1
|
Negatu DA, Aragaw WW, Dartois V, Dick T. A pairwise approach to revitalize β-lactams for the treatment of TB. Antimicrob Agents Chemother 2024:e0003424. [PMID: 38690896 DOI: 10.1128/aac.00034-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/07/2024] [Indexed: 05/03/2024] Open
Abstract
The dual β-lactam approach has been successfully applied to overcome target redundancy in nontuberculous mycobacteria. Surprisingly, this approach has not been leveraged for Mycobacterium tuberculosis, despite the high conservation of peptidoglycan synthesis. Through a comprehensive screen of oral β-lactam pairs, we have discovered that cefuroxime strongly potentiates the bactericidal activity of tebipenem and sulopenem-advanced clinical candidates-and amoxicillin, at concentrations achieved clinically. β-lactam pairs thus have the potential to reduce TB treatment duration.
Collapse
Affiliation(s)
- Dereje A Negatu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia
| | - Wassihun Wedajo Aragaw
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| |
Collapse
|
2
|
Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz MC, Ramakrishnan S, Iqbal Z. Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biol 2022; 23:147. [PMID: 35791022 PMCID: PMC9254434 DOI: 10.1186/s13059-022-02714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/20/2022] [Indexed: 12/30/2022] Open
Abstract
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).
Collapse
Affiliation(s)
- Martin Hunt
- EMBL-EBI, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | | | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | | |
Collapse
|
3
|
Silva ML, Cá B, Osório NS, Rodrigues PNS, Maceiras AR, Saraiva M. Tuberculosis caused by Mycobacterium africanum: Knowns and unknowns. PLoS Pathog 2022; 18:e1010490. [PMID: 35617217 PMCID: PMC9135246 DOI: 10.1371/journal.ppat.1010490] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB), one of the deadliest threats to human health, is mainly caused by 2 highly related and human-adapted bacteria broadly known as Mycobacterium tuberculosis and Mycobacterium africanum. Whereas M. tuberculosis is widely spread, M. africanum is restricted to West Africa, where it remains a significant cause of tuberculosis. Although several differences have been identified between these 2 pathogens, M. africanum remains a lot less studied than M. tuberculosis. Here, we discuss the genetic, phenotypic, and clinical similarities and differences between strains of M. tuberculosis and M. africanum. We also discuss our current knowledge on the immune response to M. africanum and how it possibly articulates with distinct disease progression and with the geographical restriction attributed to this pathogen. Understanding the functional impact of the diversity existing in TB-causing bacteria, as well as incorporating this diversity in TB research, will contribute to the development of better, more specific approaches to tackle TB.
Collapse
Affiliation(s)
- Marta L. Silva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Baltazar Cá
- INASA - Instituto Nacional de Saúde Pública da Guiné-Bissau, Bissau, Guinea-Bissau
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Pedro N. S. Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- * E-mail:
| |
Collapse
|
4
|
Balamurugan M, Banerjee R, Kasibhatla SM, Achalere A, Joshi R. Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches. Front Genet 2022; 13:800083. [PMID: 35495132 PMCID: PMC9043288 DOI: 10.3389/fgene.2022.800083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A total of two lineages of Mycobacterium tuberculosis var. africanum (Maf), L5 and L6, which are members of the Mycobacterium tuberculosis complex (MTBC), are responsible for causing tuberculosis in West Africa. Regions of difference (RDs) are usually used for delineation of MTBC. With increased data availability, single nucleotide polymorphisms (SNPs) promise to provide better resolution. Publicly available 380 Maf samples were analyzed for identification of “core-cluster-specific-SNPs,” while additional 270 samples were used for validation. RD-based methods were used for lineage-assignment, wherein 31 samples remained unidentified. The genetic diversity of Maf was estimated based on genome-wide SNPs using phylogeny and population genomics approaches. Lineage-based clustering (L5 and L6) was observed in the whole genome phylogeny with distinct sub-clusters. Population stratification using both model-based and de novo approaches supported the same observations. L6 was further delineated into three sub-lineages (L6.1–L6.3), whereas L5 was grouped as L5.1 and L5.2 based on the occurrence of RD711. L5.1 and L5.2 were further divided into two (L5.1.1 and L5.1.2) and four (L5.2.1–L5.2.4) sub-clusters, respectively. Unassigned samples could be assigned to definite lineages/sub-lineages based on clustering observed in phylogeny along with high-confidence posterior membership scores obtained during population stratification. Based on the (sub)-clusters delineated, “core-cluster-specific-SNPs” were derived. Synonymous SNPs (137 in L5 and 128 in L6) were identified as biomarkers and used for validation. Few of the cluster-specific missense variants in L5 and L6 belong to the central carbohydrate metabolism pathway which include His6Tyr (Rv0946c), Glu255Ala (Rv1131), Ala309Gly (Rv2454c), Val425Ala and Ser112Ala (Rv1127c), Gly198Ala (Rv3293) and Ile137Val (Rv0363c), Thr421Ala (Rv0896), Arg442His (Rv1248c), Thr218Ile (Rv1122), and Ser381Leu (Rv1449c), hinting at the differential growth attenuation. Genes harboring multiple (sub)-lineage-specific “core-cluster” SNPs such as Lys117Asn, Val447Met, and Ala455Val (Rv0066c; icd2) present across L6, L6.1, and L5, respectively, hinting at the association of these SNPs with selective advantage or host-adaptation. Cluster-specific SNPs serve as additional markers along with RD-regions for Maf delineation. The identified SNPs have the potential to provide insights into the genotype–phenotype correlation and clues for endemicity of Maf in the African population.
Collapse
|
5
|
Osei-Wusu S, Otchere ID, Morgan P, Musah AB, Siam IM, Asandem D, Afum T, Asare P, Asante-Poku A, Kusi KA, Gagneux S, Yeboah-Manu D. Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa. PLoS One 2021; 16:e0255433. [PMID: 34437584 PMCID: PMC8389432 DOI: 10.1371/journal.pone.0255433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022] Open
Abstract
Findings from previous comparative genomics studies of the Mycobacterium tuberculosis complex (MTBC) suggest genomic variation among the genotypes may have phenotypic implications. We investigated the diversity in the phenotypic profiles of the main prevalent MTBC genotypes in West Africa. Thirty-six whole genome sequenced drug susceptible MTBC isolates belonging to lineages 4, 5 and 6 were included in this study. The isolates were phenotypically characterized for urease activity, tween hydrolysis, Thiophen-2-Carboxylic Acid Hydrazide (TCH) susceptibility, nitric oxide production, and growth rate in both liquid (7H9) and solid media (7H11 and Löwenstein–Jensen (L-J)). Lineage 4 isolates showed the highest growth rate in both liquid (p = 0.0003) and on solid (L-J) media supplemented with glycerol (p<0.001) or pyruvate (p = 0.005). L6 isolates optimally utilized pyruvate compared to glycerol (p<0.001), whereas L5 isolates grew similarly on both media (p = 0.05). Lineage 4 isolates showed the lowest average time to positivity (TTP) (p = 0.01; Average TTP: L4 = 15days, L5 = 16.7days, L6 = 29.7days) and the highest logCFU/mL (p = 0.04; average logCFU/mL L4 = 5.9, L5 = 5.0, L6 = 4.4) on 7H11 supplemented with glycerol, but there was no significant difference in growth on 7H11 supplemented with pyruvate (p = 0.23). The highest release of nitrite was recorded for L5 isolates, followed by L4 and L6 isolates. However, the reverse was observed in the urease activity for the lineages. All isolates tested were resistant to TCH except for one L6 isolate. Comparative genomic analyses revealed several mutations that might explain the diverse phenotypic profiles of these isolates. Our findings showed significant phenotypic diversity among the MTBC lineages used for this study.
Collapse
Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Portia Morgan
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Abdul Basit Musah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Ishaque Mintah Siam
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Diana Asandem
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Theophilus Afum
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Asamoah Kusi
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
- * E-mail:
| |
Collapse
|