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 for pleural effusions induced by viral pleurisy:A case report

BACKGROUND Viral pleurisy is a viral infected disease with exudative pleural effusions.It is one of the causes for pleural effusions.Because of the difficult etiology diagnosis,clinically pleural effusions tend to be misdiagnosed as tuberculous pleurisy or idiopathic pleural effusion.Here,we report a case of pleural effusion secondary to viral pleurisy which is driven by infection with epstein-barr virus.Viral infection was identified by metagenomic next-generation sequencing(mNGS).CASE SUMMARY A 40-year-old male with a history of dermatomyositis,rheumatoid arthritis,and secondary interstitial pneumonia was administered with long-term oral prednisone.He presented with fever and chest pain after exposure to cold,accompanied by generalized sore and weakness,night sweat,occasional cough,and few sputums.The computed tomography scan showed bilateral pleural effusions and atelectasis of the partial right lower lobe was revealed.The pleural fluids were found to be yellow and slightly turbid after pleural catheterization.Thoracoscopy showed fibrous adhesion and auto-pleurodesis.Combining the results in pleural fluid analysis and mNGS,the patient was diagnosed as viral pleuritis.After receiving Aciclovir,the symptoms and signs of the patient were relieved.CONCLUSION Viral infection should be considered in cases of idiopathic pleural effusion unexplained by routine examination.mNGS is helpful for diagnosis.

Pulmonary nocardiosis with bloodstream infection diagnosed by metagenomic next-generation sequencing in a kidney transplant recipient:A case report

BACKGROUND Pulmonary nocardiosis is difficult to diagnose by culture and other conventional testing,and is often associated with lethal disseminated infections.This difficulty poses a great challenge to the timeliness and accuracy of clinical detection,especially in susceptible immunosuppressed individuals.Metagenomic nextgeneration sequencing(mNGS)has transformed the conventional diagnosis pattern by providing a rapid and precise method to assess all microorganisms in a sample.CASE SUMMARY A 45-year-old male was hospitalized for cough,chest tightness and fatigue for 3 consecutive days.He had received a kidney transplant 42 d prior to admission.No pathogens were detected at admission.Chest computed tomography showed nodules,streak shadows and fiber lesions in both lung lobes as well as right pleural effusion.Pulmonary tuberculosis with pleural effusion was highly suspected based on the symptoms,imaging and residence in a high tuberculosisburden area.However,anti-tuberculosis treatment was ineffective,showing no improvement in computed tomography imaging.Pleural effusion and blood samples were subsequently sent for mNGS.The results indicated Nocardia farcinica as the major pathogen.After switching to sulphamethoxazole combined with minocycline for antinocardiosis treatment,the patient gradually improved and was finally discharged.CONCLUSION A case of pulmonary nocardiosis with an accompanying bloodstream infection was diagnosed and promptly treated before the dissemination of the infection.This report emphasizes the value of mNGS in the diagnosis of nocardiosis.mNGS may be an effective method for facilitating early diagnosis and prompt treatment in infectious diseases,which overcomes the shortcomings of conventional testing.

Metagenomic next-generation sequencing in the diagnosis of neurocysticercosis:A case report

BACKGROUND The clinical symptoms and imaging manifestations of neurocysticercosis(NCC)are very different,and the difficulty and delay of clinical diagnoses may lead to an increase in mortality and disability.Rapid and accurate pathogen identification is important for the treatment of these patients.Metagenomic next-generation sequencing(mNGS)is a powerful tool to identify pathogens,especially in infections that are difficult to identify by conventional methods.CASE SUMMARY A 43-year-old male patient was admitted due to a recurrent headache for a few months.Imaging examinations showed hydrocephalus and cystic lesions,which were considered to be a central nervous system infection,but no etiology was found by routine examination.mNGS of the cerebrospinal fluid revealed high Taenia solium reads,and the positive results of a cysticercosis antibody test confirmed the infection.Combined with the patient’s clinical manifestations,the etiological evidence,and the imaging manifestation,the patient was finally diagnosed with NCC and he was prescribed dexamethasone,albendazole,neurotrophic drugs,and intracranial pressure reduction therapy.The headaches disappeared after anti-parasite treatment,and no associated symptoms recurred prior to the three-and six-month follow-up.CONCLUSION As an accurate and sensitivity detection method,mNGS can be a reliable approach for the diagnosis of NCC.

Overlapping infections of Mycobacterium canariasense and Nocardia farcinica in an immunocompetent patient:A case report

BACKGROUND Infections by non-tuberculous mycobacteria(NTM)have become more common in recent years.Mycobacterium canariasense(M.canariasense)was first reported as an opportunistic pathogen in 2004,but there have been very few case reports since then.Nocardia is a genus of aerobic and Gram-positive bacilli,and these species are also opportunistic pathogens and in the Mycobacteriales order.Conventional methods for diagnosis of NTM are inefficient.Metagenomic next-generation sequencing(mNGS)can rapidly detect many pathogenic microorganisms,even rare species.Most NTM and Nocardia infections occur in immunocompromised patients with atypical clinical symptoms.There are no previous reports of infection by M.canariasense and Nocardia farcinica(N.farcinica),especially in immunocompetent patients.This case report describes an immunocompetent 52-year-old woman who had overlapping infections of M.canariasense,N.farcinica,and Candida parapsilosis(C.parapsilosis)based on mNGS.CASE SUMMARY A 52-year-old woman presented with a productive cough and chest pain for 2 wk,and recurrent episodes of moderate-grade fever for 1 wk.She received antibiotics for 1 wk at a local hospital,and experienced defervescence,but the productive cough and chest pain persisted.We collected samples of a lung lesion and alveolar lavage fluid for mNGS.The lung tissue was positive for M.canariasense,N.farcinica,and C.parapsilosis,and the alveolar lavage fluid was positive for M.canariasense.The diagnosis was pneumonia,and application of appropriate antibiotic therapy cured the patient.CONCLUSION Etiological diagnosis is critical for patients with infectious diseases.mNGS can identify rare and novel pathogens,and does not require a priori knowledge.

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.

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.

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.

Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases of the central nervous system after empirical treatment

BACKGROUND The diagnostic value of metagenomic next-generation sequencing(mNGS)in central nervous system(CNS)infectious diseases after empirical treatment has not been reported.AIM To investigate the diagnostic value of mNGS of cerebrospinal fluid(CSF)in the empirically treated CNS infectious diseases.METHODS A total of 262 CSF samples from patients with suspected CNS infections were collected between August 2020 and December 2021.Both mNGS and conventional methods were used for testing.The conventional methods included microbial culture,smear,polymerase chain reaction,etc.RESULTS Among 262 suspected cases,183 cases(69.84%)were diagnosed as CNS infection,including 86 cases of virus infection(47.00%),70 cases of bacterial infection(38.25%)and 27 cases of fungal infection(14.76%).The sensitivity and specificity of mNGS were 65.6%(95%CI:58.2%-72.3%)and 89.6%(95%CI:79.1%-95.3%),respectively.The PPV of mNGS was 94.5%(95%CI:88.6%-97.6%),and the NPV was 48.8%(95%CI:39.7%–57.9%).The pathogen detective sensitivity and accuracy of mNGS were higher than those of conventional methods(Sensitivity:65.6%vs 37.2%;P<0.001;Accuracy:72.0%vs 50%,P<0.001).The results showed that compared with conventional methods,mNGS technology was a more sensitive method for the diagnosis of CNS infection after empirical treatment.CONCLUSION mNGS can be a better method applied in the diagnosis of CNS infection after empirical treatment.

Review of the Clinical Applications of Metagenomic Next-Generation Sequencing in Bloodstream Infection

Bloodstream infection (BSI) is an important cause of morbidity and mortality worldwide. If we can make early diagnosis and start effective antibiotic treatment in time, the hospitalization time of patients with bloodstream infection can be significantly shortened. However, the current diagnosis of bloodstream infection cannot achieve the ideal therapeutic effect to a large extent because of the matrix effect of blood and the long turnaround time of blood culture. Therefore, a new detection method with a short turnaround time and high sensitivity is needed for the early diagnosis and timely treatment to improve the prognosis of patients. Metagenomic next-generation sequencing (mNGS) is a recently developed method for the comprehensive analysis of all microorganisms and genetic materials in clinical samples and is expected to be the main method for the early diagnosis of bloodstream infections. This review discusses the clinical application of mNGS in bloodstream infections. We also discuss technical challenges that need to be addressed to improve the diagnostic applicability of mNGS.

Successful surgical treatment of polybacterial gas gangrene confirmed by metagenomic next-generation sequencing detection:A case report

BACKGROUND We report on a case of Vibrio vulnificus(V.vulnificus)detected by metagenomics next-generation sequencing(mNGS)in a 53-year-old male patient with polymicrobial gas gangrene and successful treatment by surgery.This report raises awareness among dermatologists that when a patient is clinically suspected of a special type of pathogenic infection,the mNGS method should be preferred to identify the patient’s pathogen infection as soon as possible and then take effective treatment in time to save patients’lives.CASE SUMMARY A 53-year-old male who worked in the aquatic market complained of redness and swelling of the lower limbs,blisters and ulcers with fever for 3 d.We used mNGS to test the pathogens in ulcer secretions.The results were returned in 24 h and indicated:V.vulnificus,Fusobacterium necrophorum,Staphylococcus haemolyticus,Staphylococcus aureus,Streptococcus dysgalactiae and Klebsiella aerogenes.This patient was diagnosed with V.vulnificus infection.The emergency operation was performed immediately under combined lumbar and epidural anesthesia:Left leg expansion and exploration(August 10,2021).After surgery,we continued to use piperacillin sodium tazobactam sodium 4.5 g every 8 h and levofloxacin 0.5 g for anti-infection treatment.The patient underwent further surgery under lumbar anesthesia on August 17,2021 and August 31,2021:Left leg deactivation and skin grafting,negative pressure closed drainage and right thigh skin removal.After treatment,the transplanted flap survived.CONCLUSION We could confirm the diagnosis of Vibrio vulnificus infection within 24 h through mNGS detection and then immediately performed emergency surgery.

Usefulness of metagenomic next-generation sequencing in adenovirus 7-induced acute respiratory distress syndrome:A case report

BACKGROUND Direct metagenomic next-generation sequencing(mNGS)of clinical samples is an effective method for the molecular diagnosis of infection.However,its role in the diagnosis of patients with acute respiratory distress syndrome(ARDS)of an unknown infectious etiology remains unclear.CASE SUMMARY A 33-year-old man was admitted to our center for a cough and febrile sensation.Shortly after admission,the patient was diagnosed with ARDS and treated in the intensive care unit.Subsequently,chest computed tomography features suggested an infection.mNGS was performed and the results were indicative of an infection caused by adenovirus type 7.The patient recovered after receiving appropriate treatment.CONCLUSION mNGS is a promising tool for the diagnosis of ARDS caused by infectious agents.However,further studies are required to develop strategies for incorporating mNGS into the current diagnostic process for the disease.

Metagenomic Shotgun Sequencing Provides Prevalence Data for Pathogens, and Source-Tracking Indices Useful in Public Health Risk Assessment of Environmental Waters

State-approved membrane filtration (MF) techniques for water quality assessments were contrasted with metagenomic shotgun sequencing (MSS) protocols to evaluate their efficacy in providing precise health-risk indices for surface waters. Samples from a freshwater receiving pond (ABI-1002) and two upstream storm water ditches (ABI-1003) and (ABI-1004) yielded alarmingly high Fecal coliform MF densities of 220, >2000 and >2000 CFU/100ml respectively. The indicator, Enterococcus bacteria exceeded allowable limits in all but the equipment control (ABI-1001). Using MSS, the relative numerical abundance of pathogenic bacteria, virulence and antibiotic resistance genes revealed the status and potential pollution sources of each ditch. High levels of Shigella sp. (0 (ABI-1001), 4945 (ABI-1002), 55,008 (ABI-1003), and 2221 (ABI-1004) genomic reads/100ml) correlated with virulence genes and antibiotic resistance genes found in fecal samples for ABI1003 and not ABI1004. Traditional culture methods (TCM) showed possible fecal contamination in two of the four samples, and no contamination in the others. MSS clearly distinguished between fecal and environmental bacteria contamination sources, and pinpointed actual risks from pathogens. Our data underscore the potential utility of MSS in precision risk assessment for public and biodiversity health and tracking of environmental microbiomes shifts by field managers and policy makers.

Distinct taxonomic and ecological functions of microbiome in sediments of different depth in Bohai Sea and Yellow Sea

Microorganisms in sediments are critical to marine ecosystems.The microbial communities in marine sediments of the Bohai Sea(BS)and Yellow Sea(YS),the eastern Chinese marginal seas,were uncovered in employing the metagenomic approach.In addition,the taxonomic and functional compositions of microbes were compared among various sediment core depths.Results showing the compositions,diversities,and functions of the microbial communities showed no significant variations with sea areas,and significant seasonal variations was observed in station 3500-7 only on functions of the microbial communities.Moreover,the compositions,diversities,and functions of the microbial communities changed noticeably in different sediment depths in close correlation with physical and chemical properties of sediments.However,the large fraction of the variation in functional communities remained unexplained.From bioinformatic analysis of the metagenomic data,the carbon-metabolismrelated genes such as glycosyl transferase(GT),glycoside hydrolase(GH),and carbohydrate esterase(CE)genes were rich in the microbial community,especially in the top sediment depth.Additionally,in this N-polluted habitat,nitrification and anaerobic ammonia oxidation(anammox)were dominant in the top sediment depth,whereas dissimilatory nitrate reduction to ammonium(DNRA)and denitrification were dominant in the middle and bottom depth,respectively.Further identification of possible biogeochemical links suggested that Gammaproteobacteria,Alphaproteobacteria,Nitrospirae,Nitrospinae,Chloroflexi,and Methanomicrobia might promote effective circulation of carbon and nitrogen cycling.This study expanded our knowledge about the structure and functional potential of microbial communities associated with different sediment depth,and provided further comprehensive information on element cycles in marine environments.

mNGS在疑似脓毒症患者中的应用价值

目的评估宏基因组测序技术(mNGS)在脓毒症患者中的诊断价值。方法本研究对87例疑似脓毒症患者共125例样本进行mNGS、培养法和其他传统方法检测,比较不同方法对病原体的检测效能,并分析了相关病原谱。结果mNGS总检出率显著高于传统检测方法(P<0.01)。mNGS的敏感性显著高于培养和其他病原检测方法(P<0.01)。mNGS覆盖的病原谱更加全面。结论本研究为mNGS的临床转化提供更多的临床实践依据,可以选择不同的样本类型以提高mNGS对病原的检测效率。

Critical respiratory failure due to pregnancy complicated by COVID-19 and bacterial coinfection:A case report

BACKGROUND In the past 3 years,the global pandemic of coronavirus disease 2019(COVID-19)has posed a great threat to human life and safety.Among the causes of death in COVID-19 patients,combined or secondary bacterial infection is an important factor.As a special group,pregnant women experience varying degrees of change in their immune status,cardiopulmonary function,and anatomical structure during pregnancy,which puts them at higher risk of contracting COVID-19.COVID-19 infection during pregnancy is associated with increased adverse events such as hospitalisation,admission to the intensive care unit,and mechanical ventilation.Therefore,pregnancy combined with coinfection of COVID-19 and bacteria often leads to critical respiratory failure,posing severe challenges in the diagnosis and treatment process.CASE SUMMARY We report a case of COVID-19 complicated with Staphylococcus aureus(S.aureus)coinfection in a pre-gnant woman at 34 wk of gestation.Her rapid progression of pulmonary lesions caused severe respiratory failure,and she received noninvasive ventilator-assisted respiratory treatment.Subsequently,we delivered a foetus via emergency caesarean section after accelerating the maturity of the foetal pulmonary system,and the respiratory condition of the puerperant woman significantly improved after the delivery of the foetus.Lavage fluid was taken under tracheoscopy to quickly search for pathogens by the metagenomic nextgeneration sequencing(mNGS),and both COVID-19 and S.aureus were detected.After targeted anti-infective treatment,the maternal condition gradually improved,and the patient was discharged from the hospital.CONCLUSION The coinfection of pregnancy with COVID-19 and bacteria often leads to critical respiratory failure,which is a great challenge in the process of diagnosis and treatment.It is crucial to choose the right time to deliver the foetus and to quickly find pathogens by mNGS.

Diagnosis of tuberculous uveitis by the macrogenome of intraocular fluid:A case report and review of the literature

BACKGROUND Tuberculous uveitis caused by tuberculosis infection factors is common,but tuberculous uveitis caused by Mycobacterium tuberculosis found in the intraocular fluid is rare.This report describes the use of intraocular fluid in the diagnosis of tuberculous uveitis in a patient and reviews the relevant literature.CASE SUMMARY A 24-year-old woman who was 31-wk pregnant visited Hebei Chest Hospital due to intermittent chest pain,fever,and decreased vision for 3 mo.The hydrothorax test suggested“tuberculous pleurisy”,and yellow effusion was extracted from the chest tube twice resulting in a total volume of approximately 800 mL.The patient chose to continue the pregnancy without treatment,and was hospitalized again due to high fever.Following 2 mo of anti-tuberculosis treatment,a healthy boy was delivered by cesarean section.Tuberculous uveitis was diagnosed using tuberculosis Xpert,and intraocular infection was detected by second-generation gene sequencing.Following systemic treatment,the patient gradually improved,and the corrected visual acuity of the left eye gradually increased from 0.08 to 1.0.CONCLUSION The etiology of uveitis is complex,and it is necessary to assess the patient’s general condition and apply molecular biology methods to determine the pathogenesis and guide precise treatment,to improve clinicians’awareness and standardize treatment of the disease.