Browsing by Author "João, Inês"
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- Aplicação dos testes IGRA na deteção de tuberculose latente: o geral e o particularPublication . Rodrigues, J.; Betencourt, C.; João, Inês; Sarioglou, K.; Reis, L.; Cristóvão, P.; Graça, S.; Jordão, Luísa
- Characterization of Mycobacterium tuberculosis resistant strains circulating in a Lisbon hospital: a 2 years studyPublication . Perdigão, João; João, Inês; Silva, Carla; Portugal, Isabel; Jordão, Luísa
- Contribution of freely available databases for the accurate classification of emergent pathogensPublication . João, Inês; Cristóvão, Paula; Jordão, LuísaOBJECTIVES: Nontuberculous mycobacteria (NTM) are a heterogeneous group of microorganisms. Their clinical relevance and treatment differs significantly upon NTM species, which makes identification at this level crucial. Additionally, inaccurate diagnosis can lead to therapeutic approaches consistent with Mycobacterium tuberculosis infection which are usefulness.In the present study different molecular methods were used in the identification of NTM. The aim was to evaluate and compare the performance of freely available databases in the accurate identification of NTM. METHODS: Partial sequencing of hsp65 and 16S rRNA genes of 54 strains of NTM. The resulting sequences were compared with the nucleotide sequences from GenBank, RIDOM and EzTaxon databases for 16S rRNA gene. For hsp65 gene GenBank and Web Databases were used. RESULTS: Seventy-two percent of NTM were identified to species level by 16SrRNA analysis. The remaining 28% failed this goal. Thirty-three obtained an unique outcome in all databases and 6 isolates (15%) obtained at least one different resultAnalysis of hsp65 gene sequences identified unambiguously 76% of the strains, for the remaining 22% the analysis led to the possibility of classification into more than one species. Of all the strains analyzed, this approach failed to identify only 2%. CONCLUSION: The obsolescence of databases, including the GenBank and RIDOM, made the identification of emerging pathogens, as NTM, very complex. If instead of allowing free deposit it was mandatory to update the taxonomy of mycobacteria and asserting the quality of sequences prior to deposit, e.g. in GenBank, several problems would be avoided. Among the shortcomings, we highlight the existence of non-validated "species" names, poorly classified species and even classification limited to genera. As there is no control of sequences submited to this database, identical sequences could give different percentages of similarity. Furthermore, this database contains an enormous amount of flawed sequences, which can lead to identification errors. On the other hand controlled databases which contain high quality and properly characterized sequences, have a limited usefulness due to lagging updating (RIDOM), and the absence of sequences other than from reference strains (EzTaxon and Web Database).
- Distribution of Chlamydia trachomatis ompA-genotypes over three decades in PortugalPublication . Lodhia, Zohra; Cordeiro, Dora; Correia, Cristina; João, Inês; Carreira, Teresa; Vieira, Luís; Nunes, Alexandra; Ferreira, Rita; Schäfer, Sandra; Aliyeva, Elzara; Portugal, Clara; Monge, Isabel; Pessanha, Maria Ana; Toscano, Cristina; Côrte-Real, Rita; Antunes, Marília; Gomes, Joao Paulo; Borges, Vítor; José Borrego, MariaObjectives: Chlamydia trachomatis is classified into 15 major genotypes, A to L3, based on the diversity of ompA gene. Here, we evaluated and characterised the distribution and diversity of ompA-genotypes over 32 years (1990-2021) in Portugal. Methods: The collection of the Portuguese National Reference Laboratory for Sexually Transmitted Infections includes 5824 C. trachomatis-positive samples that were successfully ompA-genotyped between 1990 and 2021. An in-depth analysis of ompA-genotypes distribution across the years, as well as by biological sex, age and anatomical site of infection was performed. Results: ompA-genotype E was consistently the most frequently detected across the years, with a median frequency of 34.6%, followed by D/Da (17.6%), F (14.3%) and G (10.7%). The prevalence of lymphogranuloma venereum (LGV) genotypes (mostly L2, 62.0%, followed by L2b, 32.1%) increased since 2016, reaching the highest value in 2019 (20.9%). LGV, G and Da genotypes were associated with biological sex, specifically with being male, and were the most frequent among anorectal specimens (37.7%, 19.4% and 17.7%, respectively). Notably, LGV ompA-genotypes represented 38.9% of the male anorectal specimens since 2016, and were also detected among oropharynx and urogenital samples. ompA-genotype E was the most frequently detected at the oropharynx (28.6%) and urogenital (33.9%) sites during the study period, followed by D/Da (17.4%) and F (16.0%) in the urogenital specimens, and by G (26.1%) and D/Da (25.7%) in oropharynx specimens. Our data also highlight the emergence of the recombinant L2b/D-Da strain since 2017 (representing between 2.0% and 15.5% of LGV cases per year) and the non-negligible detection of ompA-genotype B in urogenital and anorectal specimens. Conclusions: This study provides a comprehensive landscape of C. trachomatis molecular surveillance in Portugal, highlighting the continued relevance of ompA-genotyping as a complement to rapid LGV-specific detection tests. It also contributes to a deeper understanding of C. trachomatis epidemiology, diversity and pathogenicity.
- Distribution of Chlamydia trachomatis ompA-genotypes over three decades in PortugalPublication . Lodhia, Zohra; Cordeiro, Dora; Correia, Cristina; João, Inês; Carreira, Teresa; Vieira, Luís; Nunes, Alexandra; Ferreira, Rita; Schäfer, Sandra; Aliyeva, Elzara; Portugal, Clara; Monge, Isabel; Pessanha, Maria Ana; Toscano, Cristina; Côrte-Real, Rita; Antunes, Marília; Gomes, Joao Paulo; Borges, Vítor; Borrego, Maria JoséObjectives: Chlamydia trachomatis is classified into 15 major genotypes, A to L3, based on the diversity of ompA gene. Here, we evaluated and characterised the distribution and diversity of ompA-genotypes over 32 years (1990–2021) in Portugal. Methods: The collection of the Portuguese National Reference Laboratory for Sexually Transmitted Infections includes 5824 C. trachomatis-positive samples that were successfully ompA-genotyped between 1990 and 2021. An in-depth analysis of ompA-genotypes distribution across the years, as well as by biological sex, age and anatomical site of infection was performed. Results: ompA-genotype E was consistently the most frequently detected across the years, with a median frequency of 34.6%, followed by D/Da (17.6%), F (14.3%) and G (10.7%). The prevalence of lymphogranuloma venereum (LGV) genotypes (mostly L2, 62.0%, followed by L2b, 32.1%) increased since 2016, reaching the highest value in 2019 (20.9%). LGV, G and Da genotypes were associated with biological sex, specifically with being male, and were the most frequent among anorectal specimens (37.7%, 19.4% and 17.7%, respectively). Notably, LGV ompA-genotypes represented 38.9% of the male anorectal specimens since 2016, and were also detected among oropharynx and urogenital samples. ompA-genotype E was the most frequently detected at the oropharynx (28.6%) and urogenital (33.9%) sites during the study period, followed by D/Da (17.4%) and F (16.0%) in the urogenital specimens, and by G (26.1%) and D/Da (25.7%) in oropharynx specimens. Our data also highlight the emergence of the recombinant L2b/D-Da strain since 2017 (representing between 2.0% and 15.5% of LGV cases per year) and the non-negligible detection of ompA-genotype B in urogenital and anorectal specimens. Conclusions: This study provides a comprehensive landscape of C. trachomatis molecular surveillance in Portugal, highlighting the continued relevance of ompA-genotyping as a complement to rapid LGV-specific detection tests. It also contributes to a deeper understanding of C. trachomatis epidemiology, diversity and pathogenicity.
- Exploitation of a link between antibacterial agent-resistance and biofilm-formation by classical and emergent pathogensPublication . João, Inês; Reis, Lúcia; Carvalho, Patrícia; Duarte, Aida; Jordão, LuísaObjectives: In recent years nosocomial infections have gained growing importance. Among their etiological agents are “classical” pathogens such as S.aureus and also emergent pathogens, previously neglected, such as nontuberculous mycobacteria (MTM). The ability to resist to antibacterial agents, such as antibiotics and disinfectants, is shared by all of them. Here we aim to establish a link between bacterial virulence, antibacterial agents’ resistance and biofilm formation. Methods: Bacterial reference strains and clinical isolates were grown in adequate medium. Among the “classical” pathogens used are E.coli, K. pneumoniae, S. aureus and P. aeroginosa. The group of emergent pathogens includes M.fortuitum, M.abcessus, M.chelonae, M.avium etc. NTM susceptibility test to antibiotics was evaluated by broth based microdilution method and interpreted according to NCCLS guidelines. The desinfectant (oxygen peroxide, ammonium quaternary salts [AQS] and glutaraldehyde [GA) efficacy was performed according to the approved guidelines. The susceptibility was performed by two different methods: broth microdilution and diffusion in solid medium. In order to evaluate the effect of these agents in bacteria a scanning electron microscopy (SEM) study was performed. Biofilm forming ability was evaluated by the microtiter-plate test. The assay was performed at 25ºC and 37ºC in optimal growth media, phosphate saline buffer pH 7.4 and water during for different periods of time. Fast growing bacteria were assayed for 3 days while slow growers were assayed for 15 days.
- Exploiting a link between resistance to antimicrobial agents and pathogens structurePublication . João, Inês; Reis, Lúcia; Carvalho, Patrícia A.; Duarte, Aida; Jordão, LuísaIn recent years nosocomial infections have gained growing importance. Among their etiological agents are pathogens such as S.aureus, E. coli and also emergent pathogens, previously neglected, such as nontuberculous mycobacteria (MTM). The ability to resist to antibacterial agents, such as antibiotics and disinfectants, is shared by all of them. Here we aim to establish a link between bacterial virulence, antibacterial agents' resistance and structure. Bacterial reference strains and clinical isolates (E.coli, K. pneumoniae, S. aureus and P. aeroginosa, M.smegmatis) were grown in adequate medium. NTM susceptibility test to antibiotics was evaluated by broth based microdilution method and interpreted according to NCCLS guidelines. The desinfectant (oxygen peroxide, ammonium quaternary salts [AQS] and glutaraldehyde [GA]) efficacy was performed according to the approved guidelines. The susceptibility was performed by two different methods: broth microdilution and diffusion in solid medium. In order to evaluate the effect of these agents in bacteria a scanning electron microscopy (SEM) study was performed. The results of the antibiotic susceptibility test showed, with no surprise, that the resistant strains are the most prevalent. The resistance spectrum ranged from 1 to 5 antibiotics currently used in therapeutic schemes. Oxygen peroxide was the most effective disinfectant followed by QAS and GA. Nevertheless, among NTM we identified one isolate resistant to all disinfectants tested. The SEM analysis showed that different disinfectants caused different effects on bacteria suggesting different action mechanisms. Bacterial resistance to antibiotics and disinfectants vary in the same manner. The mechanisms involved in the resistance are not fully elucidated and more studies are needed to provide effective conclusions. Biofilm formation can be part of the mechanism involved both in resistance development and propagation of infections by these agents.
- Exploring a link between pathogens structure's and resistance to disinfectantPublication . João, Inês; Reis, Lúcia; Carvalho, Patrícia; Duarte, Aida; Jordão, LuísaIn recent years healthcare-associated infections (HAIs) infections have gained growing importance. Among their etiological agents are classical (e.g. K. pneumoniae, S. aureus) and emergent pathogens, previously neglected, such as nontuberculous mycobacteria (NTM). The ability to resist to antibacterial agents, such as antibiotics and disinfectants, is shared by all of them. Here we aim to establish a link between bacterial virulence, disinfectant resistance and structure. Bacterial reference strains and clinical isolates were grown in adequate medium. NTM susceptibility test to antibiotics was evaluated by broth microdilution method and interpreted according to NCCLS guidelines in a previous work. The susceptibility to disinfectants (hydrogen peroxide, ammonium quaternary salts [AQS] and glutaraldehyde [GA]) was performed by two different methods: broth microdilution and diffusion in solid medium. In order to evaluate the effect of these agents in bacteria a scanning electron microscopy (SEM) study was performed. Hydrogen peroxide was the less effective disinfectant. The efficiencies of QAS and GA were similar. Nevertheless, among NTM we identified one isolate resistant to all disinfectants tested (Table 1). The SEM analysis showed that different disinfectants caused different effects on bacteria suggesting different action mechanisms (Figure 1). Bacterial resistance to antibiotics and disinfectants vary in the same manner. The mechanisms involved in the resistance are not fully elucidated and more studies are needed to provide effective conclusions. Biofilm formation can be part of the mechanism involved both in antibiotic/disinfectant resistance development and infection propagation.
- General Overview on Nontuberculous Mycobacteria, Biofilms, and Human InfectionPublication . Faria, Sónia; João, Inês; Jordao, LuísaNontuberculous mycobacteria (NTM) are emergent pathogens whose importance in human health has been growing. After being regarded mainly as etiological agents of opportunist infections in HIV patients, they have also been recognized as etiological agents of several infections on immune-competent individuals and healthcare-associated infections. The environmental nature of NTMand their ability to assemble biofilms on different surfaces play a key role in their pathogenesis. Here, we review the clinical manifestations attributed to NTM giving particular importance to the role played by biofilm assembly.
- Infeções por Chlamydia trachomatis e Neisseria gonorrhoeae: resultados do diagnóstico laboratorial realizado no INSA, 2017-2022Publication . João, Inês; Cordeiro, Dora; Correia, Cristina; Carreira, Teresa; Borrego, Maria JoséChlamydia trachomatis e Neisseria gonorrhoeae são responsáveis pelas duas infeções sexualmente transmissíveis (IST) curáveis mais comuns em todo o mundo. Sendo frequentemente assintomáticas, o rastreio laboratorial destas IST é fundamental, para que possa ser efetuado o tratamento adequado que evite o desenvolvimento de sequelas clínicas graves e para quebrar cadeias de transmissão. O presente estudo teve por objetivo determinar a frequência das infeções por C. trachomatis e N. gonorrhoeae no âmbito da prestação de serviços do Laboratório Nacional de Referência das IST no INSA, no período 2017-2022. A pesquisa laboratorial de C. trachomatis e N. gonorrhoeae foi efetuada por uma técnica de PCR em tempo real, tendo sido obtidos resultados válidos para 47 136 amostras biológicas (genitais, anorretais e/ou orofaríngeas) de 21 188 pessoas que, em 22,6% (n=4799) dos casos, revelaram ser positivas para qualquer uma destas IST. Nas mulheres, a infeção por C. trachomatis foi a mais frequente (10,5%; 494/4692), enquanto nos homens a infeção por N. gonorrhoeae foi a mais comum (16,2%; 2669/16 455). C. trachomatis foi mais detetada nas amostras anorretais (10,1%; 1222/12 057), nas quais 19,3% (236/1222) revelaram pertencer ao grupo do linfogranuloma venéreo, e N. gonorrhoeae na orofaringe (11,5%; 1621/14 123). Ambas as infeções foram mais frequentemente detetadas nos homens (28,4%; 4680/16455) e nas pessoas (independentemente do sexo) com menos de 25 anos (36,8%; 1389/3777). Em conclusão, este estudo revelou infeção por C. trachomatis e N. gonorrhoeae em amostras colhidas de diferentes locais anatómicos, tendo sido observadas elevadas frequências de infeção por N. gonorrhoeae a nível orofaríngeo e anorretal, assim como de C. trachomatis neste último local anatómico, sugerindo que o rastreio destas IST não se deverá restringir à região genital. O aumento (8,6 pontos percentuais entre 2017 e 2022) das infeções por N. gonorrhoeae configura motivo de preocupação dada a potencial emergência de estirpes resistentes aos antibióticos.