Browsing by Author "Oliveira, Olena"
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- Evaluation of a gene-by-gene approach for prospective whole-genome sequencing-based surveillance of multidrug resistant Mycobacterium tuberculosisPublication . Macedo, Rita; Pinto, Miguel; Borges, Vítor; Nunes, Alexandra; Oliveira, Olena; Portugal, Isabel; Duarte, Raquel; Gomes, João PauloWhole-genome sequencing (WGS) offers unprecedented resolution for tracking Mycobacterium tuberculosis transmission and antibiotic-resistance spread. Still, the establishment of standardized WGS-based pipelines and the definition of epidemiological clusters based on genetic relatedness are under discussion. We aimed to implement a dynamic gene-by-gene approach, fully relying on freely available software, for prospective WGS-based tuberculosis surveillance, demonstrating its application for detecting transmission chains by retrospectively analysing all M/XDR strains isolated in 2013-2017 in Portugal. We observed a good correlation between genetic relatedness and epidemiological links, with strongly epilinked clusters displaying mean pairwise allele differences (AD) always below 0.3% (ratio of mean AD over the total number of shared loci between same-cluster strains). This data parallels the genetic distances acquired by the core-SNV analysis, while providing higher resolution and epidemiological concordance than MIRU-VNTR genotyping. The dynamic analysis of strain sub-sets (i.e., increasing the number of shared loci within each sub-set) also strengthens the confidence in detecting epilinked clusters. This gene-by-gene strategy also offers several practical benefits (e.g., reliance on freely-available software, scalability and low computational requirements) that further consolidated its suitability for a timely and robust prospective WGS-based laboratory surveillance of M/XDR-TB cases.
- Limited Benefit of the New Shorter Multidrug-Resistant Tuberculosis Regimen in Europe [Letters to the Editor]Publication . Lange, Christoph; Duarte, Raquel; Fréchet-Jachym, Mathilde; Guenther, Gunar; Guglielmetti, Lorenzo; Olaru, Ioana D; Oliveira, Olena; Rumetshofer, Rudolf; Veziris, Nicolas; van Leth, Frank; European MDR-TB database collaborationExtract: The emergence of multidrug-resistant tuberculosis (MDR-TB), defined as bacillary resistance to at least rifampicin and isoniazid, threatens global TB control. The number of patients notified with MDR-TB worldwide has increased by 261% from 2009 to 2014, and more than one-third of these patients currently live in the European Region of the World Health Organization (WHO). Management of patients with MDR-TB is challenging owing to the long duration of therapy required to achieve a relapse-free cure, complex drug regimens, frequent drug-related adverse events, high costs, suboptimal adherence, and overall low cure rates. [...]
- Shifting Profile of MDR-TB Patients in Northern Portugal? [Letters to the Editor]Publication . Oliveira, Olena; Gaio, A.; Silva, Anabela; Macedo, Rita; Duarte, RaquelExtract: The occurrence of multidrug and extensively drug-resistant tuberculosis (M/XDR-TB), defined as a public health crisis by the World Health Organization (WHO) in 2013, is a threat to all efforts to control TB in Europe. Despite the steady decline of TB incidence, Europe has faced the largest proportion of M/XDR-TB among individuals diagnosed with TB; this requires a stronger link between health system strengthening and M/XDR-TB control to adequately prevent and treat this deadly disease. In 2014, 15% of new TB cases and 48% of previously treated cases were estimated to be MDR-TB.The XDR-TB prevalence among MDR-TB patients was 17.5 %. Within Europe the epidemiological pattern of TB varies greatly, with some countries showing a steady progress towards elimination of the disease, while others continue to face high rates of incidence. Portugal is the only Western European country presenting an intermediate TB incidence, estimated at 20 per 100 000 inhabitants in 2014, with the infection being concentrated at the two largest cities of Porto (Northern Region) and Lisbon (Lisbon and Tagus Valley Region). Nation wide, MDR-TB was reported for 2.5 % of the cases with drug-susceptibility testing (DST) results, 26% of which XDR. MDR-TB was substantially circumscribed to the metropolitan areas of Porto and Lisbon. In the Northern Region of Portugal, MDRTB was reported for 1.3 % of the cases with DST results without any diagnosed cases of XDR-TB. [...]