Abstract
BackgroundEscherichia coli 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 E. coli usually takes more than 2 days. The object of this study is to explore the value of metagenomic next-generation sequencing (mNGS) in identifying E. coli from human cerebrospinal fluid. In addition, we investigated the infection source of E. coli through whole genome sequencing and phylogenetic analysis.MethodsWe 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 E. coli. Furthermore, we screened 20 E. coli strains from the National Center for Biotechnology Information and conducted a phylogenetic analysis.ResultsA 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 E. coli were identified. Later, E. coli was reported via the second cerebrospinal fluid culture, certifying the result of mNGS. Moreover, we also cultured carbapenem-resistant E. coli from the patient’s bloodstream. Through whole genome sequencing and phylogenetic analysis, we found that the E. coli isolated from cerebrospinal fluid and the bloodstream was 100% homologous, indicating the E. coli central nervous system infection was originated from the bloodstream.ConclusionMetagenomic 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 E. coli 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.
Highlights
Escherichia coli is a common gram-negative bacterium that can be a harmless inhabitant of the gastrointestinal tract in humans (Croxen et al, 2013)
It’s found that the patient—as in our study—with cerebrospinal fluid (CSF) WBC >300×106/L, CSF protein > 500 mg/L, or glucose ratio ≤ 0.3 had a notably higher metagenomic next-generation sequencing (mNGS) detection rate (Miao et al, 2018). Another retrospective observational study focused on CSF samples from 99 pediatric bacterial meningitis patients found that mNGS appeared with higher sensitivity (68.7%) than culture (55.6%), and the top four detected pathogens were Streptococcus pneumoniae, Streptococcus Agalactiae, Staphylococcus aureus, and Escherichia coli (Guo et al, 2019)
Our study demonstrated the usefulness of mNGS in improved identification of neurosurgical postoperative central nervous system (CNS) infection
Summary
Escherichia coli is a common gram-negative bacterium that can be a harmless inhabitant of the gastrointestinal tract in humans (Croxen et al, 2013). These symbiotic E. coli strains seldom contribute to illness. Craniopharyngioma is a rare benign epithelial tumor of the CNS derived from residual cells of Rathke’s pouch, which includes two different histopathological type, adamantinomatous and papillary craniopharyngioma (Müller, 2014). It constitutes about 2–5% of primary intracranial tumors with an overall morbidity of 0.5–2 cases per million (Erfurth et al, 2013). We investigated the infection source of E. coli through whole genome sequencing and phylogenetic analysis
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