Oral flora meningoencephalitis diagnosis by next-generation DNA sequencing

Abstract

Introduction. Standard culture methods may fail to detect the causative agents of bacterial infection for various reasons including specimen collection after antibiotic administration, or when standard techniques or environmental conditions are not appropriate for growth of the microorganisms. Conventional 16S rRNA gene sequencing is sometimes a useful alternative technique for identification of bacteria, but is confounded by polymicrobial infection. We present a case of a patient who developed a serious neurological infection for which causative oral flora organisms were observed by microscopy, failed to culture but were identified by next-generation DNA sequencing. Case presentation. A male in his forties developed sinus pain and congestion, followed by facial and eye pain, and several weeks later acute-onset confusion and neck stiffness. Cerebrospinal fluid examination revealed pleocytosis and several bacterial morphologies, which were subsequently identified by next-generation sequencing as oral flora constituents Porphyromonas endodontalis , Fusobacterium nucleatum , Streptococcus constellatus , Prevotella species and Parvimonas micra . Conclusion. Oral flora can cause meningoencephalitis and brain abscess formation if translocation occurs by injury or surgical procedures. Next-generation sequencing is often not available at healthcare facilities, or when available may not have been validated for a wide spectrum of specimen sources, but is available at reference laboratories and should be considered when routine methods fail to provide a diagnosis for serious infections.

The First Infant Anaerobic Meningitis Infected by Prevotella bivia: A Case Report and Literature Review

“… Recovery 2009 F/11 Senthilkumar Sankararaman et al 13 Prevotella spp. Peritonsillar pus culture Vancomycin, ceftriaxone, and metronidazole 6 weeks Brain abscess Recovery 2012 F/9 Xiaoqiang Li et al 14 Porphyromonas gingivalis, P. enoeca and Actinomyces israelii mNGS of cerebrospinal fluid Ceftriaxone, vancomycin, and metronidazole 1 month Brain swelling and the skull base was eroded Recovery 2020 F/16 Vyshak Chandra et al 15 Streptococcus constellatus, Fusobacterium species P. dentalis , and Parvimonas micra Culture of the tumor Vancomycin, ceftriaxone, and metronidazole 6 weeks Right hemiparesis and meningioma Recovery 2020 M/70 Wei-Wei Zhang et al 16 P. oris mNGS of cerebrospinal fluid Metronidazole and meropenem Metronidazole and meropenem 2 weeks, meropenem 2 weeks Meningitis and spinal canal infection Recovery 2023 M/9 Eric Heintz et al 17 Porphyromonas endodontalis, F.nucleatum, S.constellatus, Prevotella spp.and Parvimonas micra mNGS of cerebrospinal fluid Cefepime and metronidazole, ceftriaxone and metronidazole Cefepime and metronidazole 3weeks, ceftriaxone and metronidazole 3 weeks Hydrocephalus. Recovery 2023 M/40 <...…”

Improving the Diagnosis of Bacterial Infections: Evaluation of 16S rRNA Nanopore Metagenomics in Culture-Negative Samples

“…Addressing the widely discussed issue of background noise (Street et al, 2017 ; Sanderson et al, 2018 ; Charalampous et al, 2019 ; Yang et al, 2019 ; Chan et al, 2020 ), we found herein that setting a cut-off of 1% classified reads improved the accuracy of results, in line with many published studies (Sanderson et al, 2018 ; Charalampous et al, 2019 ; Yang et al, 2019 ; Chan et al, 2020 ). Nonetheless, using this cut-off in sample 31, collected from pleuropneumonia, led to categorising some bacteria as background noise while these are well-known oral flora bacteria (Nakazawa et al, 2002 ; Heintz et al, 2019 ). Conversely, the analysis of sample 22 (aortic valve in a context of infective endocarditis) concluded with the notable presence of six bacteria including environmental and oral flora bacteria, questioning their relevance as etiological agents.…”

Bacterial Profiles of Brain in Downer Cattle with Unknown Etiology

“…Especially, movement disorder through complication of encephalitis was detected to mice which inject with Rhodococcus genus [ 43 ]. Carnobacterium , Helcococcus , and Parvimonas genus were detected as pathogenic bacteria for neurological disorder such as encephalitis, valvular endocarditis, and meningoencephalitis by isolation and NGS technique method to fish, bovine, and human [ 44 , 45 , 46 , 47 , 48 , 49 ]. According to these previous studies, it could be suggested that Carnobacterium and Parvimonas genera may cause these diseases through an invasion by way of the nasal cavity and oral flora, respectively, which move to the brain tissue.…”