Gruber, C. E. M. | bioRxiv Science

bioRxiv2021

ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler

Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to understand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession, harboring multiple deletions and amino acid changing mutations. To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here we propose an easy-to-use SARS-CoV-2 genome Assembler: the ESCA pipeline. Results showed that ESCA can perform high quality genome assembly from IonTor-rent and Illumina raw data, and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility to compare assembled genomes of multi sample runs through an easy table format. Script and manuals are available on GitHub: https://github.com/cesaregruber/ESCA

bioinformatics↗

bioRxiv2018

Epidemiologal investigation of an Acinetobacter baumannii outbreak using Core Genome Multilocus Sequence Typing

Carbapenem-resistant (CR) Acinetobacter baumannii is a serious nosocomial pathogen able to cause a variety of serious, often life-threatening infections and outbreaks. We aimed to investigate the molecular epidemiology of clinical isolates of CR-A. baumannii from an outbreak occurred in the intensive care unit (ICU) of our hospital.\n\nFrom January to April 2017, 13 CR-A. baumannii isolates were collected at the \"L. Spallanzani\" hospital, Rome, Italy; typing was performed by repetitive extragenetic palindromic-based (rep)- PCR-based DiversiLab system and WGS data were used for in silico analysis of traditional MLST types, for identifying resistance genes and for core genome multi locus sequence typing (cgMLST) analysis. Epidemiological data were obtained from hospital records.\n\nStrains were cultured from 7 patients treated in the ICU of our hospital; all isolates showed a multi-drug resistant (MDR) profile, carrying the blaOXA-23 carbapenemase. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group while the cgMLST approach, which uses 2690 gene targets to characterize the gene-by-gene allelic profile of A. baumannii, highlighted the presence of two cluster types. These results allowed us to identify two patients who entered the ICU already colonized by two different strains of CR-A. baumannii; we hypothesize that these two patients could be the source of two separate transmission chains.\n\nOur results show that whole-genome-DNA sequencing by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.

molecular biology↗