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Hu X, Jiang L, Liu X, Chang H, Dong H, Yan J, Zhou X, Kong M. The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections. Microbiol Spectr 2024:e0045824. [PMID: 38916357 DOI: 10.1128/spectrum.00458-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/18/2024] [Indexed: 06/26/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
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Affiliation(s)
- Xiaohang Hu
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Liqing Jiang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaowei Liu
- Department of Intensive Care Unit, Affiliated Hospital of Jining Medical University,Jining Medical University, Shandong Jining, China
| | - Hong Chang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Haixin Dong
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Jinyan Yan
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaoya Zhou
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Min Kong
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
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Liu P, Sun K, Li R, Chen X. Case report: A rare case of skin abscess caused by coinfection of Actinobaculum schaalii and Actinomyces turicensis. Front Cell Infect Microbiol 2024; 14:1378197. [PMID: 38601737 PMCID: PMC11004288 DOI: 10.3389/fcimb.2024.1378197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Skin abscess is one of the most common infections of the skin and soft tissues. However, anaerobic bacteria are infrequently identified as the causative agents of this particular form of abscess. In this case, a 34-year-old pregnant woman was diagnosed with a skin abscess with the use of ultrasonography. The microbiological analysis results of the purulent fluid revealed the coinfection of Actinobaculum schaalii and Actinomyces turicensis. The patient was first treated empirically with 3 days of cefathiamidine, which resulted in no symptom improvement. Subsequently, a surgical procedure involving incision and draining was performed, with the administration of ceftriaxone. After 7 days of antibiotic intervention, the patient exhibited a satisfactory recovery. Clinicians need to be aware of other types of infections that might be attributed to Actinobaculum schaalii and Actinomyces turicensis, in addition to urinary tract infections.
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Affiliation(s)
| | | | | | - Xiaodi Chen
- Department of Clinical Laboratory, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical University, Jinan, China
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Imeneo A, Rindi LV, Di Lorenzo A, Cavasio RA, Vitale P, Spalliera I, Dauri M, Biasucci DG, Giuliano I, D'Agostini C, Minelli S, Bossa MC, Altieri A, Andreoni M, Malagnino V, Iannetta M, Sarmati L. Brain abscess caused by Actinomyces turicensis in a non-immunocompromised adult patient: a case report and systematic review of the literature. BMC Infect Dis 2024; 24:109. [PMID: 38245682 PMCID: PMC10799506 DOI: 10.1186/s12879-024-08995-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Actinomyces turicensis is rarely responsible of clinically relevant infections in human. Infection is often misdiagnosed as malignancy, tuberculosis, or nocardiosis, therefore delaying the correct identification and treatment. Here we report a case of a 55-year-old immunocompetent adult with brain abscess caused by A. turicensis. A systematic review of A. turicensis infections was performed. METHODS A systematic review of the literature was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The databases MEDLINE, Embase, Web of Science, CINAHL, Clinicaltrials.gov and Canadian Agency for Drugs and Technology in Health (CADTH) were searched for all relevant literature. RESULTS Search identified 47 eligible records, for a total of 67 patients. A. turicensis infection was most frequently reported in the anogenital area (n = 21), causing acute bacterial skin and skin structure infections (ABSSSI) including Fournier's gangrene (n = 12), pulmonary infections (n = 8), gynecological infections (n = 6), cervicofacial district infections (n = 5), intrabdominal or breast infections (n = 8), urinary tract infections (n = 3), vertebral column infections (n = 2) central nervous system infections (n = 2), endocarditis (n = 1). Infections were mostly presenting as abscesses (n = 36), with or without concomitant bacteremia (n = 7). Fever and local signs of inflammation were present in over 60% of the cases. Treatment usually involved surgical drainage followed by antibiotic therapy (n = 51). Antimicrobial treatments most frequently included amoxicillin (+clavulanate), ampicillin/sulbactam, metronidazole or cephalosporins. Eighty-nine percent of the patients underwent a full recovery. Two fatal cases were reported. CONCLUSIONS To the best of our knowledge, we hereby present the first case of a brain abscess caused by A. turicensis and P. mirabilis. Brain involvement by A. turicensis is rare and may result from hematogenous spread or by dissemination of a contiguous infection. The infection might be difficult to diagnose and therefore treatment may be delayed. Nevertheless, the pathogen is often readily treatable. Diagnosis of actinomycosis is challenging and requires prompt microbiological identification. Surgical excision and drainage and antibiotic treatment usually allow for full recovery.
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Affiliation(s)
- Alessandra Imeneo
- Infectious Diseases, Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | - Lorenzo Vittorio Rindi
- Infectious Diseases, Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | - Andrea Di Lorenzo
- Infectious Diseases, Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | | | - Pietro Vitale
- Infectious Disease Clinic, Policlinico Tor Vergata, Rome, Italy
| | | | - Mario Dauri
- Department of Anaesthesiology, Emergency and Intensive Care Medicine, Policlinico Tor Vergata, Rome, Italy
| | | | - Ilaria Giuliano
- Emergency and Reception Department, Anesthesia and Resuscitation Unit, Policlinico Tor Vergata, Rome, Italy
| | | | - Silvia Minelli
- Laboratory of Clinical Microbiology, Policlinico Tor Vergata, Rome, Italy
| | | | - Anna Altieri
- Laboratory of Clinical Microbiology, Policlinico Tor Vergata, Rome, Italy
| | - Massimo Andreoni
- Infectious Diseases, Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | - Vincenzo Malagnino
- Infectious Diseases, Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | - Marco Iannetta
- Infectious Diseases, Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | - Loredana Sarmati
- Infectious Diseases, Department of Systems Medicine, Tor Vergata University, Rome, Italy.
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Zhan Z, Lin X, Li G, Zeng J, Su D, Liao J, Shen Q. Renal abscess complicating acute pyelonephritis in children: Two cases report and literature review. Medicine (Baltimore) 2023; 102:e36355. [PMID: 38050281 PMCID: PMC10695508 DOI: 10.1097/md.0000000000036355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/26/2023] [Indexed: 12/06/2023] Open
Abstract
RATIONALE To describe the diagnostic and treatment approaches of renal abscesses complicated with acute pyelonephritis in children. PATIENT CONCERNS Two children presented with fever, vomiting, and abdominal pain with no typical manifestations, like frequent urination, urgency, dysuria, hematuria, foam urine, and lumbago. Renal abscess complicating acute pyelonephritis was diagnosed by B-ultrasound and computed tomography enhancement. Moreover, inflammatory markers were elevated significantly, but routine blood and urine cultures were repeatedly negative. The empirical anti-infection therapy had no obvious effect. A pathogenic diagnosis was confirmed in case two, and macro gene detection in blood and urine guided the follow-up treatment. DIAGNOSES Both children were diagnosed with acute gastroenteritis on admission, but renal abscess complicating acute pyelonephritis were diagnosed by imaging examination. INTERVENTIONS Both children were given anti-infection therapy of third-generation cephalosporin, which had no obvious effect. Routine blood and urine cultures were repeatedly negative. Case one was changed to piperacillin sodium tazobactam. We further carried out blood and urinary metagenomic next-generation sequencing detection for case two. Meanwhile, meropenem and linezolid anti-infection treatment was given. The results showed overlapping infection with Escherichia coli and Enterococcus faecalis. According to the genetic test results, amoxicillin clavulanate potassium combined with nitrofurantoin were prescribed after discharge. OUTCOMES Clinical symptoms of the 2 children disappeared, the infection was controlled, and imaging showed that renal abscess complicated with acute pyelonephritis disappeared. LESSONS The clinical spectrum of renal abscess complicating acute pyelonephritis is vague, with no specific manifestations, and can be easily misdiagnosed. B-ultrasound and computed tomography enhancement are helpful in making a definite diagnosis. Moreover, the sensitivity of routine culture is low, and metagenomic next-generation sequencing might be helpful to detect pathogenic microorganisms and guided treatment. Early treatment with broad-spectrum antibiotics might have favorable outcomes.
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Affiliation(s)
- Zhuqin Zhan
- Department of Nephrology, Children’s Hospital of Fudan University Xiamen Branch (Xiamen Children’s Hospital), Xiamen, Fujian, China
| | - Xiaoliang Lin
- Department of Respiratory, Children’s Hospital of Fudan University Xiamen Branch (Xiamen Children’s Hospital), Xiamen, Fujian, China
| | - Guangbo Li
- Department of Nephrology, Children’s Hospital of Fudan University Xiamen Branch (Xiamen Children’s Hospital), Xiamen, Fujian, China
| | - Jinhua Zeng
- Department of Nephrology, Children’s Hospital of Fudan University Xiamen Branch (Xiamen Children’s Hospital), Xiamen, Fujian, China
| | - Dequan Su
- Department of Nephrology, Children’s Hospital of Fudan University Xiamen Branch (Xiamen Children’s Hospital), Xiamen, Fujian, China
| | - Jianying Liao
- Department of Nephrology, Children’s Hospital of Fudan University Xiamen Branch (Xiamen Children’s Hospital), Xiamen, Fujian, China
| | - Qian Shen
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
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Gligorijevic N, Kaljevic M, Radovanovic N, Jovanovic F, Joksimovic B, Singh S, Dumic I. Adrenal Abscesses: A Systematic Review of the Literature. J Clin Med 2023; 12:4601. [PMID: 37510716 PMCID: PMC10380332 DOI: 10.3390/jcm12144601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Objective: To summarize the existing knowledge about adrenal gland abscesses, including etiology, clinical presentation, common laboratory and imaging findings, management and overall morbidity and mortality. Design: Systematic literature review. Methods: We performed a search in the PubMed database using search terms: 'abscess and adrenal glands', 'adrenalitis', 'infection and adrenal gland', 'adrenal abscess', 'adrenal infection' and 'infectious adrenalitis'. Articles from 2017 to 2022 were included. We found total of 116 articles, and after applying exclusion criteria, data from 73 articles was included in the final statistical analysis. Results: Of 84 patients included in this review, 68 were male (81%), with a mean age of 55 years (range: 29 to 85 years). Weight loss was the most frequent symptom reported in 58.3% patients, followed by fever in 49%. Mean duration of symptoms was 4.5 months. The most common laboratory findings were low cortisol (51.9%), elevated ACTH (43.2%), hyponatremia (88.2%) and anemia (83.3%). Adrenal cultures were positive in 86.4% cases, with Histoplasma capsulatum (37.3%) being the leading causative agent. Blood cultures were positive in 30% of patients. The majority of the adrenal infections occurred through secondary dissemination from other infectious foci and abscesses were more commonly bilateral (70%). A total of 46.4% of patients developed long-term adrenal insufficiency requiring treatment. Abscess drainage was performed in 7 patients (8.3%) and adrenalectomy was performed in 18 (21.4%) patients. The survival rate was 92.9%. Multivariate analysis showed that the only independent risk factor for mortality was thrombocytopenia (p = 0.048). Conclusion: Our review shows that adrenal abscesses are usually caused by fungal pathogens, and among these, Histoplasma capsulatum is the most common. The adrenal glands are usually involved in a bilateral fashion and become infected through dissemination from other primary sources of infection. Long-term adrenal insufficiency develops in 46% of patients, which is more common than what is observed in non-infectious etiology of adrenal gland disorders. Mortality is about 7%, and the presence of thrombocytopenia is associated with worse prognosis. Further prospective studies are needed to better characterize optimal testing and treatment duration in patients with this relatively rare but challenging disorder.
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Affiliation(s)
- Nikola Gligorijevic
- Division of General Internal Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Marija Kaljevic
- Department of Hospital Medicine, Saint Francis Hospital and Medical Center, Hartford, CT 06105, USA
- Division of Internal Medicine, University of Connecticut, Farmington, CT 06030, USA
| | - Natasa Radovanovic
- Department of Endocrinology, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Filip Jovanovic
- Department of Internal Medicine, Merit Health Wesley, Hattiesburg, MS 39402, USA
| | - Bojan Joksimovic
- Department of Pathological Physiology, Faculty of Medicine Foca, University of East Sarajevo, 73300 Foca, Bosnia and Herzegovina
| | - Sandra Singh
- Clinic for Endocrinology, Diabetes and Metabolic Diseases, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Igor Dumic
- Department of Hospital Medicine, Mayo Clinic Health System, Eau Claire, WI 54703, USA
- Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
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Jia K, Huang S, Shen C, Li H, Zhang Z, Wang L, Zhao G, Wu Z, Lin Y, Xia H, Tang M, Yang H, Hu H. Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS). Front Cell Infect Microbiol 2023; 13:1119020. [PMID: 36936777 PMCID: PMC10020507 DOI: 10.3389/fcimb.2023.1119020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce. Methods The medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms. Results In the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients. Conclusions mNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.
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Affiliation(s)
- Kaipeng Jia
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shiwang Huang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Chong Shen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Hongjun Li
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhe Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Lei Wang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Gangjian Zhao
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhouliang Wu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuda Lin
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Mingze Tang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Huifen Yang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
| | - Hailong Hu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
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Chen S, Kang Y, Li D, Li Z. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis. Int J Infect Dis 2022; 122:867-873. [PMID: 35907477 DOI: 10.1016/j.ijid.2022.07.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022] Open
Abstract
BACKGROUND The identification of pathogens in patients with pulmonary infection has always been a major challenge in medicine. Compared with sputum and throat swabs, bronchoalveolar lavage fluid (BALF) can better reflect the actual state in the lungs. However, there has not been a meta-analysis of the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in detecting pathogens in BALF from patients with pulmonary infections. METHODS Data sources were PubMed, Web of Science, Embase, and the China National Knowledge Infrastructure. The pooled sensitivity and specificity were estimated by using random-effects or fixed-effect models. Subgroup analysis was performed to reveal the effect of potential explanatory factors on the diagnostic performance measures. RESULTS The pooled sensitivity was 78% (95% confidence interval: 67-87%; I2 = 92%) and the pooled specificity was 77% (95% confidence interval: 64-94%; I2 = 74%) for mNGS. Subgroup analyses for the sensitivity of mNGS revealed that patients with pulmonary infections who were severely ill or immunocompromised significantly affected heterogeneity (P < 0.001). The positive detection rate of mNGS for pathogens in BALF of severely or immunocompromised pulmonary-infected patients was 92% (95% confidence interval: 78-100%). CONCLUSION mNGS has high diagnostic performance for BALF pathogens in patients with pulmonary infections, especially in critically ill or immunocompromised patients.
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Affiliation(s)
- Shenglin Chen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China
| | - Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China.
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Gubbiotti MA, LiVolsi V, Montone K, Baloch Z. A Cyst-ematic Analysis of the Adrenal Gland: A Compilation of Primary Cystic Lesions From Our Institution and Review of the Literature. Am J Clin Pathol 2022; 157:531-539. [PMID: 34596217 DOI: 10.1093/ajcp/aqab156] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES Although primary adrenal lesions and metastases are most commonly encountered, de novo cysts of the adrenal gland can occasionally occur. METHODS We analyzed the pathology archives at the Hospital of the University of Pennsylvania for diagnoses of cystic lesions of the adrenal gland between 1998 and 2020. Patient demographics and clinical information were extracted, and pathology slides and stains, as appropriate, were analyzed. The literature between 1998 and 2020 was also searched for large case series involving cystic adrenal lesions. RESULTS We found 18 cystic lesions of the adrenal gland in our archives, categorized as pseudocysts (7), endothelial cysts (5), mesothelial cysts (2), mature teratoma (1), cystic adrenal cortical adenoma (1), cystic pheochromocytoma (1), and cystic metastasis (1). The mean age at time of diagnosis was 52.3 years, and the mean size of the cysts was 6.0 cm. There was a slight female predilection, and cysts were more likely to be found on the left side. All lesions were incidental findings. The cystic metastasis was clear cell renal cell carcinoma. Our findings were also compared with those found in the literature published within the same timeframe. CONCLUSIONS Adrenal cysts are rare entities. Our findings are concordant with other large studies and provide additional cases to the existing literature. In addition, our literature search expands the possible differential diagnoses for cystic lesions arising in the adrenal gland.
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Affiliation(s)
| | - Virginia LiVolsi
- Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen Montone
- Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Zubair Baloch
- Hospital of the University of Pennsylvania, Philadelphia, PA, USA
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Zhu Y, Xu M, Ding C, Peng Z, Wang W, Sun B, Cheng J, Chen C, Chen W, Wei H, Hu Z. Metagenomic Next-Generation Sequencing vs. Traditional Microbiological Tests for Diagnosing Varicella-Zoster Virus Central Nervous System Infection. Front Public Health 2022; 9:738412. [PMID: 35127608 PMCID: PMC8814106 DOI: 10.3389/fpubh.2021.738412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/03/2021] [Indexed: 11/27/2022] Open
Abstract
Background Unbiased metagenomic next-generation sequencing (mNGS) detects pathogens in a target-independent manner. It is not well-understood whether mNGS has comparable sensitivity to target-dependent nucleic acid test for pathogen identification. Methods This study included 31 patients with chickenpox and neurological symptoms for screening of possible varicella-zoster virus (VZV) central nervous system (CNS) infection. Microbiological diagnosing of VZV cerebrospinal fluid (CSF) infection was performed on stored CSF samples using mNGS, quantitative and qualitative VZV-specific PCR assays, and VZV IgM antibodies test. Results The median age was 30.0 [interquartile range (IQR), 24.3–33.3] years. 51.6% of the patients were men. About 80.6% of the patients had normal CSF white blood cell counts (≤ 5 × 106/L). VZV IgM antibodies presented in 16.1% of the CSF samples, and nucleic acids were detectable in 16.1 and 9.7% using two different VZV-specific real-time PCR protocols. Intriguingly, maximal identification of VZV elements was achieved by CSF mNGS (p = 0.001 and p = 007; compared with qualitative PCR and VZV IgM antibody test, respectively), with sequence reads of VZV being reported in 51.6% (16/31) of the CSF samples. All VZV PCR positive samples were positive when analyzed by mNGS. Of note, human betaherpesvirus 6A with clinical significance was unexpectedly detected in one CSF sample. Conclusions Our study suggests that CSF mNGS may have higher sensitivity for VZV detection than CSF VZV PCR and antibody tests, and has the advantage of identifying unexpected pathogens.
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Affiliation(s)
- Yunqi Zhu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Miaomiao Xu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chengyuan Ding
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhihang Peng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Weixiao Wang
- Department of Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Binghu Sun
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian Cheng
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chen Chen
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Chen
- Department of Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongxia Wei
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Hongxia Wei
| | - Zhiliang Hu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Zhiliang Hu
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10
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Tabaksert A, Kumar R, Raviprakash V, Srinivasan R. Actinomyces turicensis parapharyngeal space infection in an immunocompetent host: first case report and review of literature. Access Microbiol 2021; 3:000241. [PMID: 34595393 PMCID: PMC8479964 DOI: 10.1099/acmi.0.000241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/27/2021] [Indexed: 11/18/2022] Open
Abstract
Actinomyces are common commensals of the oral cavity, gastrointestinal tract and urogenital tract. They are anaerobic, Gram-positive, non-acid-fast bacilli, which can cause invasive infection and abscesses. We present the first reported case of supraglottitis and deep neck space abscess formation secondary to Actinomyces turicensis infection. The patient was managed with intravenous antibiotics, incision and drainage of a left parapharyngeal abscess and subsequent mediastinal abscess. After 6 weeks in hospital, the patient was successfully discharged to complete a 6-month course of oral amoxicillin.
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Affiliation(s)
- Ayla Tabaksert
- Department of Otolaryngology, Darlington Memorial Hospital, Darlington, UK
| | - Ravi Kumar
- Department of Otolaryngology, Darlington Memorial Hospital, Darlington, UK
| | - Veena Raviprakash
- Department of Microbiology, Darlington Memorial Hospital, Darlington, UK
| | - Rajeev Srinivasan
- Department of Otolaryngology, Darlington Memorial Hospital, Darlington, UK
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11
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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12
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Wu H, Wei J, Yu D. Application of NGS in Diagnosis of Tuberculous Pleurisy with Multiple Negative Tests: A Case Report. Infect Drug Resist 2020; 13:3543-3550. [PMID: 33116673 PMCID: PMC7553599 DOI: 10.2147/idr.s269779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Background Tuberculous pleurisy is inflammation caused by direct infection of Mycobacterium tuberculosis (MTB) and/or delayed allergic reaction of the pleura to MTB thallus components. The diagnosis of tuberculous pleurisy is mainly confirmed by bacterial culture, smear staining or histopathology, but has some clinical limitations. Next-generation sequencing (NGS), as a new diagnostic technology, has good application prospects in the diagnosis of tuberculous pleurisy. Case Presentation A patient admitted with right pleural effusion and pneumonia was actively treated with anti-infection, anti-inflammatory and symptomatic support while various etiological tests of right pleural effusion were improved. However, all the etiological tests for MTB infection were negative. At this time, the patient’s condition worsened and pleural effusion also appeared on the left side. In order to clarify the cause of the disease as soon as possible and prevent the disease from worsening again, the left and right pleural effusions of the patient were sent for NGS testing. The test results suggested MTB infection, which finally clarified the diagnosis of tuberculous pleurisy, and the next treatment plan of the patient was timely adjusted. Conclusion NGS is instructive in the diagnosis of tuberculous pleurisy when various conventional tests and imaging methods fail.
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Affiliation(s)
- Honglin Wu
- Department of Respiratory Medicine, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.,Department of Gastroenterology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China
| | - Jiahui Wei
- Department of Respiratory Medicine, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China
| | - Dujuan Yu
- Department of Respiratory Medicine, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China
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