Correlation between the gut microbiome and neurodegenerative diseases:a review of metagenomics evidence

A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.

Metagenomic analysis revealing the metabolic role of microbial communities in the free amino acid biosynthesis of Monascus rice vinegar during fermentation

Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic network on FAA biosynthesis remains unclear.Through metagenomic analysis,this work aimed to elucidate the roles of microbes in FAA biosynthesis during Monascus rice vinegar fermentation.Taxonomic profiles from functional analyses showed 14 dominant genera with high contributions to the metabolism pathways.The metabolic network for FAA biosynthesis was then constructed,and the microbial distribution in different metabolic pathways was illuminated.The results revealed that 5 functional genera were closely involved in FAA biosynthesis.This study illuminated the metabolic roles of microorganisms in FAA biosynthesis and provided crucial insights into the functional attributes of microbiota in vinegar fermentation.

Metagenomic Insight Reveals the Microbial Structure and Function of the Full-Scale Coking Wastewater Treatment System:Gene-Based Nitrogen Removal

Microbial communities play crucial roles in pollutant removal and system stability in biological systems for coking wastewater(CWW)treatment,but a comprehensive understanding of their structure and functions is still lacking.A five month survey of four sequential bioreactors,anoxic 1/oxic 1/anoxic 2/oxic 2(A1/O1/A2/O2),was carried out in a full-scale CWW treatment system in China to elucidate operational performance and microbial ecology.The results showed that A1/O1/A2/O2 had excellent and stable performance for nitrogen removal.Both total nitrogen(TN;(17.38±6.89)mgL1)and ammonium-nitrogen(NH4 t-N;(2.10±1.34)mg·L^(-1))in the final biological effluent satisfied the Chinese national standards for CWW.Integrated analysis of 16S ribosome RNA(rRNA)sequencing and metagenomic sequencing showed that the bacterial communities and metagenomic function profiles of A1 and O1 shared similar functional structures,while those of A2 significantly varied from those of other bioreactors(p<0.05).The results indicated that microbial activity was strongly connected with activated sludge function.Nitrosospira,Nitrosomonas,and SM1A02 were responsible for nitrification during the primary anoxic-oxic(AO)stage and Azoarcus and Thauera acted as important denitrifiers in A2.Nitrogen cycling-related enzymes and genes work in the A1/O1/A2/O2 system.Moreover,the hao genes catalyzing hydroxylamine dehydrogenase(EC 1.7.2.6)and the napA and napB genes catalyzing nitrate reductase(EC 1.9.6.1)played important roles in the nitrification and denitrification processes in the primary and secondary AO stages,respectively.The mixed liquor suspended solids(MLSS)/total solids(TS),TN removal rate(RR),total organic carbon(TOC)(RR),and NH_(4)^(+)t-N(RR)were the most important environmental factors for regulating the structure of core bacterial genera and nitrogen-cycling genes.Proteobacteria were the potential main participants in nitrogen metabolism in the A1/O1/A2/O2 system for CWW treatment.This study provides an original and comprehensive understanding of the microbial community and functions at the gene level,which is crucial for the efficient and stable operation of the full-scale biological process for CWW treatment.

Lacticaseibacillus rhamnosus Probio-M9 may be vertically transmitted from mother to infant during lactation based on faeces metagenomics

Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study recruited one pregnant woman,who ingested Probio-M9 daily from 35 weeks of gestation to delivery.Feces of the mother-infant pair were regularly collected from one month before delivery to 6 months of infant's age for metagenomic sequencing.Probio-M9 genomes were mappable to all infant fecal samples,suggesting the ingested probiotics could be vertically transmitted from mother to infant.Infant-or mother-specific differential metabolic pathways were found between the maternal and infant's gut microbiome,implicating apparent differences in the intestinal metagenomic potential/function between the mother and the infant.In conclusion,maternal ingestion of Probio-M9 during the final weeks of gestation could deliver to the infant gut.The findings provided novel insights into shaping infant's gut microbiota.

Brain abscess from oral microbiota approached by metagenomic next-generation sequencing: A case report and review of literature

BACKGROUND Brain abscess is a serious and potentially fatal disease caused primarily by microbial infection.Although progress has been made in the diagnosis and treatment of brain abscesses,the diagnostic timeliness of pathogens needs to be improved.CASE SUMMARY We report the case of a 54-year-old male with a brain abscess caused by oral bacteria.The patient recovered well after receiving a combination of metagenomic next-generation sequencing(mNGS)-assisted guided medication and surgery.CONCLUSION Therefore,mNGS may be widely applied to identify the pathogenic microor-ganisms of brain abscesses and guide precision medicine.

Bronchoalveolar lavage fluid metagenomic next-generation sequencing assay for identifying pathogens in lung cancer patients

Background:For patients with lung cancer,timely identification of new lung lesions as infectious or non-infectious,and accurate identification of pathogens is very important in improving OS of patients.As a new auxiliary examination,metagenomic next-generation sequencing(mNGS)is believed to be more accurate in diagnosing infectious diseases in patients without underlying diseases,compared with conventional microbial tests(CMTs).We designed this study tofind out whether mNGS has better performance in distinguishing infectious and non-infectious diseases in lung cancer patients using bronchoalveolar lavagefluid(BALF).Materials and Methods:This study was a real-world retrospective review based on electronic medical records of lung cancer patients with bronchoalveolar lavage(BAL)and BALF commercial mNGS testing as part of clinical care from 1 April 2019 through 30 April 2022 at The First Affiliated Hospital of Sun Yat-sen University.164 patients were included in this study.Patients were categorized into the pulmonary non-infectious disease(PNID)group(n=64)and the pulmonary infectious disease(PID)group(n=100)groups based onfinal diagnoses.Results:BALF mNGS increased the sensitivity rate by 60%compared to CMTs(81%vs.21%,p<0.05),whereas there was no significant difference in specificity(75%vs.98.4%,p>0.1).Among the patients with PID,bacteria were the most common cause of infection.Fungal infections occurred in 32%of patients,and Pneumocystis Yersini was most common.Patients with Tyrosine kinase inhibitors(TKIs)therapy possess longer overall survival(OS)than other anti-cancer agents,the difference between TKIs and immuno-checkpoint inhibitors(ICIs)was insignificant(median OS TKIs vs.ICIs vs.Anti-angiogenic vs.Chemo vs.Radiotherapy=76 vs.84 vs.61 vs.58 vs.60).Conclusions:our study indicates that BALF mNGS can add value by improving overall sensitivity in lung cancer patients with potential pulmonary infection,and was outstanding in identifying Pneumocystis infection.It could be able to help physicians adjust the follow-up treatment to avoid the abuse of antibiotics.

Metagenomic next-generation sequencing may assist diagnosis of osteomyelitis caused by Mycobacterium houstonense:A case report

BACKGROUND Mycobacterium houstonense(M.houstonense)belongs to the nontuberculous mycobacterium group.Infection caused by M.houstonense is prone to recurrence.CASE SUMMARY We present a patient who was diagnosed with osteomyelitis caused by M.houstonense and treated with a combination of cefoxitin,and amikacin combined with linezolid.CONCLUSION The emergence of metagenomic next-generation sequencing(NGS)has brought new hope for the diagnosis and treatment of listeria meningitis.NGS can analyze a large number of nucleic acid sequences in a short time and quickly determine the pathogen species in the sample.Compared with traditional cerebrospinal fluid culture,NGS can greatly shorten the diagnosis time and provide strong support for the timely treatment of patients.Regarding treatment,NGS can also play an important role.Rapid and accurate diagnosis can enable patients to start targeted treatment as soon as possible and improve the treatment effect.At the same time,by monitoring the changes in pathogen resistance,the treatment plan can be adjusted in time to avoid treatment failure.

Diagnosis of Acute Q Fever in an Elderly Patient Using Metagenomic Next-Generation Sequencing:A Case Report

Query fever(Q fever)is a globally spread zoonotic disease caused by Coxiella burnetii,commonly found in natural foci but rarely seen in Hebei Province.The clinical manifestations of Q fever are diverse and nonspecific,which often leads to missed or incorrect diagnoses in clinical practice.This article reports a case of acute Q fever diagnosed in an elderly patient using metagenomic next-generation sequencing.

Washed microbiota transplantation for Crohn’s disease:A metagenomic,metatranscriptomic,and metabolomic-based study

BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transplantation(WMT).Most existing studies have focused on observing the clinical phenomena.However,the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome,metatranscriptome,and metabolome-has not yet been reported.AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.METHODS We conducted a prospective,open-label,single-center clinical study.Eleven CD patients underwent WMT.Their clinical responses(defined as a decrease in their CD Activity Index score of>100 points)and their microbiome(metagenome,metatranscriptome)and metabolome profiles were evaluated three months after the procedure.RESULTS Seven of the 11 patients(63.6%)showed an optimal clinical response three months post-WMT.Gut microbiome diversity significantly increased after WMT,consistent with improved clinical symptoms.Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains,such as Faecalibac-terium prausnitzii,Roseburia intestinalis,and Escherichia coli.In addition,metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors.However,levels of vital amino acids that may be associated with disease progression(e.g.,L-glutamic acid,gamma-glutamyl-leucine,and prolyl-glutamine)were reduced after WMT.CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment,likely due to the effective reconstruction of the patient’s microbiome.Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.

Studies on the Extraction Methods of Metagenomic DNA from Mud Volcano in Xinjiang

[Objective]To seek one effective extraction method of metagenomic DNA from mud volcano.[Method]The metagenomic DNA from mud volcano was extracted by CTAB extraction method,SDS-enzyme method,improved method,reagent kit method.The extraction of four kinds of methods were compared.[Result]The extracted rate in reagent sets method was the highest,next was improved method,the extracted quantity in SDS-enzyme method was maximum.DNA extracted by the improved method was diluted ten times for PCR.[Conclusion]Considering economy and purity,the improved method can be used as one effective extraction method of metagenomic DNA from mud volcano.

Application of metagenomics in the human gut microbiome

There are more than 1000 microbial species living in the complex human intestine.The gut microbial community plays an important role in protecting the host against pathogenic microbes,modulating immunity,regulating metabolic processes,and is even regarded as an endocrine organ.However,traditional culture methods are very limited for identifying microbes.With the application of molecular biologic technology in the field of the intestinal microbiome,especially metagenomic sequencing of the next-generation sequencing technology,progress has been made in the study of the human intestinal microbiome.Metagenomics can be used to study intestinal microbiome diversity and dysbiosis,as well as its relationship to health and disease.Moreover,functional metagenomics can identify novel functional genes,microbial pathways,antibiotic resistance genes,functional dysbiosis of the intestinal microbiome,and determine interactions and co-evolution between microbiota and host,though there are still some limitations.Metatranscriptomics,metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome.This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects.The limitations of metagenomics to be overcome are also discussed.Metatranscriptomics,metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.

Effects of viral infection and microbial diversity on patients with sepsis:A retrospective study based on metagenomic next-generation sequencing

BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.

Clinical metagenomic sequencing for rapid diagnosis of pneumonia and meningitis caused by Chlamydia psittaci

BACKGROUND Chlamydia psittaci(C.psittaci)is a gram-negative intracellular parasitic pathogenic bacterium that can infect avian and mammalian hosts,including humans.The detection of C.psittaci infections typically relies on traditional antigen-based immunoassays or serological testing that often lack sensitivity and/or specificity.Metagenomic next generation sequencing(mNGS)is an emerging tool for diagnosis.AIM To demonstrate that mNGS represents a valuable tool for rapid,sensitive,and accurate pathogen detection including C.psittaci infections.METHODS Four cases of psittacosis pneumonia and one case of pediatric psittacosis meningitis were diagnosed between December 2019 and May 2020 using mNGS at Changzhou Second People’s Hospital affiliated to Nanjing Medical University.Patients’clinical characteristics,manifestations,and treatment histories were retrospectively evaluated.RESULTS All five patients had a history of exposure to wild(psittacine or other birds)or domesticated birds(chickens).All patients had a high fever(>39℃)and three of them(60%)experienced organ insufficiency during the disease.The laboratory data showed normal to slightly increased leucocyte and neutrophil counts,and elevated procalcitonin levels in all five cases,and very high C-reactive protein levels in psittacosis pneumonia patients.mNGS identified a potential pathogen,C.psittaci,in patients’bronchoalveolar lavage fluid or cerebrospinal fluid.Computed tomography revealed lung air-space consolidation,pleural thickening,and effusion fluid buildup in psittacosis pneumonia cases,and an arachnoid cyst in the right temporal lobe of the pediatric psittacosis meningitis patient.All patients experienced complete recovery following the administration of targeted antichlamydia therapy.CONCLUSION This study not only demonstrated that mNGS represents a valuable tool for rapid,sensitive,and accurate pathogen detection,but also raised public health concerns over C.psittaci infections.

Conjunctival microbiome changes associated with fungal keratitis: metagenomic analysis

AIM: To investigate the ocular surface microbiome profile of patients with fungal keratitis(FK) through bacterial 16 S r DNA sequencing. METHODS: The swab samples were collected from 8 patients with FK(Group 1 from the corneal ulcer, Group 2 from the conjunctival sac of the infected eyes, and Group 3 from the conjunctival sac of the fellow eyes) and 10 healthy eyes(Group 4 from the conjunctival sac). Bacterial 16 S rDNA V4-V5 region sequencing was performed to characterize the bacterial communities on the ocular surfaces of the patients with FK. RESULTS: Our metagenomic data showed that 97% of the sequence reads were categorized into 245 distinct bacterial genera, with 67.75±7.79 genera detected in Group 1, 73.80±13.44 in Group 2, 74.57±14.14 in Group 3, and 89.60±27.49 in Group 4. Compared with the healthy eyes(Group 4), both infected(Groups 1 and 2) and fellow eyes(Group 3) of the patients with FK showed reduced bacterial diversity and altered ocular surface microbiota compositions, with lower abundance of Corynebacterium and Staphylo coccus and higher abundances of Pseudomonas, Achromobacter, Caulobacter and Psychrobacter. CONCLUSION: Our report depicts the altered ocular surface bacterial community structures both in the affected and fellow eyes of patients with FK. These changes may contribute to the pathogenesis of FK or the increased risk for FK.

Viral Metagenomics Analysis of Planktonic Viruses in East Lake,Wuhan,China

East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.

Construction of a Metagenomic DNA Library of Sponge Symbionts and Screening of Antibacterial Metabolites

To study the bioactive metabolites produced by sponge-derived uncultured symbionts, a metagenomic DNA library of the symbionts of sponge Gelliodes gracilis was constructed. The average size of DNA inserts in the library was 20 kb. This library was screened for antibiotic activity using paper disc assaying. Two clones displayed the antibacterial activity against Micrococcus tetragenus. The metabolites of these two clones were analyzed through HPLC. The result showed that their metabolites were quite different from those of the host E. coli DNA and the host containing vector pHZ132. This study may present a new approach to exploring bioactive metabolites of sponge symbionts.

Diversity in metagenomic sequences reveals new pathogenic fungus associated with smut in Job's tears

Smut is a serious disease in Job's tears,also known as adlay,and contributes to the reduction of crop yield in agricultural fields.In this study,the key pathogenic fungi in adlay smut disease were first identified by internal transcribed spacer region(ITS)high-throughput sequencing and then used to elucidate the composition and diversity of the fungal community in adlay smut.Results indicate that an abundance of operational taxonomic units(OTUs)were detected in the infected involucres of flowering plants and the OTUs were classified to nine phyla,20 classes,45 orders,90 families and 119 genera.A total of 4986 OTUs clustered together,sharing six core OTUs in all samples,while 145 OTUs were shared among four geographical groups.The Shannon and Simpson indices ranged from 0.137–1.629 and 0.357–0.970,respectively.Community diversity ranked as Anshun(AS)>Qinglong(QL)>Xingren(XR)>Xingyi(XY)among the four geographical groups by Shannon and Simpson indices,exhibiting complex community diversities among accessions and geographical groups.The richness and diversity data imply a weak relationship between the accession community richness and geographical origins of samples.Two closely related fungal genera,Sporisorium and Ustilago,were implicated as causes of smut disease.The genus Sporisorium appears to be more commonly found among accessions and thus is more likely to be the fungal pathogen causing smut in adlay.This work can facilitate strategies to control and prevent smut infection to improve adlay yield.

The Diagnostic Value of Metagenomic Next-Generation Sequencing in <i>Angiostrongylus cantonensis</i>Encephalitis/Meningitis

Objective: Angiostrongylus cantonensis (A. cantonensis) is an important parasite, which causes neurological infection in children, and is generally difficult to diagnose. We analyzed the significance of metagenomic next-generation sequencing in diagnosing A. cantonensis encephalitis/meningitis in children to provide a reference for clinical diagnosis. Methods: The case collection of A. cantonensis encephalitis/meningitis was from July 2018 to August 2020. The patients’ clinical characteristics and pathogen were described, and diagnostic sensitivity methods for A. cantonensis encephalitis/meningitis were compared and analyzed, including parasite antibody detection and metagenomic next-generation sequencing (mNGS) detection in different samples. Results: Eleven cases were diagnosed with A. cantonensis encephalitis/meningitis, including six males (54.5%) and five females (45.5%), and the age ranged from 1 to 13 years with a median of 21 months (IQR: 15.6, 96). All patients were undiagnosed upon admission, of which ten cases had neurological symptoms or signs, six cases (54.5%) had a history of definite or suspicious exposure to parasites, and eight cases (72.7%) had abnormal changes in cranial MRI. The results of A. cantonensis antibodies in the peripheral blood and cerebrospinal fluid (CSF) were compared with CSF’s metagenomic next-generation sequencing (mNGS). The antibody-positive rate of peripheral blood was 54.5%, CSF antibody-positive rate was 27.2%, and mNGS-positive rate of CSF was 81.8%, and the positive diagnostic rate of the latter was significantly higher than the former two (p = 0.035 < 0.05 and p = 0.030 < 0.05, respectively). Conclusion: Metagenomic next-generation sequencing has a higher positive rate for diagnosing infection and plays an important role in clarifying diagnosis and reducing misdiagnosis.

Diagnosis of cytomegalovirus encephalitis using metagenomic nextgeneration sequencing of blood and cerebrospinal fluid:A case report

BACKGROUND Cytomegalovirus(CMV)infections in the population are mostly subclinical,inapparent,or latent.However,it is rare in brain tissue.Most reported CMV encephalitis cases were patients with immunodeficiency.The diagnosis and detection rate of CMV encephalitis in patients with normal immune function needs to be further improved.CASE SUMMARY An 86-year-old male was admitted due to a sudden onset of unconsciousness for 3 h.The patient developed status epilepticus and was relieved after antiepileptic treatment.Encephalitis was considered due to the high signals of diffusionweighted imaging sequences in the right central region by magnetic resonance imaging.Metagenomic next-generation sequencing(mNGS)of blood and cerebrospinal fluid revealed CMV,with unique reads number being 614 and 1,respectively.Simultaneous quantitative PCR results showed CMV positive in blood samples and negative in cerebrospinal fluid samples.The patient was finally diagnosed as CMV encephalitis with status epilepticus.After the antiviral,hormonal,andγ-globulin pulse therapy,the patient’s condition improved,and he was finally discharged.CONCLUSION mNGS could be a reliable approach for the diagnosis of CMV encephalitis,with high efficiency,sensitivity,and specificity.

Successful treatment of disseminated nocardiosis diagnosed by metagenomic next-generation sequencing:A case report and review of literature

BACKGROUND Nocardia paucivorans is an infrequently found bacterium with the potential to cause severe infection,with a predilection for the central nervous system,both in immunocompromised and immunocompetent individuals.Rapid etiological diagnosis of nocardiosis can facilitate timely and rational antimicrobial treatment.Metagenomic next-generation sequencing(m NGS)can improve the rate and reduce the turnaround time for the detection of Nocardia.CASE SUMMARY A 49-year-old man was admitted to hospital with cough and hemoptysis.Imaging revealed pulmonary consolidation as well as multiple brain lesions.Nocardia asiatica and Nocardia beijingensis were rapidly detected by m NGS of bronchoalveolar lavage fluid(BALF)while bacterial culture of BALF and pathological biopsy of lung tissue were negative.In early stages,he was treated with trimethoprim-sulfamethoxazole(TMP-SMZ)and linezolid by individual dose adjustment based on serum concentrations and the adverse effects of thrombocytopenia and leukopenia.The treatment was then replaced by TMP-SMZ and ceftriaxone or minocycline.He was treated with 8 mo of parenteral and/or oral antibiotics,and obvious clinical improvement was achieved with resolution of pulmonary and brain lesions on repeat imaging.CONCLUSION m NGS provided fast and precise pathogen detection of Nocardia.In disseminated nocardiosis,linezolid is an important alternative that can give a better outcome with the monitoring of linezolid serum concentrations and platelet count.