EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison

Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1-6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually-time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run. EasySSR requires only a FASTA and an optional GENBANK file of one or more genomes to identify and compare STRs. The tool can automatically analyze and compare SSRs in whole genomes, convert GenBank to PTT files, identify perfect and imperfect SSRs and coding and non-coding regions, compare their frequencies, abundancy, motifs, flanking sequences, and iterations, producing many outputs ready for download such as PTT files, interactive charts, and Excel tables, giving the user the data ready for further analysis in minutes. EasySSR was implemented as a web application, which can be executed from any browser and is available for free at https://computationalbiology.ufpa.br/easyssr/. Tutorials, usage notes, and download links to the source code can be found at https://github.com/engbiopct/EasySSR.

Genomic analysis of Klebsiella pneumoniae high-risk clone ST11 co-harboring MCR-1.27 and KPC-2 recovered at a pediatric oncologic hospital in the Brazilian Amazon region

The horizontal transfer of antibiotic resistance genes in Gram-negative bacteria, mainly through plasmids, is one of the greatest concerns for health systems worldwide and has been a growing threat in hospitals related to nosocomial infection by multidrug resistant bacteria.

OBJECTIVES

Phenotypic and genomic characterization of a KPC-2 and MCR-1.27 producing Klebsiella pneumoniae strain isolated from a pediatric patient at an oncologic hospital in Belém, Pará State, Brazilian Amazon region.

METHODS

Antibiotic susceptibility test, whole genome sequencing and in silico analysis were used to characterize the bacterial isolate (IEC 48020) received in the Evandro Chagas Institute.

RESULTS

The isolate was resistant to carbapenens, colistin, polymyxin B and several other antimicrobials, and was susceptible in vitro just to tigecycline, classified as an extensively drug resistance phenotype. Genomic analysis revealed IEC48020 strain belonged to sequence type 11, clonal complex 258 high-risk clone and the presence of eight plasmids, two of them harboring mcr-1.27 and bla_KPC-2 genes, and the presence of virulence-related genes encoding yersiniabactin, phospholipase D and traT genes.

CONCLUSION

The presence and dissemination of high-risk clone bacteria with high disseminating plasmids containing antibiotic resistance genes for last resources antibiotics treatment options is a threat to the health care system and demands efforts in surveillance and epidemiological research for better knowledge of the actual situation of antibiotic resistance in health care system, especially in Amazon region, Brazil.