SARS-CoV-2 Antibody Seroprevalence in Patients With Cancer on Systemic Antineoplastic Treatment in the First Wave of the COVID-19 Pandemic in Portugal.

At the time of the first wave of the COVID-19 pandemic, patients with cancer were considered to be at high risk of serious illness and had a higher exposure risk since they needed frequent and nondeferrable hospital visits. Serological tests were not routinely used, and seroprevalence in this population was unknown. A single-center, cross-sectional study was developed to determine the seroprevalence of anti-SARS-CoV-2 antibodies (Abs) in patients with cancer undergoing systemic antineoplastic treatment. One hundred patients were consecutively recruited in a two-week period (6th-20th May 2020), and serum samples were tested for the presence of immunoglobulin M (IgM) and immunoglobulin G (IgG) Abs directed against both spike (S) and nucleocapsid (N) SARS-CoV-2 proteins in two distinct time points (at recruitment and 4-8 weeks later). IgG-positive results were subject to confirmation, in the same serum sample, using two distinct assays. At the time of the first study visit, no patient had a previously confirmed diagnosis of COVID-19, one reported previous contact with a COVID-19 patient, and all had a baseline SARS-CoV-2-negative RT-PCR. Two patients tested positive for SARS-CoV-2 IgG in the first study visit, which was not confirmed in either of the two confirmatory assays. Seventy-two patients were tested at the second study visit, all with negative IgG tests. IgM was persistently positive at both study visits in one patient and was positive in another patient at the second study visit, both with negative RT-PCR and serum IgG. No patient tested positive for RT-PCR within the study timeframe. No evidence of prior or acute SARS-CoV-2 infection was documented in this cohort of patients with cancer undergoing systemic treatment, and no additional exposure risk was documented compared to general population seroprevalence studies. The study was inconclusive regarding the role of SARS-CoV-2 serology in patients with cancer in the early phase of the pandemic. This study did show that, with adherence to recommended preventive measures, it was safe to maintain systemic cancer therapy.

Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal.

Portugal is a low incidence country for tuberculosis (TB) disease. Now figuring among TB low incidence countries, it has since the 1990s reported multidrug resistant and extensively drug resistant (XDR) TB cases, driven predominantly by two strain-types: Lisboa3 and Q1. This study describes the largest characterization of the evolutionary trajectory of M/XDR-TB strains in Portugal, spanning a time-period of two decades. By combining whole-genome sequencing and phenotypic susceptibility data for 207 isolates, we report the geospatial patterns of drug resistant TB, particularly the dispersion of Lisboa3 and Q1 clades, which underly 64.2% and 94.0% of all MDR-TB and XDR-TB isolates, respectively. Genomic-based similarity and a phylogenetic analysis revealed multiple clusters (n = 16) reflecting ongoing and uncontrolled recent transmission of M/XDR-TB, predominantly associated with the Lisboa3 and Q1 clades. These clades are now thought to be evolving in a polycentric mode across multiple geographical districts. The inferred evolutionary history is compatible with MDR- and XDR-TB originating in Portugal in the 70's and 80's, respectively, but with subsequent multiple emergence events of MDR and XDR-TB particularly involving the Lisboa3 clade. A SNP barcode was defined for Lisboa3 and Q1 and comparison with a phylogeny of global strain-types (n = 28 385) revealed the presence of Lisboa3 and Q1 strains in Europe, South America and Africa. In summary, Portugal displays an unusual and unique epidemiological setting shaped by >40 years of uncontrolled circulation of two main phylogenetic clades, leading to a sympatric evolutionary trajectory towards XDR-TB with the potential for global reach.

Improving influenza surveillance in Portuguese preschool children by parents' report.

UNLABELLED: Influenza surveillance is usually based on nationally organized sentinel networks of physicians and on hospital reports. This study aimed to test a different report system, based on parents' phone contact to the research team and in home collection of samples by a dedicated team. The identification of influenza and other respiratory viruses in children who attended a Hospital Emergency Department was also recorded. Real-time PCR and reverse transcription PCR were performed for influenza A and B, parainfluenza 1-4, adenovirus, human metapneumovirus, respiratory syncytial virus A and B, rhinovirus, enterovirus, group 1 coronaviruses, group 2 coronaviruses, and human bocavirus. One hundred children were included, 64 from the day care centers and 36 from the Hospital. Overall, 79 samples were positive for at least one respiratory virus. Influenza A (H3) was the virus most frequently detected: 25 cases, 20 of these in children under 5 years of age (ten from day care centers and ten who went to the hospital) which was higher than those reported by the National Influenza Surveillance Programme for this age. CONCLUSION: The results obtained in this study suggest that a surveillance system based on parents' reports could complement the implanted system of the National Influenza Surveillance Programme.

Genetic analysis of extensively drug-resistant Mycobacterium tuberculosis strains in Lisbon, Portugal.

OBJECTIVES: Extensively drug-resistant (XDR) tuberculosis (TB) threatens the global control of TB worldwide. Lisbon has a high XDR-TB rate [50% of the multidrug-resistant tuberculosis (MDR-TB)], which is mainly associated with Lisboa family strains. Few studies have addressed the identification of mutations associated with resistance to second-line injectable drugs, and the relative frequency of such mutations varies geographically. The aim of this study was to characterize the genetic changes associated with the high number of XDR-TB cases in Lisbon. METHODS: In the present study we analysed 26 XDR-TB clinical isolates. The gyrA, tlyA and rrs genes were screened for mutations that could be responsible for resistance to fluoroquinolones and second-line injectable drugs. Moreover, the strains under analysis were also genotyped by MIRU-VNTR ('mycobacterial interspersed repetitive unit-variable number of tandem repeats'). RESULTS: The mutational analysis identified the most frequent mutations in the resistance-associated genes: S91P in gyrA (42.3%); A1401G in rrs (30.8%); and Ins755GT in tlyA (42.3%). The occurrence of mutations in rrs was associated with the non-occurrence of mutations in tlyA. The genotypic analysis revealed that the strains were highly clonal, belonging to one of two MIRU-VNTR clusters, with the largest belonging to the Lisboa family. Association between mutations in gyrA and rrs or tlyA was verified. CONCLUSIONS: The association of specific mutations highlighted the strains' high clonality and indicates recent XDR-TB transmission. In addition, the identification of the most frequent resistance-associated mutations will be invaluable in applying XDR-TB molecular detection tests in the region in the near future.

Genotypic analysis of Mycobacterium tuberculosis isolates from a Lisbon hospital in Portugal.

Portugal has one of the highest tuberculosis notification rates of the European Union with Lisbon Health Region having an incidence rate well above the national average. The present study analyses the transmission, drug susceptibility and characteristics of a study population from a Central Lisbon's Hospital. One hundred and thirty -two Mycobacterium tuberculosis clinical isolates were previously tested for drug susceptibility to first -line drugs. The multidrug (MDR) resistance rate was found to be 3.0%, while 13.6% of the isolates were resistant to one or more first -line drugs. HIV serology was available for 98 patients, 26 (26.5%) were positive. Genotyping was performed by MIRU -VNTR and 53 (40.2%) out of the 132 isolates were found to be distributed through 17 MIRU -VNTR clusters of two or more isolates. Lisboa strains accounted for 25.8% of all strains. We conclude that transmission of resistant and susceptible Mycobacterium tuberculosis strains is occurring, with special concern for Lisboa strains.

Genetic characterisation of the ethambutol resistance-determining region in Mycobacterium tuberculosis: prevalence and significance of embB306 mutations.

Ethambutol (EMB) is a first-line antitubercular drug that inhibits arabinogalactan and lipoarabinomannan biosynthesis. Resistance to EMB has traditionally been associated with embB mutations, especially in the Met306 codon. In this study, the region encompassing the embB306 codon in 109 Mycobacterium tuberculosis clinical isolates (49 EMB-susceptible and 60 EMB-resistant) was characterised. The occurrence of embB306 mutations was verified not only in EMB-resistant isolates (55.0%) but also in EMB-susceptible isolates (16.3%), which questions the role of embB306 mutations as determinants of EMB resistance. Subsequently, four different embB alleles were created by in vitro mutagenesis and were introduced into Mycobacterium smegmatis on a multicopy plasmid. To assess the contribution of embB306 mutations to EMB resistance, the EMB minimum inhibitory concentration (MIC) of these strains was determined. Strains carrying mutant embB306 alleles were able to grow at slightly higher MICs compared with the strain carrying the wild-type embB gene. The small MIC increase obtained here does not appear to be sufficient to cause high-level EMB resistance. The results obtained in the present study suggest that acquisition of EMB resistance might be a multistep process in which embB306 mutations may represent a first-step in EMB resistance acquisition.

Multidrug-resistant tuberculosis in Lisbon, Portugal: a molecular epidemiological perspective.

Portugal has the fourth highest tuberculosis (TB) incidence rate in the European Union (EU). Thirty-nine percent of all cases originate in Lisbon Health Region. Portugal also presents high levels of multidrug-resistant tuberculosis (MDR-TB) (1.5%, primary rate and 2.4%, in retreatment cases). In the present study we have characterized 58 MDR-TB clinical isolates by: (i) determining the resistance profile to first- and second-line drugs used in the treatment of tuberculosis; (ii) genotyping all isolates by MIRU-VNTR; (iii) analyzing mutations conferring resistance to isoniazid, rifampicin, streptomycin, and ethambutol, in katG, mabA-inhA, rpoB, rpsL, rrs, and pncA genes. We have therefore established the prevalence of the most common mutations associated with drug resistance in the Lisbon Health Region: C-15T in mabA-inhA for isoniazid; S531L in rpoB for rifampicin; K43R in rpsL for streptomycin; and V125G in pncA for pyrazinamide. By genotyping all isolates and combining with the mutational results, we were able to assess the isolates' genetic relatedness and determine possible transmission events. Strains belonging to family Lisboa, characterized several years ago, are still responsible for the majority of the MDR-TB. Even more alarming is the high prevalence of extensive drug-resistant tuberculosis (XDR-TB) among the MDR-TB isolates, which was found to be 53%. The TB status in Portugal therefore requires urgent attention to contain the strains continuously responsible for MDR-TB and now, XDR-TB.

Molecular epidemiology of Mycobacterium tuberculosis in Lisbon.

We conducted a molecular epidemiology study of Mycobacterium tuberculosis strains isolated from patients in Lisbon hospitals. We used restriction fragment length polymorphism (RFLP) to detect Lisbon family strains and to determine the genetic diversity of Mycobacterium tuberculosis strains isolated in Lisbon, through identification of the most important risk factors of tuberculosis transmission analysis, with the insertion sequence IS6110 as a probe to fingerprint isolates of Mycobacterium tuberculosis. 64.8% of the 290 Mycobacterium tuberculosis isolates were grouped in clusters. This figure was 60.7% if we excluded strains with five or fewer IS6110 copies. Multidrug-resistance was observed in 4.1% of the strains and they were all in clusters. Forty-five (18.2%) strains were included in the Lisbon family. Considering the relatively high percentage of strains in cluster detected in this study, we believe that active transmission is still taking place in Lisbon. Moreover, clusters of Lisbon strains represent the predominant strains circulating in Lisbon and are still related to drug resistance although presenting a lower percentage than that observed in previous studies.

pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis isolates in Portugal.

The nucleotide sequences of the pncA genes within 55 multidrug-resistant pyrazinamide-resistant Mycobacterium tuberculosis clinical isolates were determined. Fifty-three out of the 55 isolates were pyrazinamidase (PZase) negative. Four strains contained a wild-type pncA gene, and PZase activity was undetectable in two of these strains. Seven of the 18 identified pncA mutations found have not been described in previous studies.

[Laboratory surveillance of drug resistance tuberculosis in Portugal in 2000-2001]. / Vigilância laboratorial da resistência aos antibacilares em Portugal em 2000-2001.

BACKGROUND: A network for the Surveillance of Antituberculosis Drug Resistance (VigLab-Tuberculose), including all the mycobacterial laboratories where drug susceptibility test on isolates of Mycobacterium tuberculosis complex are carried out, was established in Portugal in April 2000. VigLab-Tuberculose aims to maintain a laboratory-based surveillance system for antibiotic susceptibilities of Mycobacterium tuberculosis complex isolates in order to monitor trends in drug resistance in Portugal. OBJECTIVE: To describe the first line antituberculosis drug resistance patterns of tuberculosis cases diagnosed and reported to VigLab-Tuberculose in 2000-2001. METHODS: Collaborating laboratories collect and report data on individuals from whom a drug susceptibility test on Mycobacterium tuberculosis complex isolates has been performed in 2000-2001. Data collected included demographic, geographic, clinical and first line antibiotics susceptibility information. Data were analysed using Epi-Info version 6.04c software. RESULTS: There were 4170 reports of drug susceptibility test results on tuberculosis patients diagnosed from 1st April 2000 to 31st December 2001. Drug susceptibility results for all five first line antituberculosis drugs shows that 23% (541/2358) were resistant at least to one of them. The proportion of mono-resistance to streptomycin was 7,6% (179/2358), to isoniazid 2,6% (62/2358), to rifampicin 0,6% (15/2358) and to pyrazinamide 1,3% (30/2358). From the 4164 patients tested both to isoniazid and rifampicina, 244 (5,9%) were multidrug resistant. From patients with no history of previous tuberculosis treatment, 1,8% (28/1557) were mono-resistant to isoniazid, 0,4% (7/1557) to rifampicina, 4,2% (66/1557) to streptomycin and 1,7% (27/1557) to pyrazinamide. The proportion of primary multidrug resistance was 2,8% (43/1557) and acquired resistance was 13,3% (41/309). CONCLUSION: The laboratory participation rate was 80%, which is very encouraging for the first two years of VigLab-Tuberculose activities. The proportion of primary multidrug resistance was higher than the reported resistance from central and west Europe (less 1%), which reinforce the need and importance of maintaining and strengthening the laboratory-based surveillance in order to minimise the emergence of drug resistance.