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Zou S, Chen Z, Tan Y, Tan M, Guo W, Wu S, Liu J, Song S, Peng Y, Wang M, Liang K. Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection. HIV Med 2024. [PMID: 38515324 DOI: 10.1111/hiv.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/02/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated. METHODS We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups. RESULTS Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001). CONCLUSION CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.
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Affiliation(s)
- Shi Zou
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhong Chen
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Yuting Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Miao Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Guo
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Songjie Wu
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Liu
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Shihui Song
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongquan Peng
- Graduate Collaborative Training Base of the First Hospital of Changsha, Hengyang Medical School, Uni-versity of South China, Hengyang, China
| | - Min Wang
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Ke Liang
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
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Zeng X, Liang Y, Wang H, Chen J, Xu Y, Ou Q, Yin J, Zhuang J, Xiong W, Tang L, Li X, Tong G, Lei L, Jian X. Detection of pathogens from venous or arterial blood of patients with left-sided infective endocarditis by metagenomic next-generation sequencing: A prospective study. Clin Chim Acta 2024; 552:117698. [PMID: 38072301 DOI: 10.1016/j.cca.2023.117698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Infective endocarditis is a life-threatening uncommon infectious disease, and we aimed to explore the clinical utility of venous or arterial blood-based metagenomic next-generation sequencing (mNGS) approaches to diagnose left-sided infective endocarditis (LSIE). METHODS We prospectively studied 79 LSIE patients who received valvular surgery in our hospital. Results of blood culture, valve culture, venous blood-based mNGS, arterial blood-based mNGS, venous blood-based mNGS plus blood culture, and arterial blood-based mNGS plus blood culture were evaluated and compared. RESULTS Both venous blood- and arterial blood-based mNGS methods displayed significantly higher positive detection rates than blood culture and valve culture (43.0 %, 49.4 % vs. 32.9 %, 19.0 %; P < 0.001). Strikingly, when combining blood-based mNGS and blood culture, the positive rate could be further improved to more than 60 %. Moreover, we found mNGS LSIE detection was closely associated with preoperative leukocyte (P = 0.027), neutrophil value (P = 0.018), vegetation ≥ 14 mm (P = 0.043), and vegetations in aortic valve (P = 0.048). In addition, we discovered that blood-based mNGS had a superir capacity over blood culture to detect gram-negative bacteria, fungi, Bartonella Quintana, and mixed infections than blood culture. CONCLUSION This study indicates that venous blood- and arterial blood-based mNGS displayed high positive rate in the rapid detection of pathogens in high-risk LSIE patients.
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Affiliation(s)
- Xiaodong Zeng
- Department of Cardiac Surgical Intensive Care Unit, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
| | - Yuemei Liang
- Guangzhou Health Science College, Guangzhou, Guangdong, 510000, China
| | - Han Wang
- Department of Cardiac Surgical Intensive Care Unit, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
| | - Jimei Chen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China; Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangzhou, 510080, P.R. China
| | - Yang Xu
- Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Qiuxiang Ou
- Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Jia Yin
- Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China; Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangzhou, 510080, P.R. China
| | - Weiping Xiong
- Department of Cardiac Surgical Intensive Care Unit, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
| | - Lili Tang
- Department of Cardiac Surgical Intensive Care Unit, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
| | - Xueming Li
- Department of Cardiac Surgical Intensive Care Unit, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
| | - Guang Tong
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China
| | - Liming Lei
- Department of Cardiac Surgical Intensive Care Unit, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China; Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangzhou, 510080, P.R. China.
| | - Xuhua Jian
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, P.R. China.
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Ju C, Wang L, Xu P, Wang X, Xiang D, Xu Y, Xu X, Chen R, He J. Differentiation between lung allograft rejection and infection using donor-derived cell-free DNA and pathogen detection by metagenomic next-generation sequencing. Heliyon 2023; 9:e22274. [PMID: 38053854 PMCID: PMC10694331 DOI: 10.1016/j.heliyon.2023.e22274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023] Open
Abstract
Background In lung transplant recipients (LTRs), the primary causes of mortality are rejection and infection, which often present similar symptoms, making differentiation challenging. This study aimed to explore the diagnostic efficacy of plasma donor-derived cell-free DNA (dd-cfDNA) in conjunction with metagenomic next-generation sequencing (mNGS) for pathogen detection in differentiation between lung allograft rejection and infection in LTRs experiencing new-onset pulmonary complications. Methods We conducted a retrospective study on 188 LTRs who underwent lung or heart-lung transplantation at our institution from 2015 to 2021. The LTRs were categorized into three groups: stable, rejection, and infection. We measured plasma dd-cfDNA levels and utilized both mNGS and culture methods to identify pathogens in the bronchoalveolar lavage fluid (BALF). Results The rejection group exhibited the highest levels of plasma dd-cfDNA (median 1.34 %, interquartile range [IQR] 1.06-2.19 %) compared to the infection group (median 0.72 %, IQR 0.62-1.07 %) and the stable group (median 0.69 %, IQR 0.58-0.78 %) (both p < 0.001). Within the infection group, a significantly higher level of dd-cfDNA was observed in the cytomegalovirus infection subgroup (p < 0.001), but not in the fungal (p > 0.05) or bacterial infection subgroups (p > 0.05), when compared to the stable group. Elevated dd-cfDNA levels, in combination with negative mNGS results, strongly indicated lung allograft rejection, with a positive predictive value and negative predictive value of 88.7 % and 99.2 %, respectively. Conclusions Plasma dd-cfDNA in combination with BALF pathogen detection by mNGS shows satisfactory accuracy in differentiating lung allograft rejection from infectious complications.
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Affiliation(s)
- Chunrong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lulin Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peihang Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaohua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dong Xiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rongchang Chen
- Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Jianxing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Li J, Zhang C, Lu M, Wang Y, Wang W, Liu F, Wu S, Liu Y, Fan M, Li K. The diverse genetic genotypes of Bartonella species circulating in rodents from Inner Mongolia, Northern China. PLoS Negl Trop Dis 2023; 17:e0011462. [PMID: 37384796 DOI: 10.1371/journal.pntd.0011462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023] Open
Abstract
Bartonella are generally recognized as zoonotic pathogens of mammals, including many rodent species. However, data on the genetic diversity of Bartonella in some regions are still absent in China. In this study, we collected rodent samples (Meriones unguiculatus, Spermophilus dauricus, Eolagurus luteus, and Cricetulus barabensis) from Inner Mongolia located in Northern China. The Bartonella were detected and identified by sequencing the gltA, ftsZ, ITS, and groEL genes in them. An overall 47.27% (52/110) positive rate was observed. This may be the first report that M. unguiculatus and E. luteus harbor Bartonella. Phylogenetic and genetic analysis on gltA, ftsZ, ITS, and groEL genes indicated that the strains were divided into seven distinct clades, suggesting the diverse genetic genotypes of Bartonella species in this area. Of those, Clade 5 meets the criteria for identification as a novel species based on gene sequence dissimilarity to known Bartonella species and herein we name it "Candidatus Bartonella mongolica".
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Affiliation(s)
- Jianyun Li
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot City, Inner Mongolia Autonomous Region, China
| | - Chenxi Zhang
- Inner Mongolia Medical University, Huhehot City, Inner Mongolia Autonomous Region, China
| | - Miao Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing City, China
| | - Yu Wang
- Inner Mongolia Agricultural University, Huhehot City, Inner Mongolia Autonomous Region, China
| | - Wen Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing City, China
| | - Fang Liu
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot City, Inner Mongolia Autonomous Region, China
| | - Shaoqing Wu
- Ulanqab Center for Disease Control and Prevention, Ulanqab City, Inner Mongolia Autonomous Region, China
| | - Yang Liu
- Baotou Medical College, Baotou City, Inner Mongolia Autonomous Region, China
| | - Mengguang Fan
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot City, Inner Mongolia Autonomous Region, China
| | - Kun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing City, China
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5
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Fraz MSA, Dahle G, Skaug KM, Jarraud S, Frye S, Bjørnholt JV, Nordøy I. Case report: A prosthetic valve endocarditis caused by Legionella bozemanae in an immunocompetent patient. Front Med (Lausanne) 2022; 9:1055465. [DOI: 10.3389/fmed.2022.1055465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Extrapulmonary infections with Legionella species are rare, but important to acknowledge. We report a case of infective endocarditis (IE) with Legionella bozemanae in a 66-year-old immunocompetent man with an aortic homograft. The diagnosis was made by direct 16S rRNA gene amplification from valve material, confirmed by a targeted Legionella-PCR in serum and the detection of L. bozemanae specific antibodies. To our knowledge, this is the first confirmed case of IE with L. bozemanae as causative pathogen. The infected aortic prosthesis was replaced by a homograft, and the patient was successfully treated with levofloxacin and azithromycin for 6 weeks.
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Zeng X, Wu J, Li X, Xiong W, Tang L, Li X, Zhuang J, Yu R, Chen J, Jian X, Lei L. Application of Metagenomic Next-Generation Sequencing in the Etiological Diagnosis of Infective Endocarditis During the Perioperative Period of Cardiac Surgery: A Prospective Cohort Study. Front Cardiovasc Med 2022; 9:811492. [PMID: 35369282 PMCID: PMC8965566 DOI: 10.3389/fcvm.2022.811492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Objective The present study aimed to prospectively evaluate the role of metagenomic next-generation sequencing (mNGS) in the etiological diagnosis of patients with perioperative infective endocarditis (IE). Methods From May 1st, 2019 to December 31st, 2020, a total of 99 patients with IE were enrolled in the present study according to the modified Duke criteria, etiological, and pathological results. 11 non-IE patients undergoing heart valve surgery in the same period were selected as the control group. A blood culture test was performed immediately after admission, and the valves harvested operatively were examined by blood culture and mNGS. Results In the IE group, there were 29 cases (29.3%) with positive blood culture, 16 cases (16.2%) with positive valve culture, and 85 cases (85.9%) with positive valve mNGS. Compared to culture-based detection, mNGS achieved better performance with a sensitivity, specificity, area under the curve (AUC) of 0.859, 0.727, and 0.793, respectively. The combined approach using culture and mNGS further improved the diagnostic accuracy (sensitivity 89.9%, specificity 72.7%, AUC 0.813). Preoperative white blood cell (P = 0.029) and neutrophils (P = 0.046) were identified as independent factors affecting the detection rate of mNGS. In the mNGS-positive group, 95 strains of pathogens were found and 10 cases were identified with mixed infection. There were 72 gram-positive bacteria and 14 gram-negative bacteria. mNGS positive group displayed higher species richness than mNGS negative group with enrichment of Streptococcus sanguis, Streptococcus buccalis, and Streptococcus griseus. Proteobacteria and Actinomycetes were enriched in mNGS negative group. Notably, six patients showed disconcordant results between culture and mNGS. Rothia aeria was identified in the blood culture, valve culture, and valve mNGS in one patient. Bartonella Quintana and Coxiella burnetii, which were fastidious intracellular bacteria, were found in two blood and valve culture-negative cases. Conclusions mNGS outperformed the conventional culture method and displayed high accuracy in detecting pathogens in IE patients. This study provided support for the use of mNGS in the etiological diagnosis of IE.
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Affiliation(s)
- Xiaodong Zeng
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jinlin Wu
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xin Li
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Weiping Xiong
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Lili Tang
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xueming Li
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | | | - Jimei Chen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Xuhua Jian
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liming Lei
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
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Podgórska A, Kordybach-Prokopiuk M, Jaworska-Wilczyńska M, Hoffman P, Biernacka K, Kuśmierski K, Kuthan R, Hryniewiecki T, Lutyńska A. The First Case of Granulicatella adiacens Identified from a Resected Heart Valve by Next Generation Sequencing (NGS) in Poland. Pathogens 2022; 11:pathogens11030295. [PMID: 35335619 PMCID: PMC8950401 DOI: 10.3390/pathogens11030295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
In this report, we describe the course and successful treatment of a case of complicated infective endocarditis (IE). A patient presented with a high-grade, irregular fever with chills lasting at least 2 months along with dyspnoea, chest pain, fatigue, weight loss, and night sweats during the previous 3 months. As well as cardiac congenital disorders, he was found to have Granulicatella adiacens infective aortic valve endocarditis, presumably transmitted from the oral cavity niche. Validated metagenomic 16S rDNA next generation sequencing was used to perform taxonomic identification, allowing for specific adequate antibiotic therapy instead of empiric therapy. This paper highlights the critical role of rapid taxonomic identification of nutritionally variant streptococci and the benefit of proper IE treatment in avoiding relapses or fatal complications.
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Affiliation(s)
- Anna Podgórska
- Department of Medical Biology, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland;
- Correspondence:
| | - Maria Kordybach-Prokopiuk
- Department of Congenital Heart Diseases, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland; (M.K.-P.); (P.H.); (K.B.)
| | - Maria Jaworska-Wilczyńska
- Department of Valvular Heart Disease, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland; (M.J.-W.); (T.H.)
| | - Piotr Hoffman
- Department of Congenital Heart Diseases, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland; (M.K.-P.); (P.H.); (K.B.)
| | - Katarzyna Biernacka
- Department of Congenital Heart Diseases, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland; (M.K.-P.); (P.H.); (K.B.)
| | - Krzysztof Kuśmierski
- Department of Cardiac Surgery and Transplantology, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland;
| | - Robert Kuthan
- Department of Medical Microbiology, Medical University of Warsaw, 5 Chałubińskiego Street, 02-004 Warsaw, Poland;
| | - Tomasz Hryniewiecki
- Department of Valvular Heart Disease, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland; (M.J.-W.); (T.H.)
| | - Anna Lutyńska
- Department of Medical Biology, National Institute of Cardiology, Stefan Cardinal Wyszyński State Research Institute, 42 Alpejska Street, 04-628 Warsaw, Poland;
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Ju CR, Lian QY, Guan WJ, Chen A, Zhang JH, Xu X, Chen RC, Li SY, He JX. Metagenomic Next-Generation Sequencing for Diagnosing Infections in Lung Transplant Recipients: A Retrospective Study. Transpl Int 2022; 35:10265. [PMID: 35221789 PMCID: PMC8866178 DOI: 10.3389/ti.2022.10265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022]
Abstract
Background: Accurate identification of pathogens is essential for the diagnosis and control of infections. We aimed to compare the diagnostic performance of metagenomic next-generation sequencing (mNGS) and conventional detection methods (CDM) in lung transplant recipients (LTRs).Methods: We retrospectively analyzed 107 LTRs with suspected infection of pulmonary, blood, central nervous system or chest wall between March 2018 and November 2020. Bronchoalveolar lavage fluid and other body fluids were subject to pathogen detection by both mNGS and CDM.Results: Of the 163 specimens, 84 (51.5%) tested positive for both mNGS and culture, 19 (11.7%) of which were completely consistent, 44 (27.0%) were partially congruent, and 21 (12.9%) were discordant (kappa = .215; p = .001). Compared with CDM, mNGS detected a higher diversity of pathogens. Moreover, the turn-around time was significantly shorter for mNGS compared with culture (2.7 ± .4 vs. 5.5 ± 1.6 days, p < .001). As an auxiliary method, treatment strategies were adjusted according to mNGS findings in 31 cases (29.0%), including eight patients with non-infectious diseases, who were finally cured.Conclusion: mNGS can identify pathogens with a shorter turn-around time and therefore provide a more accurate and timely diagnostic information to ascertaining pulmonary infections. mNGS might have a role in differentiating infectious from non-infectious lung diseases in LTRs.
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Affiliation(s)
- Chun-Rong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiao-Yan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Heng Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rong-Chang Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Shi-Yue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shi-Yue Li, ; Jian-Xing He,
| | - Jian-Xing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shi-Yue Li, ; Jian-Xing He,
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9
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Santibáñez P, García-García C, Portillo A, Santibáñez S, García-Álvarez L, de Toro M, Oteo JA. What Does 16S rRNA Gene-Targeted Next Generation Sequencing Contribute to the Study of Infective Endocarditis in Heart-Valve Tissue? Pathogens 2021; 11:34. [PMID: 35055982 DOI: 10.3390/pathogens11010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
Infective endocarditis (IE) is a severe and life-threatening disease. Identification of infectious etiology is essential for establishing the appropriate antimicrobial treatment and decreasing mortality. The aim of this study was to explore the potential utility of metataxonomics for improving microbiological diagnosis of IE. Here, next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene was performed in 27 heart valve tissues (18 natives, 5 intravascular devices, and 4 prosthetics) from 27 patients diagnosed with IE (4 of them with negative blood cultures). Metataxonomics matched with conventional diagnostic techniques in 24/27 cases (88.9%). The same bacterial family was assigned to 24 cases; the same genus, to 23 cases; and the same species, to 13 cases. In 22 of them, the etiological agent was represented by percentages > 99% of the reads and in two cases, by ~70%. Staphylococcus aureus was detected in a previously microbiological undiagnosed patient. Thus, microbiological diagnosis with 16S rRNA gene targeted-NGS was possible in one more sample than using traditional techniques. The remaining two patients showed no coincidence between traditional and 16S rRNA gene-targeted NGS microbiological diagnoses. In addition, 16S rRNA gene-targeted NGS allowed us to suggest coinfections that were supported by clinical data in one patient, and minority records also verified mixed infections in three cases. In our series, metataxonomics was valid for the identification of the causative agents, although more studies are needed before implementation of 16S rRNA gene-targeted NGS for the diagnosis of IE.
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Albloshi AMK, Alqumber MAA. Infective endocarditis: Role of molecular techniques in early diagnosis. Saudi J Biol Sci 2021; 28:6844-6852. [PMID: 34866984 PMCID: PMC8626217 DOI: 10.1016/j.sjbs.2021.07.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022] Open
Abstract
Infective endocarditis (IE), a heart valve infection primarily caused by bacteria such as streptococci or staphylococci, causes significant morbidity and mortality. Despite the long-term use of broad-spectrum antimicrobials, the infection is often difficult to manage. The latest diagnostic modalities for IE are discussed in this study. Blood culture use in pathogen identification can lead to loss of precious time as well as generation of false negative reports. The first steps in diagnosis are blood cultures and echocardiography, but molecular techniques can be extremely useful and may be used for an accurate and early diagnosis.
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Affiliation(s)
| | - Mohammed A A Alqumber
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Saudi Arabia
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11
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Lian QY, Chen A, Zhang JH, Guan WJ, Xu X, Wei B, Huang DX, He JX, Ju CR. High-throughput next-generation sequencing for identifying pathogens during early-stage post-lung transplantation. BMC Pulm Med 2021; 21:348. [PMID: 34742287 PMCID: PMC8572506 DOI: 10.1186/s12890-021-01723-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput next-generation sequencing (HT-NGS) has the potential to detect a large variety of pathogens; however, the application of HT-NGS in lung transplant (LTx) recipients remains limited. We aimed to evaluate the value of HT-NGS for pathogen detection and diagnosis of pulmonary infection during early-stage post-lung transplantation. METHODS In this retrospective study, we enrolled 51 LTx recipients who underwent lung transplantation between January 2020 and December 2020. Bronchoalveolar lavage fluid (BALF) samples were collected for the detection of pathogens using both HT-NGS and conventional microbiological testing. The detection of pathogens and diagnostic performance of HT-NGS were compared with that of conventional methods. RESULTS HT-NGS provided a higher positive rate of pathogen detection than conventional microbiological testing (88.24% vs. 76.47%). The most common bacteria detected via HT-NGS during early-stage post-lung transplantation were Enterococcus, Staphylococcus, Pseudomonas and Klebsiella, while all fungi were Candida and all viruses were Herpesvirus. Uncommon pathogens, including Strongyloides, Legionella, and Mycobacterium abscesses were identified by HT-NGS. The sensitivity of HT-NGS for diagnosing pulmonary infection was significantly higher than that of conventional microbiological testing (97.14% vs. 68.57%; P < 0.001). For three LTx recipients, treatment regimens were adjusted according to the results of HT-NGS, leading to a complete recovery. CONCLUSION HT-NGS is a highly sensitive technique for pathogen detection, which may provide diagnostic advantages, especially in LTx recipients, contributing to the optimization of treatment regimens against pulmonary infection during early-stage post-lung transplantation.
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Affiliation(s)
- Qiao-Yan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Heng Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bing Wei
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dan-Xia Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Xing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Chun-Rong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Rodríguez-García R, Rodríguez-Esteban MÁ, Fernández-Suárez J, Morilla A, García-Carús E, Telenti M, Morales C, Albaiceta GM, Fernández J. Evaluation of 16S rDNA Heart Tissue PCR as a Complement to Blood Cultures for the Routine Etiological Diagnosis of Infective Endocarditis. Diagnostics (Basel) 2021; 11:1372. [PMID: 34441306 PMCID: PMC8394467 DOI: 10.3390/diagnostics11081372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/18/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative pathogen is required to optimize the effective therapy in infective endocarditis (IE). The aim of this study was to assess a 16S rDNA PCR to identify bacteria from heart valve tissues and to evaluate its usefulness as a complement to blood and removed valves cultures. A total of 266 patients diagnosed with IE from January 2015 to December 2019 were evaluated. Results between 16S rDNA PCR from heart valve tissues were compared with microbiological cultures. Blood cultures were positive in 83.5% of patients diagnosed with IE, while 39.6% and 71.8% of the evaluated heart valve samples were positive by culture and 16S rDNA PCR, respectively. For 32 (12%) patients, 16S rDNA tissue PCR provided valuable information supporting the results of blood cultures in the case of bacteria characteristic from the skin microbiota. Additionally, a microorganism was identified by using 16S rDNA PCR in 36% of blood culture-negative cases. The present study reveals that molecular diagnosis using 16S rDNA tissue PCR provides complementary information for the diagnosis of IE, and it should be recommended in surgical endocarditis, especially when blood cultures are negative.
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Affiliation(s)
- Raquel Rodríguez-García
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (R.R.-G.); (M.Á.R.-E.); (G.M.A.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - María Ángeles Rodríguez-Esteban
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (R.R.-G.); (M.Á.R.-E.); (G.M.A.)
| | - Jonathan Fernández-Suárez
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
| | - Ana Morilla
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
| | - Enrique García-Carús
- Servicio de Medicina Interna, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Mauricio Telenti
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
| | - Carlos Morales
- Servicio de Cirugía Cardiaca, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Guillermo Muñiz Albaiceta
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (R.R.-G.); (M.Á.R.-E.); (G.M.A.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220 Madrid, Spain
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33003 Oviedo, Spain
| | - Javier Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Servicio de Microbiología Clínica, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (J.F.-S.); (A.M.); (M.T.)
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Gomes C, Pons MJ, Del Valle-Mendoza J, Matsuoka M, Ruiz J. Immunogenic Peptides from Pap31 and SCS-α of Bartonella bacilliformis: One Step Closer to a Rapid Diagnostic Tool for Carrion's Disease. Pathogens 2021; 10:917. [PMID: 34451381 DOI: 10.3390/pathogens10080917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 11/17/2022] Open
Abstract
Bartonella bacilliformis is the causal agent of Carrion’s disease, an overlooked illness endemic in the Andean Mountains with Peru being the most affected country. The diagnostic of this illness is a challenge due to the limited resources and the common symptomatology with other infectious diseases. The goal of this study was to identify immunogenic peptides from Pap31 and succinyl-CoA synthetase α (SCS-α) of B. bacilliformis that might be suitable for developing a serologic tool. The immunodominant character of Pap31 and SCS-α was determined by Western blotting and in-silico analysis. Subsequently, 35 peptides were selected for epitope mapping and their immunoreactivity was tested by enzyme-linked immunosorbent assay (ELISA). A total of 30 sera were tested including pre-exposed people with high IgM levels for Pap31/SCS-α (23 sera), patients (2 sera) as well as 5 sera with no reactivity to Pap31/SCS-α. The results indicate that Pap31-8 (187QAIGSAILKGTKDTGT202) and SCS-α-12 (59IFASVAEGKEKTGANA74) are the most immunogenic peptides, with Pap31-8 showing potential to discriminate between B. bacilliformis and the remaining Bartonella spp., and SCS-α-12 differentiating Bartonella spp. from other microorganisms.
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