AUTHOR=Shi Qingmiao , Zhang Jun , Wang Jinghui , Du Lijuan , Shi Zhaoyang , Xu Min , Luo Yonggang 

TITLE=Homologous Escherichia coli Identified in Cerebrospinal Fluid and Bloodstream

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=11

YEAR=2021

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2021.674235

DOI=10.3389/fcimb.2021.674235

ISSN=2235-2988

ABSTRACT=<sec><title>Background</title><p><italic>Escherichia coli</italic> is an opportunistic bacterium that causes a wide range of diseases, such as bloodstream infection and central nervous system infection. The traditional culture-based method to detect <italic>E. coli</italic> usually takes more than 2 days. The object of this study is to explore the value of metagenomic next-generation sequencing (mNGS) in identifying <italic>E. coli</italic> from human cerebrospinal fluid. In addition, we investigated the infection source of <italic>E. coli</italic> through whole genome sequencing and phylogenetic analysis.</p></sec><sec><title>Methods</title><p>We combined a clinical example to analyze the function of mNGS in pathogen detection from cerebrospinal fluid. NextSeq 550Dx platform was applied for mNGS. Next, whole genome sequencing was performed to obtain the genomic characterization of <italic>E. coli</italic>. Furthermore, we screened 20 <italic>E. coli</italic> strains from the National Center for Biotechnology Information and conducted a phylogenetic analysis.</p></sec><sec><title>Results</title><p>A middle-aged patient who attended our hospital was diagnosed with craniopharyngioma and received surgery. The patient had recurrent fever and persistent lethargy after surgery. Cerebrospinal fluid culture firstly failed to grow the bacteria. Next the cerebrospinal fluid sample was detected by mNGS and the sequence readings of <italic>E. coli</italic> were identified. Later, <italic>E. coli</italic> was reported <italic>via</italic> the second cerebrospinal fluid culture, certifying the result of mNGS. Moreover, we also cultured carbapenem-resistant <italic>E. coli</italic> from the patient’s bloodstream. Through whole genome sequencing and phylogenetic analysis, we found that the <italic>E. coli</italic> isolated from cerebrospinal fluid and the bloodstream was 100% homologous, indicating the <italic>E. coli</italic> central nervous system infection was originated from the bloodstream.</p></sec><sec><title>Conclusion</title><p>Metagenomic next-generation sequencing is a valuable tool to identify the pathogens from cerebrospinal fluid, and seeking the infection source is of great significance in clinical diagnosis and treatment. Furthermore, carbapenem-resistant <italic>E. coli</italic> is a serious problem as the cause of bloodstream infection and central nervous system infection, and effective and adequate measures to prevent and control the present circumstance are urgent.</p></sec>