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 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 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 Genome Sequence of Listeria monocytogenes Plasmid pLM-C-273 Carrying Genes Related to Stress Resistance

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Lindsay Liang ◽  
Saravanamuttu Gnaneshan ◽  
Rafael A. Garduño ◽  
Gustavo V. Mallo
Keyword(s):  
Antibiotic Resistance ◽  
Listeria Monocytogenes ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Stress Resistance ◽  
Clinical Sample ◽  
Mobile Genetic Elements ◽  
Metal Resistance ◽  
Genetic Elements

Mobile genetic elements in bacteria, such as plasmids, act as important vectors for the transfer of antibiotic resistance, virulence, and metal resistance genes. Here, we report the genome sequence of a new plasmid pLM-C-273, identified in a Listeria monocytogenes strain isolated from a clinical sample in Ontario, Canada.

scholarly journals Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

2020 ◽  
Vol 76 (1) ◽  
pp. 101-109 ◽  
Author(s):  
Markus H K Johansson ◽  
Valeria Bortolaia ◽  
Supathep Tansirichaiya ◽  
Frank M Aarestrup ◽  
Adam P Roberts ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Mobile Genetic Elements ◽  
Metal Resistance ◽  
Animal Origin ◽  
Genetic Elements ◽  
Antimicrobial Resistance Genes

Abstract Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.

scholarly journals Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert

Diversity ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 205 ◽  
Author(s):  
Sáenz ◽  
Airo ◽  
Schulze-Makuch ◽  
Schloter ◽  
Vestergaard
Keyword(s):  
Energy Production ◽  
Essential Role ◽  
Extreme Environments ◽  
Atacama Desert ◽  
Mobile Genetic Elements ◽  
Metal Resistance ◽  
Soil Microbiome ◽  
Orthologous Group ◽  
Chlorite Dismutase ◽  
Genetic Elements

Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.

scholarly journals Antibiotic Resistance and Mobile Genetic Elements in Extensively Drug-Resistant Klebsiella pneumoniae Sequence Type 147 Recovered from Germany

Antibiotics ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 675
Author(s):  
Kyriaki Xanthopoulou ◽  
Alessandra Carattoli ◽  
Julia Wille ◽  
Lena M. Biehl ◽  
Holger Rohde ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
High Risk ◽  
Klebsiella Pneumoniae ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Genetic Variations ◽  
Drug Resistant ◽  
Genetic Elements ◽  
Resistance Determinants ◽  
Extensively Drug Resistant

Mobile genetic elements (MGEs), especially multidrug-resistance plasmids, are major vehicles for the dissemination of antimicrobial resistance determinants. Herein, we analyse the MGEs in three extensively drug-resistant (XDR) Klebsiella pneumoniae isolates from Germany. Whole genome sequencing (WGS) is performed using Illumina and MinION platforms followed by core-genome multi-locus sequence typing (MLST). The plasmid content is analysed by conjugation, S1-pulsed-field gel electrophoresis (S1-PFGE) and Southern blot experiments. The K. pneumoniae isolates belong to the international high-risk clone ST147 and form a cluster of closely related isolates. They harbour the blaOXA-181 carbapenemase on a ColKP3 plasmid, and 12 antibiotic resistance determinants on an multidrug-resistant (MDR) IncR plasmid with a recombinogenic nature and encoding a large number of insertion elements. The IncR plasmids within the three isolates share a high degree of homology, but present also genetic variations, such as inversion or deletion of genetic regions in close proximity to MGEs. In addition, six plasmids not harbouring any antibiotic resistance determinants are present in each isolate. Our study indicates that genetic variations can be observed within a cluster of closely related isolates, due to the dynamic nature of MGEs. The mobilome of the K. pneumoniae isolates combined with the emergence of the XDR ST147 high-risk clone have the potential to become a major challenge for global healthcare.

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