scholarly journals Import and transmission of Mycobacterium orygis and Mycobacterium africanum, Norway

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Vegard Eldholm ◽  
Janne O. Rønning ◽  
Anne Torunn Mengshoel ◽  
Trude Arnesen
Keyword(s):  
Phylogenetic Analyses ◽  
West African ◽  
Reference Laboratory ◽  
Line Probe Assay ◽  
Genome Sequences ◽  
African Countries ◽  
National Reference ◽  
Commercial Line ◽  
Probe Assay ◽  
Mycobacterium Africanum

Abstract Background The aim of the current study was to improve our understanding of the origins and transmission of Mycobacterium africanum (MAF) in Norway. Methods Whole-genome sequences (WGS) were generated for all (n = 29) available clinical isolates received at the Norwegian National Reference Laboratory for Mycobacteria (NRL) and identified as MAF in Norway, in the period 2010–2020. Phylogenetic analyses were performed. Results The analyses indicated several imports of MAF lineage 6 from both East and West African countries, whereas MAF lineage 5 was restricted to patients with West African connections. We also find evidence for transmission of MAF in Norway. Finally, our analyses revealed that a group of isolates from patients originating in South Asia, identified as MAF by means of a commercial line-probe assay, in fact belonged to Mycobacterium orygis. Conclusions Most MAF cases in Norway are the result of import, but transmission is occurring within Norway.

scholarly journals Import and Transmission of Mycobacterium Orygis and Mycobacterium Africanum, Norway

2021 ◽  
Author(s):  
vegard and eldholm ◽  
Janne Oseberg rønning ◽  
Anne Torunn Mengshoel ◽  
Trude Arnesen
Keyword(s):  
Phylogenetic Analyses ◽  
West African ◽  
Whole Genome ◽  
Immigrant Communities ◽  
Line Probe Assay ◽  
Genome Sequences ◽  
African Countries ◽  
Commercial Line ◽  
Probe Assay ◽  
Mycobacterium Africanum

Abstract Background : The aim of the current study was to improve our understanding of the origins and transmission of Mycobacterium africanum (MAF) in Norway.Methods : Whole-genome sequences (WGS) were generated for all (n=29) available clinical isolates identified as in Norway in the period 2010 – 2020. Phylogenetic analyses were performed.Results : The analyses indicated multiple imports of MAF lineage 6 from both East and West African countries, whereas MAF lineage 5 was restricted to patients with West African connections. We also find evidence for transmission of MAF in Norway. Finally, our analyses revealed that a group of isolates from patients originating in South Asia, identified as MAF by means of a commercial line-probe assay, in fact belonged to Mycobacterium orygis.Conclusions : Most MAF cases in Norway are the result of import, but transmission is occurring in immigrant communities.

scholarly journals Speeding up the diagnosis of multidrug-resistant tuberculosis in a high-burden region with the use of a commercial line probe assay

2019 ◽  
Vol 45 (2) ◽  
Author(s):  
Angela Pires Brandao ◽  
Juliana Maira Watanabe Pinhata ◽  
Rosangela Siqueira Oliveira ◽  
Vera Maria Neder Galesi ◽  
Helio Hehl Caiaffa-Filho ◽  
...  
Keyword(s):  
Susceptibility Testing ◽  
Drug Susceptibility ◽  
Multidrug Resistant ◽  
Drug Susceptibility Testing ◽  
Reference Laboratory ◽  
Line Probe Assay ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis ◽  
Commercial Line ◽  
Probe Assay

ABSTRACT Objective: To evaluate the rapid diagnosis of multidrug-resistant tuberculosis, by using a commercial line probe assay for rifampicin and isoniazid detection (LPA-plus), in the routine workflow of a tuberculosis reference laboratory. Methods: The LPA-plus was prospectively evaluated on 341 isolates concurrently submitted to the automated liquid drug susceptibility testing system. Results: Among 303 phenotypically valid results, none was genotypically rifampicin false-susceptible (13/13; 100% sensitivity). Two rifampicin-susceptible isolates harboured rpoB mutations (288/290; 99.3% specificity) which, however, were non-resistance-conferring mutations. LPA-plus missed three isoniazid-resistant isolates (23/26; 88.5% sensitivity) and detected all isoniazid-susceptible isolates (277/277; 100% specificity). Among the 38 (11%) invalid phenotypic results, LPA-plus identified 31 rifampicin- and isoniazid-susceptible isolates, one isoniazid-resistant and six as non-Mycobacterium tuberculosis complex. Conclusions: LPA-plus showed excellent agreement (≥91%) and accuracy (≥99%). Implementing LPA-plus in our setting can speed up the diagnosis of multidrug-resistant tuberculosis, yield a significantly higher number of valid results than phenotypic drug susceptibility testing and provide further information on the drug-resistance level.

scholarly journals Pan-Genome Analysis of Mycobacterium Africanum: Insights to Dynamics and Evolution.

2020 ◽  
Author(s):  
Idowu Olawoye ◽  
Simon D.W. Frost ◽  
Christian T. Happi
Keyword(s):  
West Africa ◽  
Genome Analysis ◽  
West African ◽  
Multiple Copy ◽  
Genome Sequences ◽  
Animal Reservoir ◽  
Pan Genome ◽  
Lineage Specificity ◽  
Mycobacterium Africanum ◽  
Core Genes

Abstract Background: Mycobacterium tuberculosis complex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.We tested the hypothesis that M. africanum West African 2 (lineage 6) might have emigrated out of West Africa but was outcompeted by more virulent modern strains of M. tuberculosis (MTB).Whole genome sequences of M. tuberculosis from Nigeria (n=21), South Africa (n=24) and M. africanum West African 2 from Mali (n=22) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. Results: The outcome of this analysis shows that Lineages 2, 4 and 6 all have a close pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.Conclusions: The findings in this study provides a perspective to one of the hypotheses that M. africanum West African 2 might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.

scholarly journals Comparison of GeneXpert and Line Probe Assay for Detection of Mycobacterium tuberculosis and Rifampicin-Mono resistance at the National Tuberculosis Reference Laboratory, Kenya

2019 ◽  
Author(s):  
S.A. Aricha ◽  
Leonard King'wara ◽  
N.W. Mwirigi ◽  
Linda Chaba ◽  
T. Kiptai ◽  
...  
Keyword(s):  
Predictive Value ◽  
Performance Characteristics ◽  
Reference Laboratory ◽  
Drug Resistant ◽  
Line Probe Assay ◽  
Perfect Agreement ◽  
Predictive Values ◽  
National Tuberculosis ◽  
Probe Assay ◽  
Sensitivity Specificity

Abstract Introduction The dual challenge of low diagnostic sensitivity of microscopy test and technical challenge of performing a TB culture test poses a problem for case detection and initiation of Tuberculosis (TB) second-line treatment. There is thus need for a rapid, reliable and easily accessible assay. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF and Line Probe Assay (LPA) Methods 329 sputum samples of patients across the 47 counties in Kenya suspected to have drug resistant TB were picked and subjected to GeneXpert, LPA and Culture MGIT at the National TB Reference Laboratory. Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of various assays. Results GeneXpert had a sensitivity, specificity, positive predictive value, and negative predictive value of 78.5%, 64.9%, 59.4% and 82.2% respectively while LPA had 98.4%, 66.0%, 65.4% and 98.4%. For diagnosis of rifampicin mono-resistance GeneXpert had a moderate agreement (Kappa=0.59, P<0.01) (sensitivity= 62.50%, specificity = 96.50%) while LPA that had almost perfect agreement (Kappa= 0.89, p<0.01) with a (sensitivity= 90.0% and specificity= 99.1%). Conclusion LPA has a better performance characteristic to GeneXpert and an alternative to culture with regards to detection of RIF’s mono-resistance.

scholarly journals The Previously Unidentified, Divergent Badnavirus Species Cacao red vein-banding virus is Associated with Cacao Swollen Shoot Disease in Nigeria

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1302-1308 ◽  
Author(s):  
Nomatter Chingandu ◽  
Lelia Dongo ◽  
Osman A. Gutierrez ◽  
Judith K. Brown
Keyword(s):  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
West African ◽  
Open Reading Frames ◽  
Nucleotide Identity ◽  
Genome Sequences ◽  
Foliar Symptoms ◽  
Field Samples ◽  
Polymerase Chain ◽  
Reading Frames

Cacao swollen shoot disease (CSSD) of Theobroma cacao was reported in Nigeria in 1944; however, no badnaviral genome sequences have been found associated with the symptomatic trees. In 2017, leaf samples (n = 18) were collected from cacao trees from Osun and Oyo, Nigeria showing foliar symptoms that included red vein-banding and shoot swelling, and variable secondary mosaic, mottling, and fern-like pattern symptoms. Abutting primers designed around previously determined 500-bp intergenic region sequences were used for polymerase chain reaction (PCR) amplification. Of the 18 samples, 9 yielded an approximately 7,000-bp, apparently genome-size product. The nine genomes were sequenced and found to encode four open reading frames, and to share 86 to 99% nucleotide identity. Pairwise analysis of the Nigerian genomes with 21 previously reported CSSD badnaviruses, at the complete genome and reverse-transcription ribonuclease H (1,230 bp) sequence levels, indicated 71 to 75 and 72 to 76% nucleotide identity, respectively. Phylogenetic analysis of the nine complete genomes indicated that the closest relatives of the divergent Nigerian isolates were previously described West African CSSD badnaviruses. Based on pairwise comparisons and phylogenetic analyses, the Nigerian CSSD isolates constitute a previously unrecognized Badnavirus sp., herein named Cacao red vein-banding virus (CRVBV). Primers designed based on the CRVBV genome sequences amplified a 1,068-bp fragment from 16 of 18 field samples tested by PCR, suggesting the possible existence of additional CRVBV variants.

scholarly journals Draft Genome Sequence of aMycobacterium africanumClinical Isolate from Antioquia, Colombia

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
U. A. Hurtado ◽  
J. S. Solano ◽  
A. Rodriguez ◽  
J. Robledo ◽  
F. Rouzaud
Keyword(s):  
Mycobacterium Tuberculosis ◽  
South America ◽  
Clinical Isolate ◽  
Genome Sequence ◽  
Draft Genome ◽  
West African ◽  
Draft Genome Sequence ◽  
African Countries ◽  
Mycobacterium Africanum

Mycobacterium africanumis a member of theMycobacterium tuberculosiscomplex. Most commonly found in West African countries, it has scarcely been described in South America. Here, we report the first genome sequence of a ColombianM. africanumclinical isolate. It is composed of 4,493,502 bp, with 4,069 genes.

scholarly journals Comparison of GeneXpert and Line Probe Assay for Detection of Mycobacterium tuberculosis and Rifampicin-Mono resistance at the National Tuberculosis Reference Laboratory, Kenya

2019 ◽  
Author(s):  
S.A. Aricha ◽  
Leonard King'wara ◽  
N.W. Mwirigi ◽  
Linda Chaba ◽  
T. Kiptai ◽  
...  
Keyword(s):  
Predictive Value ◽  
Performance Characteristics ◽  
Reference Laboratory ◽  
Drug Resistant ◽  
Line Probe Assay ◽  
Perfect Agreement ◽  
Predictive Values ◽  
National Tuberculosis ◽  
Probe Assay ◽  
Sensitivity Specificity

Abstract Background: The dual challenge of low diagnostic sensitivity of microscopy test and technical challenge of performing a TB culture test poses a problem for case detection and initiation of Tuberculosis (TB) second-line treatment. There is thus need for a rapid, reliable and easily accessible assay. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF and Line Probe Assay (LPA) Methods: 329 sputum samples of patients across the 47 counties in Kenya suspected to have drug resistant TB were picked and subjected to GeneXpert, LPA and Culture MGIT at the National TB Reference Laboratory. Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of the various assays. Results: Against culture MGIT as the gold standard for TB diagnosis, GeneXpert had a sensitivity, specificity, positive predictive value, and negative predictive value of 78.5%, 64.9%, 59.4 % and 82.2% respectively while LPA had 98.4%, 66.0 %, 65.4% and 98.4%. For diagnosis of rifampicin mono-resistance GeneXpert had a moderate agreement (Kappa=0.59, P<0.01) (sensitivity= 62.50%, specificity = 96.50 %) while LPA that had almost perfect agreement (Kappa= 0.89, p<0.01) with a (sensitivity= 90.0% and specificity= 99.1%). Conclusion: LPA has a better performance characteristic to GeneXpert and an alternative to culture with regards to detection of RIF’s mono-resistance. Keywords: LPA, GeneXpert, Sensitivity, Specificity, Drug-resistant TB

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