ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents

Abstract

In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like Chlamydia trachomatis and Legionella pneumophila. In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub.

Unveiling a Listeria monocytogenes Outbreak in a Rabbit Farm: Clinical Manifestation, Antimicrobial Resistance, Genomic Insights and Environmental Investigation

“…A threshold of seven ADs can provide a proxy for the identification of genetic clusters with potential epidemiological concordance (i.e., "outbreaks") [37]. Reads and/or assemblies were screened for the presence of antimicrobial resistance genes with ABRicate v.1.0.1 (https://github.com/tseemann/ABRIcate) (accessed on 11 March 2024), though ReporType (https://github.com/insapathogenomics/ReporType) (accessed on 11 March 2024) [38] using NCBI AMRFinderPlus [39], CARD [40], Resfinder [41], and ARG-ANNOT [42] databases, and with the online BIGSdb-Lm (https://bigsdb.pasteur.fr/listeria/) (accessed on 11 March 2024) [43] and Centre for Genomic and Epidemiology (ResFinder 4.42, http://www.genomicepidemiology.org; accessed on 30 January 2024) tools.…”