Biology subjects

Hirabayashi, A.

Publications and source records attributed to Hirabayashi, A..

3 recordsLinked to original sources

bioRxiv2020

Plasmidome analysis of carbapenem-resistant Enterobacteriaceae isolated in Vietnam

Carbapenem-resistant Enterobacterales (CRE) represent a serious threat to public health due to the lack of treatment and high mortality. The rate of antimicrobial resistance of Enterobacterales isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene blaNDM, spread via plasmids among Enterobacterales in Vietnam. In this study, we characterized blaNDM-carrying plasmids in Enterobacterales isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Almost identical 73 kb IncFII(pSE11)::IncN hybrid plasmids carrying blaNDM-1 were found in a P. mirabilis isolate and an M. morganii isolate. A 112 kb IncFII(pRSB107)::IncN hybrid plasmid carrying blaNDM-1 in an E. coli isolate had partially identical sequences with a 39 kb IncR plasmid carrying blaNDM-1 and an 88 kb IncFII(pHN7A8)::IncN hybrid plasmid in a C. freundii isolate. 148-149 kb IncFIA(Hl1)::IncA/C2 plasmids and 75-76 kb IncFII(Yp) plasmids, both carrying blaNDM-1 were shared among three sequence type 11 (ST11) isolates and three ST395 isolates of K. pneumoniae, respectively. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to blaNDM-1. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.

microbiology↗

bioRxiv2020

Long-read shotgun metagenome sequencing using PromethION uncovers novel bacteriophages, their abundance, and interaction with host bacterial immunity in the oral microbiota

Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conducted a long-read metagenomic study of human saliva for the first time using PromethION that requires a smaller amount of DNA than PacBio. Our analyses, which integrated both PromethION and HiSeq data of >30 Gb per sample, revealed N50 ranging from 187-345 kb and thousands of contigs with >1 kb accounting for > 99% of all contigs on which 94-96% of HiSeq reads were mapped. We identified hundreds of viral contigs (95 phages and 333 prophages on an average per sample); 0-43.8% and 12.5-56.3% of the "most confident" phages and prophages, respectively, didnt cluster with those reported previously and were identified as novel. Our integrated analyses identified highly abundant oral phages/prophages, including a novel Streptococcus phage cluster and nine jumbo phages/prophages. Interestingly, 86% of the phage cluster and 67% of the jumbo phages/prophages contained remote homologs of antimicrobial resistance genes, suggesting their potential role as a source of recombination to generate new resistance genes. Pan-genome analysis of the phages/prophages revealed remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Functional annotation revealed that the highest fraction of the core genes was enriched in phage morphogenesis, followed by the fraction enriched in host cellular processes. Furthermore, our study suggested that oral phages present in human saliva are under selective pressure for escaping CRISPR immunity. ImportanceDespite the abundance and grave implications oral bacterial viruses in health and disease, little is known regarding the different groups of oral bacterial viruses, their relative abundances under various conditions, and their activities. We provided answers to these questions for the first time utilizing a recently developed sequencer that can capture and sequence long DNA fragments, including viruses, and requires only a small amount of DNA input, making it suitable for analyzing human oral samples. We identified hundreds of viral sequences, including "jumbo" viruses and a distinctive group of highly abundant oral viruses, which often contained parts of antimicrobial resistance genes; the entire repertoire of these viral genes showed remarkable diversity and supported a recently proposed hypothesis that phages modulate oral microbiota through multiple mechanisms. We also revealed genomic signs of coevolution of viruses and host bacteria that have been missed in large viromic studies in humans.

microbiology↗

bioRxiv2020

Comparison of de-duplication methods used by WHO Global Antimicrobial Resistance Surveillance System (GLASS) and Japan Nosocomial Infections Surveillance (JANIS) in the surveillance of antimicrobial resistance

A major issue in the surveillance of antimicrobial resistance (AMR) is "de-duplication" or removal of repeated isolates, for which there exist multiple methods. The World Health Organization (WHO) Global Antimicrobial Resistance Surveillance System (GLASS) requires de-duplication by selecting only the first isolate of a given bacterial species per patient per surveillance period per specimen type per age group, gender, and infection origin stratification. However, no study on the comparative application of this method has been reported. The objective of this study was to evaluate differences in data tabulation between the WHO GLASS and the Japan Nosocomial Infections Surveillance (JANIS) system, which counts both patients and isolates after removing repeated isolates of the same bacterial species per multiresistance phenotype isolated from a patient within 30 days, regardless of specimen type. All bacterial data, consisting of approximately 8 million samples from 1795 Japanese hospitals in 2017 were exported from the JANIS database, and were tabulated using either the de-duplication algorithm of GLASS, or JANIS. We compared the tabulated results of the total number of patients whose blood and urine cultures were taken and of the percentage of resistant isolates of Escherichia coli for each priority antibiotic. The number of patients per specimen type tabulated by the JANIS method was always smaller than that of GLASS. There was a small (< 3%) difference in the percentage of resistance of E. coli for any antibiotic between the two methods in both out- and inpatient settings and blood and urine isolates. The two tabulation methods did not show considerable differences in terms of the tabulated percentages of resistance for E. coli. We further discuss how the use of GLASS tabulations to create a public software and website that could help to facilitate the understanding of and treatment against AMR.

microbiology↗