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.

Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.

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gMeat and meat products are important sources of human intestinal infections. We report the isolation of Helicobacter pullorum strains from chicken meat. Bacteria were isolated from 4 of the 17 analyzed fresh chicken meat samples, using a membrane filter method. MIC determination revealed that the four strains showed acquired resistance to ciprofloxacin; one was also resistant to erythromycin, and another one was resistant to tetracycline. Whole-genome sequencing of the four strains and comparative genomics revealed important genetic traits within the H. pullorum species, such as 18 highly polymorphic genes (including a putative new cytotoxin gene), plasmids, prophages, and a complete type VI secretion system (T6SS). The T6SS was found in three out of the four isolates, suggesting that it may play a role in H. pullorum pathogenicity and diversity. This study suggests that the emerging pathogen H. pullorum can be transmitted to humans by chicken meat consumption/contact and constitutes an important contribution toward a better knowledge of the genetic diversity within the H. pullorum species. In addition, some genetic traits found in the four strains provide relevant clues to how this species may promote adaptation and virulence. Infectious diarrhea is a major cause of morbidity and mortality throughout the world, particularly in children (1). Besides the most commonly associated pathogens, such as Salmonella enterica, Campylobacter spp., and Shiga toxin-producing Escherichia coli, infectious intestinal pathogens also include Helicobacter species. Among these, Helicobacter pullorum has been detected in poultry as well as in human samples (2, 3).H. pullorum is a Gram-negative, gently curved rod, with an unsheathed monopolar flagellum (4). This enterohepatic Helicobacter species was initially isolated from the liver, duodenum, and cecum of asymptomatic poultry, but it has also been associated with enteritis and vibrionic hepatitis in broiler chickens and laying hens (4). In poultry, H. pullorum was found to colonize the cecum at high concentrations, as well as to be present on poultry carcasses, possibly due to contamination during slaughtering. Therefore, the potential role of this bacterium as an emerging foodborne human pathogen needs to be considered (3, 5-7). In humans, H. pullorum is considered an emergent agent implicated in several digestive pathologies, such as gastroenteritis (2) and chronic inflammatory conditions of the intestine (8, 9) and liver (for a review, see reference 10 and references cited therein). However, the lack of available detection tools and the difficulties in cultivating this fastidious organism result in an underdetection of the pathogen and underdiagnosis of the associated infection. Despite its zoonotic potential, there is no proof to date that one can acquire H. pullorum infection by the handling and consumption of raw or undercooked broiler chicken meat.In the present work, we report the isolation of H. pullorum from chicken meat and present antimicrobial susceptibility data and ...

Background: Acute septic arthritis (SA) still remains a challenge with significant worldwide morbidity. In recent years, Kingella kingae has emerged and treatment regimens have become shorter. We aim to analyze trends in SA etiology and management and to identify risk factors for complications. Methods: Longitudinal observational, single center study of children (<18 years old) with SA admitted to a tertiary care pediatric hospital, from 2003 to 2018, in 2 cohorts, before and after implementation of nucleic acid amplification assays (2014). Clinical, treatment and disease progression data were obtained. Results: A total of 247 children were identified, with an average annual incidence of 24.9/100,000, 57.9% males with a median age of 2 (1-6) years. In the last 5 years, a 1.7-fold increase in the annual incidence, a lower median age at diagnosis and an improved microbiologic yield (49%) was noticed. K. kingae became the most frequent bacteria (51.9%) followed by MSSA (19.2%) and S. pyogenes (9.6%). Children were more often treated for fewer intravenous days (10.7 vs. 13.2 days, P = 0.01) but had more complications (20.6% vs. 11.4%, P = 0.049) with a similar sequelae rate (3.7%). Risk factors for complications were C-reactive protein ≥80 mg/L and Staphylococcus aureus infection, and for sequelae at 6 months, age ≥4 years and CRP ≥ 80 mg/L. Conclusions: The present study confirms that K. kingae was the most common causative organism of acute SA. There was a trend, although small, for decreasing antibiotic duration. Older children with high inflammatory parameters might be at higher risk of sequelae.