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Khan MF, Ali A, Rehman HM, Noor Khan S, Hammad HM, Waseem M, Wu Y, Clark TG, Jabbar A. Exploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis. Sci Rep 2024; 14:10904. [PMID: 38740859 DOI: 10.1038/s41598-024-61752-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, ranks among the top causes of global human mortality, as reported by the World Health Organization's 2022 TB report. The prevalence of M. tuberculosis strains that are multiple and extensive-drug resistant represents a significant barrier to TB eradication. Fortunately, having many completely sequenced M. tuberculosis genomes available has made it possible to investigate the species pangenome, conduct a pan-phylogenetic investigation, and find potential new drug targets. The 442 complete genome dataset was used to estimate the pangenome of M. tuberculosis. This study involved phylogenomic classification and in-depth analyses. Sequential filters were applied to the conserved core genome containing 2754 proteins. These filters assessed non-human homology, virulence, essentiality, physiochemical properties, and pathway analysis. Through these intensive filtering approaches, promising broad-spectrum therapeutic targets were identified. These targets were docked with FDA-approved compounds readily available on the ZINC database. Selected highly ranked ligands with inhibitory potential include dihydroergotamine and abiraterone acetate. The effectiveness of the ligands has been supported by molecular dynamics simulation of the ligand-protein complexes, instilling optimism that the identified lead compounds may serve as a robust basis for the development of safe and efficient drugs for TB treatment, subject to further lead optimization and subsequent experimental validation.
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Affiliation(s)
- Muhammad Fayaz Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Sadiq Noor Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Hafiz Muhammad Hammad
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Maaz Waseem
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yurong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK.
| | - Abdul Jabbar
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan.
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Silva-Pereira TT, Soler-Camargo NC, Guimarães AMS. Diversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures. Microbiol Spectr 2024; 12:e0228923. [PMID: 38230932 PMCID: PMC10871547 DOI: 10.1128/spectrum.02289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.
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Affiliation(s)
- Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Khan MT, Mahmud A, Islam MM, Sumaia MSN, Rahim Z, Islam K, Iqbal A. Multi-epitope vaccine against drug-resistant strains of Mycobacterium tuberculosis: a proteome-wide subtraction and immunoinformatics approach. Genomics Inform 2023; 21:e42. [PMID: 37813638 PMCID: PMC10584640 DOI: 10.5808/gi.23021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 10/11/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Toll-like receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.
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Affiliation(s)
- Md Tahsin Khan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Araf Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md. Muzahidul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mst. Sayedatun Nessa Sumaia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Zeaur Rahim
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kamrul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Asif Iqbal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
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Liu W, Ou P, Tian F, Liao J, Ma Y, Wang J, Jin X. Anti- Vibrio parahaemolyticus compounds from Streptomyces parvus based on Pan-genome and subtractive proteomics. Front Microbiol 2023; 14:1218176. [PMID: 37485508 PMCID: PMC10361664 DOI: 10.3389/fmicb.2023.1218176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Vibrio parahaemolyticus is a foodborne pathogen commonly found in seafood, and drug resistance poses significant challenges to its control. This study aimed to identify novel drug targets for antibacterial drug discovery. Methods To identify drug targets, we performed a pan-genome analysis on 58 strains of V. parahaemolyticus genomes to obtain core genes. Subsequently, subtractive proteomics and physiochemical checks were conducted on the core proteins to identify potential therapeutic targets. Molecular docking was then employed to screen for anti-V. parahaemolyticus compounds using a in-house compound library of Streptomyces parvus, chosen based on binding energy. The anti-V. parahaemolyticus efficacy of the identified compounds was further validated through a series of experimental tests. Results and Discussion Pangenome analysis of 58 V. parahaemolyticus genomes revealed that there were 1,392 core genes. After Subtractive proteomics and physiochemical checks, Flagellar motor switch protein FliN was selected as a therapeutic target against V. parahaemolyticus. FliN was modeled and docked with Streptomyces parvus source compounds, and Actinomycin D was identified as a potential anti-V. parahaemolyticus agent with a strong binding energy. Experimental verification confirmed its effectiveness in killing V. parahaemolyticus and significantly inhibiting biofilm formation and motility. This study is the first to use pan-genome and subtractive proteomics to identify new antimicrobial targets for V. parahaemolyticus and to identify the anti-V. parahaemolyticus effect of Actinomycin D. These findings suggest potential avenues for the development of new antibacterial drugs to control V. parahaemolyticus infections.
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Affiliation(s)
- Wenbin Liu
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Peiyu Ou
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Fangyuan Tian
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jingyang Liao
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yan Ma
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jie Wang
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaobao Jin
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
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Negrete-Paz AM, Vázquez-Marrufo G, Gutiérrez-Moraga A, Vázquez-Garcidueñas MS. Pangenome Reconstruction of Mycobacterium tuberculosis as a Guide to Reveal Genomic Features Associated with Strain Clinical Phenotype. Microorganisms 2023; 11:1495. [PMID: 37374997 DOI: 10.3390/microorganisms11061495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). There is no consensus on the genetic determinants of this pathogen that may contribute to EPTB. In this study, we constructed the M. tuberculosis pangenome and used it as a tool to seek genomic signatures associated with the clinical presentation of TB based on its accessory genome differences. The analysis carried out in the present study includes the raw reads of 490 M. tuberculosis genomes (PTB n = 245, EPTB n = 245) retrieved from public databases that were assembled, as well as ten genomes from Mexican strains (PTB n = 5, EPTB n = 5) that were sequenced and assembled. All genomes were annotated and then used to construct the pangenome with Roary and Panaroo. The pangenome obtained using Roary consisted of 2231 core genes and 3729 accessory genes. On the other hand, the pangenome resulting from Panaroo consisted of 2130 core genes and 5598 accessory genes. Associations between the distribution of accessory genes and the PTB/EPTB phenotypes were examined using the Scoary and Pyseer tools. Both tools found a significant association between the hspR, plcD, Rv2550c, pe_pgrs5, pe_pgrs25, and pe_pgrs57 genes and the PTB genotype. In contrast, the deletion of the aceA, esxR, plcA, and ppe50 genes was significantly associated with the EPTB phenotype. Rv1759c and Rv3740 were found to be associated with the PTB phenotype according to Scoary; however, these associations were not observed when using Pyseer. The robustness of the constructed pangenome and the gene-phenotype associations is supported by several factors, including the analysis of a large number of genomes, the inclusion of the same number of PTB/EPTB genomes, and the reproducibility of results thanks to the different bioinformatic tools used. Such characteristics surpass most of previous M. tuberculosis pangenomes. Thus, it can be inferred that the deletion of these genes can lead to changes in the processes involved in stress response and fatty acid metabolism, conferring phenotypic advantages associated with pulmonary or extrapulmonary presentation of TB. This study represents the first attempt to use the pangenome to seek gene-phenotype associations in M. tuberculosis.
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Affiliation(s)
- Andrea Monserrat Negrete-Paz
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58020, Michoacán, Mexico
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro 58893, Michoacán, Mexico
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro 58893, Michoacán, Mexico
| | - Ana Gutiérrez-Moraga
- Instituto de Ciencias Biomédicas, Vicerrectoría de Investigación y Doctorados, Universidad Autónoma de Chile, Santiago 7500912, Chile
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58020, Michoacán, Mexico
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Usharani N, Kanth SV, Saravanan N. Current nanotechnological strategies using lipids, carbohydrates, proteins and metal conjugates-based carrier systems for diagnosis and treatment of tuberculosis - A review. Int J Biol Macromol 2023; 227:262-272. [PMID: 36521715 DOI: 10.1016/j.ijbiomac.2022.12.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Tuberculosis is a fatal disease caused by Mycobacterium tuberculosis with highest morbidity and mortality every year. The evolution of anti-TB drugs is promising in controlling and treating TB. Yet, the drug response varies depending on the bacterial load and host immunological profiles. The prolonged anti-TB treatment regimen and high pill burden leads to poor adherence to treatment and acquired drug resistance. In the clinical arena, sustainable nanotechnology improves the targeted strategies leading to enhance therapeutic recovery with minimum treatment duration and virtuous drug adherence. Determinants of nanosystems are the size, nature, formulation techniques, stable dosing patterns, bioavailability and toxicity. In the treatment of chronic illness, nanomedicines inclusive of biological macromolecules such as lipids, peptides, and nucleic acids occur to be a successive alternative to synthetic carriers. Most biological nanomaterials possess antimicrobial properties with other intrinsic characteristics. Recently, the pulmonary delivery of anti-TB drugs through polymeric nanocarrier systems is shown to be effective in achieving optimal drug levels in lungs for longer duration, enhanced tissue permeation and sustained systemic clearance. This thematic review provides a holistic insight into the nanodelivery systems pertinent to the therapeutic applications in pulmonary tuberculosis describing the choice of carriers, optimized process, metabolic action and excretion processes.
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Affiliation(s)
- Nagarajan Usharani
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Swarna Vinodh Kanth
- Centre for Human and Organizational Resources Development, CSIR-Central Leather Research Institute, Chennai, India
| | - Natarajan Saravanan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai, India.
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Hurtado-Páez U, Álvarez Zuluaga N, Arango Isaza RE, Contreras-Moreira B, Rouzaud F, Robledo J. Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia. Front Microbiol 2023; 13:1076797. [PMID: 36687645 PMCID: PMC9846648 DOI: 10.3389/fmicb.2022.1076797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.
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Affiliation(s)
- Uriel Hurtado-Páez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,*Correspondence: Uriel Hurtado-Páez,
| | | | - Rafael Eduardo Arango Isaza
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,Facultad de Ciencias, Universidad Nacional de Colombia (UNAL), Medellín, Colombia
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei–Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain,Fundación ARAID, Zaragoza, Spain
| | | | - Jaime Robledo
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana (UPB), Medellín, Colombia
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Morey-León G, Andrade-Molina D, Fernández-Cadena JC, Berná L. Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador. BMC Genomics 2022; 23:844. [PMID: 36544084 PMCID: PMC9769008 DOI: 10.1186/s12864-022-09042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador. RESULTS Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected. CONCLUSION This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance. In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.
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Affiliation(s)
- Gabriel Morey-León
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.442157.10000 0001 1183 0630Universidad de Guayaquil, Guayaquil, Ecuador ,grid.442156.00000 0000 9557 7590Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Derly Andrade-Molina
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Juan Carlos Fernández-Cadena
- grid.442156.00000 0000 9557 7590Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | - Luisa Berná
- grid.418532.90000 0004 0403 6035Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay ,grid.11630.350000000121657640Facultad de Ciencias, Unidad de Genómica Evolutiva, Universidad de La República, Montevideo, Uruguay
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Almuhayawi MS, Al Jaouni SK, Selim S, Alkhalifah DHM, Marc RA, Aslam S, Poczai P. Integrated Pangenome Analysis and Pharmacophore Modeling Revealed Potential Novel Inhibitors against Enterobacter xiangfangensis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192214812. [PMID: 36429532 PMCID: PMC9691136 DOI: 10.3390/ijerph192214812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 06/02/2023]
Abstract
Enterobacter xiangfangensis is a novel, multidrug-resistant pathogen belonging to the Enterobacter genus and has the ability to acquire resistance to multiple antibiotic classes. However, there is currently no registered E. xiangfangensis drug on the market that has been shown to be effective. Hence, there is an urgent need to identify novel therapeutic targets and effective treatments for E. xiangfangensis. In the current study, a bacterial pan genome analysis and subtractive proteomics approach was employed to the core proteomes of six strains of E. xiangfangensis using several bioinformatic tools, software, and servers. However, 2611 nonredundant proteins were predicted from the 21,720 core proteins of core proteome. Out of 2611 nonredundant proteins, 372 were obtained from Geptop2.0 as essential proteins. After the subtractive proteomics and subcellular localization analysis, only 133 proteins were found in cytoplasm. All cytoplasmic proteins were examined using BLASTp against the virulence factor database, which classifies 20 therapeutic targets as virulent. Out of these 20, 3 cytoplasmic proteins: ferric iron uptake transcriptional regulator (FUR), UDP-2,3diacylglucosamine diphosphatase (UDP), and lipid-A-disaccharide synthase (lpxB) were chosen as potential drug targets. These drug targets are important for bacterial survival, virulence, and growth and could be used as therapeutic targets. More than 2500 plant chemicals were used to molecularly dock these proteins. Furthermore, the lowest-binding energetic docked compounds were found. The top five hit compounds, Adenine, Mollugin, Xanthohumol C, Sakuranetin, and Toosendanin demonstrated optimum binding against all three target proteins. Furthermore, molecular dynamics simulations and MM/GBSA analyses validated the stability of ligand-protein complexes and revealed that these compounds could serve as potential E. xiangfangensis replication inhibitors. Consequently, this study marks a significant step forward in the creation of new and powerful drugs against E. xiangfangensis. Future studies should validate these targets experimentally to prove their function in E. xiangfangensis survival and virulence.
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Affiliation(s)
- Mohammed S. Almuhayawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Soad K. Al Jaouni
- Department of Hematology/Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 Calea Mănă ¸stur Street, 400372 Cluj-Napoca, Romania
| | - Sidra Aslam
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Punjab 38000, Pakistan
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Peter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
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Effect of samarium oxide nanoparticles on virulence factors and motility of multi-drug resistant Pseudomonas aeruginosa. World J Microbiol Biotechnol 2022; 38:209. [PMID: 36040540 DOI: 10.1007/s11274-022-03384-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/09/2022] [Indexed: 10/14/2022]
Abstract
Biofilm formation and quorum sensing (QS) dependent virulence factors are considered the major causes of the emergence of drug resistance, therapeutic failure and development of Pseudomonas aeruginosa infections. This study aimed to investigate the effects of samarium oxide nanoparticles (Sm2O3NPs) on biofilm, virulence factors, and motility of multidrug-resistant P. aeruginosa. Sm2O3NPs were synthesized using curcumin and characterized by Transmission Electron Microscopy, X-ray diffractometer, Field Emission Scanning Electron Microscopy, and Energy-dispersive X-ray spectroscopy. Minimum inhibitory concentration (MIC) was determined using broth microdilution method. The antibiofilm potential of Sm2O3NPs was also evaluated by crystal violet staining and light microscopy examination. Then, the effect of sub-MICs concentrations of Sm2O3NPs on the proteolytic and hemolytic activities of P. aeruginosa was investigated. Finally, the effect of Sm2O3NPs on various types of motility including swarming, swimming, and twitching was studied. Our results showed that Sm2O3NPs significantly inhibited biofilm formation of P. aeruginosa by 49-61%. Additionally, sub-MICs concentrations of Sm2O3NPs effectively decreased virulence factors including pyocyanin (33-55%), protease (24-45%), and hemolytic activity (22-41%). Moreover, swarming, swimming, and twitching motility remarkably was reduced after exposure to the NPs. The findings of this work showed that Sm2O3NPs have a high potential in inhibiting QS-dependent virulence of P. aeruginosa, which could be considered for antibacterial chemotherapy after further characterization.
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Ceres KM, Stanhope MJ, Gröhn YT. A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation. Microb Genom 2022; 8. [PMID: 35763423 PMCID: PMC9455707 DOI: 10.1099/mgen.0.000839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The increased accessibility of next generation sequencing has allowed enough genomes from a given bacterial species to be sequenced to describe the distribution of genes in the pangenome, without limiting analyses to genes present in reference strains. Although some taxa have thousands of whole genome sequences available on public databases, most genomes were sequenced with short read technology, resulting in incomplete assemblies. Studying pangenomes could lead to important insights into adaptation, pathogenicity, or molecular epidemiology, however given the known information loss inherent in analyzing contig-level assemblies, these inferences may be biased or inaccurate. In this study we describe the pangenome of a clonally evolving pathogen,
Mycobacterium bovis
, and examine the utility of gene content variation in
M. bovis
outbreak investigation. We constructed the
M. bovis
pangenome using 1463 de novo assembled genomes. We tested the assumption of strict clonal evolution by studying evidence of recombination in core genes and analyzing the distribution of accessory genes among core monophyletic groups. To determine if gene content variation could be utilized in outbreak investigation, we carefully examined accessory genes detected in a well described
M. bovis
outbreak in Minnesota. We found significant errors in accessory gene classification. After accounting for these errors, we show that
M. bovis
has a much smaller accessory genome than previously described and provide evidence supporting ongoing clonal evolution and a closed pangenome, with little gene content variation generated over outbreaks. We also identified frameshift mutations in multiple genes, including a mutation in glpK, which has recently been associated with antibiotic tolerance in
Mycobacterium tuberculosis
. A pangenomic approach enables a more comprehensive analysis of genome dynamics than is possible with reference-based approaches; however, without critical evaluation of accessory gene content, inferences of transmission patterns employing these loci could be misguided.
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Affiliation(s)
- Kristina M Ceres
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.,Population and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.,Population and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yrjö T Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.,Population and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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Stiens J, Arnvig KB, Kendall SL, Nobeli I. Challenges in defining the functional, non-coding, expressed genome of members of the Mycobacterium tuberculosis complex. Mol Microbiol 2021; 117:20-31. [PMID: 34894010 DOI: 10.1111/mmi.14862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/14/2022]
Abstract
A definitive transcriptome atlas for the non-coding expressed elements of the members of the Mycobacterium tuberculosis complex (MTBC) does not exist. Incomplete lists of non-coding transcripts can be obtained for some of the reference genomes (e.g., M. tuberculosis H37Rv) but to what extent these transcripts have homologues in closely related species or even strains is not clear. This has implications for the analysis of transcriptomic data; non-coding parts of the transcriptome are often ignored in the absence of formal, reliable annotation. Here, we review the state of our knowledge of non-coding RNAs in pathogenic mycobacteria, emphasizing the disparities in the information included in commonly used databases. We then proceed to review ways of combining computational solutions for predicting the non-coding transcriptome with experiments that can help refine and confirm these predictions.
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Affiliation(s)
- Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Kristine B Arnvig
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Sharon L Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
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