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Rajendiran V, Devaraju N, Haddad M, Ravi NS, Panigrahi L, Paul J, Gopalakrishnan C, Wyman S, Ariudainambi K, Mahalingam G, Periyasami Y, Prasad K, George A, Sukumaran D, Gopinathan S, Pai AA, Nakamura Y, Balasubramanian P, Ramalingam R, Thangavel S, Velayudhan SR, Corn JE, Mackay JP, Marepally S, Srivastava A, Crossley M, Mohankumar KM. Base editing of key residues in the BCL11A-XL-specific zinc finger domains derepresses fetal globin expression. Mol Ther 2024; 32:663-677. [PMID: 38273654 PMCID: PMC10928131 DOI: 10.1016/j.ymthe.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
BCL11A-XL directly binds and represses the fetal globin (HBG1/2) gene promoters, using 3 zinc-finger domains (ZnF4, ZnF5, and ZnF6), and is a potential target for β-hemoglobinopathy treatments. Disrupting BCL11A-XL results in derepression of fetal globin and high HbF, but also affects hematopoietic stem and progenitor cell (HSPC) engraftment and erythroid maturation. Intriguingly, neurodevelopmental patients with ZnF domain mutations have elevated HbF with normal hematological parameters. Inspired by this natural phenomenon, we used both CRISPR-Cas9 and base editing at specific ZnF domains and assessed the impacts on HbF production and hematopoietic differentiation. Generating indels in the various ZnF domains by CRISPR-Cas9 prevented the binding of BCL11A-XL to its site in the HBG1/2 promoters and elevated the HbF levels but affected normal hematopoiesis. Far fewer side effects were observed with base editing- for instance, erythroid maturation in vitro was near normal. However, we observed a modest reduction in HSPC engraftment and a complete loss of B cell development in vivo, presumably because current base editing is not capable of precisely recapitulating the mutations found in patients with BCL11A-XL-associated neurodevelopment disorders. Overall, our results reveal that disrupting different ZnF domains has different effects. Disrupting ZnF4 elevated HbF levels significantly while leaving many other erythroid target genes unaffected, and interestingly, disrupting ZnF6 also elevated HbF levels, which was unexpected because this region does not directly interact with the HBG1/2 promoters. This first structure/function analysis of ZnF4-6 provides important insights into the domains of BCL11A-XL that are required to repress fetal globin expression and provide framework for exploring the introduction of natural mutations that may enable the derepression of single gene while leaving other functions unaffected.
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Affiliation(s)
- Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Mahdi Haddad
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Chandrasekar Gopalakrishnan
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA
| | | | - Gokulnath Mahalingam
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Dhiyaneshwaran Sukumaran
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Sandhiya Gopinathan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | | | - Rajasekaran Ramalingam
- Department of Integrative Biology, School of Bioscience and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu 632014, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Shaji R Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Jacon E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA; Institute of Molecular Health Sciences, Department of Biology, Zurich, Switzerland
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Department of Haematology, Christian Medical College & Hospital, Vellore, Tamil Nadu 632 004, India
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India.
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Ravi NS, George A, Mohankumar KM. Protocol for arrayed gRNA screening by base editors in mammalian cell lines using lentiviral system. STAR Protoc 2023; 4:102668. [PMID: 37922314 PMCID: PMC10656259 DOI: 10.1016/j.xpro.2023.102668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/25/2023] [Accepted: 10/04/2023] [Indexed: 11/05/2023] Open
Abstract
Base editing, a CRISPR-based genome engineering technique, enables precise single-nucleotide modifications while minimizing double-strand breaks. Here, we present a protocol for arrayed mutagenesis using base editors to identify regulatory elements within the gamma-globin locus. We describe steps for guide RNA (gRNA) cloning into lentiviral vectors, establishing stable cell lines with base editor expression, transducing gRNAs, and assessing editing efficiency. This protocol can be applied to diverse genomic regions and cell lines for arrayed screening, facilitating genetic research, and target discovery. For complete details on the use and execution of this protocol, please refer to Ravi et al. (2022)1.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India.
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India.
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3
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George A, Ravi NS, Prasad K, Panigrahi L, Koikkara S, Rajendiran V, Devaraju N, Paul J, Pai AA, Nakamura Y, Kurita R, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, Mohankumar KM. Efficient and error-free correction of sickle mutation in human erythroid cells using prime editor-2. Front Genome Ed 2022; 4:1085111. [PMID: 36605051 PMCID: PMC9808041 DOI: 10.3389/fgeed.2022.1085111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Sickle cell anaemia (SCA) is one of the common autosomal recessive monogenic disorders, caused by a transverse point mutation (GAG > GTG) at the sixth codon of the beta-globin gene, which results in haemolytic anaemia due to the fragile RBCs. Recent progress in genome editing has gained attention for the therapeutic cure for SCA. Direct correction of SCA mutation by homology-directed repair relies on a double-strand break (DSB) at the target site and carries the risk of generating beta-thalassaemic mutations if the editing is not error-free. On the other hand, base editors cannot correct the pathogenic SCA mutation resulting from A > T base transversion. Prime editor (PE), the recently described CRISPR/Cas 9 based gene editing tool that enables precise gene manipulations without DSB and unintended nucleotide changes, is a viable approach for the treatment of SCA. However, the major limitation with the use of prime editing is the lower efficiency especially in human erythroid cell lines and primary cells. To overcome these limitations, we developed a modular lenti-viral based prime editor system and demonstrated its use for the precise modelling of SCA mutation and its subsequent correction in human erythroid cell lines. We achieved highly efficient installation of SCA mutation (up to 72%) and its subsequent correction in human erythroid cells. For the first time, we demonstrated the functional restoration of adult haemoglobin without any unintended nucleotide changes or indel formations using the PE2 system. We also validated that the off-target effects mediated by the PE2 system is very minimal even with very efficient on-target conversion, making it a safe therapeutic option. Taken together, the modular lenti-viral prime editor system developed in this study not only expands the range of cell lines targetable by prime editor but also improves the efficiency considerably, enabling the use of prime editor for myriad molecular, genetic, and translational studies.
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Affiliation(s)
- Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanya Koikkara
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Aswin Anand Pai
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India,Department of Haematology, Christian Medical College and Hospital, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | | | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Shaji R. Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Department of Haematology, Christian Medical College and Hospital, Vellore, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Department of Haematology, Christian Medical College and Hospital, Vellore, India
| | - Kumarasamypet M. Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India,Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India,*Correspondence: Kumarasamypet M. Mohankumar,
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4
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Ravi NS, Wienert B, Wyman SK, Bell HW, George A, Mahalingam G, Vu JT, Prasad K, Bandlamudi BP, Devaraju N, Rajendiran V, Syedbasha N, Pai AA, Nakamura Y, Kurita R, Narayanasamy M, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, DeWitt MA, Crossley M, Corn JE, Mohankumar KM. Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin. eLife 2022; 11:65421. [PMID: 35147495 PMCID: PMC8865852 DOI: 10.7554/elife.65421] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Naturally occurring point mutations in the HBG promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous HBG proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the –123 region. Base editing at –123 and –124 bp of HBG promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of –123T > C and –124T > C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the HBG promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Beeke Wienert
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Henry William Bell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anila George
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | - Jonathan T Vu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Kirti Prasad
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | | | - Vignesh Rajendiran
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Nazar Syedbasha
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Japan, Tokyo, Japan
| | | | | | | | - Srujan Marepally
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Mark A DeWitt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Jacob E Corn
- Department of Biology, ETH Zurich, Zurich, Switzerland
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5
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Devaraju N, Rajendiran V, Ravi NS, Mohankumar KM. Genome Engineering of Hematopoietic Stem Cells Using CRISPR/Cas9 System. Methods Mol Biol 2022; 2429:307-331. [PMID: 35507170 DOI: 10.1007/978-1-0716-1979-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ex vivo genetic manipulation of autologous hematopoietic stem and progenitor cells (HSPCs) is a viable strategy for the treatment of hematologic and primary immune disorders. Targeted genome editing of HSPCs using the CRISPR-Cas9 system provides an effective platform to edit the desired genomic locus for therapeutic purposes with minimal off-target effects. In this chapter, we describe the detailed methodology for the CRISPR-Cas9 mediated gene knockout, deletion, addition, and correction in human HSPCs by viral and nonviral approaches. We also present a comprehensive protocol for the analysis of genome modified HSPCs toward the erythroid and megakaryocyte lineage in vitro and the long-term multilineage reconstitution capacity in the recently developed NBSGW mouse model that supports human erythropoiesis.
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Affiliation(s)
- Nivedhitha Devaraju
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Mangalore, Karnataka, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India.
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Christopher AC, Venkatesan V, Karuppusamy KV, Srinivasan S, Babu P, Azhagiri MKK, C K, Bagchi A, Rajendiran V, Ravi NS, Kumar S, Marepally SK, Mohankumar KM, Srivastava A, Velayudhan SR, Thangavel S. Preferential expansion of human CD34+CD133+CD90+ hematopoietic stem cells enhances gene-modified cell frequency for gene therapy. Hum Gene Ther 2021; 33:188-201. [PMID: 34486377 DOI: 10.1089/hum.2021.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CD34+CD133+CD90+ hematopoietic stem cells (HSCs) are responsible for long-term multi-lineage hematopoiesis and the high frequency of gene-modified HSCs is crucial for the success of hematopoietic stem and progenitor cell (HSPC) gene therapy. However, the ex vivo culture and gene manipulation steps of HSPC graft preparation significantly reduce the frequency of HSCs, thus necessitating large doses of HSPCs and reagents for the manipulation. Here, we identified a combination of small molecules, Resveratrol, UM729, and SR1 that preferentially expands CD34+CD133+CD90+ HSCs over other subpopulations of adult HSPCs in ex vivo culture. The preferential expansion enriches the HSCs in ex vivo culture, enhances the adhesion and results in a 6-fold increase in the long-term engraftment in NSG mice. Further, the culture enriched HSCs are more responsive to gene modification by lentiviral transduction and gene editing, increasing the frequency of gene-modified HSCs up to 10-fold in vivo. The yield of gene-modified HSCs obtained by the culture enrichment is similar to the sort-purification of HSCs and superior to Cyclosporin-H treatment. Our study addresses a critical challenge of low frequency of gene-modified HSCs in HSPC graft by developing and demonstrating a facile HSPC culture condition that increases the frequency of gene-modified cells in vivo. This strategy will improve the outcome of HSPC gene therapy and also simplify the gene manipulation process.
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Affiliation(s)
| | - Vigneshwaran Venkatesan
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | - Karthik V Karuppusamy
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | | | - Prathibha Babu
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | - Manoj Kumar K Azhagiri
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India.,Manipal Academy of Higher Education, 76793, Manipal, Karnataka, India;
| | - Karthik C
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India;
| | - Abhirup Bagchi
- Center for Stem Cell Research, 302927, Vellore, Tamil nadu, India;
| | | | - Nithin Sam Ravi
- Center for Stem Cell Research, 302927, Vellore, Tamil Nadu, India;
| | - Sanjay Kumar
- Christian Medical College and Hospital Vellore, 30025, Center for Stem Cell Research, Vellore, Tamil Nadu, India;
| | | | | | - Alok Srivastava
- Christian Medical College, Centre for Stem Cell Research, CMC Campus, Bagayam, Vellore, Tamilnadu, India, 632002.,Christian Medical College, Haematology, Ida Scudder Road, Vellore, Tamil Nadu, India, 632004;
| | | | - Saravanabhavan Thangavel
- Center for Stem Cell Research, 302927, Christian Medical College Campus Bagayam,, Vellore, Tamil nadu, India, 632002;
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Ravi NS, Aslam RF, Veeraraghavan B. A New Method for Determination of Minimum Biofilm Eradication Concentration for Accurate Antimicrobial Therapy. Methods Mol Biol 2019; 1946:61-67. [PMID: 30798544 DOI: 10.1007/978-1-4939-9118-1_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial susceptibility testing (AST) is an important technique to find the susceptibility pattern of clinical isolates in order to administer the appropriate drug. One such technique is minimum inhibitory concentration (MIC), which not only identifies the right drug but also suggests the appropriate concentration necessary to neutralize the organisms in planktonic form. MIC can vary in case of adherent organisms since they form biofilms and activate survival mechanisms like quorum sensing. Here we have strategized a new method which used an inoculator plate, a resazurin dye, and a standard plate to identify minimum biofilm eradication concentration (MBEC) of adherent organisms.
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Affiliation(s)
- Nithin Sam Ravi
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Raziya Fathima Aslam
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India.
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Ravi NS, Anandan S, Vijayakumar S, Gopi R, Lopes BS, Veeraraghavan B. The potential of different molecular biology methods in tracking clones of Acinetobacter baumannii in an ICU setting. J Med Microbiol 2018; 67:1340-1347. [DOI: 10.1099/jmm.0.000797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nithin Sam Ravi
- 1Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Shalini Anandan
- 1Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Saranya Vijayakumar
- 1Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Radha Gopi
- 1Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Bruno S. Lopes
- 2School of Medicine, Medical Sciences and Nutrition, Medical Microbiology, University of Aberdeen, Aberdeen, UK
| | - Balaji Veeraraghavan
- 1Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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