Deciphering the removal of antibiotics and the antibiotic resistome from typical hospital wastewater treatment systems

Hospital wastewater treatment systems (HWTSs) are a significant source and reservoir of antibiotic resistance genes (ARGs) and a crucial hub for transmitting ARGs from clinical to natural environments. However, there is a lack of research on the antibiotic resistome of clinical wastewater in HWTSs. In this study, we used metagenomics to analyze the prevalence and abundance of ARGs in five typical HWTSs. A total of 17 antibiotics from six categories were detected in the five HWTSs; β-lactam antibiotics were found at the highest concentrations, with up to 4074.08 ng·L-1. We further found a total of 21 ARG types and 1106 subtypes of ARGs with the highest percentage of multi-drug resistance genes (evgS, msbA, arlS, and baeS). The most abundant last-resort ARGs were mcr, which were detected in 100 % of the samples. HWTSs effluent is a major pathway for the transmission of last-resort ARGs into urban wastewater networks. The removal of antibiotics, antibiotic-resistant bacteria, and ARGs from HWTSs was mainly achieved by tertiary treatment, i.e., chlorine disinfection, but antibiotics and ARGs were still present in the HWTSs effluent or even increased after treatment. Moreover, antibiotics and heavy metals (especially mercury) in hospital effluents can exert selective pressure for antibiotic resistance, even at low concentrations. Qualitative analyses based on metagenome-assembled genome analysis revealed that the putative hosts of the identified ARGs are widely distributed among Pseudomonas, Acidovorax, Flavobacterium, Polaromonas, and Arcobacter. Moreover, we further assessed the clinical availability of ARGs and found that multidrug ARGs had the highest clinical relevance values. This study provides new impulses for monitoring and removing antibiotics and ARGs in the hospital sewage treatment process.

Effect of biochar on the SPNA system at ambient temperatures

Biochar has been extensively studied in wastewater treatment systems. However, the role of biochar in the single-stage partial nitritation anammox (SPNA) system remains not fully understood. This study explored the impact of biochar on the SPNA at ambient temperatures (20 °C and 15 °C). The nitrogen removal rate of the system raised from 0.43 to 0.50 g N/(L·d) as the biochar addition was raised from 2 to 4 g/L. Metagenomic analysis revealed that gene abundances of amino sugar metabolism and nucleotide sugar metabolism, amino acid metabolism, and quorum sensing were decreased after the addition of biochar. However, the gene abundance of enzymes synthesizing NADH and trehalose increased, indicating that biochar could stimulate electron transfer reactions in microbial metabolism and assist microorganisms in maintaining a steady state at lower temperatures. The findings of this study provide valuable insights into the mechanism behind the improved nitrogen removal facilitated by biochar in the single-stage partial nitritation anammox system.

Performances of antibiotic resistance genes profile upon the action of biochar-activated peroxydisulfate in composting

In this study, the amendment of biochar-activated peroxydisulfate during composting to remove antibiotic resistance genes (ARGs) by direct (microbial community succession) and indirect methods (physicochemical factors) was analyzed. When implementing indirect methods, the synergistic effect of peroxydisulfate with biochar optimized the physicochemical habitat of compost, maintaining its moisture within a range of 62.95%-65.71%, and a pH of 6.87-7.73, and causing the compost to mature 18 days earlier than the control groups. The direct methods caused the optimized physicochemical habitat to adjust the microbial communities and reduce the abundance of most of the ARG host bacteria (Thermopolyspora, Thermobifida, and Saccharomonospora), thus inhibiting this substance's amplification. Heatmap analysis confirmed the necessary connection between physicochemical factors, microbial communities, and ARGs. Moreover, a mantel test confirmed the direct significant effect of the microbial communities on ARGs and the indirect significant effect of physicochemical factors on ARGs. The results showed that the abundance of more ARGs was down-regulated at the end of composting and regulated by biochar-activated peroxydisulfate, especially for the abundance of AbaF, tet(44), golS, and mryA, which was significantly decreased by 0.87-1.07 fold. These results provide new insights into the removal of ARGs during composting.

Nitrogen contribution and microbial community of size-fractionated anammox sludge in continuous stirred-tank reactors

In this study, the microbial diversity of size-fractionated anammox sludge in a well-mixed system and their contribution to nitrogen transformation were investigated. Results showed that small granules (0.2-1.0 mm) contributed to the major part of the nitrogen removal rate (56 %) due to its largest mixed liquor volatile suspended solids (1240 ± 80 mg·L^-1). However, large granules (>1.0 mm) possessed the highest relative abundances of Ca. Kuenenia stuttgartiensis and specific anammox activity, representing 49.34 % and 24.45 ± 0.01 mg-N·g^-1-mixed liquor volatile suspended solids·h^-1, respectively. The microbial diversity decreased as the increase of granular size, resulting in microbial community shifting to a simpler model. Metagenomic analysis showed that fine sludge might be the potential major for NO/N₂O production in the mature well-mixed system under inorganic conditions. This study provides guidance for the evaluation of nitrogen contribution by anammox size-fractionated sludge and the inhibition of the potential NO/N₂O emission in anammox processes.

Synergistic effect of bioanode and biocathode on nitrobenzene removal: Microbial community structure and functions

This study aimed to reveal the synergistic effect of bioanode and biocathode on nitrobenzene (NB) removal with different microbial community structures and functions. Single-chamber bioelectrochemical reactors were constructed and operated with different initial concentrations of NB and glucose as the substrate. With the synergistic effect of biocathode and bioanode, NB was completely removed within 8 h at a kinetic rate constant of 0.8256 h^-1, and high conversion rate from NB to AN (92%) was achieved within 18 h. The kinetic rate constant of NB removal was linearly correlated with the maximum current density and total coulombs (R² > 0.95). Increase of glucose and NB concentrations had significantly positive and negative effects, respectively, on the NB removal kinetics (R² > 0.97 and R² > 0.93, respectively). Geobacter sp. and Enterococcus sp. dominated in the bioanode and biocathode, respectively. The presence of Klebsiella pneumoniae in the bioanode was beneficial for Geobacter species to produce electricity and to alleviate the NB inhibition. As one of the dominant species at the biocathode, Methanobacterium formicicum has the ability of nitroaromatics degradation according to KEGG analysis, which played a crucial role for NB reduction. Fermentative bacteria converted glucose into volatile fatty acids or H₂, to provide energy sources to other species (e.g., Geobacter sulfurreducens and Methanobacterium formicicum). The information from this study is useful to optimize the bioelectrocatalytic system for nitroaromatic compound removal.

Identification and profiling of microbial community from industrial sludge

The purpose of this study is to identify microbial communities in pulp and paper industry sludge and their metagenomic profiling on the basis of; phylum, class, order, family, genus and species level. Results revealed that the dominant phyla in 16S rRNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. Metagenomics is a molecular biology-based technology that uses bioinformatics to evaluate huge gene sequences extracted from environmental samples to assess the composition and function of microbiota. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their diversity (%) in highly contaminated sludge to perform in situ bioremediation.

Immobilization of metribuzin-degrading bacteria on biochar: Enhanced soil remediation and bacterial community restoration

Metribuzin (MB), a triazinone herbicide is extensively sprayed for weed control in agriculture, has been reported to contaminate soil, groundwater, and surface waters. In soil, MB residues can negatively affect not only the germination of subsequent crops but also disturb soil bacterial community. The present study describes the use of biochar as a carrier material to immobilize MB-degrading bacterial consortium, for remediation of MB-contaminated soil and restoration of soil bacterial community in soil microcosms. The bacterial consortium (MB3R) comprised four bacterial strains, i.e., Rhodococcus rhodochrous AQ1, Bacillus tequilensis AQ2, Bacillus aryabhattai AQ3, and Bacillus safensis AQ4. Significantly higher MB remediation was observed in soil augmented with bacterial consortium immobilized on biochar compared to the soil augmented with un-immobilized bacterial consortium. Immobilization of MB3R on biochar resulted in higher MB degradation rate (0.017 Kd^-1) and reduced half-life (40 days) compared to 0.010 Kd^-1 degradation rate and 68 day half-life in treatments where un-immobilized bacterial consortium was employed. It is worth mentioning that the MB degradation products metribuzin-desamino (DA), metribuzin-diketo (DK), and metribuzin desamino-diketo (DADK) were detected in the treatments where MB3R was inoculated either alone or in combination with biochar. MB contamination significantly altered the composition of soil bacteria. However, soil bacterial community was conserved in response to augmentation with MB3R immobilized on biochar. Immobilization of the bacterial consortium MB3R on biochar can potentially be exploited for remediation of MB-contaminated soil and protecting its microbiota.

Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system

Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.

The influences of illite/smectite clay on lignocellulose decomposition and maturation process revealed by metagenomics analysis during cattle manure composting

The purpose of this study was to analyze the effects of illite/smectite clay (I/S) on lignocellulosic degradation and humification process via metagenomics analysis during cattle manure composting. The test group (TG) with 10% I/S and the reference group (RG) were established. The results indicated that the addition of I/S made the degradation rate of cellulose, hemicellulose and lignin in TG (1.56%, 29.01%, 19.95%) was higher than that in RG (1.16%, 17.24%, 13.14%). Compared with RG, the abundance values of AA2, AA10, GH1 and GH10 in TG increased by 15.18%, 29.28%, 31.08%, 21.65%, respectively. Meanwhile, humic substance (HS) content was increased by 3.49% and 7.16% during RG and TG composting. Furthermore, the microbial community in TG changed, in which the relative abundance of Actinobacteria increased and Proteobacteria decreased. Redundancy analysis (RDA) showed that the temperature was positively correlated with the abundance of AA2, AA10, GH1 and GH10, whereas the organic matter content was negatively correlated. Overall, adding I/S to the composting could stimulate microbial activity, promote the degradation of lignocellulose and humification process.

Cyclocarya paliurus polysaccharides alleviate type 2 diabetic symptoms by modulating gut microbiota and short-chain fatty acids

BACKGROUND

Cyclocarya paliurus polysaccharide (CCPP), a primary active component in the leaves of Cyclocarya paliurus (Batal.) Iljinsk (C. paliurus), has the ability to treat type 2 diabetes mellitus (T2DM), but cannot be digested by our digestive system. Therefore, mechanisms of regulating the gut microbiota and intestinal metabolites might exist.

PURPOSE

To reveal the potential mechanism of CCPP treatment, this study aimed to investigate the alterations of the gut microbiota and intestinal metabolites especially short chain fatty acids (SCFAs) in type 2 diabetic rats.

STUDY DESIGN AND METHODS

Type 2 diabetic rat models were developed, and the therapeutic effects of CCPP were evaluated. Metagenomics analysis was utilized to analyze the alterations to the gut microbiota, and UHPLC-QTOF/MS-based untargeted metabolomics analysis of colon contents was used to identify the differential intestinal metabolites. GC/MS was used to measure the SCFAs in rat's colon contents and human fecal inoculums. Furthermore, the expression of SCFA receptors including GPR41, GPR43 and GPR109a was verified by qRT-PCR and the concentration of glucagon-like peptide-1(GLP-1) and peptide tyrosinetyrosine (PYY) was measured by Elisa.

RESULTS

Inhibition of the blood glucose levels and improvements in glucose tolerance and serum lipid parameters were observed after CCPP treatment. Eleven SCFA-producing species including Ruminococcus_bromii, Anaerotruncus_colihominis, Clostridium_methylpentosum, Roseburia_intestinalis, Roseburia_hominis, Clostridium_asparagiforme, Pseudoflavonifractor_capillosus, Intestinimonas_butyriciproducens, Intestinimonas_sp._GD2, Oscillibacter_valericigenes and Oscillibacter_ruminantium were clearly increased in the CCPP group. Furthermore, our study indicated that CCPP increases the production of SCFAs both in vivo and in vitro, and the gut microbiota are the key factor of this process. The SCFA receptors including GPR41, GPR43 and GPR109a, were significantly stimulated in the CCPP treated rats, which was accompanied by the upregulated expression of GLP-1 and PYY.

CONCLUSION

These results demonstrated that CCPP could alleviate type 2 diabetic symptoms by increasing the SCFA-producing bacteria, promoting the production of SCFAs and upregulating SCFA-GLP1/PYY associated sensory mediators.

Assessing the benefits of composting poultry manure in reducing antimicrobial residues, pathogenic bacteria, and antimicrobial resistance genes: a field-scale study

The poultry industry in the European Union produces 13 million tons of manure annually, which represents a major health and environmental challenge. Composting is an environmental-friendly technique for the management of manure, but there are few studies about antibiotic residues and antimicrobial resistances at a field scale. The goal of this study was to determine if the composting of poultry manure at a field scale would result in the reduction of antibiotic residues, pathogenic bacteria, and antibiotic resistance genes (ARGs) in the final fertilizer product. A 10-week composting of poultry manure spiked with enrofloxacin, doxycycline, and ciprofloxacin was performed. The determination of antibiotics residues and 22 selected ARGs was carried out together with the identification of bacteria by metagenomics. In the case of ciprofloxacin and doxycycline, a 90% decrease was observed after composting for 3 weeks. Sixteen ARGs were detected at the beginning of the experiment; 12 of them decreased from week 0 to week 10 (reduction of 73.7-99.99%). The presence of potentially pathogenic bacteria, such as, Campylobacter coli or commensal bacteria such as Escherichia coli decreases along the composting process. In conclusion, 10-week composting of poultry manure promotes the reduction of antibiotic residues and most of the ARGs and pathogenic bacteria.

Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.)

Tuber species may be regarded as complex microhabitats hosting diverse microorganisms inside their fruiting bodies. Here, we investigated the structure of microbial communities inhabiting the gleba of wild growing (in stands) T. aestivum, using Illumina sequencing and culture-based methods. The two methods used in combination allowed to extract more information on complex microbiota of Tuber aestivum gleba. Analysis of the V3-V4 region of 16S rDNA identified nine phyla of bacteria present in the gleba of T. aestivum ascomata, mostly Proteobacteria from the family Bradyrhizobiaceae. Our results ideally match the earlier data for other Tuber species where the family Bradyrhizobiaceae was the most represented. The ITS1 region of fungal rDNA represented six alien fungal species belonging to three phyla. To complement the metagenomic analysis, cultivable fungi and bacteria were obtained from the gleba of the same T. aestivum fruiting bodies. The identified fungi mostly belong to the phylum Basidiomycota and same to Ascomycota. Analysis of cultivable bacteria revealed that all the specimens were colonized by different strains of Bacillus. Fungal community inhabiting T. aestivum fruiting bodies was never shown before.

Viral metagenomic analysis of fecal samples reveals an enteric virome signature in irritable bowel syndrome

BACKGROUND

Changes in the enteric microbiota have been suggested to contribute to gastrointestinal diseases, including irritable bowel syndrome. Most of the published work is on bacterial dysbiosis with meager data on the role of the virome in irritable bowel syndrome and other gastrointestinal diseases. In the current study, we therefore aimed to investigate the viral community composition of the gut and test for potential dysbiosis linked to irritable bowel syndrome.

RESULTS

A metagenomics analysis on fecal samples of 50 individuals - 30 of whom met the Rome IV criteria for IBS and 20 healthy controls- was conducted. There was a noticeable alteration in viral taxa observed in association with irritable bowel syndrome when compared to healthy individuals - where some eukaryotic viral taxa noticeably prevail over others. We observed a significant decrease in the diversity and abundance of enteric virome particularly in eukaryotic viruses of Megavirales in patients with irritable bowel syndrome.

CONCLUSIONS

These findings shed light on a new hypothesis that the alteration of the viral taxa contributes to the pathogenesis of irritable bowel syndrome and related symptoms, and therefore, pave the way for developing a new diagnostic biomarker or anti-viral drugs for the treatment of irritable bowel syndrome.

Deciphering the microbiota data from termite mound soil in South Africa using shotgun metagenomics

We present the metagenomic dataset of the microbial DNA of a termite mound in the North West Province of South Africa. This is the foremost account revealing the microbial diversity of a termite mound soil using the shotgun metagenomics approach in the Province. Next-generation sequencing of the community DNA was carried out on an Illumina Miseq platform. The metagenome comprised of 7,270,818 sequences representing 1,172,099,467 bps with a mean length of 161 bps and 52% G + C content. The sequence data is accessible at the NCBI SRA under the bioproject number PRJNA526912. Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) was employed for community analysis and it was observed that 0.36% sequences were of archeal origin, 9.51% were eukaryotes and 90.01% were fit to bacteria. A total of 5 archeal, 27 bacterial, and 22 eukaryotic phyla were revealed. Abundant genera were Sphingomonas (6.00%), Streptomyces (5.00%), Sphingobium (4.00%), Sphingopyxis (3.00%), and Mycobacterium (3.00%), representing 19.23% in the metagenome. For functional examination, Cluster-of-Orthologous-Group (COG) based annotation showed that 46.44% sequences were metabolism associated and 17.45% grouped in the poorly characterized category. Subsystem based annotation method indicated that 14.00% sequences were carbohydrates, 13.00% were clustering-based subsystems, and 10.00% genes for amino acids and derivatives together with the presence of useful traits needed in the body of science.

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities

Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

Diminishing microbiome richness and distinction in the lower respiratory tract of lung cancer patients: A multiple comparative study design with independent validation

OBJECTIVES

Current evidence suggests that microorganisms are associated with neoplastic diseases; however, the role of the airway microbiome in lung cancer remains unknown. To investigate the taxonomic profiles of the lower respiratory tract (LRT) microbiome in patients with lung cancer.

MATERIALS AND METHODS

BALF samples were collected in a discovery set comprising 150 individuals, including 91 patients with lung cancer, 29 patients with nonmalignant pulmonary diseases and 30 healthy subjects, and an independent validation set including 85 participants. The samples were assessed by metagenomics analysis. Random forest regression analysis was performed to select a diagnostic panel.

RESULTS

In the discovery set, richness was reduced in lung cancer patients compared with that in healthy subjects, and the microbiome of patients with nonmalignant diseases resembled that of patients with lung cancer. Interestingly, Bradyrhizobium japonicum was only found in patients with lung cancer, whereas Acidovorax was found in patients with cancer and nonmalignant pulmonary diseases. A microbiota-related diagnostic model consisting of age, pack year of smoking and eleven types of bacteria was built, and the area under the curve (AUC) for discriminating the patients with cancer was 0.882 (95%CI: 0.807-0.957) in the training set and 0.796 (95%CI: 0.673-0.920) in the independent validation set.

CONCLUSION

Our study demonstrates that the LRT microbiome richness is diminished in lung cancer patients compared with that in healthy subjects and that microbiota-specific biomarkers may be useful for diagnosing patients for whom lung biopsy is not feasible.

Understanding the cumulative effects of salinity, temperature and inoculation size for the design of optimal halothermotolerant bioanodes from hypersaline sediments

The main objective of this study was to understand the interaction between salinity, temperature and inoculum size and how it could lead to the formation of efficient halothermotolerant bioanodes from the Hypersaline Sediment of Chott El Djerid (HSCE). Sixteen experiments on bioanode formation were designed using a Box-Behnken matrix and response surface methodology to understand synchronous interactions. All bioanode formations were conducted on 6 cm² carbon felt electrodes polarized at -0.1 V/SCE and fed with lactate (5 g/L) at pH 7.0. Optimum levels for salinity, temperature and inoculum size were predicted by NemrodW software as 165 g/L, 45 °C and 20%, respectively, under which conditions maximum current production of 6.98 ± 0.06 A/m² was experimentally validated. Metagenomic analysis of selected biofilms indicated a relative abundance of the two phyla Proteobacteria (from 85.96 to 89.47%) and Firmicutes (from 61.90 to 68.27%). At species level, enrichment of Psychrobacter aquaticus, Halanaerobium praevalens, Psychrobacter alimentaris, and Marinobacter hydrocarbonoclasticus on carbon-based electrodes was correlated with high current production, high salinity and high temperature. Members of the halothermophilic bacteria pool from HSCE, individually or in consortia, are candidates for designing halothermotolerant bioanodes applicable in the bioelectrochemical treatment of industrial wastewater at high salinity and temperature.

Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination

Next-generation sequencing (NGS) followed by metagenomic enables the detection and identification of known as well as novel pathogens. It could be potentially useful in the diagnosis of encephalitis, caused by a variety of microorganisms. The aim of the present study was to evaluate the sensitivity of isothermal RNA amplification (Ribo-SPIA) followed by NGS metagenomic analysis in the detection of human immunodeficiency virus (HIV) and herpes simplex virus (HSV) in cerebrospinal fluid (CSF). Moreover, we analyzed the contamination background. We detected 102 HIV copies and 103 HSV copies. The analysis of control samples (two water samples and one CSF sample from an uninfected patient) revealed the presence of human DNA in the CSF sample (91 % of all reads), while the dominating sequences in water were qualified as 'other', related to plants, plant viruses, and synthetic constructs, and constituted 31 % and 60 % of all reads. Bacterial sequences represented 5.9 % and 21.4 % of all reads in water samples and 2.3 % in the control CSF sample. The bacterial sequences corresponded mainly to Psychrobacter, Acinetobacter, and Corynebacterium genera. In conclusion, Ribo-SPIA amplification followed by NGS metagenomic analysis is sensitive for detection of RNA and DNA viruses. Contamination seems common and thus the results should be confirmed by other independent methods such as RT-PCR and PCR. Despite these reservations, NGS seems to be a promising method for the diagnosis of viral infections.