SIDRA vasconcellos - Academia.edu (original) (raw)

Papers by SIDRA vasconcellos

Frontiers in Tropical Diseases

Leprosy is a neglected tropical disease that leads to physical disability and social discriminati... more Leprosy is a neglected tropical disease that leads to physical disability and social discrimination. The active surveillance of new cases and vigilance for drug resistance can decrease the incidence, and improve the clinical outcomes of people affected by it. We analyzed, with molecular biology techniques, a set of skin biopsy samples from 25 Venezuelan patients. The patients had been diagnosed with leprosy in 2014 and early 2015, and 15 were relapse cases. The samples were tested for molecular drug resistance to dapsone, rifampicin, and fluoroquinolones. In addition, we performed molecular epidemiology analysis through multiple-locus variable-number tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP) typing. We did not find evidence of drug resistance and 76% of the samples (n = 16) had isolates belonging to SNP type 3. Genotype profiles allowed us to rule out the possibility of re-infection in a patient with persistent symptoms after treatment, as well as that o...

*Worldwide distribution is reported for regions with more than 3% of a given SITs as com... more *Worldwide distribution is reported for regions with more than 3% of a given SITs as compared to their total number in the SITVIT2 database. The definition of macro-geographical regions and sub-regions (<a href="http://unstats.un.org/unsd/methods/m49/m49regin.htm" target="_blank">http://unstats.un.org/unsd/methods/m49/m49regin.htm</a>) is according to the United Nations; Regions: AFRI (Africa), AMER (Americas), ASIA (Asia), EURO (Europe), and OCE (Oceania), subdivided in: E (Eastern), M (Middle), C (Central), N (Northern), S (Southern), SE (South-Eastern), and W (Western). Furthermore, CARIB (Caribbean) belongs to Americas, while Oceania is subdivided in 4 sub-regions, AUST (Australasia), MEL (Melanesia), MIC (Micronesia), and POLY (Polynesia). Note that in our classification scheme, Russia has been attributed a new sub-region by itself (Northern Asia) instead of including it among rest of the Eastern Europe. It reflects its geographical localization as well as due to the similarity of specific TB genotypes circulating in Russia (a majority of Beijing genotypes) with those prevalent in Central, Eastern and South-Eastern Asia.**The 3 letter country codes are according to <a href="http://en.wikipedia.org/wiki/ISO_3166-1_alpha-3" target="_blank">http://en.wikipedia.org/wiki/ISO_3166-1_alpha-3</a>; countrywide distribution is only shown for SITs with ≥3% of a given SITs as compared to their total number in the SITVIT2 database.Description of clusters containing 3 or more isolates in this study and their worldwide distribution in the SITVIT2 database (interrogation made on September 25th 2013).</p

Frequencies of strains according to classification by Spoligotyping (SITVIT2) and 24 loc... more Frequencies of strains according to classification by Spoligotyping (SITVIT2) and 24 loci MIRU-VNTR (MIRUVNTRPlus).</p

Notes: The Venn diagram was constructed based on LAM isolates defined by 24 loci MIURU-V... more Notes: The Venn diagram was constructed based on LAM isolates defined by 24 loci MIURU-VNTR. The sizes of the circles is not proportional to the real frequency of these markers. Twenty isolates classified with LAM by MIRU-VNTRs were removed from the final analysis because of showing a mixed genotype or failure in at least one of the three genotype procedures. * absence of spacers 33–36 in the spoligotyping profile, ** absence of spacers 21–24 in the spoligotyping profile, ***Two isolates RDRio but not RD174 (LAM2 SIT3908).</p

Classification according to SITIVIT2. For unknown Spoligotypes, we used SpotClust. <s... more Classification according to SITIVIT2. For unknown Spoligotypes, we used SpotClust. 2 Patterns were classified based on a VNTRplus database that allows construction of a Neighbor-Joining based phylogenetic tree, visualizing proximity of a particular genotype with that of a set of reference strains to the genotype family level.</p

The Lancet Microbe

Background Despite strong leprosy control measures, including effective treatment, leprosy persis... more Background Despite strong leprosy control measures, including effective treatment, leprosy persists in the Comoros. As of May, 2022, no resistance to anti-leprosy drugs had been reported, but there are no nationally representative data. Post-exposure prophylaxis (PEP) with rifampicin is offered to contacts of patients with leprosy. We aimed to conduct a countrywide drug resistance survey and investigate whether PEP led to the emergence of drug resistance in patients with leprosy. Methods In this observational, deep-sequencing analysis we assessed Mycobacterium leprae genomes from skin biopsies of patients in Anjouan and Mohéli, Comoros, collected as part of the ComLep (NCT03526718) and PEOPLE (NCT03662022) studies. Skin biopsies that had sufficient M leprae DNA (>2000 bacilli in 2 μl of DNA extract) were assessed for the presence of seven drug resistance-associated genes (ie, rpoB, ctpC, ctpI, folP1, gyrA, gyrB, and nth) using Deeplex Myc-Lep (targeted next generation deep sequencing), with a limit of detection of 10% for minority M leprae bacterial populations bearing a polymorphism in these genes. All newly registered patients with leprosy for whom written informed consent was obtained were eligible for inclusion in the survey. Patients younger than 2 years or with a single lesion on the face did not have biopsies taken. The primary outcome of our study was the proportion of patients with leprosy (ie, new cases, patients with relapses or reinfections, patients who received single (double) dose rifampicin-PEP, or patients who lived in villages where PEP was distributed) who were infected with M leprae with a drug-resistant mutation for rifampicin, fluoroquinolone, or dapsone in the Comoros.

*Classification based on construction of phylogenetic tree using the N-J Algorithm and e... more *Classification based on construction of phylogenetic tree using the N-J Algorithm and evaluating proximity of particular isolate with a set of 182 reference strains in the MIRU-VNTRPlus. Note: Strains with RDRio (LAM, Like-LAM and Non LAM).**In bold the same number of copy of hypothetic Ancestral RDRio as suggested by lazzarini et al, 2007 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107747#pone.0107747-Lazzarini1" target="_blank">[2]</a> and n the probable number of copy of hypothetic Ancestral RDRio in the additional 12 loci.Descripition of RDRio by 24 loci MIRU-VNTRs, fbpC103 and RD174.</p

Figure S8. Computer-generated UPGMA dendrogram based on combined 12 loci MIRU-spoligotyping analy... more Figure S8. Computer-generated UPGMA dendrogram based on combined 12 loci MIRU-spoligotyping analysis of selected strains from Caracas-Venezuela, From left to right i) Boxes colors: in red RDRio strains, in green no-RDRio strains, in blue mixed RDRio/no-RDRio, Boxes identification: SNP or NO SNP refers to Ag85C SNP positive or negative strains respectively, ii) strain identification, iii) SITVITWEB classification iv) SIT form SITVITWEB, v) SIT from SpolDB4, vi) SpolDB4 classification, vii) 12 loci MIRU profile (MIRU02, MIRU04, MIRU40, MIRU10, MIRU16, MIRU20, MIRU23, MIRU24, MIRU26, MIRU27, MIRU31, MIRU39, MIRU40), viii) spoligotyping profile. (TIF 1017 kb)

Figure S7. Computer-generated UPGMA dendrogram based on combined 12 loci MIRU-spoligotyping analy... more Figure S7. Computer-generated UPGMA dendrogram based on combined 12 loci MIRU-spoligotyping analysis of selected strains from Buenos Aires-Argentina, From left to right i) Boxes colors: in red RDRio strains, in green no-RDRio strains, in blue mixed RDRio/no-RDRio, Boxes identification: SNP or NO SNP refers to Ag85C SNP positive or negative strains respectively, ii) strain identification, iii) SITVITWEB classification iv) SIT form SITVITWEB, v) SIT from SpolDB4, vi) SpolDB4 classification, vii) 12 loci MIRU profile (MIRU02, MIRU04, MIRU40, MIRU10, MIRU16, MIRU20, MIRU23, MIRU24, MIRU26, MIRU27, MIRU31, MIRU39, MIRU40), viii) spoligotyping profile. (TIF 422 kb)

Figure S2. Minimum spanning Tree based on 12 loci MIRU-VNTR profiles of Ag85C SNP positive strain... more Figure S2. Minimum spanning Tree based on 12 loci MIRU-VNTR profiles of Ag85C SNP positive strains from Paraguay. Each node represents a MIRU-VNTR type. The size of the circle is relative to the number of isolates with the MIRU pattern and the colors indicate clusters containing either RDRio (red), WT (green) genotypes or mixed pattern (blue). In orange are strains with RDRio deletion but no RD174 deletion. (TIF 759 kb)

Figure S1. Computer-generated dendrogram according to UPGMA IS6110-RFLP analysis of selected stra... more Figure S1. Computer-generated dendrogram according to UPGMA IS6110-RFLP analysis of selected strains from Paraguay using Bionumerics v4.50 (Applied Maths). Spoligotyping results are also displayed. (TIF 716 kb)

The Genetic profile of Mycobacterium tuberculosis RDRio in Minas Gerais as defined by spoligotypi... more The Genetic profile of Mycobacterium tuberculosis RDRio in Minas Gerais as defined by spoligotyping (DOCX 23 kb)

PLOS ONE, 2014

The frequency of fbpC103, RDRio<... more The frequency of fbpC103, RDRio and RD174 in LAM, LAM-like and Non LAM isolates, as designated by spoligotyping and 24 MIRU-VNTR typing.</p

Revista do Instituto de Medicina Tropical de São Paulo, 2019

This is an open-access article distributed under the terms of the Creative Commons Attribution Li... more This is an open-access article distributed under the terms of the Creative Commons Attribution License.

BMC Microbiology, 2019

Background: The Latin American & Mediterranean (LAM) spoligotype family is one of the most succes... more Background: The Latin American & Mediterranean (LAM) spoligotype family is one of the most successful genotype of Mycobacterium tuberculosis worldwide and particularly prevalent in South-America. Within this family, a sublineage named Region of Difference Rio (RD Rio) was reported initially in Brazil and is characterized by a genomic deletion of about 26.3 kb. This lineage seems to show a specific adaptation to the Euro-Latin American population. In this context, we sought to evaluate the LAM family and the presence of the RD Rio genotype in samples from three Latin American countries including Paraguay, Venezuela and Argentina. To detect LAM strains reliably we applied a typing scheme using spoligotyping, 12 loci MIRU-VNTR, the Ag85C 103 SNP and the regions of difference RD Rio and RD174. IS6110-RFLP results were also used when available. Results: Genotyping of 413 M. tuberculosis isolates from three Latin-American countries detected LAM (46%) and the ill-defined T clade (16%) as the most frequent families. The highest clustering rate was detected in the sample population from the city of Caracas in Venezuela. We observed considerable differences in the presence of the RD Rio lineage, with high frequency in Caracas-Venezuela (55%) and low frequency in Buenos Aires-Argentina (11%) and Paraguay (10%). The molecular markers (RD174, Ag85C 103 , MIRU02-MIRU40 signature) of the RD Rio lineage were essentially confirmed. For the LAM family, the most polymorphic loci were MIRU40, MIRU31, MIRU10, MIRU26, MIRU16 and the least polymorphic MIRU24, MIRU20, MIRU04, MIRU23. Conclusions: Our results suggest a differential adaptation of LAM-sublineages in neighboring populations and that RD Rio strains spread regionally with different rates of distribution. The Ag85C SNP and RDs (RD174, RD Rio) tested in this study can in fact facilitate molecular epidemiological studies of LAM strains in endemic settings and low-income countries.

The American journal of tropical medicine and hygiene, Feb 4, 2017

We conducted a population-based study of tuberculosis (TB) from 2009 to 2015 in an indigenous com... more We conducted a population-based study of tuberculosis (TB) from 2009 to 2015 in an indigenous community of Brazil, the largest in the country, to investigate risk factors associated with recent TB transmission. The clinical isolates of Mycobacterium tuberculosis were genotyped by IS6110-RFLP (restriction fragment length polymorphism) and spoligotyping analysis. Among 67 isolates typed by RFLP, 69% fell into fifteen clusters, and 91% of TB cases with shared IS6110-RFLP pattern were diagnosed within 2 years of another case in the cluster. Individual risk factors associated with genetic clustering were domestic overcrowding (odds ratio [OR]: 6.10; 95% confidence interval [CI]: 1.50-24.88) and low social class (OR: 3.72; 95% CI: 1.00-13.98). Most reported contacts (76%) were identified within the household of the index TB case, but most of the genetic clustering of M. tuberculosis occurred outside of household (79%). Expanded contacts investigation and prophylaxis outside of household s...

Genome Announcements, 2015

Mycobacterium tuberculosisof the Bejing subtype (MtbB) is transmitted efficiently in high burden ... more Mycobacterium tuberculosisof the Bejing subtype (MtbB) is transmitted efficiently in high burden countries for this genotype. A higher virulence was associated with isolates of the “modern” Beijing genotype sub-lineages when compared to “ancient” ones. Here, we report the full genomes of the strain representing these two genotypes from Brazil, a country with a low incidence ofMtbB.

International Journal of Leprosy and Other Mycobacterial Diseases, 2004

Lupus vulgaris is a variant of cutaneous tuberculosis. Its more destructive and mutilating clinic... more Lupus vulgaris is a variant of cutaneous tuberculosis. Its more destructive and mutilating clinical forms have become rarer in consonance of a general decline of cutaneous tuberculosis. It is rarely seen now in developed countries due to stringent control measures, improved quality of living and effective therapeutic regimens. Misdiagnosis, neglect, or late diagnosis may result in severe, ulcerative and mutilating &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;wolf eaten&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; skin lesions. This paper describes four such cases of &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;were-wolf&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; cutaneous tuberculosis. Early diagnosis and treatment is important to prevent much of the disfigurement.

BMC Infectious Diseases, 2012

Background Tuberculosis is one of the most infectious diseases in the world. Molecular typing met... more Background Tuberculosis is one of the most infectious diseases in the world. Molecular typing methods such as spoligotyping, and VNTR (variable number tandem repeats), IS6110 in the NTF region and LSP (large sequence polymorphisms) analysis are generally useful tools for the resolution of various issues related to the classical epidemiology of Mycobacterium tuberculosis (M. tuberculosis). Methods To determine the transmission characteristics of M. tuberculosis strains isolated in Beijing, China, and their genetic relationships, especially those among Beijing family strains, 260 M. tuberculosis strains isolated from patients presenting pulmonary tuberculosis were analyzed by spoligotyping, and by examining 22 VNTR loci and the presence/absence of IS6110 in the NTF region, RD105 and RD181. Results 81% (211 strains) of the isolates studied were Beijing family strains, 174 (82.5%) of which were identified as modern Beijing strains based on the presence of IS6110 upstream of the NTF regi...