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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [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: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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Sharma R, Avendaño Rangel F, Reis-Cunha JL, Marques LP, Figueira CP, Borba PB, Viana SM, Beneke T, Bartholomeu DC, de Oliveira CI. Targeted Deletion of Centrin in Leishmania braziliensis Using CRISPR-Cas9-Based Editing. Front Cell Infect Microbiol 2022; 11:790418. [PMID: 35252020 PMCID: PMC8892584 DOI: 10.3389/fcimb.2021.790418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Leishmania braziliensis is the main causative agent of Tegumentary Leishmaniasis in the Americas. However, difficulties related to genome manipulation, experimental infection, and parasite growth have so far limited studies with this species. CRISPR-Cas9-based technology has made genome editing more accessible, and here we have successfully employed the LeishGEdit approach to attenuate L. braziliensis. We generated a transgenic cell line expressing Cas9 and T7 RNA polymerase, which was employed for the targeted deletion of centrin, a calcium-binding cytoskeletal protein involved in the centrosome duplication in eukaryotes. Centrin-deficient Leishmania exhibit growth arrest at the amastigote stage. Whole-genome sequencing of centrin-deficient L. braziliensis (LbCen−/−) did not indicate the presence of off-target mutations. In vitro, the growth rates of LbCen−/− and wild-type promastigotes were similar, but axenic and intracellular LbCen−/− amastigotes showed a multinucleated phenotype with impaired survival following macrophage infection. Upon inoculation into BALB/c mice, LbCen−/− were detected at an early time point but failed to induce lesion formation, contrary to control animals, infected with wild-type L. braziliensis. A significantly lower parasite burden was also observed in mice inoculated with LbCen−/−, differently from control mice. Given that centrin-deficient Leishmania sp. have become candidates for vaccine development, we propose that LbCen−/− can be further explored for the purposes of immunoprophylaxis against American Tegumentary Leishmaniasis.
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Affiliation(s)
- Rohit Sharma
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
| | - Francys Avendaño Rangel
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - João Luís Reis-Cunha
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Sayonara M. Viana
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Camila I. de Oliveira
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- INCT—Instituto de Investigação em Doenças Tropicais, Salvador, Brazil
- *Correspondence: Camila I. de Oliveira,
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Zhang WW, Karmakar S, Gannavaram S, Dey R, Lypaczewski P, Ismail N, Siddiqui A, Simonyan V, Oliveira F, Coutinho-Abreu IV, DeSouza-Vieira T, Meneses C, Oristian J, Serafim TD, Musa A, Nakamura R, Saljoughian N, Volpedo G, Satoskar M, Satoskar S, Dagur PK, McCoy JP, Kamhawi S, Valenzuela JG, Hamano S, Satoskar AR, Matlashewski G, Nakhasi HL. A second generation leishmanization vaccine with a markerless attenuated Leishmania major strain using CRISPR gene editing. Nat Commun 2020; 11:3461. [PMID: 32651371 PMCID: PMC7351751 DOI: 10.1038/s41467-020-17154-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/13/2020] [Indexed: 01/16/2023] Open
Abstract
Leishmaniasis is a neglected tropical disease caused by Leishmania protozoa transmitted by infected sand flies. Vaccination through leishmanization with live Leishmania major has been used successfully but is no longer practiced because it resulted in occasional skin lesions. A second generation leishmanization is described here using a CRISPR genome edited L. major strain (LmCen-/-). Notably, LmCen-/- is a genetically engineered centrin gene knock-out mutant strain that is antibiotic resistant marker free and does not have detectable off-target mutations. Mice immunized with LmCen-/- have no visible lesions following challenge with L. major-infected sand flies, while non-immunized animals develop large and progressive lesions with a 2-log fold higher parasite burden. LmCen-/- immunization results in protection and an immune response comparable to leishmanization. LmCen-/- is safe since it is unable to cause disease in immunocompromised mice, induces robust host protection against vector sand fly challenge and because it is marker free, can be advanced to human vaccine trials.
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Affiliation(s)
- Wen-Wei Zhang
- Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Subir Karmakar
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
| | - Sreenivas Gannavaram
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
| | - Ranadhir Dey
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
| | - Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Nevien Ismail
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
| | - Abid Siddiqui
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
| | - Vahan Simonyan
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
| | - Fabiano Oliveira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Iliano V Coutinho-Abreu
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Thiago DeSouza-Vieira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Claudio Meneses
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - James Oristian
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Tiago D Serafim
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Abu Musa
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), The Joint Usage/Research Center on Tropical Disease, Nagasaki University, Nagasaki, Japan and Nagasaki University Graduate School of Biomedical Sciences Doctoral Leadership Program, Nagasaki, Japan
| | - Risa Nakamura
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), The Joint Usage/Research Center on Tropical Disease, Nagasaki University, Nagasaki, Japan and Nagasaki University Graduate School of Biomedical Sciences Doctoral Leadership Program, Nagasaki, Japan
| | - Noushin Saljoughian
- Department of Pathology and Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Greta Volpedo
- Department of Pathology and Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Monika Satoskar
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
- Northeast Ohio Medical University, Rootstown, Ohio, 44272, USA
| | - Sanika Satoskar
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA
- Northeast Ohio Medical University, Rootstown, Ohio, 44272, USA
| | - Pradeep K Dagur
- National Institute of Heart, Lung and Blood Institute, NIH, Bethesda, MD, 20852, USA
| | - J Philip McCoy
- National Institute of Heart, Lung and Blood Institute, NIH, Bethesda, MD, 20852, USA
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Jesus G Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Shinjiro Hamano
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), The Joint Usage/Research Center on Tropical Disease, Nagasaki University, Nagasaki, Japan and Nagasaki University Graduate School of Biomedical Sciences Doctoral Leadership Program, Nagasaki, Japan
| | - Abhay R Satoskar
- Department of Pathology and Microbiology, Ohio State University, Columbus, OH, 43210, USA.
| | - Greg Matlashewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC, H3A 2B4, Canada.
| | - Hira L Nakhasi
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, 20993, USA.
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Lamotte S, Aulner N, Späth GF, Prina E. Discovery of novel hit compounds with broad activity against visceral and cutaneous Leishmania species by comparative phenotypic screening. Sci Rep 2019; 9:438. [PMID: 30679614 PMCID: PMC6345745 DOI: 10.1038/s41598-018-36944-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/28/2018] [Indexed: 12/22/2022] Open
Abstract
The limited success of recent phenotypic anti-leishmanial drug screening campaigns calls for new screening strategies for the discovery of clinically relevant hits. Here we present such a novel strategy based on physiologically relevant, ex vivo biology. We established high content phenotypic assays that combine primary murine macrophages and lesion-derived, virulent L. donovani and L. amazonensis amastigotes, which we applied to validate previously identified, anti-leishmanial hit compounds referred to as ‘GSK Leish-Box’. Together with secondary screens using cultured promastigotes, our pipeline distinguished stage- and/or species-specific compounds, including 20 hits with broad activity at 10 µM against intracellular amastigotes of both viscerotropic and dermotropic Leishmania. Even though the GSK Leish-Box hits were identified by phenotypic screening using THP-1 macrophage-like cells hosting culture-derived L. donovani LdBob parasites, our ex vivo assays only validated anti-leishmanial activity at 10 µM on intra-macrophagic L. donovani for 23 out of the 188 GSK Leish-Box hits. In conclusion, our comparative approach allowed the identification of hits with broad anti-leishmanial activity that represent interesting novel candidates to be tested in animal models. Physiologically more relevant screening approaches such as described here may reduce the very high attrition rate observed during pre-clinical and clinical phases of the drug development process.
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Affiliation(s)
- S Lamotte
- Institut Pasteur, Molecular Parasitology and Signaling, INSERM U1201, Department of Parasites and Insect Vectors, Paris, France
| | - N Aulner
- Institut Pasteur, UTechS Photonic BioImaging, Center for Technological Research and Resources, 75015, Paris, France
| | - G F Späth
- Institut Pasteur, Molecular Parasitology and Signaling, INSERM U1201, Department of Parasites and Insect Vectors, Paris, France.
| | - E Prina
- Institut Pasteur, Molecular Parasitology and Signaling, INSERM U1201, Department of Parasites and Insect Vectors, Paris, France.
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