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Hirai, I.

Publications and source records attributed to Hirai, I..

2 recordsLinked to original sources
bioRxiv2024

A rapid method to determine the genetic lineage of Escherichia coli using open reading frame composition in the shallow sequencing

Determining the genetic background of bacterial isolates and evaluating the genetic relatedness among these isolates in a short time period are important to identify the spreading route(s) in cases of healthcare-associated infections and outbreaks caused by antimicrobial-resistant bacteria. Previously, we proposed a shallow sequencing (Shall-seq) procedure to determine the genetic backgrounds of clinical isolates using the minimum amount of sequence data. However, it took a longer time, such as longer than 10 h, to determine the genetic background of one clinical isolate. In this study, we developed a search procedure using open reading frame (ORF) composition to select the reference genome sequence with the highest matching ratio (>90%), the indicator genome sequence (IGS), for the examined bacterial isolate. Consequently, IGSs were selected for 28 (96.6%) of the examined 29 isolates and selection was performed within 30 min for each bacterial isolate. More importantly, the comparison of IGSs indicated that the IGSs, determined by ORF composition, of the examined bacterial isolates were closely related to the genome sequences determined using the Shall-seq procedure. Taken together, these results suggest that our newly developed search procedure can quickly determine the genetic background of bacterial isolates.

microbiology↗
bioRxiv2024

Shallow sequencing (Shall-seq) procedure: A method for determining the genetic lineages and detecting antimicrobial resistance genes of antimicrobial-resistant bacteria using minimum Nanopore sequencing data

Antimicrobial-resistant bacteria could cause nosocomial infections and outbreaks in healthcare facilities. Phylogenetic analyses based on whole-genome sequencing (WGS) could become the gold-standard method for understanding the route of antimicrobial-resistant bacterial spreading. However, generally, the WGS needs to analyze much amount of data. Therefore, sufficient resources such as budget and data analysis system are needed and it is a burden for introduction of the WGS in the routine clinical examination of pathogenic bacterial isolates. In this study, we used Escherichia coli as a model and evaluated whether determination of the genetic background and detection of antimicrobial-resistance genes of 29 E. coli clinical isolates were achieved by searching databases using sequence reads output by the Nanopore sequencer as the search keys. Consequently, only 66.2 MB data was sufficient to search for a genome sequence with [≥]90% range of coverage rate. Importantly, AMR genes and plasmid replicon types were also detected with minimum data, and the detected AMR genes and phenotypes of the E. coli isolates did not present any discrepancy. Taken together, this shallow sequencing (Shall-seq) procedure consists of "shallow of coverage" sequencing using the Nanopore sequencer and data search using minimum data could be used to analyze bacterial isolates cost-effectively.

microbiology↗