Project description:Using Nanopore sequencing, our study has revealed a close correlation between genomic methylation levels and antibiotic resistance rates in Acinetobacter Baumannii. Specifically, the combined genome-wide DNA methylome and transcriptome analysis revealed the first epigenetic-based antibiotic-resistance mechanism in A. baumannii. Our findings suggest that the precise location of methylation sites along the chromosome could provide new diagnostic markers and drug targets to improve the management of multidrug-resistant A. baumannii infections.
Project description:Overall design Hi-C experiments were performed on untreated wild type cells at stationary and drug-treated cells (Novobiocin) of Mycoplasma Pneumoniae MPN129. We studied the chromosome organization of the genome-reduced bacterium, Mycoplasma pneumoniae, which has minimal genetic components and lacks several structural DNA-binding proteins. Platforms : Illumina HiSeq 2000 (Mycoplasma Pneumoniae MPN129)
Project description:To unravel distinct pattern of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and explore the impact of COVID-19 pandemic on epidemiological features
Project description:With the global increase in the use of carbapenems, several gram-negative bacteria have acquired carbapenem resistance, thereby limiting treatment options. Klebsiella pneumoniae is one of such notorious pathogen that is being widely studied to find novel resistance mechanisms and drug targets. These antibiotic-resistant clinical isolates generally harbor many genetic alterations, and identification of causal mutations will provide insights into the molecular mechanisms of antibiotic resistance. We propose a method to prioritize mutated genes responsible for antibiotic resistance, in which mutated genes that also show significant expression changes among their functionally coupled genes become more likely candidates. For network-based analyses, we developed a genome-scale co-functional network of K. pneumoniae genes, KlebNet (www.inetbio.org/klebnet). Using KlebNet, we could reconstruct functional modules for antibiotic-resistance, and virulence, and retrieved functional association between them. With complementation assays with top candidate genes, we could validate a gene for negative regulation of meropenem resistance and four genes for positive regulation of virulence in Galleria mellonella larvae. Therefore, our study demonstrated the feasibility of network-based identification of genes required for antimicrobial resistance and virulence of human pathogenic bacteria with genomic and transcriptomic profiles from antibiotic-resistant clinical isolates.
Project description:We developed a multi recombinase engineering rationale, that combines oligonucleotide recombineering with the selective capacity of antibiotic resistance via transient insertion of selector plasmids. We tested this method in Mycoplasma pneumoniae, a bacterium with a very inefficient native recombination machinery. A wide variety of targeted genome modifications were carried out. We did whole genome sequencing of some clones to confirm that the engineering method is not mutagenic and ensure that genome modifications only occurred at the intended loci. Specifically we sequenced clones carrying 1 kb deletion at 4 different chromosomal locations (i.e., M129-GP35-PtetCre Δ1kbmpn088::lox scar, M129-GP35-PtetCre Δ1kbmpn256::lox scar, M129-GP35-PtetCre Δ1kbmpn440::lox scar, M129-GP35-PtetCre Δ1kbmpn583::lox scar), a clone carrying a 30 kb deletion (M129-GP35-PtetCre Δ30kbNE region::pLoxPuro) and a clone carrying a 5.5 kb deletion that was complemented with the two essential genes found in this area (M129-GP35 Δ5.5kbmpn633-mpn638::mpn636-637lox scar)
