The complete mitochondrial genome sequence of the pathogenic yeast Candida ( Torulopsis ) glabrata

International audienceWe report here the complete sequence of the mitochondrial (mt) genome of the pathogenic yeast Candida glabrata . This 20 kb mt genome is the smallest among sequenced hemiascomycetous yeasts. Despite its compaction, the mt genome contains the genes encoding the apocytochrome b (COB ), three subunits of ATP synthetase (ATP6 , 8 and 9 ), three subunits of cytochrome oxidase (COX1 , 2 and 3 ), the ribosomal protein VAR1 , 23 tRNAs, small and large ribosomal RNAs and the RNA subunit of RNase P. Three group I introns each with an intronic open reading frame are present in the COX1 gene. This sequence is available under accession number AJ511533

Summary statistics of the potentially selective «neutral» microsatellite markers (34) for albacore (<i>Thunnus alalunga</i>).

<p>Number of individuals (Nind). Number of alleles (A). Expected (He), unbiased Nei's (1978) expected (H.n.b) and observed (HO) heterozygosity. Polymorphism information content (PIC). Null allele frequency (Fnull). Fisher’s inbreeding coefficient (Fis). Probability of identity (PI). Probability of exclusion (PE1, single parent; PE2, a second parent given a first parent assigned; PE3, a pair of parents). Number of repeated genotypes (Nrep and percentage (%) of the total number of individuals genotyped for each loci). Genotyping error rate per allele, E1 referring to allelic dropout rate and E2 to the false allele rate, and the 95% confidence interval (CI). Significant values are highlighted in bold (P<0.05) for heterozygote excess, Fnull, and Fis.</p><p>Summary statistics of the potentially selective «neutral» microsatellite markers (34) for albacore (<i>Thunnus alalunga</i>).</p

PCR amplification results of 37 microsatellites markers tested on Scombridae species (<i>Thunnus albacares</i>, <i>Thunnus thynnus</i>, <i>Thunnus obesus</i>, <i>Acanthocybium solandri</i>) with 4 or 5 individuals per species.

<p>Weak amplified product in bold. Very weak amplified product in bold and italic. Smear in grey.</p><p>PCR amplification results of 37 microsatellites markers tested on Scombridae species (<i>Thunnus albacares</i>, <i>Thunnus thynnus</i>, <i>Thunnus obesus</i>, <i>Acanthocybium solandri</i>) with 4 or 5 individuals per species.</p

Geographic location of albacore sampled.

<p>Circles are proportional to the number of individuals collected. (A) southwest Indian Ocean (n = 42), (B) northwest Indian Ocean (n = 31), (C) South Africa (n = 31), and (D) southeast Atlantic Ocean (n = 32).</p

Probability of detecting a particular level of differentiation (FST) among populations of albacore with 1 000 replicates.

<p>Probability of detecting a particular level of differentiation (FST) among populations of albacore with 1 000 replicates.</p

Characteristics of two «non-neutral» microsatellite markers for albacore (<i>Thunnus alalunga</i>).

<p>Number of individuals (Nind). Number of alleles (A). Expected (He), unbiased Nei's (1978) expected (H.n.b) and observed (Ho) heterozygosity. Polymorphism information content (PIC). Null allele frequency (Fnull). Fisher’s inbreeding coefficient (Fis). Probability of identity (PI). Probability of exclusion (PE1, single parent; PE2, a second parent given a first parent assigned; PE3, a pair of parents). Number of repeated genotypes (Nrep and percentage (%) of the total number of individuals genotyped for each loci). Genotyping error rate per allele, E1 referring to allelic dropout rate and E2 to the false allele rate, and the 95% confidence interval (CI). Significant values are highlighted in bold (P<0.05) for heterozygote excess, Fnull, and Fis.</p><p>Characteristics of two «non-neutral» microsatellite markers for albacore (<i>Thunnus alalunga</i>).</p

Microsatellite markers developed for Thunnus alalunga (43) with the corresponding GenBank number.

<p>Sequence range size in base pairs (complete sequence—primers, microsatellites and flanking region), primers sequence, number of repeats in the microsatellite motif determinate, microsatellite sequence corresponding at >75% alignment from GenBank NR and BOLD sequences, summary on the «non-neutral» gene alignment details, and information on the class of the markers («neutral», «non-neutral» and selected or not in the final panel).</p><p>Microsatellite markers developed for Thunnus alalunga (43) with the corresponding GenBank number.</p

Read length distribution and number of reads throughout QDD bioinformatics pipeline steps.

<p>Read length distribution and number of reads throughout QDD bioinformatics pipeline steps.</p

Summary of the selection steps used to develop microsatellite markers.

<p>Summary of the selection steps used to develop microsatellite markers.</p

Z oonotic tuberculosis in humans assessed by next-generation sequencing: an 18-month nationwide study in Lebanon

International audienceThe World Health Organization (WHO) and other international organisations, including the Food and Agriculture Organization of the United Nations, the World Organisation for Animal Health and the International Union Against Tuberculosis and Lung Disease recently called for formally assessing and (re)prioritising the burden of zoonotic tuberculosis (TB) in people, due to Mycobacterium bovis [1, 2]. Its global contribution to human TB, otherwise principally caused by Mycobacterium tuberculosis, might be underestimated [2]. Nationally representative prevalence data are virtually non-existent on continents with the highest presumed burdens, i.e. in Africa and Asia [3]. In addition to causing hard-to-diagnose extrapulmonary TB more frequently, M. bovis is naturally resistant to pyrazinamide [4], a crucial drug for the standard short-course anti-TB therapy. Due to reliability issues, phenotypic susceptibility to pyrazinamide is often not tested [5]. The most commonly used phenotypic and molecular diagnostics, including the WHO-endorsed GeneXpert MTB/RIF test (Cepheid, Sunnyvale, CA, USA), do not differentiate M. bovis from M. tuberculosis [1]. Thus, M. bovis-infected patients may receive inadequate treatment, risking poorer outcomes [6]. Underdiagnosis in people also implies the existence of undetected animal and food sources and zoonotic risks escaping common TB control measures [1, 2]. In Europe, patients with M. bovis infection are often African-or southern Mediterranean-born, suggesting regional endemicity [6, 7]. We determined the prevalence of M. bovis-caused TB in a survey including all TB patients reported to the national TB programme over an 18-month period in Lebanon. In addition to its national population and >1.5 million Syrian and Palestinian refugees, this Mediterranean country hosts large numbers of migrant workers from Africa and Asia [8]. Many are from Ethiopia [8], where proportions of extrapulmonary TB and M. bovis-caused disease among TB patients apparently culminate, reaching ∼30% [9] and 15-30% (in focal studies; [10]), respectively. We used a novel targeted next-generation sequencing-based assay for extensive drug resistance detection, including resistance to pyrazinamide, and genotypic differentiation between M. bovis and M. tuberculosis [11]. This survey was approved by the Azm Center/Lebanese University ethical committee (document CE-EDST-3-2016). Clinical samples were collected from all 1104 different TB patients with presumption of pulmonary or extrapulmonary TB, based on the presence of symptoms and prior tuberculin skin testing or radiological examination in local hospitals for a number of patients, and reported to all national anti-TB centres between June 1, 2016 and November 31, 2017. All of these 1104 patients were tested by at least one of the following assays: solid (Lowenstein-Jensen) and/or liquid (BBL MGIT; Beckton Dickinson, Franklin Lakes, NJ, USA) culturing, GeneXpert MTB/RIF on sputum, and Anyplex MTB/NTM Real-time (Seegene, Seoul, Republic of Korea) on sputum or culture on solid or liquid medium. Out of these 1104, 417 were confirmed as TB positive by GeneXpert and/or Anyplex. Among these 417 patients, 354 were culture positive. Among the 354 corresponding patients, 325 were new TB patients, 22 had a previous TB history, while TB history information was unavailable for seven patients. Available DNA extracts, obtained from 348 out of 354 primary cultures by using MasterPure™ DNA Purification Kit (Epicentre, Illumina, Madison, WI, USA), were subjected to targeted sequencing, more @ERSpublications In response to recent international calls, this study reveals the nationally representative prevalence of zoonotic tuberculosis in people in a non-high income country, highlighting the need for appropriate diagnostics and treatment of these patients http://bit.ly/2l3ydD