About: Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report

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About: Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report
Creator	Lu, Yihan Huang, Weifeng Li, Manshi Yang, Fuhuo
source	Medline; PMC
abstract	BACKGROUND: Urinary tract infection (UTI) caused by various pathogenic microorganisms is ubiquitous in the parts of the urinary system such as kidney, ureter, bladder, and urethra. Currently, clinical detection of UTI is mainly focused on urine culture; however, the diagnostic value of urine culture remains limited due to the time-consuming procedure and low detection rate, especially in patients who have used antibiotics. Generally, treatment for UTI relies on empirical medication rather than pathogen diagnosis, which leads to the inappropriate use of antimicrobial agents and a significant increase in resistant strains. Comparatively, metagenomic next-generation sequencing (mNGS) is capable of overcoming the disadvantages of clinical culture, and identifying pathogens for further treatment. CASE PRESENTATION: A 33-year-old male patient was admitted to hospital with a high fever and chills. None of his autoimmune disease or thyroid function related indicators were positive, and he had no risk of endocarditis. His white blood cell count, C-reactive protein, procalcitonin, interleukin 6, and neutrophil proportion were markedly elevated. He was initially diagnosed as having an infection of unknown etiology. Since empirical treatment of Sulperazon and Metronidazole did not relieve his symptoms, both the blood and urine specimens were examined using traditional culture, serological testing, and mNGS assay. Traditional culture and serological testing produced negative results, while the mNGS assay revealed the presence of a potential pathogen, Enterococcus faecalis, in the urine specimen, which was further confirmed by both Sanger sequencing and qPCR analysis. A CT scan of the patient’s whole abdomen showed stones in the right kidney. Once targeted antibiotic therapy was administered, the patient recovered quickly. CONCLUSIONS: Our case illustrated that mNGS, as a novel culture-independent approach, demonstrated the capability of rapid, sensitive, and accurate pathogen identification. Furthermore, this technology provides strong support for guiding clinicians to determine appropriate treatment.
has issue date	2020-07-02(xsd:dateTime)
bibo:doi	10.1186/s12879-020-05179-0
bibo:pmid	32615925
has license	cc-by
sha1sum (hex)	d12af0a7df23c606019102136d69a173889c4241
schema:url	https://doi.org/10.1186/s12879-020-05179-0
resource representing a document's title	Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report
has PubMed Central identifier	PMC7330266
has PubMed identifier	32615925
schema:publication	BMC Infect Dis
resource representing a document's body	covid:d12af0a7df23c606019102136d69a173889c4241#body_text
is schema:about of	named entity 'presence' named entity 'demonstrated' named entity 'infection' named entity 'etiology' named entity 'technology' named entity 'C-reactive protein' named entity 'initially' named entity 'detection' named entity 'kidney' named entity 'elevated' named entity 'urine culture' named entity 'resistant strains' named entity 'Urinary tract infection' named entity 'urine specimen' named entity 'antimicrobial agents' named entity 'antibiotic therapy' named entity 'interleukin 6' named entity 'pathogenic microorganisms' named entity 'metagenomic' named entity 'UTI' named entity 'thyroid function' named entity 'next-generation sequencing' named entity 'assay' named entity 'etiology' named entity 'Enterococcus faecalis' named entity 'urinary-tract infection' named entity 'primers' named entity 'E. faecalis' named entity 'polyomavirus' named entity 'infection' named entity 'ftp' named entity 'E. faecalis' named entity 'focal infection' named entity 'fungi' named entity 'bacteria' named entity 'viruses' named entity 'urine specimen' named entity 'bacteria' named entity 'specific antigens' named entity 'infection' named entity 'pathogen' named entity 'UTI' named entity 'pathogens' named entity 'WBC' named entity 'parathyroid hormone' named entity 'influenza A and B viruses' named entity 'inflammation' named entity 'human herpesvirus 6' named entity 'Linezolid' named entity 'follow-up' named entity 'Staphylococcus lugdunensis' named entity 'Laboratory testing' named entity 'pathogenic microorganisms' named entity 'antifungals' named entity 'Urinary tract infection' named entity 'KAPA' named entity 'bacteria' named entity 'hospital-acquired infections' named entity 'Parvimonas micra' named entity 'antibodies' named entity 'human genome' named entity 'antibiotic resistance' named entity 'NCBI' named entity 'high fever' named entity 'E. faecalis' named entity 'bacteria' named entity 'enterococci' named entity 'nucleic acid sequences' named entity 'infection' named entity 'clinical laboratories' named entity 'Liver' named entity 'UTI' named entity 'Escherichia coli' named entity 'Chlamydia pneumoniae' named entity 'microorganism' named entity 'viruses' named entity 'autoimmune diseases' named entity 'PCR'

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