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Diversity and antimicrobial resistance profiles of Mycobacterium avium complex clinical isolates in Thailand based on whole genome comparative analysis.
Sci Rep
January 2025
Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
The Mycobacterium avium complex (MAC) is a group of closely related nontuberculous mycobacteria that can cause various diseases in humans. In this study, genome sequencing, comprehensive genomic analysis, and antimicrobial susceptibility testing of 66 MAC clinical isolates from King Chulalongkorn Memorial Hospital, Bangkok, Thailand were carried out. Whole-genome average nucleotide identity (ANI) revealed the MAC species distribution, comprising 54 (81.
View Article and Find Full Text PDFFast exact gap-affine partial order alignment with POASTA.
Bioinformatics
January 2025
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States.
Motivation: Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial order alignment do not scale well to larger graphs and sequences. While heuristic approaches exist, they do not guarantee optimal alignment and sacrifice alignment accuracy.
View Article and Find Full Text PDFWhole genome sequencing analysis of enteropathogenic from human and companion animals in Korea.
J Vet Sci
December 2024
College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Korea.
Importance: This study is essential for comprehending the zoonotic transmission, antimicrobial resistance, and genetic diversity of enteropathogenic (EPEC).
Objective: To improve our understanding of EPEC, this study focused on analyzing and comparing the genomic characteristics of EPEC isolates from humans and companion animals in Korea.
Methods: The whole genome of 26 EPEC isolates from patients with diarrhea and 20 EPEC isolates from companion animals in Korea were sequenced using the Illumina HiSeq X (Illumina, USA) and Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) platforms.
Can a plant biologist fix a thermostat?
New Phytol
January 2025
Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037-100210, USA.
The shift to reductionist biology at the dawn of the genome era yielded a 'parts list' of plant genes and a nascent understanding of complex biological processes. Today, with the genomics era in full swing, advances in high-definition genomics enabled precise temporal and spatial analyses of biological systems down to the single-cell level. These insights, coupled with artificial intelligence-driven in silico design, are propelling the development of the first synthetic plants.
View Article and Find Full Text PDFFirst report on comprehensive genomic analysis of a multidrug-resistant Enterobacter asburiae isolated from diabetic foot infection from Bangladesh.
Sci Rep
January 2025
Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
Enterobacter asburiae (E. asburiae) is a gram-negative rod-shaped bacterium which has emerging significance as an opportunistic pathogen having high virulence pattern and drug resistant properties. In this study, we present the detailed analysis of the whole genome sequence of a multidrug-resistant (MDR) E.
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