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- Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogenPublication . Isidro, Joana; Ferreira, Susana; Pinto, Miguel; Domingues, F. C.; Oleastro, Mónica; Gomes, João Paulo; Borges, VítorArcobacter butzleri is a foodborne emerging human pathogen, frequently displaying a multidrug resistant character. Still, the lack of comprehensive genome-scale comparative analysis has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small but diverse core-genome with 1165 genes. It presents a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a type I secretion system (T1SS) harboring another agglutinin and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) and other antibiotic resistant determinants. We unprecedentedly describe a genetic mechanism of A. butzleri macrolides resistance, (inactivation of a TetR repressor likely regulating an EP). Fluoroquinolones resistance correlated with Thr-85-Ile in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the main antigen PorA, we show that A. butzleri is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats indicates that phase variation likely modulates A. butzleri key adaptive functions. In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast and diverse virulence and antibiotic resistance arsenals that open a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.
- Prevalence of Arcobacter: From farm to retail – A systematic review and meta-analysisPublication . Mateus, Cristiana; Martins, Rodrigo; Luís, Ângelo; Oleastro, Mónica; Domingues, F.C.; Pereira, L.; Ferreira, SusanaArcobacter is a group of bacteria widely distributed in several habitats and throughout the food chain. Considering the pathogenic potential of some species within this group, it is important to understand their distribution along the food chain, as well as the possible routes of transmission. Aiming this, a systematic review and meta-analysis-based method was used to investigate the prevalence of Arcobacter species throughout the food chain, from farm to fork, using the worldwide available data. Database search was performed using related keywords and considering studies up to March 2020. The pooled prevalence of Arcobacter in food chain was 30% (0.300; 95% CI: 0.262–0.342), ranging from 0.5 to 99.4%. The highest prevalence of Arcobacter was observed in Belgium (0.575; 95% CI:0.427–0.710) and the lower in Ireland (0.031; 95% CI:0.022–0.042). Oceania continent (0.409; 95% CI:0.173–0.697) and the countries with high income level (0.342; 95% CI:0.293–0.394) presented the highest prevalence when considering the analysis of subgroups. Arcobacter spp. presented the highest prevalence at the processing stage (0.335; 95% CI:0.270–0.406), when compared with primary and retail stage. Also, data points to the relevance of environmental sources in food contamination. Arcobacter seems to be more frequently found in animal origin products, with the highest prevalence observed for poultry-associated products (0.404; 95% CI: 0.338–0.473), being Arcobacter butzleri the most frequently found species. The results of this meta-analysis highlight the high prevalence and distribution of Arcobacter along the food chain, suggesting a high risk to human health, and the relevance of taking preventive actions in order to reduce the burden of this pathogen in food sector.
- Natural Transformation as a Mechanism of Horizontal Gene Transfer in Aliarcobacter butzleriPublication . Bonifácio, Marina; Mateus, Cristiana; Alves, Ana R.; Maldonado, Emanuel; Duarte, Ana Paula; Domingues, Fernanda; Oleastro, Mónica; Ferreira, SusanaAliarcobacter butzleri is an emergent enteropathogen, showing high genetic diversity, which likely contributes to its adaptive capacity to different environments. Whether natural transformation can be a mechanism that generates genetic diversity in A. butzleri is still unknown. In the present study, we aimed to establish if A. butzleri is naturally competent for transformation and to investigate the factors influencing this process. Two different transformation procedures were tested using exogenous and isogenic DNA containing antibiotic resistance markers, and different external conditions influencing the process were evaluated. The highest number of transformable A. butzleri strains were obtained with the agar transformation method when compared to the biphasic system (65% versus 47%). A. butzleri was able to uptake isogenic chromosomal DNA at different growth phases, and the competence state was maintained from the exponential to the stationary phases. Overall, the optimal conditions for transformation with the biphasic system were the use of 1 µg of isogenic DNA and incubation at 30 ◦C under a microaerobic atmosphere, resulting in a transformation frequency ~8 × 10−6 transformants/CFU. We also observed that A. butzleri favored the transformation with the genetic material of its own strain/species, with the DNA incorporation process occurring promptly after the addition of genomic material. In addition, we observed that A. butzleri strains could exchange genetic material in co-culture assays. The presence of homologs of well-known genes involved in the competence in the A. butzleri genome corroborates the natural competence of this species. In conclusion, our results show that A. butzleri is a naturally transformable species, suggesting that horizontal gene transfer mediated by natural transformation is one of the processes contributing to its genetic diversity. In addition, natural transformation can be used as a tool for genetic studies of this species.
- The Prevalence of Arcobacteraceae in Aquatic Environments: A Systematic Review and Meta-AnalysisPublication . Venâncio, Igor Miguel Antunes; Luís, Ângelo; Domingues, F.C.; Oleastro, Mónica; Pereira, L.; Ferreira, SusanaMembers of the family Arcobacteraceae are distributed widely in aquatic environments, and some of its species have been associated with human and animal illness. However, information about the diversity and distribution of Arcobacteraceae in different water bodies is still limited. In order to better characterize the health risk posed by members in the family Arcobacteraceae, a systematic review and meta-analysis-based method was used to investigate the prevalence of Arcobacteraceae species in aquatic environments based on available data published worldwide. The database search was performed using related keywords and considering studies up to February 2021. The pooled prevalence in aquatic environments was 69.2%, ranging from 0.6 to 99.9%. These bacteria have a wide geographical distribution, being found in diverse aquatic environments with the highest prevalence found in raw sewage and wastewater treatment plants (WWTP), followed by seawater, surface water, ground water, processing water from food processing plants and water for human consumption. Assessing the effectiveness of treatments in WWTP in eliminating this contamination, it was found that the wastewater treatment may not be efficient in the removal of Arcobacteraceae. Among the analyzed Arcobacteraceae species, Al. butzleri was the most frequently found species. These results highlight the high prevalence and distribution of Arcobacteraceae in different aquatic environments, suggesting a risk to human health. Further, it exposes the importance of identifying and managing the sources of contamination and taking preventive actions to reduce the burden of members of the Arcobacteraceae family.