Direct diagnosis of Pasteurella multocida meningitis using next-generation sequencing

Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art

“…Two studies used the PACEseq mNGS test (Hugobiotech, Beijing, China) ( Mao et al, 2021 ; Zeng et al, 2021 ), two studies used VIDISCA and Ion Torrent end-repair library ( Edridge et al, 2019 ; Gao et al, 2021 ), and one study each used the NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs, Ipswich, MA, United States) ( Carbo et al, 2020 ; Leon et al, 2020 ), the KAPA Hyper Prep Kit (Kapa Biosystem, Potters Bar, United Kingdom) ( Yin et al, 2021 ), the NuGEN Ovation Ultralow Library System V2 kit (NuGEN Technologies, United States) ( Guan et al, 2015 ) the Trio RNA-Seq kit (NuGEN Technologies) ( Li et al, 2021 ), and the Roche 454 GS FLX single-end library (Roche Diagnostics, Branford, CT, United States) ( Joanna María et al, 2016 ). In three studies, the mNGS library was constructed following the single-end Oxford Nanopore library preparation protocol ( Morsli et al, 2021a , b , 2022 ). Finally, the library preparation protocol and kits were not reported in 14 studies ( Table 1 and Figure 3 ).…”

“…BGISEQ platforms were used in 12/51 (24%) of studies ( Table 1 ), including BGISEQ-50, 100, and 500 platforms, while three studies used the Roche 454 GS FLX Titanium system platform, Ion PGM System platforms and Ion Torrent Proton Sequencer (Life Technologies, United States), respectively ( Joanna María et al, 2016 ; Edridge et al, 2019 ; Gao et al, 2021 ). Real-time sequencing with the Oxford Nanopore MinION sequencer was used in three studies ( Morsli et al, 2021a , b , 2022 ) and no information about the sequencer was reported in five studies ( Table 1 ). The use of Nanopore technologies, i.e., single-long-read sequencing platforms combined with direct read blasting against the NCBI GenBank database using EPI2ME online software 1 or against an internal database using in-house pipelines, allowed for pathogen identification within the first minutes of sequencing ( Morsli et al, 2021a ).…”

“…The use of Nanopore technologies, i.e., single-long-read sequencing platforms combined with direct read blasting against the NCBI GenBank database using EPI2ME online software 1 or against an internal database using in-house pipelines, allowed for pathogen identification within the first minutes of sequencing ( Morsli et al, 2021a ). Furthermore, all additional pieces of information such as bacteria profiling and genotyping, was obtained in less than 6 h ( Morsli et al, 2021a , b , 2022 ).…”

“…Virus genotyping based on hit-blast identified strains could be confirmed by phylogenetic analysis based on sequence similarity level, while bacteria genotyping could be predicted online by Multi-Locus Sequence Typing online platform ( Figure 3 ). Also, the in silico antibiotic resistance pattern could be predicted by aligning bacterial genome sequences against online databases of antibiotic-resistance encoding genes ( Table 1 ; Guan et al, 2015 ; Miller et al, 2019 ; Carbo et al, 2020 ; Manso et al, 2020 ; Morsli et al, 2021a , c ; Piantadosi et al, 2021 ), mostly represented by ResFinder on the Centre for Genomic Epidemiology server ( Bortolaia et al, 2020 ; Morsli et al, 2021a , b , 2022 ).…”

“…Of the 217 CSF samples in which mNGS investigation yielded results discordant with the routine method, mNGS conclusively found a pathogen in 38/103 CSF samples in which routine investigations found no pathogen, as reported in 25/51 studies: mNGS over-detected RNA viruses, including Human rhinovirus and Human coronavirus ( Li et al, 2021 ), Coxsackievirus 9 and Mumps virus ( Kawada et al, 2016 ), Saint-Louis Encephalitis virus ( Chiu et al, 2017 ), Powassan Virus ( Piantadosi et al, 2018 ), Toscana virus ( Tschumi et al, 2019 ), Jamestown Canyon virus ( Solomon et al, 2021 ), Enterovirus A71 ( Leon et al, 2020 ), and Hepatitis E virus ( Carbo et al, 2020 ), while only HSV-1, HHV-6, and EBV were identified as DNA viruses ( Zhang Y. et al, 2019 ; Carbo et al, 2020 ). Bacterial pathogens documented in 11% of these cases included Listeria monocytogenes in four cases ( Yao et al, 2016 ; Lan et al, 2020 ), Ureaplasma parvum in three cases ( Wang et al, 2020 ; Xing X.-W. et al, 2021 ; Zhan et al, 2021 ) and one case each was detected of Klebsiella pneumoniae ( Zeng et al, 2021 ), Pasteurella multocida ( Morsli et al, 2022 ), Enterococcus faecalis ( Zhang et al, 2021a ), Nocardia farcinica ( Zhang et al, 2021b ), Streptococcus suis ( Zhang et al, 2020 ), and Psychrobacter sp. ( Joanna María et al, 2016 ).…”