Browsing by Author "Rodrigues, Irene"
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- An Overview of Monkeypox Virus Detection in Different Clinical Samples and Analysis of Temporal Viral Load DynamicsPublication . Cordeiro, Rita; Pelerito, Ana; de Carvalho, Isabel Lopes; Lopo, Sílvia; Neves, Raquel; Rocha, Raquel; Palminha, Paula; Verdasca, Nuno; Palhinhas, Cláudia; Borrego, Maria José; Manita, Carla; Ferreira, Idalina; Bettencourt, Célia; Vieira, Patrícia; Silva, Sónia; Água-Doce, Ivone; Roque, Carla; Cordeiro, Dora; Brondani, Greice; Santos, João Almeida; Martins, Susana; Rodrigues, Irene; Ribeiro, Carlos; Núncio, Maria Sofia; Gomes, João Paulo; Batista, Fernando da ConceiçãoMpox is a zoonotic disease caused by the Monkeypox virus (MPXV), and since May 2022, tens of thousands of cases have been reported in non-endemic countries. We aimed to evaluate the suitability of different sample types for mpox diagnostic and assess the temporal dynamics of viral load. We evaluated 1914 samples from 953 laboratory-confirmed cases. The positivity rate was higher for lesion (91.3%) and rectal swabs (86.1%) when compared with oropharyngeal swabs (69.5%) and urines (41.2%), indicating higher viral loads for the former. Supporting this, lesion and rectal swabs showed lower median PCR C values (C = 23 and C = 24), compared to oropharyngeal swabs and urines (C = 31). Stable MPXV loads were observed in swabs from lesions up to 30 days after symptoms onset, contrasting with a considerable decrease in viral load in rectal and oropharyngeal swabs. Overall, these results point to lesion swabs as the most suitable samples for detecting MPXV in the 2022-2023 multicountry outbreak and show comparable accuracy to rectal swabs up to 8 days after symptoms onset. These findings, together with the observation that about 5% of patients were diagnosed through oropharyngeal swabs while having negative lesions, suggest that multisite testing should be performed to increase diagnostic sensitivity.
- Genome-Scale Characterization of Mycobacterium abscessus Complex Isolates from PortugalPublication . Carneiro, Sofia; Pinto, Miguel; Silva, Sónia; Santos, Andrea; Rodrigues, Irene; Santos, Daniela; Duarte, Sílvia; Vieira, Luís; Gomes, João Paulo; Macedo, RitaThe Mycobacterium abscessus complex (MABC) is an emerging, difficult to treat, multidrug-resistant nontuberculous mycobacteria responsible for a wide spectrum of infections and associated with an increasing number of cases worldwide. Dominant circulating clones (DCCs) of MABC have been genetically identified as groups of strains associated with higher prevalence, higher levels of antimicrobial resistance, and worse clinical outcomes. To date, little is known about the genomic characteristics of MABC species circulating in Portugal. Here, we examined the genetic diversity and antimicrobial resistance profiles of 30 MABC strains isolated between 2014 and 2022 in Portugal. The genetic diversity of circulating MABC strains was assessed through a gene-by-gene approach (wgMLST), allowing their subspecies differentiation and the classification of isolates into DCCs. Antimicrobial resistance profiles were defined using phenotypic, molecular, and genomic approaches. The majority of isolates were resistant to at least two antimicrobials, although a poor correlation between phenotype and genotype data was observed. Portuguese genomes were highly diverse, and data suggest the existence of MABC lineages with potential international circulation or cross-border transmission. This study highlights the genetic diversity and antimicrobial resistance profile of circulating MABC isolates in Portugal while representing the first step towards the implementation of a genomic-based surveillance system for MABC at the Portuguese NIH.
- Microevolution of a Mycobacteroides abscessus subsp. bolletii strain in a clinical persistent infectionPublication . Santos, Andrea; Pinto, Miguel; Carneiro, Sofia; Silva, Sónia; Rodrigues, Irene; Munhá, João; Gomes, João Paulo; Macedo, RitaMycobacteroides abscessus complex (MAB), a fast-growing nontuberculous mycobacterium, is emerging as a significant infectious disease threat, due to both intrinsic and acquired resistance mechanisms to antibiotics and disinfectants and the need for extensive and multidrug regimens for treatment. Despite the prolonged regimens, outcomes are poor and persistence cases have been reported. Here, we describe clinical, microbiologic and genomic features of a M. abscessus subsp. bolletii (M. bolletii) strain consecutively isolated from a patient within an eight-year infection period. From April 2014 to September 2021, the National Reference Laboratory for Mycobacteria received eight strains isolated from a male patient. Species identification, molecular resistance profile and phenotypic drug susceptibility were determined. Five of these isolates were recovered for further in-depth genomic analysis. Genomic analysis confirmed the multidrug resistant pattern of the strain and also other genetic changes associated with adaptation to environment and defence mechanisms. We highlight the identification of new mutations in locus MAB_1881c and in locus MAB_4099c (mps1 gene), already described as associated with macrolides resistance and morphotype switching, respectively. Additionally, we also observed the emergence and fixation of a mutation in locus MAB_0364c that appeared at a frequency of 36% for the 2014 isolate, 57% for the 2015 isolate and 100% for the 2017 and 2021 isolates, clearly illustrating a fixation process underlying a microevolution of the MAB strain within the patient. Altogether these results suggest that the observed genetic alterations are a reflection of the bacterial population's continuous adaptation and survival to the host environment during infection, contributing to persistence and treatment failure.
- Tuberculose em Portugal no período 2008-2012: avaliação da taxa de confirmação laboratorial no INSA e padrão de susceptibilidade aos antibacilaresPublication . Macedo, Rita; Silva, Anabela Santos; Rodrigues, Irene; João, Inês; Simões, Maria João
- Vigilância laboratorial da tuberculose em Portugal: relatório 2012Publication . Macedo, Rita; Silva, Anabela Santos; Rodrigues, Inês João; Rodrigues, Irene; Furtado, Cristina; Simões, Maria JoãoEm Portugal, e de acordo com o último relatório do Programa Nacional de luta contra a Tuberculose da Direção-Geral da Saúde, em 2012 foram notificados 2480 casos de tuberculose (TB), dos quais 2286 correspondem a casos novos (taxa de incidência de 21,6/100.000 habitantes). Embora Portugal continue entre os países de incidência intermédia, o único na Europa Ocidental, a incidência dos casos novos parece vir a diminuir desde o início da década de 2000. A incidência de tuberculose multirresistente (TB-MR) tem também vindo a diminuir. Em 2012 a incidência de TB-MR foi de 0,56% (14 casos) do total dos casos de TB registados. Esta é uma proporção inferior à média na UE e encontra-se praticamente circunscrita às áreas metropolitanas do Porto e, principalmente, de Lisboa. De acordo com os dados deste mesmo relatório, o número de casos de TB confirmados dos quais se conhece o perfil de suscetibilidade aos antibacilares tem vindo a diminuir, sendo que é cada vez mais frequente os doentes iniciarem tratamento empiricamente com base apenas em critérios clínicos e radiológicos. De facto, não sendo os laboratórios do INSA os únicos a nível nacional a efetuar isolamento em cultura e respetivo teste de suscetibilidade aos antibacilares (TSA), pode verificar-se, pela análise dos dados laboratoriais, que, embora o número de casos de TB notificados tenha aumentado em 2012, o número de casos de TB confirmados no INSA e com resultado de TSA tem vindo a diminuir. Por outro lado, e em relação aos casos de TB-MR verificamos que, entre 2008-2011, o número de casos notificados ao SVIG tem sido discordante em relação ao número de casos com resultado laboratorial. Em 2012 acentua-se essa diferença,com aumento do número de casos de TB-MR com confirmação laboratorial e que se mantêm sem notificação clínica. Este facto, alerta por si só, para a importância de se avaliarem periodicamente os vários componentes dos sistemas de vigilância, concretamente, no que diz respeito aos atrasos de notificação e consequentes implicações nas decisões a adoptar no controlo e prevenção da transmissão da tuberculose.