Percorrer por autor "Ramos, Miguel"
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- Genomic epidemiology and resistome dynamics of species in a Portuguese Open Air Laboratory: the emergence of the FRI-8 carbapenemasePublication . Teixeira, Pedro; Ramos, Miguel; Rivière, Rani; Azevedo, Mónica; Ferreira, Mário; Cano, Maria Manuela; Vieira, Patrícia; Reis, Lígia; Matias, Rui; Rodrigues, João; Menezes, Carina; Rosado, Tânia; Sequeira, António; Moreira, Olga; Ruppitsch, Werner; Cabal-Rosel, Adriana; Mo, Solveig Sølverød; Dias, Elsa; Woegerbauer, Markus; Caniça, Manuela; Manageiro, VeraInterconnected reservoirs contribute to the global spread of antimicrobial resistance (AMR), including carbapenem- and colistin-resistant , highlighting the need for a One Health approach. We assessed the genomic epidemiology, diversity and AMR mechanisms of spp. across interconnected human, animal, plant, and environmental reservoirs in a Portuguese Open Air Laboratory. Over a one year monitoring period, samples from 12 different compartments were collected and processed using selective media to isolate spp., which were subjected to antibiotic susceptibility testing, whole-genome sequencing and subsequent analyses to identify AMR determinants, characterize plasmids and phylogenetic relationships. We established a collection of 61 isolates spanning nine species and 32 sequence types, including 16 novel ones, across nine compartments (river water, wastewater, soil, manure, feed, air, farmers, pigs, wild animals), reflecting the diversity and ubiquity of species. Core-genome analysis revealed eight genetic clusters, suggesting clonal transmission across compartments. In total, 29 antibiotic resistance genes were detected across all isolates. Notably, this is the first documentation of -harbouring in European environmental settings and the first to describe , and genes in Portugal. was detected in all isolates ( = 17), located on four different IncFII(Yp) plasmids, and in an isolate, flanked by IS3 family transposases. and the -harbouring isolate were resistant to carbapenems. A gene was identified in an isolate on an IncFII(pECLA) plasmid. These plasmids exhibited high sequence similarity with global counterparts, indicating potential for horizontal gene transfer. Other antimicrobial resistance genes included , , and . Our findings underscore the importance of as vectors for AMR and the critical role of environmental compartments in its dissemination, reinforcing the importance of adopting a One Health approach to fully understand AMR dynamics.
- Mapping the evidence of the effects of environmental factors on the prevalence of antibiotic resistance in the non-built environmentPublication . Deza-Cruz, Iñaki; de Menezes, Alexandre; Gardner, Brian; Aktan, Ílknur; Alnajjar, Sarhad; Betson, Martha; Cabal Rosel, Adriana; Caniça, Manuela; Chambers, Mark A.; Tarrant, Georgina; Contadini, Francesca; Daramola, Olukayode; de la Rivière, Rani; Egan, Bernadette; Ekiri, Abel; Finnegan, Catherine; Gonzalez Villeta, Laura C.; Green, Richard; Hall, Belinda; Hassan, Marwa M.; Hawes, Martin; Healy, Sara; Holbrook, Lisa; Kaya, Damla; Kumar, Prashant; La Ragione, Roberto M.; Maupin, Daniel; Mehat, Jai W.; Messina, Davide; Moon, Kelly; Mumford, Elizabeth; Nichols, Gordon; Olivença, Daniel V.; Prada, Joaquin M.; Price, Claire; Proudman, Christopher; Queenan, Retha; Ramos, Miguel; Closa, Jaime Riccomini; Ritchie, Jennifer M.; Santorelli, Lorenzo A.; Selemetas, Nick; Spick, Matt; Subbannayya, Yashwanth; Surendran, Shelini; Teixeira, Pedro; Tharmakulasingam, Mukunthan; Valle, Damian; van Vliet, Arnoud H.M.; Videira, Marco; Wallace-Williams, Hazel; Wanelik, Klara M.; Woegerbauer, Markus; Wright, Sydney; Lo Iacono, GiovanniBackground: Antibiotic resistance increasingly threatens the interconnected health of humans, animals, and the environment. While misuse of antibiotics is a known driver, environmental factors also play a critical role. A balanced One Health approach-including the environmental sector-is necessary to understand the emergence and spread of resistance. Methods: We systematically searched English-language literature (1990-2021) in MEDLINE, Embase, and Web of Science, plus grey literature. Titles, abstracts, and keywords were screened, followed by full-text reviews using a structured codebook and dual-reviewer assessments. Results: Of 13,667 records screened, 738 met the inclusion criteria. Most studies focused on freshwater and terrestrial environments, particularly associated with wastewater or manure sources. Evidence of research has predominantly focused on Escherichia coli and Pseudomonas spp., with a concentration on ARGs conferring resistance to sulphonamides (sul1-3), tetracyclines (tet), and beta-lactams. Additionally, the People's Republic of China has produced a third of the studies-twice that of the next country, the United States-and research was largely domestic, with closely linked author networks. Conclusion: Significant evidence gaps persist in understanding antibiotic resistance in non-built environments, particularly in marine, atmospheric, and non-agricultural settings. Stressors such as climate change and microplastics remain notably under-explored. There is also an urgent need for more research in low-income regions, which face higher risks of antibiotic resistance, to support the development of targeted, evidence-based interventions.
- Unraveling the genome-wide repertoire of the novel chromosomally encoded mcr-8.6 gene variant in Klebsiella michiganensis isolated from manurePublication . Rivière, Rani; Teixeira, Pedro; Silva, Catarina; Ramos, Miguel; Dias, Elsa; Manageiro, Vera; Caniça, ManuelaThe increasing rates of colistin resistance worldwide poses a significant threat to public health. While the most commonly described variant is , other variants such as have been detected, typically associated with . However, little is known about the prevalence of in other bacterial species and environmental reservoirs. This study aimed to characterize a novel subvariant identified in a strain isolated from manure in Portugal, collected during an annual longitudinal survey at an Open Air laboratory, as well as to depict its genomic context and potential mobility mechanisms. The strain was subjected to phenotypic susceptibility testing, whole-genome sequencing and hybrid genome assembly. analysis included identification of resistance genes and mobile genetic element. The new gene variant and its genetic environment were characterized. The F731 strain presented susceptibility to colistin with a MIC = 0.25 mg/L, despite carrying a novel subvariant, , which was located within a 61.6 kb chromosomal genomic island. This variant presented 23-24 amino acid substitutions compared to previous characterized MCR-8 proteins. The genomic island also harbored multiple insertion sequences (IS, IS, IS), virulence factors, and metabolic and regulatory proteins, among others. Synteny analysis revealed high sequence identity between this genomic island and both chromosomal and plasmid regions from other bacterial strains isolated from different reservoirs worldwide, indicating prior mobility. Furthermore, other antimicrobial resistance genes were detected [e.g., ', ], but no plasmid replicons were identified. This is the first report of a gene in a , as well as the first occurrence in Portugal. Although F731 remains colistin-susceptible, the presence of a novel chromosomally encoded but located in a mobile genomic island underscores the risk of future horizontal gene transfer. These findings highlight the importance of further monitoring and continued surveillance in environmental and animal compartments in order to track the dissemination of antimicrobial resistance.