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- Cross-sectional study on protective antibodies against influenza A virus subtypes and cross-protection against influenza A(H3N2) subclade K, Portugal, August 2025Publication . Guiomar, Raquel; Henriques, Camila; Pereira da Silva, Susana; Gomes, Licínia; Dias, Daniela; Verdasca, Nuno; Portuguese Laboratory Network for the Diagnosis of Influenza and Respiratory Viruses; Nunes, Baltazar; Rodrigues, Ana PaulaThe 2025/26 season was marked by co-circulation of influenza A subtypes, with the first detection of A(H3N2) subclade K in September 2025. In August 2025 in Portugal, 14.8% (95% CI: 12.2-17.8) of 886 persons tested had cross-protective antibodies against this subclade. The overall seroprevalence against circulating A(H1N1)pdm09 strains was 28.1% (95% CI: 24.4-32.0). These data highlight the presence of previous cross-reactive antibodies and the possible advantage of vaccination in the extent of detectable antibodies against influenza viruses.
- Rapid drug resistance prediction in positive clinical samples using an extensive targeted next-generation sequencing panelPublication . Rosendal, Ebba; Isidro, Joana; Carneiro, Sofia; Gomes, João Paulo; Macedo, RitaTuberculosis (TB) remains a global health challenge, exacerbated by the emergence of drug-resistant strains. Most methods for drug susceptibility testing (DST) are culture-dependent and time consuming, possibly delaying optimal TB-treatment. This study aimed to develop an extensive targeted next-generation sequencing (tNGS) approach for rapid genotypic DST directly from clinical samples. We designed a tNGS panel comprising 30 amplicons targeting 19 genomic regions associated with resistance to 20 antibiotics. This method was applied to 71 smear-positive (0-3+) pulmonary TB clinical samples collected at the Portuguese National Reference Laboratory. DNA was extracted and amplified using multiplex PCRs, followed by sequencing on Oxford Nanopore Technologies MinION platform. Sequencing data were using TB-Profiler and the tNGS results compared to phenotypic DST and whole genome sequencing (WGS) data from corresponding isolates. The tNGS demonstrated high concordance with both phenotypic and WGS-based DST across different sample types and smear positivity levels. For first-line drugs, tNGS showed 88% categorical agreement (CA) with pDST, increasing to 97% when excluding undetermined results. Compared to WGS across all analysed antibiotics, tNGS achieved 92% CA, increasing to >99% when excluding undetermined results. Validation of the tNGS panel showed 90% (1,895/2,076) of amplicons reaching >10x coverage at all analysed positions and 43 (61%) samples with all complete amplicons above this threshold. Non-specific amplification of contaminant bacterial DNA was minimal, with most mapped off-target reads being of human origin. This method enables comprehensive resistance prediction directly from clinical samples and signifies an important development in TB diagnostics and resistance monitoring.
- Challenges of Congenital HHV6 Infection Diagnosis and Treatment: Two Case Reports and Literature ReviewPublication . Fernandes, Andreia; Pereira, Mafalda; Oliveira, Íris; Novo, Marta; Soares, Marta; Ramalho, Ana Raquel; Santos, Vera; Vinagre, Elsa; Lopo, Silvia; Gaspar, LuísaIntroduction: Congenital human herpesvirus 6 (HHV6) infection occurs in 1% of the general population and may result from the transmission of an inherited chromosomally integrated HHV6 (iciHHV6) or transplacental infection. It is mostly asymptomatic. Case reports: Case 1: a 29th-week-old female preterm newborn, admitted to the neonatal intensive care unit, became clinically unstable and irritable on the 20th day of hospitalization. Cranial ultrasound, revealed a significant posthemorrhagic tetraventricular dilation, with signs of ventriculitis. Investigations revealed HHV6 positivity on cerebrospinal fluid polymerase chain reaction multiplex panel testing and HHV6-DNA high viral loads in plasma samples. Case 2: a female late preterm newborn was admitted to the neonatal intensive care unit due to early-onset sepsis. Investigations revealed group B streptococcus positive blood cultures and cerebrospinal fluid HHV6 positivity on polymerase chain reaction multiplex panel testing, with negative bacterial culture. After 3 days of adequate antibiotic treatment, she maintained persistent moaning, which motivated a cranial ultrasound, revealing mild brain edema. Clinical improvement was observed only after beginning antiviral treatment in both newborns. Due to the persistency of high viral loads in both cases, despite antiviral treatment and clinical improvement, an iciHHV6 was suspected and posteriorly confirmed. Discussion/conclusion: Congenital iciHHV6 infection diagnosis is challenging because the presence of an iciHHV6 results in persistently high viral loads, even in the absence of active infection. Only a few diagnostic techniques can confirm active replication; unfortunately, these are not available in most countries. The decision to initiate antiviral treatment should be based on clinical judgment. Better ways for the diagnosis of active infection are needed.
- Enhancing Entomological Surveillance: Real-Time Monitoring of Mosquito Activity with the VECTRACK System in Rural and Urban AreasPublication . Silva, Manuel; Gouveia, Bruna R.; Santos, José Maurício; Guerreiro, Nélia; Monteiro, Alexandra; Almeida, Soraia; Osório, Hugo CostaBackground: Mosquitoes from the Aedes (Ae.) genus are vectors of dengue, Zika, chikungunya, and other arboviruses, posing a significant public health threat. In 2005, Aedes aegypti was detected for the first time in Madeira Island, Portugal, in the city of Funchal, and has since become established in the region. In 2017, Aedes albopictus was detected for the first time in mainland Portugal. These invasion events require targeted entomological surveillance, which demands substantial human resources and a high management capacity for traditional vector monitoring. Following promising results obtained in laboratory conditions, a field-deployable model of a bioacoustic sensor for the automatic classification of mosquitoes integrated with a Biogents Sentinel trap as part of the VECTRACK system was tested in three regions in Portugal. Methods: The VECTRACK system was deployed in three locations: Funchal on Madeira Island, and Palmela and Algarve on mainland Portugal. Catch bags were manually inspected at intervals ranging from daily to weekly, resulting in a total of 38 captures in Madeira, 10 in Palmela, and 7 in the Algarve. Manual identifications were compared with those generated by the VECTRACK system, and the degree of correlation between the two datasets was assessed using Spearman's rank correlation coefficient. Results: A total of 176 mosquitoes were captured in Madeira, 732 in Palmela, and 143 in the Algarve. Both manual and sensor-based identifications demonstrated similar performance, with high correlation observed between the two methods. Spearman's rank correlation coefficients indicated high agreement for both female and male mosquitoes across all sites: Madeira: females = 0.84, males = 0.92, Palmela: females = 0.99, males = 0.84, Algarve: females = 0.98, and males = 0.99, all with p-values < 0.001. Conclusions: The VECTRACK system demonstrated strong performance in accurately distinguishing mosquitoes from non-mosquitoes, differentiating between Aedes and Culex genera, and identifying the sex of individual specimens. These promising results provide a solid foundation for the development of automated early warning systems and enhance mosquito surveillance strategies, which are critical for timely responses to potential vector-borne disease outbreaks.
- An update of histoplasmosis focusing on Portuguese epidemiological specificitiesPublication . Sabino, Raquel; Veríssimo, Cristina; Antunes, FranciscoNo abstract available.
- Extensive Recalcitrant Tinea Corporis Caused by Trichophyton indotineaePublication . Sun, Lanyu; Ferreira, João; Vidal, Bruno; Veríssimo, Cristina; Sabino, Raquel; Marques, Tiago; Soares-de-Almeida, Luís; Filipe, PauloNo abstract available
- Phenotypic and genomic characterization of azole resistance in Portuguese isolatesPublication . Papuc, Alexandru-Marian; Veríssimo, Cristina; Simões, Helena; Toscano, Cristina; Gomes, João Paulo; Mixão, Verónica; Sabino, RaquelIntroduction: Candida parapsilosis is a clinically important etiological agent of systemic infections associated with hospital outbreaks, which prevalence has been increasing in the last decade. Moreover, in recent years, fluconazole resistance in this species has been emerging in different countries, being a subject of significant interest and concern. In this context, the present study aims to determine the frequency of fluconazole resistance in C. parapsilosis sensu stricto isolates collected in Portugal (2003-2007 and 2017-2024), understand its associated molecular mechanisms, and relate it all with worldwide genomic data. Methods: To this end, we performed phenotypic assays of 145 isolates of C. parapsilosis collected from different biological and environmental products in Portugal (majority from the Lisbon Metropolitan area), and explored the genomic features of the fluconazole-resistant ones. Results: We found eight C. parapsilosis fluconazole-resistant isolates between 2017 and 2024, corresponding to a frequency of 8.5% in this period, and contrasting with the absence of fluconazole-resistant isolates collected before 2007. Sequencing of the ERG11 gene showed that all fluconazole-resistant isolates had the Y132F and R398I mutations. Discussion: A phylogenomic analysis including publicly available isolates from other countries revealed that our Portuguese isolates are more closely related to those from the USA and Germany than to the isolates sequenced thus far from the neighbor country, Spain. Furthermore, although three distinct C. parapsilosis genetic clades were found in our dataset, all the fluconazole-resistant isolates detected in this study cluster together, raising the question of whether the increased fluconazole-resistance in the country could possibly be associated with the emergence or introduction of this particular lineage. Altogether, these results provide valuable insights on fluconazole resistance in a set of Portuguese C. parapsilosis isolates and their associated mechanisms, representing an important step towards a better understanding of the increasing C. parapsilosis fluconazole resistance in Southern Europe.
- Diagnostic algorithms for tuberculosis in Europe: insights from the European Reference Laboratory Network for Tuberculosis (ERLTB-Net)Publication . Saluzzo, Francesca; Cabibbe, Andrea Maurizio; Anthony, Richard; Aubry, Alexandra; Drobniewski, Francis; Holicka, Yen; Lillebaek, Troels; Macedo, Rita; Mansjö, Mikael; Szél, Viktoria; Žmak, Ljiljana; Cirillo, Daniela M.; Groenheit, RamonaThe reported poor treatment outcomes for extensively drug-resistant tuberculosis (TB) in the European region highlight the urgent need for effective and context-appropriate diagnostic strategies. While the World Health Organisation (WHO) provides model algorithms, these require adaptation to the European Union/European Economic Area (EU/EEA) context, a setting with low TB incidence but high resources. This viewpoint from the European Reference Laboratory Network for TB (ERLTB-Net) proposes a tailored diagnostic algorithm that prioritises the universal use of WHO-recommended molecular rapid diagnostic tests, systematic culture, and whole genome sequencing (WGS). This approach integrates phenotypic drug susceptibility testing strategically and outlines the possible role of targeted next-generation sequencing (tNGS) in the EU/EEA setting. The algorithm also addresses the importance of diagnostic harmonisation, cross-border collaboration, and sustained investment in sequencing capacity. By aligning diagnostic practices with the regional epidemiology and laboratory infrastructure, this stepwise, resource-sensitive approach aims to strengthen TB control, improve treatment outcomes, and guide public health action in the EU/EEA.
- Europe needs a sustainably funded influenza research and response networkPublication . Krammer, Florian; Barclay, Wendy S.; Beer, Martin; Brown, Ian H.; Cox, Rebecca Jane; de Jong, Menno D.; Fodor, Ervin; Fouchier, Ron A.M.; Gabriel, Gülsah; García-Sastre, Adolfo; Guiomar, Raquel; Horby, Peter; Koopmans, Marion; Lewis, Nicola S.; Maggi, Stefania; Monne, Isabella; Naffakh, Nadia; Nohynek, Hanna; Osterhaus, Albert; Prosenc, Katarina; Prymula, Roman; Rappuoli, Rino; Redlberger-Fritz, Monika; Rimmelzwaan, Guus F.; Russell, Colin A.; Saelens, Xavier; Schwemmle, Martin; Smith, Derek J.; Stertz, Silke; Tähtinen, Paula A.; Terregino, Calogero; Thålin, CharlotteNo abstract available
- Acute flaccid myelitis in Europe between 2016 and 2023: indicating the need for better registrationPublication . Helfferich, Jelte; Calvo, Cristina; Alpeter, Ekkehardt; Andrés, Cristina; Antón, Andrés; Aubart, Melodie; Bova, Stefania Maria; Cabrerizo, Maria; von Eije, Karin; Fabiola, Stollar; Felipe, Ana; Iordanova, Ralitsa; Thomsen, Marianne Kragh; Knudsen, Per Kristian; van Loenen, Freek; Lopez, Noemi; Mirand, Audrey; Molenkamp, Richard; Midgley, Sofie; Neves, Raquel; Glomb, Lubomira Nikolaeva; Øverbø, Joakim; Öztürk, Gülten; Palminha, Paula; Viekilde Pfeiffer, Helle Cecilie; Prochazka, Birgit; Ribeiro, Carlos; Rodesch, Martine; Schuffenecker, Isabelle; Shetty, Jay; Siegert, Sandy; Solberg, Silje Lae; Sulik, Artur; Türkdoğan, Dilşad; Ünver, Olcay; Verweij, Jaco; Vila, Jorgina; Vuorinen, Tytti; Wickström, Ronny; Fischer, Thea K.; Harvala, Heli; Benschop, Kimberley S.M.Background: Acute flaccid myelitis (AFM) is a rare polio-like condition affecting mainly children and characterised by severe, often persistent, weakness. It is one of several causes of acute flaccid paralysis (AFP), which manifests as acute onset of limb weakness and reduced muscle tone. Some non-polio enteroviruses (EV), such as EV-D68 may cause AFM. Little is known about AFM incidence in Europe.AimWe aimed to better understand AFM incidence, aetiology and current surveillance policies in Europe.MethodsIn 28 countries, members of the European non-polio enterovirus network (ENPEN) and a newly established AFM network of clinicians under ENPEN received a survey asking them how AFM surveillance was performed in their countries in 2016-2023 and the numbers of AFM cases including those diagnosed with EV-D68 infection during this period.ResultsSurveillance information was obtained for 16 countries. In eight countries, AFP surveillance initiated for poliomyelitis eradication was still ongoing, while non-polio AFM cases were only systematically reported in Norway. The survey revealed 130 AFM cases for 14 countries, with 48 (37%) EV-D68-laboratory-confirmed. Among the AFM cases, 70% (n = 91) occurred in 2016, 2018 and 2022, when EV-D68 circulation increased.ConclusionsThis report provides some indication of AFM case numbers in Europe since 2016. However, as 15 of 16 countries with AFM monitoring information lacked structural AFM surveillance, numbers should be interpreted with caution. Knowing AFM incidence matters to determine its impact and detect future outbreaks. Thus, the newly established clinical network will develop a European AFM repository.