Journal: Heliyon

Article Title: Diagnostic Accuracy of the Abbott SD Bioline MPT64 antigen test for identification of MTB Complex in a U.S. Clinical Mycobacteriology Laboratory

doi: 10.1016/j.heliyon.2024.e30501

Figure Lengend Snippet: Total number of tests performed for phase I and phase II.

Article Snippet: The MTBC and NTM strains used in this study came from both the Johns Hopkins clinical strain repository as well as the American Type Culture Collection (ATCC, Manassas Virginia) and included a variety of both drug-susceptible and drug-resistant MTBC cultures across multiple Lineages (1–5, data not shown).

Techniques: Bacteria

Journal: Heliyon

Article Title: Diagnostic Accuracy of the Abbott SD Bioline MPT64 antigen test for identification of MTB Complex in a U.S. Clinical Mycobacteriology Laboratory

doi: 10.1016/j.heliyon.2024.e30501

Figure Lengend Snippet: Phase I limit of detection results (TB isolate CAM144).

Article Snippet: The MTBC and NTM strains used in this study came from both the Johns Hopkins clinical strain repository as well as the American Type Culture Collection (ATCC, Manassas Virginia) and included a variety of both drug-susceptible and drug-resistant MTBC cultures across multiple Lineages (1–5, data not shown).

Techniques:

Journal: medRxiv

Article Title: Host-pathogen co-adaptation shapes susceptibility to infection with Mycobacterium tuberculosis

doi: 10.1101/2022.08.04.22278337

Figure Lengend Snippet: a) Flowchart of included tuberculosis index cases and linked contacts; b) Density plot of contact group sizes per city; c) Maximum likelihood phylogenetic tree of included strains, clades are coloured by genetic lineage, the rings denote (from inner to outer) the city, clustering based on a 12 Single Nucleotide Substitution cut-off, phenotypic drug resistance to Rifampicin and Isoniazid; d) Proportion of isolated strains by specialist or generalist Mtbc lineages over the study period; e) Bar plot showing the proportions of isolated specialist or generalist Mtbc lineages by age groups. TB = tuberculosis, IGRA = Interferon Gamma Release Assay, SNS = Single Nucleotide Substitution, Mtbc = M. tuberculosis complex.

Article Snippet: We compared the Mtbc phagocytosis/uptake and intracellular growth of three generalist L4 strains with that of three specialist Mtbc L6 strains, in each group we included the references strains: ATCC H37Rv (L4) and M. africanum ATCC reference strain (L6).

Techniques: Isolation, Ifn? elispot

Journal: medRxiv

Article Title: Host-pathogen co-adaptation shapes susceptibility to infection with Mycobacterium tuberculosis

doi: 10.1101/2022.08.04.22278337

Figure Lengend Snippet: a) Violin plot of the terminal branch lengths of Mtbc strains; b) Numbers of genetic clusters and number of clustered strains by specialist or generalist Mtbc lineage (legend as in a); c) Forest plot of a multivariable Poisson rate model quantifying the effect of several predictor variables (y-axis) on the outcome ‘Count of tuberculosis infected contacts’ (in orange) or ‘Count of secondary active tuberculosis cases among contacts’ (in yellow); d) Bar plot of secondary active tuberculosis among close contacts inferred by Phybreak stratified by specialist or generalist Mtbc lineage (legend as in a)); e) Forest plot of a multivariable Poisson rate model quantifying the effect of Mtbc lineage on tuberculosis infection (orange) or secondary active tuberculosis (yellow) among close contacts (same legend as in c); f) Host Propensity to Propagate by specialist or generalist Mtbc lineage; f) Host propensity to propagate stratified by M. tuberculosis complex lineage. Mtbc = M. tuberculosis complex

Article Snippet: We compared the Mtbc phagocytosis/uptake and intracellular growth of three generalist L4 strains with that of three specialist Mtbc L6 strains, in each group we included the references strains: ATCC H37Rv (L4) and M. africanum ATCC reference strain (L6).

Techniques: Infection

Journal: medRxiv

Article Title: Host-pathogen co-adaptation shapes susceptibility to infection with Mycobacterium tuberculosis

doi: 10.1101/2022.08.04.22278337

Figure Lengend Snippet: a) Violin plot of the terminal branch lengths of the included Mtbc genetic lineages. b) Proportions of strains in clusters based on several different Single Nucleotide Substitution thresholds by genetic lineage and city.

Article Snippet: We compared the Mtbc phagocytosis/uptake and intracellular growth of three generalist L4 strains with that of three specialist Mtbc L6 strains, in each group we included the references strains: ATCC H37Rv (L4) and M. africanum ATCC reference strain (L6).

Techniques:

Journal: medRxiv

Article Title: Host-pathogen co-adaptation shapes susceptibility to infection with Mycobacterium tuberculosis

doi: 10.1101/2022.08.04.22278337

Figure Lengend Snippet: a - b) Global maps displaying the countries that were considered endemic (or sympatric) to the specialist Mtbc lineages detailed in the figure legends. c) Bar plot showing the proportions of Mtbc lineages isolated from the 2,279 pulmonary tuberculosis index cases included in this study; d) Permutation analysis (n = 1000) of the expected proportion of sympatric host ancestry – Mtbc lineage proportions. Vertical dashed line represents the proportion (0.75) among the index cases included in the study; e) Forest plot of the effects estimated using a Generalized Estimating Equation model to quantify the variable ‘sympatry’. The outcome is tuberculosis infection per contact, and sympatry was defined using the maps in panel a) and b). f) Permutation test assuming 14% mixed ancestry in the sample (flipping the sympatry variable from 1 to 0 and vice versa in 14% of the sample) while rerunning the model in panel e).

Article Snippet: We compared the Mtbc phagocytosis/uptake and intracellular growth of three generalist L4 strains with that of three specialist Mtbc L6 strains, in each group we included the references strains: ATCC H37Rv (L4) and M. africanum ATCC reference strain (L6).

Techniques: Isolation, Infection

Journal: medRxiv

Article Title: Host-pathogen co-adaptation shapes susceptibility to infection with Mycobacterium tuberculosis

doi: 10.1101/2022.08.04.22278337

Figure Lengend Snippet: a) Bar plot detailing the proportions of isolation country and Mtbc lineage in a global sample of 25,243 strains. b) Adjusted odds ratios for the variable contact allopatry using different sympatry assumptions from multivariate Generalized Estimation Equation models (see in main text).

Article Snippet: We compared the Mtbc phagocytosis/uptake and intracellular growth of three generalist L4 strains with that of three specialist Mtbc L6 strains, in each group we included the references strains: ATCC H37Rv (L4) and M. africanum ATCC reference strain (L6).

Techniques: Isolation

Journal: medRxiv

Article Title: Host-pathogen co-adaptation shapes susceptibility to infection with Mycobacterium tuberculosis

doi: 10.1101/2022.08.04.22278337

Figure Lengend Snippet: Mtbc uptake by lineage and strain in African (a-b) and European Caucasian (c-d) blood monocyte derived macrophages. Mtbc intracellular growth by lineage in African (e-f) and European (g-h) blood-derived macrophages. Mtbc uptake by macrophages (CFU at 4hpi x 100%/ CFU count of infection dose) was determined immediately at 4hpi and intracellular growth at 24h, 96h, and 168h post-infection. i) Mtbc L4 and j) Mtbc L6 uptake by human macrophage donor ancestry. Figures represent mean and standard deviations of European Caucasian macrophage infections compromising three independent experiments of which two compromised two donors (See supplementary Figure S3). Nine technical replicates of infection were performed and 27 CFU technical replicates per strain. African macrophages infections compromised 4 independent experiments, 12 technical replicates of infection, and 36 CFU replicates per strain. Macrophages were infected at MOI ∼1:1 (0.5 x10 6 cells: 0.5 x10 6 Mtbc bacilli). Statistical results represent T-test among Mtbc lineages (average of strains belonging to a specific lineage) and One-way ANOVA with Bonferroni post hoc test considering CFU values between the clinical strains and the reference laboratory strain H37Rv (9679-00). Mean, standard deviation, and statistical significances (*P <0.05 **P < 0.01; ***P < 0.001 and ****P < 0.0001) are depicted in the figures.

Article Snippet: We compared the Mtbc phagocytosis/uptake and intracellular growth of three generalist L4 strains with that of three specialist Mtbc L6 strains, in each group we included the references strains: ATCC H37Rv (L4) and M. africanum ATCC reference strain (L6).

Techniques: Derivative Assay, Infection, Standard Deviation