
Purva Mathur ◽  
Manigandan Venkatesan ◽  
Agila Kumari Pragasam ◽  
Shalini Anandan ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Mobile Genetic Elements ◽  
Genetic Elements

scholarly journals Accurate Localization of the Integration Sites of Two Genomic Islands at Single-Nucleotide Resolution in the Genome ofBacillus cereusATCC 10987

2008 ◽  
Vol 2008 ◽  
pp. 1-6 ◽  
Author(s):  
Ren Zhang ◽  
Chun-Ting Zhang
Keyword(s):  
Bacillus Cereus ◽  
Genomic Islands ◽  
Intergenic Sequence ◽  
Single Nucleotide ◽  
Daughter Cells ◽  
Accurate Localization ◽  
Genes Encoding ◽  
Integration Sites ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

We have identified two genomic islands, that is, BCEGI-1 and BCEGI-2, in the genome ofBacillus cereusATCC 10987, based on comparative analysis withBacillus cereusATCC 14579. Furthermore, by using the cumulative GC profile and performing homology searches between the two genomes, the integration sites of the two genomic islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and D. It is generally believed that unlike the TnsABC+E pathway, the TnsABC+D pathway would only promote vertical transmission to daughter cells. The evidence presented in this paper, however, suggests a role of the TnsABC+D pathway in the horizontal transfer of some genomic islands.

scholarly journals Shifts in Abundance and Diversity of Mobile Genetic Elements after the Introduction of Diverse Pesticides into an On-Farm Biopurification System over the Course of a Year

2014 ◽  
Vol 80 (13) ◽  
pp. 4012-4020 ◽  
Author(s):  
Simone Dealtry ◽  
Peter N. Holmsgaard ◽  
Vincent Dunon ◽  
Sven Jechalke ◽  
Guo-Chun Ding ◽  
...  
Keyword(s):  
Blot Hybridization ◽  
Pcr Amplification ◽  
Southern Blot Hybridization ◽  
Mobile Genetic Elements ◽  
Replication Initiation ◽  
Genetic Elements ◽  
Class 1 ◽  
Genes Encoding ◽  
Abundance And Diversity ◽  
And Shifts

ABSTRACTBiopurification systems (BPS) are used on farms to control pollution by treating pesticide-contaminated water. It is assumed that mobile genetic elements (MGEs) carrying genes coding for enzymes involved in degradation might contribute to the degradation of pesticides. Therefore, the composition and shifts of MGEs, in particular, of IncP-1 plasmids carried by BPS bacterial communities exposed to various pesticides, were monitored over the course of an agricultural season. PCR amplification of total community DNA using primers targeting genes specific to different plasmid groups combined with Southern blot hybridization indicated a high abundance of plasmids belonging to IncP-1, IncP-7, IncP-9, IncQ, and IncW, while IncU and IncN plasmids were less abundant or not detected. Furthermore, the integrase genes of class 1 and 2 integrons (intI1,intI2) and genes encoding resistance to sulfonamides (sul1,sul2) and streptomycin (aadA) were detected and seasonality was revealed. Amplicon pyrosequencing of the IncP-1trfAgene coding for the replication initiation protein revealed high IncP-1 plasmid diversity and an increase in the abundance of IncP-1β and a decrease in the abundance of IncP-1ε over time. The data of the chemical analysis showed increasing concentrations of various pesticides over the course of the agricultural season. As an increase in the relative abundances of bacteria carrying IncP-1β plasmids also occurred, this might point to a role of these plasmids in the degradation of many different pesticides.

scholarly journals Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses

2021 ◽  
Author(s):  
Fatima Aysha Hussain ◽  
Javier Dubert ◽  
Joseph Elsherbini ◽  
Mikayla Murphy ◽  
David VanInsberghe ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Bacterial Genome ◽  
Mobile Genetic Elements ◽  
Bacterial Strains ◽  
Genomic Features ◽  
Genetic Elements ◽  
Flexible Genome ◽  
In The Wild ◽  
Putative Phage ◽  
Resistance To Viruses

AbstractAlthough it is generally accepted that viruses (phages) drive bacterial evolution, how these dynamics play out in the wild remains poorly understood. Here we show that the arms race between phages and their hosts is mediated by large and highly diverse mobile genetic elements. These phage-defense elements display exceedingly fast evolutionary turnover, resulting in differential phage susceptibility among clonal bacterial strains while phage receptors remain invariant. Protection afforded by multiple elements is cumulative, and a single bacterial genome can harbor as many as 18 putative phage-defense elements. Overall, elements account for 90% of the flexible genome amongst closely related strains. The rapid turnover of these elements demonstrates that phage resistance is unlinked from other genomic features and that resistance to phage therapy might be as easily acquired as antibiotic resistance.

scholarly journals Abundance of mobile genetic elements in an Acinetobacter lwoffii strain isolated from Transylvanian honey sample

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexandra Veress ◽  
Tibor Nagy ◽  
Tímea Wilk ◽  
János Kömüves ◽  
Ferenc Olasz ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Rapid Evolution ◽  
Mobile Genetic Elements ◽  
Metal Resistance ◽  
Honey Sample ◽  
Common Pattern ◽  
Is Elements ◽  
Genetic Elements ◽  
Resistance Determinants ◽  
Close Relatives

AbstractBased on phylogenetic analyses, strain M2a isolated from honey, an unexpected source of acinetobacters, was classified as Acinetobacter lwoffii. The genome of this strain is strikingly crowded with mobile genetic elements. It harbours more than 250 IS elements of 15 IS-families, several unit and compound transposons and 15 different plasmids. These IS elements, including 30 newly identified ones, could be classified into at least 53 IS species. Regarding the plasmids, 13 of the 15 belong to the Rep-3 superfamily and only one plasmid, belonging to the “Low-GC” family, possesses a seemingly complete conjugative system. The other plasmids, with one exception, have a mobilization region of common pattern, consisting of the divergent mobA/mobL-family and mobS-, mobC- or traD-like genes separated by an oriT-like sequence. Although two plasmids of M2a are almost identical to those of A. lwoffi strains isolated from gold mine or Pleistocene sediments, most of them have no close relatives. The presence of numerous plasmid-borne and chromosomal metal resistance determinants suggests that M2a previously has also evolved in a metal-polluted environment. The numerous, possibly transferable, plasmids and the outstanding number of transposable elements may reflect the high potential of M2a for rapid evolution.

scholarly journals Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e99209 ◽  
Author(s):  
Corey M. Hudson ◽  
Zachary W. Bent ◽  
Robert J. Meagher ◽  
Kelly P. Williams
Keyword(s):  
Klebsiella Pneumoniae ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Resistance Determinants

scholarly journals Carbapenemase-Producing Klebsiella pneumoniae From Transplanted Patients in Brazil: Phylogeny, Resistome, Virulome and Mobile Genetic Elements Harboring blaKPC–2 or blaNDM–1

2020 ◽  
Vol 11 ◽  
Author(s):  
Otávio Hallal Ferreira Raro ◽  
Ravena Maya Cardoso da Silva ◽  
Edison Moraes Rodrigues Filho ◽  
Teresa Cristina Teixeira Sukiennik ◽  
Claudio Stadnik ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Mobile Genetic Elements ◽  
Genetic Elements
Sign in / Sign up

Export Citation Format

Share Document