Metagenomic next generation sequencing of bronchoalveolar lavage fluids for the identification of pathogens in patients with pulmonary infection: A retrospective study.

Due to the limitations of traditional laboratory methods (TMs), identification of causative pathogens of numerous pulmonary infections (PIs) remains difficult. This study evaluated the value of metagenomic next generation sequencing (mNGS) in the identification of various respiratory pathogens. A total of 207 patients with TMs and mNGS data were collected for this retrospective study. TMs included sputum culture, blood, and bronchoalveolar lavage fluid (BALF) analysis, or polymerase chain reaction analysis of throat swabs. Otherwise, BALF was collected and analyzed using mNGS. For bacterial pathogens, sensitivities of mNGS as compared to TMs were 76.74 % and 58.14 % (P=0.012). For fungal pathogens, the detection rate of mNGS sensitivity was higher as compared to that of TMs (93.68 % vs 22.11 %; P<0.001). The positive predictive value and negative predictive value were also greater for mNGS. Use of mNGS for BALF analysis offers good specificity and thus facilitates to the clinical diagnosis of PIs.

RNA-Seq-based transcriptomic profiling of primary interstitial cells of Cajal in response to bovine viral diarrhea virus infection.

Infections with bovine viral diarrhea virus (BVDV) contribute significantly to health-related economic losses in the beef and dairy industries and are widespread throughout the world. Severe acute BVDV infection is characterized by a gastrointestinal (GI) inflammatory response. The mechanism of inflammatory lesions caused by BVDV remains unknown. The interstitial cells of Cajal (ICC) network plays a pivotal role as a pacemaker in the generation of electrical slow waves for GI motility, and it is crucial for the reception of regulatory inputs from the enteric nervous system. The present study investigated whether ICC were a good model for studying GI inflammatory lesions caused by BVDV infection. Primary ICC were isolated from the duodenum of Merino sheep. The presence of BVDV was detected in ICC grown for five passages after BVDV infection, indicating that BVDV successfully replicated in ICC. After infection with BVDV strain TC, the cell proliferation proceeded slowly or declined. Morphological changes, including swelling, dissolution, and formation of vacuoles in the ICC were observed, indicating quantitative, morphological and functional changes in the cells. RNA sequencing (RNA-Seq) was performed to investigate differentially expressed genes (DEGs) in BVDV-infected ICC and explore the molecular mechanism of underlying quantitative, morphological and functional changes of ICC. Eight hundred six genes were differentially expressed after BVDV infection, of which 538 genes were upregulated and 268 genes were downregulated. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the 806 DEGs were significantly enriched in 27 pathways, including cytokine-cytokine receptor interaction, interleukin (IL)-17 signaling and mitogen-activated protein kinase (MAPK) signaling pathways. The DEGs and raw files of high-throughput sequencing of this study were submitted to the NCBI Gene Expression Omnibus (GEO) database (accession number GSE122344). Finally, 21 DEGs were randomly selected, and the relative repression levels of these genes were tested using the quantitative real-time PCR (qRT-PCR) to validate the RNA-Seq results. The results showed that the related expression levels of 21 DEGs were similar to RNA-Seq. This study is the first to establish a new infection model for investigating GI inflammatory lesions induced by BVDV infection. RNA-Seq-based transcriptomic profiling can provide a basis for study on BVDV-associated inflammatory lesions.

Bta-miR-2411 attenuates bovine viral diarrhea virus replication via directly suppressing Pelota protein in Madin-Darby bovine kidney cells.

MicroRNAs (miRNAs) are endogenous ∼22 nt noncoding RNAs that control the translation initiation and stability of target genes in a sequence-specific manner and, thus, play important regulatory roles in animals and plants. Homologs of Dom34, called Pelota or PELO, are broadly conserved in eukaryotes and archaea. Biochemical and genetic studies indicate that eukaryotic Dom34/Pelota plays an important role in cell division, differentiation of germline stem cells, and stem cell self-renewal by controlling the expression of specific genes at the translational level. Additionally, it is reported that Pelota is specifically required for high efficiency synthesis of proteins in numerous viruses. In earlier studies, we found the Bos taurus bta-miR-2411 (shortly miR-2411 herein) was significantly upregulated by more than 2.1 times in bovine viral diarrhea virus (BVDV) strain NADL-infected Madin-Darby bovine kidney (MDBK) cells after 8 h post-infection (pi) compared to normal MDBK cells without BVDV infection. Moreover, miR-2411 overexpression significantly reduced the BVDV E1 mRNA level and viral titer. Nevertheless, the mechanisms of miR-2411 attenuating on viral replication remain unclear. Here, we report that miR-2411 as a novel microRNA regulates BVDV NADL replication via directly targeting the Pelota gene in MDBK cells. We investigated whether the potential target sequences of miR-2411, located in the Pelota 3'UTR, and miR-2411 agomir transfection attenuated Pelota mRNA and protein levels. Indeed, upon miR-2411 overexpression, BVDV NADL replication was prevented. Importantly, BVDV NADL replication levels were reversed to normal levels as a result of the Pelota rescuing experiment even though miR-2411 was existent. Overall, we profiled the unique role of miR-2411 in regulating BVDV NADL replication and provided a novel strategy for generalized inhibition of viral infection.