INNUENDO: A cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens

Abstract

In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole‐genome sequencing in surveillance and outbreak investigation of food‐borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross‐sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user‐centered design strategy involving the end‐users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand‐alone, portable, open‐source, end‐to‐end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species‐specific protocols that can be run using a user‐friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species‐specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene‐by‐gene methodology; quality control measures from raw reads to allele calling; reporting system; a built‐in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof‐of‐concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web‐sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open‐source software in genomic epidemiology.

Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal

“…Applying a cut-off of 0.5% to this subset, corresponding to an AD of 16, two main clusters containing PT isolates remain and one isolate segregates independently (PT10). Nevertheless, when a 3 International Journal of Genomics more restrict cut-off is applied (0.25%; 8 AD), more consistent with outbreak clustering investigation [51], all the PT isolates separate from strains of other countries (with the exception of an isolate from the United Kingdom, ENA accession # SAMN09298461) and two main clusters containing most of the PT isolates are observed, suggesting two main circulating clones.…”

“…All allelic distance thresholds used during cluster investigation were expressed as percentages of allele differences (AD) (i.e., the number of observed allelic differences divided by the total number of shared loci under comparison). Thus, to explore isolate subsets, a conservative step-by-step approach was performed by applying three allelic distance cut-offs of 1, 0.5, and 0.25% to both initial MSTs, based on previously described data for cluster investigation in a wgMLST-based surveillance [51].…”

Chlamydia trachomatisoutbreak: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature

“…In order to confirm the outbreak and characterize the genomic backbone and mosaicism of the hybrid L2b/D C. trachomatis strain, the following bioinformatics activities were conducted: i ) reads’ quality analysis and cleaning/improvement, de novo genome assembly and post-assembly optimization using the integrative pipeline INNUca version 4.0.1 (https://github.com/B-UMMI/INNUca) (Llarena et al 2018); ii ) reference-based mapping and SNP/indel analysis against representative genome sequences of both the worldwide disseminated proctitis-associated C. trachomatis L2b strain (L2b/UCH-1/proctitis; NCBI accession numbers: AM884177.2/NC_010280.2 for chromosome and AM886279.1 for the plasmid) and the detected L2b/D C. trachomatis strain (strain Ct_L2b/D_PT05; ENA accession number ERZ870055) using Snippy version 4.1.0 (https://github.com/tseemann/snippy); iii) whole genome alignment and inspection using Mauve software version 2.3.1 (http://darlinglab.org/mauve/mauve.html); iv ) coreSNP-based alignment and recombination inspection/visualization using Parsnp and Gingr tools available at Harvest suite (https://github.com/marbl/harvest). respectively (Treangen et al 2014); v) integration of the hybrid L2b/D C. trachomatis strain in the ompA -based and genome-based species trees (Harris et al 2012) by constructing approximately-maximum-likelihood phylogenetic trees using the double-precision mode of FastTree2 under the General Time-Reversible (GTR) model (1000 bootstraps) (Price et al 2010); and, vi) locus-based sequence alignment and manipulation using MEGA software (version 7; http://www.megasoftware.net) (Kumar et al 2016).…”

Genome–scale approach to study the genetic relatedness among Brucella melitensis strains

“…All allelic distance thresholds used during cluster investigation were expressed as percentages of allele differences (AD), expressed as the number of allelic differences over the total number of shared loci under comparison. To explore strain sub-sets among our 37 PT strains, a conservative step-by-step approach was performed by applying allelic distance cut-offs ranging from 1 to 0.1% to the initial MST, based on previously described data for cluster investigation in gene-by-gene based surveillance [26].…”