ABSTRACT
OBJECTIVES: Confirming the diagnosis in viral central nervous system (CNS) infections can be difficult with the currently available diagnostic tools. Virus discovery cDNA-amplified fragment length polymorphism next-generation sequencing (VIDISCA-NGS) is a promising viral metagenomic technique that enables the detection of all viruses in a single assay. We performed a retrospective study on the diagnostic accuracy of VIDISCA-NGS in cerebrospinal fluid (CSF) of individuals with suspected CNS infections. METHODS: Consecutive adult patients presenting to the Emergency Department or inpatients, who underwent a lumbar puncture for the suspicion of a CNS infection, were included if they were diagnosed with a viral CNS infection, or if a viral CNS infection was initially suspected but eventually a different diagnosis was made. A quantitative PCR panel of the most common causative viruses was performed on CSF of these patients as reference standard and compared with the results of VIDISCA-NGS, the index test. RESULTS: We included 38 individuals with viral CNS infections and 35 presenting with suspected CNS infection for whom an alternative aetiology was finally established. Overall sensitivity and specificity were 52% (95% CI 31%-73%) and 100% (95% CI 91%-100%), respectively. One enterovirus, detected by VIDISCA-NGS, was only identified by quantitative PCR upon retesting. Additional viruses identified by VIDISCA-NGS consisted of GB virus C, human papillomavirus, human mastadenovirus C, Merkel cell polyoma virus and anelloviruses. CONCLUSION: In patients for whom routine diagnostics do not yield a causative pathogen, VIDISCA-NGS can be of additional value as it can detect a broader range of viruses, but it does not perform well enough to replace quantitativePCR.
Subject(s)
Amplified Fragment Length Polymorphism Analysis/methods , Central Nervous System Infections/diagnosis , Central Nervous System Infections/virology , High-Throughput Nucleotide Sequencing/methods , Virus Diseases/diagnosis , Viruses/isolation & purification , Adult , Aged , DNA, Viral/analysis , Female , Humans , Male , Middle Aged , Retrospective Studies , Sensitivity and Specificity , Virus Diseases/cerebrospinal fluidABSTRACT
A survey for the presence of Listeria spp., Yersinia enterocolitica and motile aeromonads in 203 samples of ready-to-eat fleshfoods purchased from retail outlets was conducted. Overall, 39.4%, 3.4% and 23.2% of samples were positive for the presence of Listeria spp., Y. enterocolitica and motile aeromonads respectively. Two factors have been identified as contributing to contamination of fleshfoods by these cold-tolerant bacteria. These are (i) the method of sale; delicatessen-bought foods were notably more contaminated than similar products bought pre-packaged, and (ii) the method of preservation. For motile aeromonads fermented foods were the least contaminated, whereas smoked and cooked products had similar incidence rates. For L. monocytogenes, significantly more (41.9%) smoked products were contaminated than fleshfoods preserved by other methods. For Y. enterocolitica, only cooked products were contaminated. In the case of cooked fleshfoods it must be assumed that most contamination occurs post-cooking and that contamination rates are increased by poor food handling procedures. Of the three possible pairwise combinations of these organisms, the coincidence of Y. enterocolitica and motile aeromonads was the only one that differed significantly from a random distribution (P less than 0.001), indicating that fleshfoods contaminated with Y. enterocolitica are probably also contaminated by motile aeromonads.
