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- In silico scrutiny of genes revealing phylogenetic congruence with clinical prevalence or tropism properties of Chlamydia trachomatis strainsPublication . Ferreira, R.; Antelo, M.; Nunes, A.; Borges, V.; Damião, V.; Borrego, M.J.; Gomes, João PauloMicrobes possess a multiplicity of virulence factors that confer them the ability to specifically infect distinct biological niches. Contrary to what is known for other bacteria, for the obligate intracellular human pathogen Chlamydia trachomatis, the knowledge of the molecular basis underlying serovars’ tissue specificity is scarce. We examined all ~900 genes to evaluate the association between individual phylogenies and cell-appetence or ecological success of C. trachomatis strains. Only ~1% of the genes presented a tree topology showing the segregation of all three disease groups (ocular, urogenital, and lymphatic) into three wellsupported clades. Approximately 28% of the genes, which include the majority of the genes encoding putative type III secretion system effectors and Inc proteins, present a phylogenetic tree where only lymphogranuloma venereum strains form a clade. Similarly, an exclusive phylogenetic segregation of the most prevalent genital serovars was observed for 61 proteins. Curiously, these serovars are phylogenetically cosegregated with the lymphogranuloma venereum serovars for ~20% of the genes. Some clade-specific pseudogenes were identified (novel findings include the conserved hypothetical protein CT037 and the predicted a-hemolysin CT473), suggesting their putative expendability for the infection of particular niches. Approximately 3.5% of the genes revealed a significant overrepresentation of nonsynonymous mutations, and the majority encode proteins that directly interact with the host. Overall, this in silico scrutiny of genes whose phylogeny is congruent with clinical prevalence or tissue specificity of C. trachomatis strains may constitute an important database of putative targets for future functional studies to evaluate their biological role in chlamydial infections.
- Early detection of influenza activity using telephone helpline dataPublication . Mexia, Ricardo; Louro, Carlota; Nunes, Baltazar; Contreiras, Teresa; Dias, Carlos MatiasThe annual influenza season is a recurring time period characterized by the prevalence of outbreaks of influenza. Early detection of these outbreaks is paramount to allocating resources and effective counter measures. Methods: Using data from the Portuguese health helpline we selected 17 triage algorithms that relate with the influenza case definition used by ECDC. We listed the weekly number of calls for each algorithm and the total number of calls to the counselling line, from week 40 to 20 (seasonal influenza) from 2010-2013. Data was then compared with data from the sentinel system (standard surveillance in Portugal) with up to 5 weeks lag, using a cross correlation function. Correlations above 0,5 were considered of interest. In parallel, the MEM - Moving Epidemic Method was applied to determine a baseline threshold for the beginning of the epidemic period. Results: We analysed 1.032.724 calls (an average of 10.432 calls each week), and the “cough algorithm” presented the highest correlation (0,83) to data from the sentinel network, with a 3 weeks lag. Using MEM, we were able to detect the beginning of the epidemic period 3 to 5 weeks in advance, comparing to data from the sentinel network. Conclusion: The baseline provided by the selected algorithms allowed, on average, three weeks of advanced warning for seasonal influenza activity. Using two techniques (cross correlation and MEM) we were able to detect early signs of seasonal influenza activity, specifically with influenza related symptoms, namely coughing.
- In Silico Scrutiny of Genes Revealing Phylogenetic Congruence with Clinical Prevalence or Tropism Properties of Chlamydia trachomatis StrainsPublication . Ferreira, R.; Antelo, M.; Nunes, A.; Borges, V.; Damião, V.; Borrego, M.J.; Gomes, João PauloMicrobes possess a multiplicity of virulence factors that confer them the ability to specifically infect distinct biological niches. Contrary to what is known for other bacteria, for the obligate intracellular human pathogen Chlamydia trachomatis, the knowledge of the molecular basis underlying serovars' tissue specificity is scarce. We examined all ~900 genes to evaluate the association between individual phylogenies and cell-appetence or ecological success of C. trachomatis strains. Only ~1% of the genes presented a tree topology showing the segregation of all three disease groups (ocular, urogenital, and lymphatic) into three well-supported clades. Approximately 28% of the genes, which include the majority of the genes encoding putative type III secretion system effectors and Inc proteins, present a phylogenetic tree where only lymphogranuloma venereum strains form a clade. Similarly, an exclusive phylogenetic segregation of the most prevalent genital serovars was observed for 61 proteins. Curiously, these serovars are phylogenetically cosegregated with the lymphogranuloma venereum serovars for ~20% of the genes. Some clade-specific pseudogenes were identified (novel findings include the conserved hypothetical protein CT037 and the predicted α-hemolysin CT473), suggesting their putative expendability for the infection of particular niches. Approximately 3.5% of the genes revealed a significant overrepresentation of nonsynonymous mutations, and the majority encode proteins that directly interact with the host. Overall, this in silico scrutiny of genes whose phylogeny is congruent with clinical prevalence or tissue specificity of C. trachomatis strains may constitute an important database of putative targets for future functional studies to evaluate their biological role in chlamydial infections.
- Surveillance in the time of austerity; Portuguese HIV/AIDS Surveillance achieves a 30% improvement in efficiency after LEAN inspired changes to processingPublication . Shivaji, Tara; Cortes Martins, Helena; Diniz, Antonio; Nogueira, Paulo J; Vasconcelos, Paula; Silva, AndreiaBackground In 2013, following reminders about statutory notification of HIV/AIDS, Portuguese clinicians notified all cases, irrespective of previous notification. At the same time, hospitals introduced electronic records that automatically generated additional paper notification reports. No supplemental resources were available to process the 10-fold increase in notifications. The ensuing backlog caused delays in providing timely information for HIV program planning and evaluation. We investigated whether management principles from the automobile industry (LEAN) could improve data management efficiency. Methods Efficiency was defined as the time spent processing the paper report into electronic surveillance information. We used value stream mapping to understand the process and employed focus groups to identify areas for improvement (LEAN methodology). We recorded the time taken to complete this process for randomly selected batches of reports and calculated the average time per report. Results When consulted, stakeholders expressed the need for information about recent HIV/AIDS diagnoses. We prioritized processing cases diagnosed between 2011-2013. We reduced data-entry errors and transcribing time by inserting drop-down menus and automatic variable calculators. We implemented auto-search during data entry to prevent duplication. We redesigned the data entry mask to match the paper report. Before intervention, processing time was 9 minutes and 28 seconds (95%CI 8:53-10:58) per report. Two months post-intervention, this was 6 minutes and 34 seconds (95% CI 6:25-6:43), reducing the time to process the remaining backlog (10,000 reports) by 54 days. Conclusion Applying LEAN techniques to HIV/AIDS surveillance in Portugal enabled delivery of crucial information to national and international HIV stakeholders through a 30% reduction in data processing time and optimization of data quality. Public health practitioners should consider LEAN techniques to improve data quality and efficiency of surveillance systems.