Browsing by Author "Sampaio, Daniel A"
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- Draft Genomic Analysis of an Avian Multidrug Resistant Morganella morganii Isolate Carrying qnrD1Publication . Jones-Dias, Daniela; Clemente, Lurdes; Moura, Inês B; Sampaio, Daniel A; Albuquerque, Teresa; Vieira, Luís; Manageiro, Vera; Caniça, ManuelaMorganella morganii is a commensal bacterium and opportunistic pathogen often present in the gut of humans and animals. We report the 4.3 Mbp draft genome sequence of a M. morganii isolated in association with an Escherichia coli from broilers in Portugal that showed macroscopic lesions consistent with colisepticemia. The analysis of the genome matched the multidrug resistance phenotype and enabled the identification of several clinically important and potentially mobile acquired antibiotic resistance genes, including the plasmid-mediated quinolone resistance determinant qnrD1. Mobile genetic elements, prophages, and pathogenicity factors were also detected, improving our understanding toward this human and animal opportunistic pathogen.
- Genetic Background and Expression of the New qepA4 Gene Variant Recovered in Clinical TEM-1- and CMY-2-Producing Escherichia coliPublication . Manageiro, Vera; Félix, David; Jones-Dias, Daniela; Sampaio, Daniel A; Vieira, Luís; Sancho, Luísa; Ferreira, Eugénia; Caniça, ManuelaA new QepA4 variant was detected in an O86:H28 ST156-fimH38 Escherichia coli, showing a multidrug-resistance phenotype. PAβN inhibition ofqepA4-harboring transconjugant resulted in increase of nalidixic acid accumulation. TheqepA4andcatA1genes were clustered in a 26.0-kp contig matching an IncF-type plasmid, and containing a Tn21-type transposon with multiple mobile genetic elements. This QepA variant is worrisome because these determinants might facilitate the selection of higher-level resistance mutants, playing a role in the development of resistance, and/or confer higher-level resistance to fluoroquinolones in association with chromosomal mutations.
- NDM-1-producing Providencia stuartii isolates in a Portuguese HospitalPublication . Manageiro, Vera; Ferreira, Eugénia; Rodrigues, João; Sampaio, Daniel A; Vieira, Luís; Pereira, Patrícia; Rodrigues, Paulo; Palos, Carlos; Caniça, ManuelaObjective: Providencia stuartii is an opportunistic pathogen typically associated with urinary infections, and is intrinsically resistance to a wide range of antibiotics. The main aim of this study was to characterize five carbapenemase (CA) NDM-1-producing P. stuartii isolates obtained during an outbreak detected in a Hospital. Methods: MICs were obtained by the reference microdilution broth method, according to EUCAST guidelines. PCR amplification and DNA sequencing were applied to identify the presence of CA genes from class A, B and D. Direct transfer of the CA resistance phenotype was attempted by mating-out assays. Genetic relatedness was examined by PFGE. One isolate, INSRA21868, recovered from the urine of an 88-year-old male patient admitted to the intensive care unit, was selected for genetic characterization using whole-genome sequencing (WGS), performed using 150 bp paired-end reads on a MiSeq (Illumina). A set of bioinformatic web tools were used to estimate the presence of pathogenicity determinants, antibiotic resistance (AR) genes, and clinically relevant mobile genetic elements. Results: All isolates, genetically indistinguishable by PFGE, presented multidrug-resistance with non-susceptibility to all carbapenems tested. Transconjugants had AR profiles similar to those of their parental clinical isolates. All NDM-1 determinants tested were found to be carried on conjugative plasmids. In silico AR analyses using ResFinder-v2.1 revealed genes conferring resistance to β-lactams [blaNDM-1, blaCMY-4 and ΔblaDHA-1), aminoglycosides (aac(2’)-Ia, armA), tetracycline (tetB), macrolides (mphE and msrE), chloramphenicol (catB3), and sulfonamides (sul1). PlasmidFinder-v1.2 analyses revealed the presence of an IncA/C2, which has been associated with wide dissemination of blaNDM-1. In the 3’ region, the blaNDM-1 gene was adjacent to a bleomycin resistance-encoding gene (bleMBL), followed by a trpF and part of the blaDHA-1-ampR region. The ISAba125 element upstream of blaNDM-1 was interrupted by an IS26 element. Conclusion: This study emphasizes the elements involved in dissemination of nosocomial infections and the potential of WGS in epidemiological investigations in the prevention of CA dissemination among hospitals as well as to other bacterial genera.
- Salmonella Enteritidis Isolate Harboring Multiple Efflux Pumps and Pathogenicity Factors, Shows Absence of O Antigen Polymerase GenePublication . Jones-Dias, Daniela; Clemente, Lurdes; Egas, Conceição; Froufe, Hugo; Sampaio, Daniel A; Vieira, Luís; Fookes, Maria; Thomson, Nicholas R; Manageiro, Vera; Caniça, ManuelaBACKGROUND: Salmonella enterica is one of the most important causes of gastrointestinal infection in humans, being the great majority of infections related to the consumption of poultry meat and eggs (Foley and Lynne, 2008; EFSA/ECDC, 2015). In animals, infections caused by serotype Enteritidis are rarely responsible for severe disease with animals frequently becoming asymptomatic carriers, except in the case of young chicks and poults, where outbreaks exhibiting clinical disease are often accompanied by high mortality rates (Foley et al., 2008, 2013). Indeed, S. enterica subsp. enterica serovar Enteritidis (S. Enteritidis) has been responsible for severe disease in industrial poultry farming facilities worldwide, posing a potential hazard for public health (Lutful Kabir, 2010). In order to be infectious, Salmonella needs to adapt to different niches and conditions, where virulence and heavy-metal-tolerance factors play an important role, through co-selection events and the formation of pathogenicity islands, respectively (Hensel, 2004; Medardus et al., 2014). Furthermore, antibiotic resistance determinants can also facilitate their survival, with ubiquitous chromosomally encoded efflux mechanisms, playing an important role in both intrinsic, and acquired multidrug resistance. Other resistance mechanisms, such as changes in the membrane permeability, enzymatic modification, and target alterations may increase the levels of bacterial resistance, contributing to the success of the infection (Poole, 2004; Delmar et al., 2014; Li et al., 2015). Both antibiotic susceptibility determination and serotyping constitute very useful tools for the epidemiologic classification of S. enterica isolates. Indeed, in S. enterica, the resistance rates fluctuate according to the serotype and with the antibiotic (Clemente et al., 2015). Classically, serotyping is based on the antigenic reactivity of lipolysaccharide (O antigen) and flagellar proteins (H antigen), followed by a designation using names or formulas (Grimont and Weill, 2007). In this study, we aimed to analyze the genome of a S. Enteritidis isolate responsible for omphalitis in chicks, exploring the molecular features associated with antibiotic resistance and pathogenicity, as well as the ability to spread the respective determinants.