Prediction of Antibiotic Susceptibility in E. coli Isolates Using Machine Learning.

Antimicrobial resistance (AMR) poses a significant global health threat, resulting in 4.96 million deaths in 2019, with projections reaching 10 million by 2050. This resistance, primarily due to the overuse of antibiotics, complicates the treatment of infections caused by various microorganisms, including the gram-negative bacterium Escherichia coli.

Solving genomic puzzles: computational methods for metagenomic binning.

Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels.

Discovery of thermophilic Bacillales using reduced-representation genotyping for identification.

Background: This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin.

Short-read fastA files dataset from complexity-reduced genotyping by sequencing data of bacterial isolates from a public hospital in Australia.

This data article contains short-read sequences (length 30-69 bp) obtained from complexity-reduced genotyping by sequencing (GBS) of 165 samples bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015. These samples represented 14 bacterial species. Data format is shown as filtered fastA files obtained from an Illumina HiSeq2500 sequencer.

Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping.

Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing.