@article {8467, title = {The conundrum of bacteria-specific antibiotics [Bugworks Research Pvt. Ltd., a C-CAMP Startup]}, journal = {J Antimicrob Chemother}, volume = {78}, year = {2023}, month = {2023 Jun 01}, pages = {1354-1358}, abstract = {

There is a continual debate on the pros and cons of broad-spectrum versus pathogen-specific antibiotics. The unmet need for a solution for antimicrobial resistance (AMR) has put this argument into sharper focus. A shortage of clinically differentiated antibiotics in late-stage clinical development coupled with the global unmet need in the face of the AMR onslaught has exacerbated the treatment options of drug-resistant bacterial infections. An added dimension to this problem is the current understanding of dysbiosis caused by antibiotics, often leading to negative fallout in immunocompromised patients. We attempt to deconstruct the nuances of this debate from an antibiotics discovery and a clinical standpoint.

}, keywords = {Anti-Bacterial Agents, Bacteria, Bacterial Infections, Drug Resistance, Bacterial, Dysbiosis, Humans}, issn = {1460-2091}, doi = {10.1093/jac/dkad130}, author = {Datta, Santanu} } @article {8318, title = {High-quality single amplicon sequencing method for illumina MiSeq platform using pool of {\textquoteright}N{\textquoteright} (0-10) spacer-linked target specific primers without PhiX spike-in [Next Gen Genomics Facility (INT)]}, journal = {BMC Genomics}, volume = {24}, year = {2023}, month = {2023 Mar 23}, pages = {141}, abstract = {

BACKGROUND: Illumina sequencing platform requires base diversity in the initial 11 cycles for efficient cluster identification and colour matrix estimation. This limitation yields low-quality data for amplicon libraries having homogeneous base composition. Spike-in of PhiX library ensures base diversity but reduces the overall number of sequencing reads for data analysis. To overcome such low diversity issues during amplicon sequencing on illumina platforms, we developed a high throughput single amplicon sequencing method by introducing {\textquoteright}N{\textquoteright} (0-10) spacers in target gene amplification primers that are pooled for simple handling.

RESULT: We evaluated the efficiency of {\textquoteright}N{\textquoteright} (0-10) spacer-linked primers by targeting bacterial 16S V3-V4 region, demonstrating heterogeneous base library construction. The addition of {\textquoteright}N{\textquoteright} (0-10) spacers causes sequencing frameshift at every base that leads to base diversity and produces heterogeneous high quality reads within a single amplicon library. We have written a python based command-line software,"MetReTrim", to trim the {\textquoteright}N{\textquoteright} (0-10) spacers from the raw reads ( https://github.com/Mohak91/MetReTrim ). We further demonstrated the accuracy of this method by comparative mock community analysis with standard illumina V3-V4 primer method. The ZymoBIOMICS{\texttrademark} microbial community DNA standard was used as a control for this study. We performed data analysisusing the DADA2 pipeline where taxonomy was assigned using SILVA database as reference. We observed no difference between the communities represented by our method and standard illumina V3-V4 primer method.

CONCLUSION: This method eliminates the need for PhiX spike-in for single amplicon sequencing on illumina MiSeq platform. This allows for sequencing of more number of samples in a run and a reduction in the overall cost. Given that Illumina sequencing works on SBS chemistry irrespective of the platform (such as HiSeq, MiSeq, NextSeq, NovaSeq, etc.) we propose that this strategy of using {\textquoteright}N{\textquoteright} (0-10) spacer-linked primer design can be adopted for generating high-quality single locus amplicon sequencing in a high throughput manner across the illumina platform subject to further validation.

}, keywords = {Bacteria, Gene Library, High-Throughput Nucleotide Sequencing, Microbiota, RNA, Ribosomal, 16S, Sequence Analysis, DNA}, issn = {1471-2164}, doi = {10.1186/s12864-023-09233-4}, author = {Naik, Tejali and Sharda, Mohak and C P, Lakshminarayanan and Virbhadra, Kumar and Pandit, Awadhesh} } @article {7616, title = {Identification and molecular characterization of drug targets of methicillin resistant Staphylococcus aureus [Mass Spectrometry - Proteomics]}, journal = {Journal of Applied and Natural Science}, volume = {14}, year = {2022}, month = {11/2022}, chapter = {1152}, abstract = {

Antimicrobial resistance is a major world health concern and drug-resistant Staphylococcus aureus is a serious threat. Due to the emergence of multidrug-resistant bacterial strains, there is an urgent need to develop novel drug targets to meet the challenge of multidrug-resistant organisms. The main objective of the current study was to determine molecular targets against S. aureus using by computational approach. S. aureus was cultured in brain heart infusion broth medium and MRSA (Methicillin resistant S. aureus) protein was extracted acetone-sodium dodecyl sulfate method. The cell lysate was treated with various antibiotics and proteinase K stable proteins were analyzed. The molecular weight of Geninthiocin-targeted protein of interest in S. aureus ranged from 46 to 50 kDa. A prominent protein band in SDS-PAGE indicated that the protein corresponding 50 kDa was resistant against proteinase K. The SDS-PAGE separated sample was excised and trypsinated, and the peptides were characterized using Nano Liquid Chromatography with tandem mass spectrometry (LC-MS/MS) analysis. Spectrum with clusters of molecular peptides and peptide fragments ranging from 110.0716 to 1002.7093 mass/charge ratio (m/z) were displayed against intensity or relative abundance in the excised gel band. The spectral data from nano LC-MS/MS was subjected to mascot search in the NCBIprot database (taxonomy-bacteria (eubacteria), resulting in seven bacterial proteins. Geninthiocin target proteins were determined against MRSA. To conclude, antibiotic target proteins were identified using a machine learning approach and these targets may have a lot of applications in developing a novel lead molecule against drug-resistant bacteria.\ 

}, keywords = {Bacteria, Drug resistance, Drug target, Geninthiocin, Virulence}, url = {https://journals.ansfoundation.org/index.php/jans/article/view/3693}, author = {Subha Lakshmi and Gopalakrishnan Nair and Santha Kumari and Samuel Gnana and Prakash Vincent} } @article {489, title = {Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T. [Next Generation Genomics facility]}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Jul}, pages = {3746}, abstract = {

We report the 4.98-Mb genome sequence of Marinilabilia salmonicolor JCM 21150(T), which was isolated from marine mud in the year 1961. The draft genome of strain Marinilabilia salmonicolor JCM 21150(T) contains 4,982,627 bp with a G+C content of 41.92\% and 4,227 protein coding genes, 52 tRNAs, and 3 rRNAs.

}, keywords = {Bacteria, Gene Expression Regulation, Bacterial, Genome, Bacterial, Molecular Sequence Data}, issn = {1098-5530}, doi = {10.1128/JB.00649-12}, author = {Kumar, Shailesh and Subramanian, Srikrishna and Raghava, Gajendra Pal Singh and Pinnaka, Anil Kumar} }