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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.
- Chlamydia trachomatis outbreak: when the virulence-associated genome backbone imports a prevalence-associated major antigen signaturePublication . Borges, Vitor; Cordeiro, Dora; Salas, Ana Isabel; Lodhia, Zohra; Correia, Cristina; Isidro, Joana; Fernandes, Cândida; Rodrigues, Ana; Azevedo, Jacinta; Alves, João; Rôxo, João; Rocha, Miguel; Corte-Real, Rita; Vieira, Luís; Borrego, Maria José; Gomes, João PauloChlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM).
- Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signaturePublication . Borges, Vítor; Cordeiro, Dora; Salas, Ana Isabel; Lodhia, Zohra; Correia, Cristina; Isidro, Joana; Fernandes, Cândida; Rodrigues, Ana Maria; Azevedo, Jacinta; Alves, João; Roxo, João; Rocha, Miguel; Côrte-Real, Rita; Vieira, Luís; Borrego, Maria José; Gomes, João PauloChlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.
- Clinical and Epidemiological Characterization of Lymphogranuloma Venereum in a Sexually Transmitted Diseases Clinic in Lisbon, 2001 to 2020Publication . Bonito, Frederico; Alves, João; Lodhia, Zohra; Cordeiro, Dora; Borges, Vítor; Azevedo, Jacinta; Borrego, Maria JoséBetween 2001 and 2020, 54 LGV cases were diagnosed in a sexually transmitted disease clinic in Lisbon, most in men who have sex with men (87%), HIV negative (63%), from the anorectal mucosa (72.2%). Cases among heterosexuals were also identified (13%). Surveillance programs irrespective of sexual orientation and HIV status are needed to avoid the morbidity associated with LGV.
- CMV and HCV infections in HIV/non-HIV mothers and newborns: prevalence, frequency and risk factorsPublication . Lopo, Sílvia; Pereira, Maria Amável; Mendonça, Joana; Vinagre, Elsa; Reis, Tânia; Cordeiro, Dora; Almeida, Catarina; Água-Doce, Ivone; Manita, Carla; Palminha, Paula; Pádua, Elizabeth; Paixão, Maria Teresa; Carreiro, Helena; Barroso, Rosalina; Campos, Teresa; Marques, TâniaThe incidence of HIV infections in gestational age is an important Public Health issue as are concerns about co-infection with opportunistic viruses, such as CMV/HCV. Several authors refer higher ratios of congenital CMV infection in children born to HIV infected mother than in uninfected. In the case of HCV, perinatal transmission increases in cases of mothers co-infected with HIV. Aims:To study CMV/HCV infection/co-infection in HIV/non-HIV women and their newborns between 2006-2010, according to epidemiological, laboratory and clinical data; to evaluate frequency of CMV/HIV/HCV maternal-fetal transmission and analyse risk factors for infections. Methods:Plasma and/or urine of 137 HIV and 140 non-HIV women, attending a Lisbon Hospital and their 140 newborns were analysed at NIH. HIV-1 and/or HIV-2 proviral DNA nested-PCR was performed on HIV mothers and their newborn’s plasma. Maternal plasma was screened for CMV and HCV antibodies; RNA determination, genotyping and viral load were performed on women with HCV antibodies, their newborn’s plasma was also screened for HCV. Newborn’s urine was inoculated for CMV detection. Data analysis was performed using SPSS 17.0 and Fisher's exact test. Results:HIV1 vertical transmission was diagnosed in 3/140(2.1%) cases. CMV congenital infection was diagnosed in 4(2.9%) newborns from HIV women and no congenital CMV infection was diagnosed in newborns from non-HIV women. 2/137(1.5%) HIV women and 14/140(10.0%) non-HIV women were CMV seronegative. HCV infection was detected in 6(4.4%) HIV women; all had HCV positive viral load; different genotypes were found. One case of HCV perinatal transmission was diagnosed. No HCV antibodies were found in non-HIV women. No children were HIV/HCV or CMV/HCV coinfected but 2 were HIV/CMV coinfected. There is evidence of significant statistical associations with race/ethnicity and time of pregnancy. Conclusion:In this study HIV women had higher CMV/HCV antibody prevalence and frequency of maternal-fetal transmission than non-HIV women. 2/137 HIV seronegative newborns and 2/3 HIV newborns were CMV congenitally infected; this difference should be further studied, as the consequences of CMV/HCV infections may become increasingly serious and complex in the presence of HIV. This specific group is not representative of the Portuguese infected women, nevertheless the significant risk factors found and other risk factors studied without strong associations should be considered in larger studies.
- Diagnóstico laboratorial da infeção por Chlamydia trachomatis, 1991-2014Publication . Dinis, Margarida; Cordeiro, Dora; Santo, Irene; Azevedo, Jacinta; Gomes, João Paulo; Borrego, Maria JoséObjetivo: O presente trabalho tem por objetivo apresentar os resultados do diagnóstico laboratorial das infeções por C. trachomatis realizado no Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA) entre 1991 e 2014.
- 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.
- Fifteen years of a nationwide culture collection of Neisseria gonorrhoeae antimicrobial resistance in PortugalPublication . Pinto, Miguel; Rodrigues, João Carlos; Matias, Rui; Água-Doce, Ivone; Cordeiro, Dora; Correia, Cristina; Gomes, João Paulo; Borrego, Maria José; PTGonoNetNeisseria gonorrhoeae antimicrobial resistance (AMR) and gonorrhea disease burden remain major public health concerns worldwide. To contribute to the supranational demands to monitor and manage the spread of antimicrobial-resistant N. gonorrhoeae, the Portuguese NIH promoted the creation of the National Laboratory Network for Neisseria gonorrhoeae Collection (PTGonoNet). The present study reports the N. gonorrhoeae major AMR trends observed from 2003 up to 2018. All isolates described in the present study constitute the opportunistic ongoing N. gonorrhoeae isolate collection supported by the National Reference Laboratory for Sexually Transmitted Infections of the Portuguese NIH, enrolling strains isolated in 35 different public and private laboratories. Minimum inhibitory concentrations were determined using E-tests for azithromycin, benzylpenicillin, cefixime, ceftriaxone, ciprofloxacin, gentamicin, spectinomycin and tetracycline. Molecular typing was determined using NG-MAST. AMR data of 2596 country-spread isolates show that 87.67% of all N. gonorrhoeae isolates presented decreased susceptibility to at least one antimicrobial. A continuous decreased susceptibility and resistance to penicillin, tetracycline and ciprofloxacin can be observed along the years. However, no decreased susceptibility to cephalosporins was observed until 2018, while for azithromycin, this was always low. The most common observed NG-MAST genogroups were G1407, G7445, G225, G2, and G1034. This study evidences the advantages of a nationwide collection of isolates and of centralized AMR testing to respond to supranational (EURO-GASP) requirements while providing unprecedented data on AMR in the context of 15 years of surveillance.
- 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.