IMPACT OF OUR WORK

Karishma presented the progress of the research group at the Ramalingawami Research Conclave 2022 (virtual), Department of Biotechnology, Government of India


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2022

New publication alert!

Ravichandran S, Avatapalli Sai Supriya, Narasimhan Y, Kaushik KS and Yenamalli R. Frontiers in Cellular and Infection Microbiology (2022).


‘Targeting’ the Search: An Upgraded Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies (B-AMP v2.0) with a Focus on Biofilm Protein Targets

In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases.


With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.

New publication alert!

Dhekane R, Mhade S, Kaushik KS. Biofilm (2022).


Adding a new dimension: Multi-level structure and organization of mixed-species Pseudomonas aeruginosa and Staphylococcus aureus biofilms in a 4-D wound microenvironment.


We have built a 4-D wound microenvironment consisting of 3-D host cell surfaces and an in vitro wound milieu (from our previous work) to study the structure and organization of mixed-species P. aeruginosa and S. aureus biofilms.


Mixed species biomass of P. aeruginosa and S. aureus grown in the recapitulated microenvironment, display distinct structure and organization, that varies between species and across biomass growth.


We place our findings in the context of the current understanding on P. aeruginosa and S. aureus organization in the wound bed, notably the niche partitioning observed in prolonged, chronic wounds.

New book chapter alert!

Shaikh N, Kaushik KS (2022).

Historical Medical Remedies as Potential Anti-Biofilm Approaches: Can We Look Back to Move Forward?

Antibiofilm Strategies, Part of the Springer Series on Biofilms Book Series (2022).

Editors: Katharina Richter, Kaspa N Kragh

While the study of biofilms has grown in the last few decades, evidence of human infections per se has existed since ancient times. In this chapter, we review descriptions of biofilm infections across ancient compendia and treatises and summarize traditional and historical medical remedies suggested and used for these infections, classifying them into plant, animal, and inanimate sources. Finally, we discuss possible considerations towards developing these historical remedies as contemporary anti-biofilm approaches.

New book chapter alert!

Ricardo Franaco-Duarte, Snehal Kadam, Karishma S Kaushik, Sakshi Painuli, Prabhaka Semwal, Natalia Cruz-Martins, Celia Fortuna Rordrigues (2022).

Quick Detection and Confirmation of Microbes in Food and Water

Present Knowledge in Food Safety: A Risk-Based Approach Through The Food Chain. Academic Press (2022).

Editors: Micheal E Knowles, Lucia E Anelich, Alan R Boobis, Bert Popping

The ingestion of contaminated food or water is a great threat to public health. In fact, food and water contamination can result in serious infections, and are associated with high morbidity and mortality. The food and water supply chain need to guarantee the safety and quality of all food products; however, this can be laborious, since it depends on several segments, starting from food sample handling, storage, sample processing, transport, and retail. Essentially, for food and waterborne pathogen detection, cell culture methods continue to be the “gold standard” (low-cost, sensitive and microorganism specific), but traditional methods do have several drawbacks: high time spent for sample preparation, large volumes of reagents needed, and prerequisite of qualified personnel. In order to surpass these issues, rapid, sensitive, on-site, and reliable methods have been developed and implemented in modern food production systems. This chapter will recapitulate available methods, and discuss them in the context of their applications, and possible use as alternatives to gold-standard methods.

2021

New publication and repository alert!

Mhade S, Panse S, Tendulkar G, Awate R, Kadam S, Pravanan Y, Yenamalli R, Kaushik KS. Frontiers in Cellular and Infection Microbiology (2021).

AMPing up the game: A structural and functional repository of antimicrobial peptides (AMPs) for biofilm studies (Biofilm-AMP), and a case study of its application to Corynebacterium striatum, an emerging pathogen.

In collaboration with Dr. Ragothaman Yennamalli, SASTRA University, Thanjavur, India.

Biofilm-AMP (A structural repository of AMP models and protein-peptide interactions relevant for biofilm studies

Mhade S, Panse S, Tendulkar G, Awate R, Kaushik KS (2021).

Biofilm-AMP (B-AMP), a user-friendly, search-enabled repository of AMP structures and AMP interactions with biofilm targets. The repository includes predicted structures for 5544 AMPs, searchable by their Pep ID, DRAMP ID, name and source, and a separate subset of 2534 AMPs filtered by known anti-Gram positive activity. For each peptide, the repository includes FASTA files, PDB files, and predicted and chosen 3D models. For the 100 AMPs selected for in silico molecular docking, the repository hosts input & output PDBQT files, images, and a text file detailing hydrogen interactions. Further, the repository hosts AMP annotations to a vast library of existing biofilm literature sources, making it a one stop databse of AMPs for biofilm studies.

Radhika and Nizam presented their recent work on in vitro systems to study biofilms at the EMBL Microbiology Conference (virtual)

December 2021

Get in touch with us for any Qs!

Kadam S, Madhusoodhanan V, Dhekane R, Bhide D, Ugale R, Tikhole U, Kaushik K. Biofilm (2021).

Milieu Matters: An in vitro wound milieu to recapitulate key features of, and probe new insights into, mixed-species bacterial biofilms.

Based on previous reports of clinical wound fluid composition, we have developed an in vitro wound milieu (IVWM) that includes, in addition to serum (to recapitulate wound fluid), matrix elements and biochemical factors. We demonstrate that the IVWM recapitulates widely reported in vivo biofilm features such as metabolic activity, increased antibiotic tolerance, 3D structure, and interspecies interactions for single- and co-species biofilms. Further, the IVWM is simple to formulate, uses laboratory-grade components, and is compatible with standard biofilm assays. Given this, it holds potential as a tractable approach to study wound biofilms under host-relevant conditions.

Karishma worked with Dr. Celia Fortunae Rodrigues (University of Porto, Portugal) and Dr. Caitlin Light (Binghamton University, USA) to put together a Special Issue on Biofilms in Wounds: New Advances in Therapy and in Healing Management for Biomedicines (2021).

Looking beyond the smokescreen: Can the oral microbiome be a tool or target in the management of tobacco-associated oral cancer?

Kadam S, Madhusoodhanan V, Patwardhan S, Kaushik KS. eCancer (2021).


This is a new focus area of our group!

2020

Kadam S, Madhusoodhanan V, Bandgar A, Kaushik K. Front Pharmacol (2020).

From Treatise to Test: Evaluating Traditional Remedies for Anti-Biofilm Potential

We identified and reconstituted plant-based medicinal formulations from historical treatises of Indian traditional medicine, and analyzed their efficacy using microtiter based assays, that constitute the cornerstone of biofilm studies. Through this study, we provide insights into considerations and challenges relevant to the "treatise to test" phase of the "ancientbiotics" pipeline.

This primer serves as a starting point for future studies exploring anti-biofilm approaches at the interface of historical and modern medicine.

A more human-relevant approach that reduces the use of animal products in research.

Kadam S, Madhusoodhanan V, Kaushik K. Biotechniques (2020).

Reduced-serum based approaches for contact-based co-culture of human dermal fibroblasts and epidermal keratinocytes.

In this methods paper, we have developed two reduced-serum based approaches (1-2% serum), using commonly-available media components, to support the contact-based co-culture of HDFa and HaCaT cells. Taken together, these formulations result in effective concentrations of 1-2% FBS, representing a 5–10 fold reduction in serum concentration as compared with previous studies (using up to 10% serum).

Kadam S, Nadkarni S, Lele J, Sakhalkar S, Mokashi P, Kaushik K (2020).

Bioengineered platforms for Chronic Wound Infection Studies: How can we make them more Human-Relevant? Front Bioeng Biotechnol.


Using chronic wounds as an example, we discuss that infection microenvironments can be bioengineered using a two-compartment approach, with the upper compartment the ‘infected wound bed’ and the lower compartment the capillary immune interface.


2019

Franco-Duarte R, Černáková L, Kadam S, Kaushik K, et al (2019). Advances in chemical and biological methods to identify microorganisms – from past to present. Microorganisms.

This invited review discusses methods of detection and identification of microorganisms, from past methods based on microbial isolation to current approaches employing molecular techniques. An international collaboration with Portugal, Iran, Italy, Poland and Brazil; we contributed to the section on molecular diagnostic tools.

Kadam S, Shai S, Shahane A, Kaushik K (2019). Recent advances in non-conventional antimicrobial approaches for chronic wound biofilms: Have we found the ‘chink in the armor’? Biomedicines.

We discuss recent therapeutic approaches for chronic wound biofilms that go beyond antibiotics, focusing on non-conventional strategies that directly kill or inhibit microbes or modify infection microenvironmental factors. We propose that most approaches will serve as adjunct therapies with antibiotics, while nanoantimicrobials can offer a new treatment paradigm.

Kaushik K, Kadam S (2019). Abandon or Administer? Moving Beyond Oversimplified Approaches and Developing Strategies that Target the Composite Infected Wound Microecosystem. Letter to the Editor. Wounds.

In this Letter to Editor, we argue that an all-or-none approach to the use of antibiotics is reductionist, and therapeutics need to account for and target the complexity of the infection state.

Kaushik K (2019). Defining the path of physician-scientist. Nature Medicine.

Featured as part of Nature Medicine's 25th year anniversary series to highlight 25 physician-scientists' the world over.

Education publications (2018-till date)

Kadam S, Methwani K, Kaushik KS.

Biofilms with a dash of color: A hands-on acrtivity for school students to build a biofilm model and use it to understand antibiotic tolerance in biofilms.

J Microbiol Biol Educ (2022).

This model was built and executed by Talk To A Scientist for India Science Festival (January 2022).

Kadam S, Chattopadhaya A, Kaushik KS.

Of Biofilms and Beehives: An Analogy-Based Instructional Tool to Introduce Biofilms in School and Undergraduate Curriculum.

Biofilm, 2022.

We have developed and implemented an analogy-based instructional tool to introduce biofilms to high school and undergraduate students, using beehives for comparison.

Please find pre- and post-session feedback, and guidelines for delivery.

If you are an undergraduate educator or school teacher and would like to implement this in your class, please get in touch with us!

Kaushik K, Zinjarde S. An Interactive, Accessible and Affordable Science-Art Based Activity to Foster Team-Building among New Students. J Microbiol Biol Educ (2020).

We describe a hands-on science-art based activity organized as part of an orientation program for new students at our institute. Based on developing team-building skills and serving as an ‘ice-breaker’ for incoming students, this activity aims at creating a composite piece of art work depicting a scientific theme. In our experience, this activity is well-suited for implementation and improvisations as a collaborative, time-and cost-effective tool for new student engagement in a classroom setting.

The entire activity was executed at a cost of ~$1.50 (INR 100) per participant!

We thank the 2019-2024 batch of students for their participation, enthusiasm and for bringing the activity to life.

Our previous publications (prior to 2018)

Hutchison J, Kaushik K, Lilleholm T, Bakhtiari L, Gordon VD (2018). Increased production of the extracellular polysaccharide Psl can give a growth advantage to Pseudomonas areruginosa under low iron conditions. bioRxiv. https://www.biorxiv.org/content/10.1101/355339v1.

Using quantitative time-lapse confocal microscopy and image analysis of biofilm growth, my work discovered that aggregates of P. aeruginosa (red) have a growth advantage over single cells in the presence of S. aureus (yellow), under low-iron conditions. Our results suggested that this effect was linked to the high EPS content of aggregates, and its ability to posit iron acquisition, likely from S. aureus.

Kaushik K, Stolhandske J, Shindell O, Smyth H, Gordon VD (2016). Tobramycin and Bicarbonate synergize to kill planktonic Pseudomonas aeruginosa, but antagonize to promote biofilm survival. npj Biofilms and Microbiomes.

Using checkerboard assays and an interpolated surface methodology, I determined that bicarbonate synergizes with tobramycin to enhance killing of planktonic bacteria, but antagonizes to promote biofilm survival. This has clinical implications since bicarbonate is being evaluated as a replacement therapy for Cystic Fibrosis

Kaushik K, Ratnayeke N, Katira P, Gordon VD (2015). The spatial profiles and metabolic capabilities of microbial populations impact the growth of antibiotic-resistant mutants. J R Soc Interface.

I discovered that microbial population structure, via density and spatial organization, impacts the survival of antibiotic-resistant mutants, in the presence of antibiotic. This effect is mediated by alkaline metabolic by-products of bacterial growth, likely ammonia or amines, that enhance the efficacy of aminoglycosides against antibiotic-resistant mutants. This opens the possibility that microbial population structure and nutrient environments could enhance antibiotic efficacy

Kaushik K, Kessel A, Ratnayeke N, Gordon VD (2015). A low-cost, hands-on module to characterize antimicrobial compounds using an interdisciplinary, biophysical approach. PLoS Biology.

As part of a hands-on school held at the International center for Theoretical Physics, Trieste, Italy, I developed an ultra-low cost, hands-on experimental module that combines biology experiments with a physics-based analytical model to test antimicrobial compound and characterize the active ingredient. In doing so, this module addresses the paucity of structured training programs that integrate diverse fields, and is suitable for implementation in resource-limited settings

Hutchison J, Rodesney C, Kaushik K, Le H, Hurwitz D, Irie Y, Gordon VD (2014). Single cell control of initial spatial structure in biofilm development using laser trapping. Langmuir.

Using laser-trapping, we present a method for growing biofilms from initiating cells controlled with single-cell precision. For co-pathogens, P. aeruginosa and S. aureus native growth, motility and surface adhesion of positioned microbes is preserved, and trapping and placing bacteria on surfaces reveals the effects of spatial structure on bacterial growth

First Large-Scale Characterization of Clinical Varicella Zoster (Chicken Pox) strains in India

Kaushik K, Lahiri KK, Chumber SK, et al (2008). Molecular characterization of clinical varicella-zoster strains from India and differentiation from the Oka vaccine strain. Jpn J Infect Dis.

This study was the first large-scale characterization of clinical VZV strains in India. Using PCR-RFLP and Gene Sequencing targeting two ORFs, I determined that circulating Indian VZV strains were genotypically distinct from the vaccine Oka strain licensed for use. This work opened the possibility of developing strain-specific VZV vaccines for India.

Kaushik K, Lahiri KK, Kumar S, et al (2008). Differentiation of wild-type varicella- zoster strains from India and the Oka vaccine strain using a VZV ORF-62 based PCR-RFLP Technique. Braz J Infect Dis.

I developed a PCR-RFLP approach to distinguish Indian VZV strains from the vaccine Oka strain using a single ORF based analysis, which reduces time-cost-resources compared to the two ORF approach.

Dr. Karishma was awarded the Ranbaxy Young Science Scholar award (2008) from Nobel Laureate Prof. David Baltimore for this work.

Clinical Publications and Case Reports

Kaushik K, Kapila K, Chumber SK (2013). Photo Quiz: Lady in Red. J Clin Microbiol 51: 3915.

Kaushik K, Kapila K, Praharaj AK (2011). Shooting Up: The interface of microbial infections and drug abuse. J Med Microbiol 60: 408-422.

Kaushik K, Kapila K (2009). Women in Medical Microbiology: Reflections on contributions. Indian J Med Microbiol 27: 285-288.

Kaushik K, Kapila K (2009). Laboratory microbiology to clinical microbiology: Are we ready for the transition? Indian J Med Microbiol 27: 378-379.

Kaushik K, Kumar S, Kapila K, et al (2007). Tuberculous brain abscess in a patient with HIV infection. Indian J Tuberc 54: 196-198.

Chumber SK, Kaushik K, Savy S (2007). Bacteriological profile of street foods in Pune. Indian J Pub Health 51.

We are a unique research group in India that works at the intersection of

basic science, clinical science, industry and technology commercialization