@article {43934,
	title = {Scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD(+)/NADH(+) imbalanceA scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceu},
	journal = {BMC Syst Biol. },
	volume = {11},
	year = {2017},
	month = {APR},
	abstract = {<p>BACKGROUND: The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens using benign metabolites. RESULTS: Controlled laboratory evolutions established chloramphenicol and streptomycin resistant pathogens of Chromobacterium. These resistant pathogens showed higher growth rates and required higher lethal doses of antibiotic. Growth and viability testing identified malate, maleate, succinate, pyruvate and oxoadipate as resensitising agents for antibiotic therapy. Resistant genes were catalogued through whole genome sequencing. Intracellular metabolomic profiling identified violacein as a potential biomarker for resistance. The temporal variance of metabolites captured the linearized dynamics around the steady state and correlated to growth rate. A constraints-based flux balance model of the core metabolism was used to predict the metabolic basis of antibiotic susceptibility and resistance. CONCLUSIONS: The model predicts electron imbalance and skewed NAD/NADH ratios as a result of antibiotics - chloramphenicol and streptomycin. The resistant pathogen rewired its metabolic networks to compensate for disruption of redox homeostasis. We foresee the utility of such scalable workflows in identifying metabolites for clinical isolates as inevitable solutions to mitigate antibiotic resistance.</p>},
	keywords = {Antibiotic resistance; Flux balance analysis; Flux variability analysis; Metabolism; Metabolomic; NAD; NADH; Redox homeostasis},
	doi = {10.1186/s12918-017-0427-z},
	author = {Banerjee, Deepanwita and Parmar, Dharmeshkumar and Bhattacharya, Nivedita and Ghanate, Avinash D. and Panchagnula, Venkateswarlu and Raghunathan, Anu}
}
@article {45413,
	title = { Integrated constraints based analysis of an engineered violacein pathway in escherichia coli},
	journal = {Biosystems },
	volume = {171},
	year = {2018},
	month = {SEP},
	pages = {10-19},
	type = {Article},
	abstract = {Strategies towards optimal violacein biosynthesis, a potential drug molecule, need systems level coordination of enzymatic activities of individual genes in a multigene operon vioABCDE. Constraints-based flux balance analysis of an extended iAF1260 model (iAF1260vio) with a reconstructed violacein module predicted growth and violacein yields in Escherichia coli accurately. Shadow price (SP) analysis identified tryptophan metabolism and NADPH as limiting. Increased tryptophan levels in Delta pgi \& Delta pheA were validated using in silico gene deletion analysis. Phenotypic phase plane (PhPP) analysis highlighted sensitivity between tryptophan and NADPH for violacein synthesis at molar growth yields. A synthetic VioABCDE operon (SYNO) sequence was designed to maximize Codon Adaptive Index (CAI: 0.9) and tune translation initiation rates (TIR: 2-50 fold higher) in E. coli. All pSYN E. coli transformants produced higher violacein, with a maximum six-fold increase in yields. The rational design E. coli: Delta pheA SYN: gave the highest violacein titers (33.8 mg/I). Such integrated approaches targeting multiple molecular hierarchies in the cell can be extended further to increase violacein yields.},
	doi = {10.1016/j.biosystems.2018.06.002},
	author = {Immanuel, Selva Rupa Christinal and Banerjee, Deepanwita and Rajankar, Mayooreshwar P. and Raghunathan, Anu}
}
@article {44377,
	title = {Knowledge, attitude and practice of antibiotic use and antimicrobial resistance: a study post the {\textquoteright}Red Line{\textquoteright} initiative},
	journal = {Current Science},
	volume = {114},
	year = {2018},
	month = {MAY},
	pages = {1866-1877},
	abstract = {Antimicrobial resistance (AMR) is propagated by irrational use of antibiotics by healthcare practitioners and the uninformed public. This study assessed a select cohort of 504 urban Indians for their knowledge, awareness and practice of antibiotic use and AMR. Forty seven per cent were unaware of the differences between over-the-counter drugs and antibiotics. One in four believes that dose-skipping does not contribute to AMR. One in ten tends to self-medicate. One in five bought medicines without prescription or started an antibiotic course by calling a doctor. Our results mandate educational campaigns, stewardship and surveillance at the national level for prudent antimicrobial use in the Indian community.},
	doi = {10.18520/cs/v114/i09/1866-1877},
	author = {Banerjee, Deepanwita and Raghunathan, Anu}
}
@article {45520,
	title = {Constraints-based analysis identifies NAD(+) recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum},
	journal = {PLoS One},
	volume = {14},
	year = {2019},
	month = {JAN },
	pages = {Article Number: e0210008},
	type = {Article},
	abstract = {<p>In the post genomic era, high throughput data augment stoichiometric flux balance models to compute accurate metabolic flux states, growth and energy phenotypes. Investigating altered metabolism in the context of evolved resistant genotypes potentially provide simple strategies to overcome drug resistance and induce susceptibility to existing antibiotics. A genome-scale metabolic model (GSMM) for Chromobacterium violaceum, an opportunistic human pathogen, was reconstructed using legacy data. Experimental constraints were used to represent antibiotic susceptible and resistant populations. Model predictions were validated using growth and respiration data successfully. Differential flux distribution and metabolic reprogramming were identified as a response to antibiotics, chloramphenicol and streptomycin. Streptomycin resistant populations (StrpR) redirected tricarboxylic acid (TCA) cycle flux through the glyoxylate shunt. Chloramphenicol resistant populations (ChlR) resorted to overflow metabolism producing acetate and formate. This switch to fermentative metabolism is potentially through excess reducing equivalents and increased NADH/NAD ratios. Reduced proton gradients and changed Proton Motive Force (PMF) induced by antibiotics were also predicted and verified experimentally using flow cytometry based membrane potential measurements. Pareto analysis of NADH and ATP maintenance showed the decoupling of electron transfer and ATP synthesis in StrpR. Redox homeostasis and NAD(+) cycling through rewiring metabolic flux was implicated in re-sensitizing antibiotic resistant C. violaceum. These approaches can be used to probe metabolic vulnerabilities of resistant pathogens. On the verge of a post-antibiotic era, we foresee a critical need for systems level understanding of pathogens and host interaction to extend shelf life of antibiotics and strategize novel therapies.</p>},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0210008},
	author = {Banerjee, Deepanwita and Raghunathan, Anu}
}
