基因组
生物
微生物群
全基因组测序
基因组
肠道微生物群
霰弹枪测序
肠道菌群
遗传学
计算生物学
免疫学
基因
作者
Christopher Gu,Layla A. Khatib,Ayannah S. Fitzgerald,Jevon Graham-Wooten,C.A.G. Ittner,Scott Sherrill-Mix,Yu‐Chung Chuang,Laurel Glaser,Nuala J. Meyer,Frederic D. Bushman,Ronald G. Collman
出处
期刊:PLOS ONE
[Public Library of Science]
日期:2023-10-10
卷期号:18 (10): e0289923-e0289923
标识
DOI:10.1371/journal.pone.0289923
摘要
Background The gut microbiome is believed to contribute to bloodstream infection (BSI) via translocation of dominant gut bacteria in vulnerable patient populations. However, conclusively linking gut and blood organisms requires stringent approaches to establish strain-level identity. Methods We enrolled a convenience cohort of critically ill patients and investigated 86 bloodstream infection episodes that occurred in 57 patients. Shotgun metagenomic sequencing was used to define constituents of their gut microbiomes, and whole genome sequencing and assembly was done on 23 unique bloodstream isolates that were available from 21 patients. Whole genome sequences were downloaded from public databases and used to establish sequence-identity distribution and define thresholds for unrelated genomes of BSI species. Gut microbiome reads were then aligned to whole genome sequences of the cognate bloodstream isolate and unrelated database isolates to assess identity. Results Gut microbiome constituents matching the bloodstream infection species were present in half of BSI episodes, and represented >30% relative abundance of gut sequences in 10% of episodes. Among the 23 unique bloodstream organisms that were available for whole genome sequencing, 14 were present in gut at the species level. Sequence alignment applying defined thresholds for identity revealed that 6 met criteria for identical strains in blood and gut, but 8 did not. Sequence identity between BSI isolates and gut microbiome reads was more likely when the species was present at higher relative abundance in gut. Conclusion In assessing potential gut source for BSI, stringent sequence-based approaches are essential to determine if organisms responsible for BSI are identical to those in gut: of 14 evaluable patients in which the same species was present in both sites, they were identical in 6/14, but were non-identical in 8/14 and thus inconsistent with gut source. This report demonstrates application of sequencing as a key tool to investigate infection tracking within patients.
科研通智能强力驱动
Strongly Powered by AbleSci AI