digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes

Background The insertion sequence elements (IS elements) represent the smallest and the most abundant mobile elements in prokaryotic genomes. It has been shown that they play a significant role in genome organization and evolution. To better understand their function in the host genome, it is desirable to have an effective detection and annotation tool. This need becomes even more crucial when considering rapid-growing genomic and metagenomic data. The existing tools for IS elements detection and annotation are usually based on comparing sequence similarity with a database of known IS families. Thus, they have limited ability to discover distant and putative novel IS elements. Results In this paper, we present digIS, a software tool based on profile hidden Markov models assembled from catalytic domains of transposases. It shows a very good performance in detecting known IS elements when tested on datasets with manually curated annotation. The main contribution of digIS is in its ability to detect distant and putative novel IS elements while maintaining a moderate level of false positives. In this category it outperforms existing tools, especially when tested on large datasets of archaeal and bacterial genomes. Conclusion We provide digIS, a software tool using a novel approach based on manually curated profile hidden Markov models, which is able to detect distant and putative novel IS elements. Although digIS can find known IS elements as well, we expect it to be used primarily by scientists interested in finding novel IS elements. The tool is available at https://github.com/janka2012/digIS.

Draft Genome Sequences of 27 Northern Maine Clinical Isolates

ABSTRACT We report the draft genome sequences of 27 common pathogens collected from a northern Maine hospital in 2017. These were sequenced in order to determine temporal and biogeographical patterns of antibiotic gene distribution. A total of 908 antibiotic resistance genes, 848 insertion sequence elements, and 57 plasmids were identified.

Prevalence and Distribution of Resistance and Enterotoxins/Enterotoxin-likes Genes in Different Clinical Isolates of Coagulase-negative Staphylococcus

Background CoNS serve as a major reservoir for genes facilitating the evolution of S. aureus as a successful pathogen. The present study aimed to determine the occurrence of genes conferring resistance to fluoroquinolone, determining of the prevalence of insertion sequence elements IS256 and IS257 and different superantigenes (SAgs) among CoNS isolates obtained from various clinical sources. Materials and Methods The current study conducted on a total of 91 CoNS species isolated from clinical specimens in Hamadan hospitals in western Iran in 2017-19. The Antimicrobial susceptibility testing was performed using disk diffusion method and the presence of the IS256 and IS257, genes conferring resistance to fluoroquinolone and enterotoxins/enterotoxin-likes encoding genes were investigated by PCR method. Results Among genes encoding classic enterotoxins, sec was the most frequent which was carried by 48.4% of isolates, followed by seb in 27.5%. None of the CoNS isolates were found to be positive to enterotoxin-like encoding genes. Among the 11 CoNS isolates that have shown phenotypically resistant to levofloxacin, 9 isolates (81.8%) with gyrB , 8 isolates (72.7%) with gyrA, 8 isolates (72.7%) with grlB and 7 isolates (63.6%) with grlA were identified. The IS256 and IS257 were identified in 31.8% and 74.7% of CoNS isolates. The results of statistical analysis showed a significant association between the occurrence of SEs encoding genes and antimicrobial resistance. Conclusion Antimicrobial resistant determinants and staphylococcus enterotoxins (SEs) are co-present in clinical CoNS isolates that confer selective advantage for colonization and survival in hospital settings. The coexistence of insertion elements and antibiotic resistance indicate their role in pathogenesis and infectious disease.

Genome rearrangements and megaplasmid loss in the filamentous bacteriumKitasatospora viridifaciensare associated with protoplast formation and regeneration

Filamentous Actinobacteria are multicellular bacteria with linear replicons.Kitasatospora viridifaciensDSM 40239 contains a linear 7.8 Mb chromosome and an autonomously replicating plasmid KVP1 of 1.7 Mb. Here we show that lysozyme-induced protoplast formation of the multinucleated mycelium ofK. viridifaciensdrives morphological diversity. Characterization and sequencing of an individual revertant colony that had lost the ability to differentiate revealed that the strain had not only lost most of KVP1 but also carried lesions in the right arm of the chromosome. Strikingly, the lesion sites were preceded by insertion sequence elements, suggesting that the rearrangements may have been caused by replicative transposition and homologous recombination between both replicons. These data indicate that protoplast formation is a stressful process that can lead to profound genetic changes.RepositoriesGenomic sequence data for strain B3.1 has been deposited in the NCBI SRA database under accession code SAMN11514356.

The Genome Sequence of Avibacterium paragallinarum Strain CL Has a Large Repertoire of Insertion Sequence Elements

ABSTRACT The draft genome sequence of Avibacterium paragallinarum strain CL serovar C is reported here. The genome comprises 154 contigs corresponding to 2.4 Mb with 41% G+C content and many insertion sequence (IS) elements, a characteristic not previously reported in A. paragallinarum.

A Novel Hybrid Plasmid Carrying Multiple Antimicrobial Resistance and Virulence Genes in Salmonella enterica Serovar Dublin

ABSTRACT Virulence plasmids and antibiotic resistance plasmids are usually maintained separately in Salmonella spp.; however, we report an instance of a hybrid plasmid (pN13-01125) in Salmonella enterica serovar Dublin. Review of the complete sequence of the 172,265-bp plasmid suggests that pN13-01125 is comprised of the previously described pSDVr and pSH696_135 plasmids and that the mechanism of hybridization likely involves IS6 (IS26) insertion sequence elements. The plasmid has a low conjugation frequency, confers resistance to six classes of antimicrobials, and contains a complete spv virulence operon.