1
|
Lv T, Zhao Q, Liu J, Wang S, Wu W, Miao L, Zhan P, Chen X, Huang M, Ye M, Ou Q, Zhang Y. Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice. Infection 2024; 52:625-636. [PMID: 38368306 DOI: 10.1007/s15010-024-02185-1] [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: 07/13/2023] [Accepted: 01/12/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Infectious etiologies of lower respiratory tract infections (LRTIs) by the conventional microbiology tests (CMTs) can be challenging. Metagenomic next-generation sequencing (mNGS) has great potential in clinical use for its comprehensiveness in identifying pathogens, particularly those difficult-to-culture organisms. METHODS We analyzed a total of 205 clinical samples from 201 patients with suspected LRTIs using mNGS in parallel with CMTs. mNGS results were used to guide treatment adjustments for patients who had negative CMT results. The efficacy of treatment was subsequently evaluated in these patients. RESULTS mNGS-detected microorganisms in 91.7% (188/205) of the clinical samples, whereas CMTs demonstrated a lower detection rate, identifying microorganisms in only 37.6% (77/205) of samples. Compared to CMT results, mNGS exhibited a detection sensitivity of 93.5% and 95.4% in all 205 clinical samples and 180 bronchoalveolar lavage fluid (BALF) samples, respectively. A total of 114 patients (114/201; 56.7%) showed negative CMT results, among which 92 received treatment adjustments guided by their positive mNGS results. Notably, 67.4% (62/92) of patients demonstrated effective treatment, while 25% (23/92) experienced a stabilized condition. Subgroup analysis of cancer patients revealed that 41.9% (13/31) exhibited an effective response to treatment, and 35.5% (11/31) maintained a stable condition following medication adjustments guided by mNGS. CONCLUSION mNGS demonstrated great potential in identifying microorganisms of clinical significance in LRTIs. The rapid turnaround time and reduced susceptibility to the impact of antimicrobial administration make mNGS a valuable supplementary tool for diagnosis and treatment decision-making for suspected LRTIs in clinical practice.
Collapse
Affiliation(s)
- Tangfeng Lv
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Qi Zhao
- Department of Pulmonary and Critical Care Medicine, Nanjing Drum Tower Hospital, Nanjing, 210008, Jiangsu, China
| | - Jia Liu
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Song Wang
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Weiwei Wu
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Liyun Miao
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
- Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng, 224002, Jiangsu, China
| | - Ping Zhan
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Xiaoli Chen
- Department of Respiratory and Critical Care Medicine, Jiangsu Provincial Hospital of Integrated Chinese and Western Medicine, 100 Cross Street, Hongshan Road, Nanjing, 210028, Jiangsu, China
| | - Manman Huang
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Mingxiang Ye
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, Jiangsu, China
| | - Qiuxiang Ou
- Dinfectome Inc., Nanjing, 210000, Jiangsu, China
| | - Yeqing Zhang
- Department of Respiratory and Critical Care Medicine, Jiangsu Provincial Hospital of Integrated Chinese and Western Medicine, 100 Cross Street, Hongshan Road, Nanjing, 210028, Jiangsu, China.
| |
Collapse
|
2
|
Yuan L, Zhu Q, Chen Q, Lai LM, Liu P, Liu Y. The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases. Lab Med 2024; 55:132-139. [PMID: 37289931 DOI: 10.1093/labmed/lmad046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens in clinical infectious diseases through the sequencing analysis of microbial and host nucleic acids in clinical samples. This study aimed to assess the diagnostic performance of mNGS in patients with infections. METHODS In this study, 641 patients with infectious diseases were enrolled. These patients simultaneously underwent pathogen detection by both mNGS and microbial culture. Through statistical analysis, we judged the diagnostic performance of mNGS and microbial culture on different pathogens. RESULTS Among 641 patients, 276 cases of bacteria and 95 cases of fungi were detected by mNGS, whereas 108 cases of bacteria and 41 cases of fungi were detected by traditional cultures. Among all mixed infections, combined bacterial and viral infections were the highest (51%, 87/169), followed by combined bacterial with fungal infections (16.57%, 28/169) and mixed bacterial, fungal, and viral infections (13.61%, 23/169). Among all sample types, bronchoalveolar lavage fluid (BALF) samples had the highest positive rate (87.8%, 144/164), followed by sputum (85.4%, 76/89) and blood samples (61.2%, 158/258). For the culture method, sputum samples had the highest positive rate (47.2%, 42/89), followed by BALF (37.2%, 61/164). The positive rate of mNGS was 69.89% (448/641), which was significantly higher than that of traditional cultures (22.31% [143/641]) (P < .05). CONCLUSIONS Our results show that mNGS is an effective tool for the rapid diagnosis of infectious diseases. Compared with traditional detection methods, mNGS also showed obvious advantages in mixed infections and infections with uncommon pathogens.
Collapse
Affiliation(s)
- Lei Yuan
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qing Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Lan Min Lai
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Peng Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| |
Collapse
|
3
|
Alsanea MS, Al-Qahtani AA, Almaghrabi RS, AlAbdulkareem MA, Alahideb BM, Obeid D, Alsuwairi FA, Alhamlan FS. Diagnosis of Human Cytomegalovirus Drug Resistance Mutations in Solid Organ Transplant Recipients-A Review. Diagnostics (Basel) 2024; 14:203. [PMID: 38248079 PMCID: PMC10814084 DOI: 10.3390/diagnostics14020203] [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: 05/02/2023] [Revised: 06/11/2023] [Accepted: 06/21/2023] [Indexed: 01/23/2024] Open
Abstract
Human cytomegalovirus (HCMV) infection may be asymptomatic in healthy individuals but can cause severe complications in immunocompromised patients, including transplant recipients. Breakthrough and drug-resistant HCMV infections in such patients are major concerns. Clinicians are first challenged to accurately diagnose HCMV infection and then to identify the most effective antiviral drug and determine when to initiate therapy, alter drug dosage, or switch medication. This review critically examines HCMV diagnostics approaches, particularly for immunocompromised patients, and the development of genotypic techniques to rapidly diagnose drug resistance mutations. The current standard method to identify prevalent and well-known resistance mutations involves polymerase chain reaction amplification of UL97, UL54, and UL56 gene regions, followed by Sanger sequencing. This method can confirm clinical suspicion of drug resistance as well as determine the level of drug resistance and range of cross-resistance with other drugs. Despite the effectiveness of this approach, there remains an urgent need for more rapid and point-of-care HCMV diagnosis, allowing for timely lifesaving intervention.
Collapse
Affiliation(s)
- Madain S. Alsanea
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
| | - Maha A. AlAbdulkareem
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Basma M. Alahideb
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Dalia Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
| | - Feda A. Alsuwairi
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Fatimah S. Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| |
Collapse
|
4
|
Mallory MA, Hymas WC, Simmon KE, Pyne MT, Stevenson JB, Barker AP, Hillyard DR, Hanson KE. Development and validation of a next-generation sequencing assay with open-access analysis software for detecting resistance-associated mutations in CMV. J Clin Microbiol 2023; 61:e0082923. [PMID: 38092673 PMCID: PMC10729743 DOI: 10.1128/jcm.00829-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/29/2023] [Indexed: 12/20/2023] Open
Abstract
Cytomegalovirus (CMV) resistance testing by targeted next-generation sequencing (NGS) allows for the simultaneous analysis of multiple genes. We developed and validated an amplicon-based Ion Torrent NGS assay to detect CMV resistance mutations in UL27, UL54, UL56, and UL97 and compared the results to standard Sanger sequencing. NGS primers were designed to generate 83 overlapping amplicons of four CMV genes (~10 kb encompassing 138 mutation sites). An open-access software plugin was developed to perform read alignment, call variants, and interpret drug resistance. Plasmids were tested to determine NGS error rate and minor variant limit of detection. NGS limit of detection was determined using the CMV WHO International Standard and quantified clinical specimens. Reproducibility was also assessed. After establishing quality control metrics, 185 patient specimens previously tested using Sanger were reanalyzed by NGS. The NGS assay had a low error rate (<0.05%) and high accuracy (95%) for detecting CMV-associated resistance mutations present at ≥5% in contrived mixed populations. Mutation sites were reproducibly sequenced with 40× coverage when plasma viral loads were ≥2.6 log IU/mL. NGS detected the same resistance-associated mutations identified by Sanger in 68/69 (98.6%) specimens. In 16 specimens, NGS detected 18 resistance mutations that Sanger failed to detect; 14 were low-frequency variants (<20%), and six would have changed the drug resistance interpretation. The NGS assay showed excellent agreement with Sanger and generated high-quality sequence from low viral load specimens. Additionally, the higher resolution and analytic sensitivity of NGS potentially enables earlier detection of antiviral resistance.
Collapse
Affiliation(s)
- Melanie A. Mallory
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Weston C. Hymas
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Keith E. Simmon
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Michael T. Pyne
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Jeffery B. Stevenson
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Adam P. Barker
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - David R. Hillyard
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Kimberly E. Hanson
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| |
Collapse
|
5
|
Pednekar P, Graf M, Tuly R, Batt K, Wang C. Gaining consensus around patient risk groups and prognostic profiles to guide CMV management among patients with solid organ transplant: Insights from a Delphi panel with SOT experts. Clin Transplant 2023; 37:e14905. [PMID: 36603193 DOI: 10.1111/ctr.14905] [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: 09/30/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023]
Abstract
INTRODUCTION This study aimed to characterize patient risk groups and respective prognostic profiles to optimize clinical decision-making and guide appropriate medical cytomegalovirus (CMV) management among patients with solid organ transplant (SOT). METHODS Between September 2021 and February 2022, a three-round modified Delphi study was conducted to generate consensus among 14 international experts in virology and organ transplantation. Experts were asked about treatment and prognoses for patients in seven distinct clinical scenarios. Furthermore, experts were asked to risk-stratify patients by pre-/post-transplant characteristics. Consensus around opting for/against a treatment was observed if ≥75% or <25% of experts reported ≥50% likelihood to recommend or if treatments were ranked inside/outside the top two options and ≥75% of experts were within 1 standard deviation of the mean rank. RESULTS Experts agreed on several unmet needs in CMV disease management post-SOT, particularly avoidance of treatment-limiting toxicities with conventional CMV therapy and emergence of both primary refractory and drug resistant treatment failures. Experts considered CMV viral load, resistance profile, and route of administration as critical to treatment selection. For newer CMV therapeutic options, experts listed lack of long-term use data, concerns over potential resistance, high cost and limited availability as challenges restricting adoption, and successful patient management. CONCLUSION Experts achieved consensus around patient risk stratifications and factors influencing therapeutic options. Recommendations emerging from this Delphi study may support practicing physicians when confronted with challenging CMV scenarios in SOT patients, but additional experiences with newer anti-CMV agents are needed to re-validate expert consensus and update post-transplant CMV guidelines.
Collapse
Affiliation(s)
| | | | | | | | - Connie Wang
- Hennepin Healthcare, Minneapolis, Minnesota, USA
| |
Collapse
|
6
|
von Bredow B, Caldera JR, Cerón S, Chan JL, Gray HK, Garner OB, Yang S. Clinical next-generation sequencing assay combining full-length gene amplification and shotgun sequencing for the detection of CMV drug resistance mutations. J Clin Virol 2023; 165:105520. [PMID: 37336174 DOI: 10.1016/j.jcv.2023.105520] [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: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
Cytomegalovirus (CMV) causes severe systemic and tissue-invasive disease in immunocompromised patients, particularly solid organ and hematopoietic stem cell transplant recipients. While antiviral drugs offer promising efficacy, clinical management is complicated by the high frequency of drug resistance-associated mutations. The most commonly encountered mutations occur in the genes encoding for the drug targets: UL54 (DNA polymerase), UL56 (terminase complex), and UL97 (phosphotransferase), conferring resistance to ganciclovir/cidofovir/foscarnet, letermovir, and ganciclovir/maribavir, respectively. Currently, standard practice for detecting drug resistance is sequencing-based genotypic analysis by commercial reference laboratories with strictly prescribed sample requirements and reporting parameters that can often restrict testing in a highly vulnerable population. In order to circumvent these limitations, we developed a dual-step next-generation sequencing (NGS)-based clinical assay that utilizes full-length gene amplification by long-range PCR followed by shotgun sequencing for mutation analysis. This laboratory-developed test (LDT) achieved satisfactory performance with 96.4% accuracy, 100% precision, and an analytical sensitivity of 300IU/mL with 20% allele frequency. Highlighted by two clinical cases, our NGS LDT was able to provide critical results from patient specimens with viral loads <500IU/mL and volumes <0.5 mL - conditions otherwise unacceptable by reference laboratories. Here, we describe the development and implementation of a robust NGS LDT that offers greater testing flexibility and sensitivity to accommodate a more diverse patient population.
Collapse
Affiliation(s)
- Benjamin von Bredow
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States; Department of Pathology, Oakland University William Beaumont School of Medicine, Rochester, MI, United States
| | - J R Caldera
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Stacey Cerón
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - June L Chan
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Hannah K Gray
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
| |
Collapse
|
7
|
Hume J, Sweeney EL, Lowry K, Fraser C, Clark JE, Whiley DM, Irwin AD. Cytomegalovirus in children undergoing haematopoietic stem cell transplantation: a diagnostic and therapeutic approach to antiviral resistance. Front Pediatr 2023; 11:1180392. [PMID: 37325366 PMCID: PMC10267881 DOI: 10.3389/fped.2023.1180392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Cytomegalovirus (CMV) is a ubiquitous virus which causes a mild illness in healthy individuals. In immunocompromised individuals, such as children receiving haematopoietic stem cell transplantation, CMV can reactivate, causing serious disease and increasing the risk of death. CMV can be effectively treated with antiviral drugs, but antiviral resistance is an increasingly common complication. Available therapies are associated with adverse effects such as bone marrow suppression and renal impairment, making the choice of appropriate treatment challenging. New agents are emerging and require evaluation in children to establish their role. This review will discuss established and emerging diagnostic tools and treatment options for CMV, including antiviral resistant CMV, in children undergoing haematopoietic stem cell transplant.
Collapse
Affiliation(s)
- Jocelyn Hume
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Brisbane, QLD, Australia
| | - Emma L. Sweeney
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Kym Lowry
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Chris Fraser
- Blood and Bone Marrow Transplant Program, Queensland Children’s Hospital, Brisbane, QLD, Australia
| | - Julia E. Clark
- Infection Management and Prevention Service, Queensland Children’s Hospital, Brisbane, QLD, Australia
| | - David M. Whiley
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Brisbane, QLD, Australia
| | - Adam D. Irwin
- The University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Infection Management and Prevention Service, Queensland Children’s Hospital, Brisbane, QLD, Australia
| |
Collapse
|
8
|
Gao L, Yang T, Zhang X, Lei W, Huang JA. Rapid detection of pulmonary nocardiosis by metagenomic next generation sequencing. Diagn Microbiol Infect Dis 2023; 106:115928. [PMID: 37001227 DOI: 10.1016/j.diagmicrobio.2023.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/01/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
We retrospectively analyzed 3 cases of pulmonary nocardiosis. Patients were identified by metagenomic next generation sequencing (mNGS) in the First Affiliated Hospital of Soochow University, from January 2019 to April 2022. All patients had underlying diseases, and were in immunocompromised state, with membranous nephropathy, acute lymphoblastic leukemia (ALL), and systemic lupus erythematosus (SLE), respectively. Symptoms common to all cases included fever, cough and expectoration. Chest computed tomography (CT) presented patchy shadows or nodules, with or without cavitation lesions, or pleural effusion. mNGS detected Nocardia spp. via bronchoalveolar lavage fluid (BALF) or blood samples from patients. All the patients were discharged with recovery after using the trimethoprim-sulfamethoxazole (TMP-SMX) and remained without evidence of disease during regular follow-ups. mNGS may be a tool for rapid and accurate detection and identification of pulmonary nocardiosis, but interpreting the mNGS results should be more cautious because the mNGS assay can also detect colonization.
Collapse
|
9
|
Hong D, Wang P, Chen Y, Zhang J, Jiang W, Ye B, Li G, Zhou J, Mao W, Tong Z, Li W, Ke L. Detection of potential pathogen in pancreatic fluid aspiration with metagenomic next-generation sequencing in patients with suspected infected pancreatic necrosis. Dig Liver Dis 2023; 55:243-248. [PMID: 35948458 DOI: 10.1016/j.dld.2022.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Timely and accurate microbial diagnosis is important in managing patients with infected pancreatic necrosis (IPN). AIMS To evaluate the diagnostic performance of Metagenomic next-generation sequencing (mNGS) in patients with suspected IPN. METHODS The clinical data of 40 patients with suspected IPN who underwent CT-guided pancreatic fluid aspiration were retrospectively analyzed. Microbial culture and mNGS were simultaneously applied to identify the potential pathogens. The diagnostic performance of the mNGS was assessed by sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). RESULTS The mNGS report can be obtained significantly earlier than culture methods (42 (36-62 h) vs. 60 (42-124 h), P = 0.032). Across all the study samples, seven species of bacteria and two species of fungi were reported accordingly to the culture results, while 22 species of bacteria and two species of fungi were detected by mNGS. The sensitivity, specificity, NPV, and PPV of mNGS were 88.0%, 100%, 83.33%, and 100%, respectively. CONCLUSIONS The diagnostic accuracy of mNGS in patients with suspected IPN is satisfactory. Moreover, mNGS may broaden the range of identifiable infectious pathogens and provide a more timely diagnosis.
Collapse
Affiliation(s)
- Donghuang Hong
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China; Department of Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, China
| | - Peng Wang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yingjie Chen
- Department of Critical Care Medicine, Jinjiang Hospital of Traditional Chinese Medicine, Jinjiang, China
| | - Jingzhu Zhang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wendi Jiang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Bo Ye
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Gang Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jing Zhou
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wenjian Mao
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhihui Tong
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Weiqin Li
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China; Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China; National Institute of Healthcare Data Science, Nanjing University, Nanjing, China.
| | - Lu Ke
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China; National Institute of Healthcare Data Science, Nanjing University, Nanjing, China.
| |
Collapse
|
10
|
Acquier M, Taton B, Alain S, Garrigue I, Mary J, Pfirmann P, Visentin J, Hantz S, Merville P, Kaminski H, Couzi L. Cytomegalovirus DNAemia Requiring (Val)Ganciclovir Treatment for More Than 8 Weeks Is a Key Factor in the Development of Antiviral Drug Resistance. Open Forum Infect Dis 2023; 10:ofad018. [PMID: 36817745 PMCID: PMC9933945 DOI: 10.1093/ofid/ofad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Background Prolonged (val)ganciclovir [(V)GCV] exposure for ≥6 weeks is a known predisposing factor for cytomegalovirus (CMV) drug resistance. However, the selection of this threshold was based on limited data. In this study, we sought to reappraise the risk factors for the development of (V)GCV resistance through a specific focus on kidney transplant recipients (KTRs). Methods This single-center retrospective study included 313 consecutive KTRs treated for a first CMV episode. Adjusted Cox multivariate regression analysis was used for identifying independent risk factors. Results Antiviral drug resistance was identified in 20 (6%) KTRs. A cumulative (V)GCV exposure for more than 6 weeks (regardless of the viral load) was not associated with antiviral drug resistance (hazard ratio [HR] = 2.45, 95% confidence interval [CI] = 0.33-18.30, P = .38). In contrast, persistent CMV DNAemia requiring (V)GCV treatment for more than 8 weeks was the main independent risk factor for antiviral drug resistance (HR = 11.68, 95% CI = 2.62-52.01, P = .001). The (V)GCV treatment for more than 8 weeks was given to 9% and 18% of patients who had persistent or recurrent CMV DNAemia, respectively. These scenarios were associated with the occurrence of drug resistance in 39% and 12% of cases, respectively. Conclusions Cumulative (V)GCV exposure ≥6 weeks regardless of the viral load is not associated with antiviral drug resistance. In contrast, prolonged exposure to (V)GCV during CMV replication (with a cutoff ³8 weeks) seems to be a key factor.
Collapse
Affiliation(s)
- M Acquier
- Department of Nephrology, Transplantation, Dialysis and Apheresis, Bordeaux University Hospital, Bordeaux, France
| | - B Taton
- Department of Nephrology, Transplantation, Dialysis and Apheresis, Bordeaux University Hospital, Bordeaux, France
| | - S Alain
- National Reference Center for Herpes Viruses, Virology Department, Limoges University Hospital, LimogesFrance.,UMR INSERM U1092, RESINFIT, Limoges University, LimogesFrance
| | - I Garrigue
- Laboratory of Virology, Bordeaux University Hospital, Bordeaux, France
| | - J Mary
- Department of Nephrology, Transplantation, Dialysis and Apheresis, Bordeaux University Hospital, Bordeaux, France
| | - P Pfirmann
- Department of Nephrology, Transplantation, Dialysis and Apheresis, Bordeaux University Hospital, Bordeaux, France
| | - J Visentin
- CNRS-UMR 5164 ImmunoConcEpT, Bordeaux University, Bordeaux, France.,Laboratory of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
| | - S Hantz
- National Reference Center for Herpes Viruses, Virology Department, Limoges University Hospital, LimogesFrance.,UMR INSERM U1092, RESINFIT, Limoges University, LimogesFrance
| | - P Merville
- Department of Nephrology, Transplantation, Dialysis and Apheresis, Bordeaux University Hospital, Bordeaux, France.,CNRS-UMR 5164 ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - H Kaminski
- Department of Nephrology, Transplantation, Dialysis and Apheresis, Bordeaux University Hospital, Bordeaux, France.,CNRS-UMR 5164 ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - L Couzi
- Department of Nephrology, Transplantation, Dialysis and Apheresis, Bordeaux University Hospital, Bordeaux, France.,CNRS-UMR 5164 ImmunoConcEpT, Bordeaux University, Bordeaux, France
| |
Collapse
|
11
|
Kotton CN, Kamar N. New Insights on CMV Management in Solid Organ Transplant Patients: Prevention, Treatment, and Management of Resistant/Refractory Disease. Infect Dis Ther 2023; 12:333-342. [PMID: 36583845 PMCID: PMC9925645 DOI: 10.1007/s40121-022-00746-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
Cytomegalovirus (CMV) infection can have both direct and indirect effects after solid-organ transplantation, with a significant impact on transplant outcomes. Prevention strategies decrease the risk of CMV disease, although CMV still occurs in up to 50% of high-risk patients. Ganciclovir (GCV) and valganciclovir (VGCV) are the main drugs currently used for preventing and treating CMV. Emerging data suggest that letermovir is as effective as VGCV with fewer hematological side effects. Refractory and resistant CMV also still occur in solid-organ-transplant patients. Maribavir has been shown to be effective and have less toxicity in the treatment of refractory and resistant CMV. In this review paper, we discuss prevention strategies, refractory and resistant CMV, and drug-related side effects and their impact, as well as optimal use of novel anti-CMV therapies.
Collapse
Affiliation(s)
- Camille Nelson Kotton
- grid.32224.350000 0004 0386 9924Transplant and Immunocompromised Host Infectious Diseases, Infectious Diseases Division, Massachusetts General Hospital, 55 Fruit Street, Cox 5, Boston, MA 02114 USA
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Nassim Kamar
- grid.414295.f0000 0004 0638 3479Department of Nephrology and Organ Transplantation, Toulouse Rangueil University Hospital, CHU Toulouse Rangueil, TSA 50032, 31059 Toulouse Cedex 9, France
- grid.7429.80000000121866389INSERM UMR 1291, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, France
- grid.15781.3a0000 0001 0723 035XPaul Sabatier University, Toulouse, France
| |
Collapse
|
12
|
Lin KP, Yeh TK, Chuang YC, Wang LA, Fu YC, Liu PY. Blood Culture Negative Endocarditis: A Review of Laboratory Diagnostic Approaches. Int J Gen Med 2023; 16:317-327. [PMID: 36718144 PMCID: PMC9884005 DOI: 10.2147/ijgm.s393329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Infective endocarditis is a potentially fatal condition, and identifying the pathogen is crucial to optimizing antibiotic treatment. While a blood culture takes time and may yield negative results, it remains the gold standard for diagnosis, blood culture-negative endocarditis, which accounts for up to 20% of infective endocarditis cases, poses a clinical challenge with increasing mortality. To better understand the etiology of blood culture-negative infective endocarditis, we reviewed non-culture-based strategies and compared the results. Serology tests work best in limited pathogens, such as Coxiella burnetii and Bartonella infections. Most of the pathogens identified by broad-range PCR tests are Streptococcus spp, Staphylococcus spp and Propionibacterium spp. adding specific real-time PCR assays to the systematic PCR testing of patients with blood culture-negative endocarditis will increase the efficiency of diagnosis. Recently, metagenomic next-generation sequencing has also shown promising results.
Collapse
Affiliation(s)
- Kuan-Pei Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Chuan Chuang
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Li-An Wang
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yun-Ching Fu
- Children’s Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan,Correspondence: Yun-Ching Fu; Po-Yu Liu, Taichung Veterans General Hospital, No. 1650, Section 4, Taiwan Blvd, Xitun District, Taichung City, 40705, Taiwan, Tel +886-4-2359-2525 ext.3110, Fax +886-4-2359-5046, Email ;
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
13
|
The Ten Most Common Questions on Cytomegalovirus Infection in Hematopoietic Stem Cell Transplant Patients. Clin Hematol Int 2022; 5:21-28. [PMID: 36577863 PMCID: PMC9797381 DOI: 10.1007/s44228-022-00025-3] [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: 09/06/2022] [Accepted: 11/15/2022] [Indexed: 12/30/2022] Open
Abstract
With the rising number of patients undergoing hematopoietic stem cell transplantation (HSCT), clinicians are more likely to encounter infectious complications in immunocompromised hosts, particularly cytomegalovirus (CMV) infection. Besides the high mortality of CMV end-organ disease, patients with detectable CMV viremia may have worse outcomes and decreased survival even in the absence of end-organ disease. In view of the implications on morbidity and mortality, clinicians should maintain a high index of suspicion and initiate antiviral drugs promptly when CMV infection is confirmed. High-risk patients should be identified in order to provide optimal management. Additionally, novel antiviral agents with a good safety profile and minor adverse events are now available for prophylaxis in high-risk patients and for treatment of resistant or refractory CMV infection. The following review provides concise, yet comprehensive, guidance on the burden and risk factors of CMV in this population, as well as an update on the latest evidence for the management of CMV infection.
Collapse
|
14
|
Demin MV, Tikhomirov DS, Tupoleva TA, Filatov FP. [Resistance to antiviral drugs in human viruses from the subfamily Betaherpesvirinae]. Vopr Virusol 2022; 67:285-294. [PMID: 36515284 DOI: 10.36233/0507-4088-136] [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: 10/02/2022] [Indexed: 12/07/2022]
Abstract
The review provides information on the mechanisms of the emergence of resistance to antiviral drugs in human viruses from the subfamily Betaherpesvirinae. Data on the principles of action of antiviral drugs and their characteristics are given. The occurrence rates of viral resistance in various groups of patients is described and information about the possible consequences of the emergence of resistance to antiviral drugs is given. Information is provided regarding the virus genes in which mutations occur that lead to viral resistance, and a list of such mutations that have described so far is given. The significance of the study of mutations leading to the resistance of the virus to antiviral drugs for medical practice is discussed.
Collapse
Affiliation(s)
- M V Demin
- National Medical Research Center of Hematology of the Ministry of Health of Russia
| | - D S Tikhomirov
- National Medical Research Center of Hematology of the Ministry of Health of Russia
| | - T A Tupoleva
- National Medical Research Center of Hematology of the Ministry of Health of Russia
| | - F P Filatov
- I.I. Mechnikov Research Institute of Vaccines and Serums of the Ministry of Education and Science of Russia.,National Research Center of Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya of the Ministry of Health of Russia
| |
Collapse
|
15
|
Tian Y, Xia H, Zhang L, Zhou JX. Detection of multidrug-resistant Acinetobacter baumannii by metagenomic next-generation sequencing in central nervous system infection after neurosurgery: A case report. Front Public Health 2022; 10:1028920. [PMID: 36339188 PMCID: PMC9634161 DOI: 10.3389/fpubh.2022.1028920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/10/2022] [Indexed: 01/29/2023] Open
Abstract
Background Central nervous system (CNS) infection is one of the most serious complications after neurosurgery. Traditional clinical methods are difficult to diagnose the pathogen of intracranial infection. Due to recent advances in genomic approaches, especially sequencing technologies, metagenomic next-generation sequencing (mNGS) has been applied in many research and clinical settings. Case presentation Here, we report a case of CNS infection with Acinetobacter baumannii in a 15-year-old woman, who previously underwent surgery for recurrence of ependymoma in the fourth ventricle. On the eleventh postoperative day, the patient had a high fever and leukocytosis in the cerebrospinal fluid (CSF). mNGS using CSF rapidly and accurately identified the causative pathogen as A. baumannii with carbapenem resistance genes blaOXA-23 and blaOXA-51, which were confirmed by subsequent culture and susceptibility tests within 5 days. During the disease, mNGS, culture, and drug susceptibility testing were continued to monitor changes in pathogenic bacteria and adjust medication. At present, there are no case reports on to the use of mNGS for detecting pathogens in postoperative infection with ependymoma and guide medication. Conclusion mNGS has great advantages in pathogen identification and even pathogen resistance prediction. Multiple mNGS examinations during the course of the disease play an important role in the dynamic monitoring of pathogens.
Collapse
Affiliation(s)
- Ying Tian
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Han Xia
- Department of Scientific Affairs, Hugo Biotechnologies, Co., Ltd, Beijing, China
| | - Linlin Zhang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China,Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, China,*Correspondence: Linlin Zhang
| | - Jian-Xin Zhou
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China,Beijing Engineering Research Center of Digital Healthcare for Neurological Diseases, Beijing, China,Beijing Shijitan Hospital, Capital Medical University, Beijing, China,Jian-Xin Zhou
| |
Collapse
|
16
|
Torii Y, Horiba K, Kawada JI, Haruta K, Yamaguchi M, Suzuki T, Uryu H, Kashiwa N, Goishi K, Ogi T, Ito Y. Detection of antiviral drug resistance in patients with congenital cytomegalovirus infection using long-read sequencing: a retrospective observational study. BMC Infect Dis 2022; 22:568. [PMID: 35733089 PMCID: PMC9219161 DOI: 10.1186/s12879-022-07537-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital human cytomegalovirus (cCMV) infection can cause sensorineural hearing loss and neurodevelopmental disabilities in children. Ganciclovir and valganciclovir (GCV/VGCV) improve long-term audiologic and neurodevelopmental outcomes for patients with cCMV infection; however, antiviral drug resistance has been documented in some cases. Long-read sequencing can be used for the detection of drug resistance mutations. The objective of this study was to develop full-length analysis of UL97 and UL54, target genes with mutations that confer GCV/VGCV resistance using long-read sequencing, and investigate drug resistance mutation in patients with cCMV infection. METHODS Drug resistance mutation analysis was retrospectively performed in 11 patients with cCMV infection treated with GCV/VGCV. UL97 and UL54 genes were amplified using blood DNA. The amplicons were sequenced using a long-read sequencer and aligned with the reference gene. Single nucleotide variants were detected and replaced with the reference sequence. The replaced sequence was submitted to a mutation resistance analyzer, which is an open platform for drug resistance mutations. RESULTS Two drug resistance mutations (UL54 V823A and UL97 A594V) were found in one patient. Both mutations emerged after 6 months of therapy, where viral load increased. Mutation rates subsided after cessation of GCV/VGCV treatment. CONCLUSIONS Antiviral drug resistance can emerge in patients with cCMV receiving long-term therapy. Full-length analysis of UL97 and UL54 via long-read sequencing enabled the rapid and comprehensive detection of drug resistance mutations.
Collapse
Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan.,Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Hideko Uryu
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Naoyuki Kashiwa
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Keiji Goishi
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan. .,Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, 173-8610, Tokyo, Japan.
| |
Collapse
|
17
|
Lee H, Oh EJ. Laboratory diagnostic testing for cytomegalovirus infection in solid organ transplant patients. KOREAN JOURNAL OF TRANSPLANTATION 2022; 36:15-28. [PMID: 35769434 PMCID: PMC9235525 DOI: 10.4285/kjt.22.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/12/2022] Open
Abstract
Human cytomegalovirus (CMV) infection, which is one of the most common complications in transplant recipients, increases the risk of graft loss and rejection. Laboratory strategies for diagnosing CMV infection rely on the measurement of viral DNAemia and CMV-specific cell-mediated immunity (CMV-CMI). The CMV quantitative nucleic acid amplification test (QNAT) enabled the spread of preemptive therapy and prompted recommendations for surveillance, diagnosis, and monitoring. Despite the implementation of the World Health Organization international standard for calibration, variability of QNAT persists due to technical issues. CMV immunoglobulin G serology is the standard method for CMV immune screening of transplant candidates and donors. Assays for CMV-CMI play an important role in helping to predict the risk and to develop an individualized CMV management plan. Genotypic testing for resistance is needed when drug-resistant CMV infection is suspected. Here, we review the state of the art of laboratory tests for CMV infection in solid organ transplantation.
Collapse
Affiliation(s)
- Hyeyoung Lee
- Department of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon, Korea
| | - Eun-Jee Oh
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Research and Development Institute for In Vitro Diagnostic Medical Devices of Catholic University of Korea, College of Medicine, The Catholic University of Korea, Seoul, Korea
| |
Collapse
|
18
|
Lodding IP, Jørgensen M, Bennedbæk M, Kirkby N, Naegele K, Gustafsson F, Perch M, Rasmussen A, Sengeløv H, Sørensen SS, Hirsch HH, Lundgren JD. Development and Dynamics of Cytomegalovirus UL97 Ganciclovir Resistance Mutations in Transplant Recipients Detected by Next-Generation Sequencing. Open Forum Infect Dis 2021; 8:ofab462. [PMID: 34660835 PMCID: PMC8514173 DOI: 10.1093/ofid/ofab462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/03/2021] [Indexed: 11/13/2022] Open
Abstract
Background (Val)ganciclovir resistance mutations in CMV UL97 (UL97-GCV-R) complicate anti-CMV therapy in recipients of solid organ and hematopoietic stem cell transplants, but comprehensive data on prevalence, emergence, and outcome are scarce. Methods Using next-generation sequencing (NGS; Illumina MiSeq platform), we analyzed UL97-GCV-R in patients with available plasma samples and refractory CMV replication/DNAemia (n = 87) containing viral loads ≥910 IU/mL. Twenty-one patients with CMV DNAemia resolving under antiviral therapy were analyzed as controls. Detected mutations were considered induced and of potential clinical significance if they increased by ≥10% compared with the first detected frequency or if they had a maximum frequency ≥25%. Results Nineteen of 87 (21.8%) with refractory CMV replication had ≥1 UL97-GCV-R detected by NGS, in comparison to 0/21 of the controls (P = .02). One-third of the recipients had 2 or more induced UL97-GCV-R mutations. The most frequently induced mutations affected codons 595 (42% [8/19]), 594 (32% [6/19]), and 603 (32% [6/19]). C592G was present in all episodes of both cases and controls at frequencies <15%, but never induced. UL97-GCV-R tended to be more frequent in donor/recipient CMV immunoglobulin G mismatch or following failure to complete primary prophylaxis, and many developed invasive CMV disease. Conclusions UL97-GCV-R is common among transplant patients with refractory CMV replication. Early testing by NGS allows for identification of major mutations at codons 595, 594, and 603 and excludes a major role of C592G in ganciclovir resistance. Large prospective studies on UL97-GCV-R are warranted.
Collapse
Affiliation(s)
- Isabelle P Lodding
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, Copenhagen, Denmark.,Department of Haematology, Rigshospitalet, Copenhagen, Denmark
| | - Mette Jørgensen
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, Copenhagen, Denmark
| | - Marc Bennedbæk
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, Copenhagen, Denmark
| | - Nikolai Kirkby
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Klaudia Naegele
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland.,Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Finn Gustafsson
- Department of Cardiology, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael Perch
- Department of Cardiology, Section for Lung Transplantation, Rigshospitalet, Copenhagen, Denmark
| | - Allan Rasmussen
- Department of Abdominal Surgery, Rigshospitalet, Copenhagen, Denmark
| | - Henrik Sengeløv
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
| | - Søren S Sørensen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Nephrology, Rigshospitalet, Copenhagen, Denmark
| | - Hans H Hirsch
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland.,Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Jens D Lundgren
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
19
|
Tamura S, Osawa S, Ishida N, Miyazu T, Tani S, Yamade M, Iwaizumi M, Hamaya Y, Kosugi I, Furuta T, Sugimoto K. Prevalence of UL97 gene mutations and polymorphisms in cytomegalovirus infection in the colon associated with or without ulcerative colitis. Sci Rep 2021; 11:13676. [PMID: 34211066 PMCID: PMC8249415 DOI: 10.1038/s41598-021-93168-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Cytomegalovirus (CMV) reactivation in the colon is common in patients with severe ulcerative colitis (UC). Ganciclovir (GCV) resistance conferring CMV UL97 gene mutations have been reported in recent years. However, the prevalence of UL97 gene mutations in GCV-naive CMV infection in the colon remains unknown. We investigated the prevalence of CMV UL97 gene mutations in patients with colonic CMV infection associated with or without UC. Twenty-two GCV-naive patients with colonic CMV infection, 15 with UC and 7 with other diseases, were enrolled. Frozen biopsy samples or formalin-fixed paraffin-embedded samples were used for nested polymerase chain reaction (PCR) amplification of the UL97 gene. Sanger DNA sequencing was performed. In comparison with AD169 reference strain, natural polymorphisms were frequently detected in codons N68D (100%), I244V (100%), and D605E (86.4%). Seven polymorphisms were detected infrequently (< 10%) outside the kinase domain. However, no known GCV resistance mutations were found. There seemed to be no difference between the ratio of polymorphisms in patients with and without UC. In conclusions, we did not detect UL97 gene mutations associated with GCV resistance in GCV-naive patients with or without UC. Consistent with previous reports, D605E polymorphism may be used as a genetic marker for CMV in East Asian countries.
Collapse
Affiliation(s)
- Satoshi Tamura
- Department of Endoscopic and Photodynamic Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
- First Department of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Satoshi Osawa
- Department of Endoscopic and Photodynamic Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.
| | - Natsuki Ishida
- First Department of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Takahiro Miyazu
- First Department of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Shinya Tani
- First Department of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Mihoko Yamade
- First Department of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Moriya Iwaizumi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Yasushi Hamaya
- First Department of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Isao Kosugi
- Department of Regenerative and Infectious Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Takahisa Furuta
- Center for Clinical Research, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Ken Sugimoto
- First Department of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| |
Collapse
|
20
|
Yu U, Wang X, Zhang X, Wang C, Yang C, Zhou X, Li Y, Huang X, Wen J, Wen F, Liu S. Cytomegalovirus Infection and the Implications of Drug-Resistant Mutations in Pediatric Allogeneic Hematopoietic Stem Cell Transplant Recipients: A Retrospective Study from a Tertiary Hospital in China. Infect Dis Ther 2021; 10:1309-1322. [PMID: 33966176 PMCID: PMC8322184 DOI: 10.1007/s40121-021-00452-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 10/28/2022] Open
Abstract
INTRODUCTION Drug-resistant cytomegalovirus (CMV) infection remains a challenge in the management of pediatric recipients of hematopoietic stem cell transplantation (HSCT). In this study, we retrospectively reviewed the clinical data on pediatric recipients of HSCT and identified known and unknown drug-resistant CMV variants. METHODS A total of 221 children underwent allogeneic HSCT between October 2017 and November 2019 at Shenzhen Children's Hospital; of these, 35 patients were suspected of having drug-resistant CMV infections and were tested for drug-resistant mutations in the UL97 and UL54 genes by Sanger sequencing. RESULTS Mutations in UL97 or UL54, or in both, were detected in 11 patients. Most of these mutations have not been previously reported. The UL97 mutation (A582V) was detected in only one patient who also harbored two UL54 mutations (T760X and R876W). One patient with both the G604S and T691A mutations in the UL54 gene died of CMV pneumonia. We investigated the risk factors associated with the development of drug-resistant CMV infection. Patients in whom both the donor and recipient had positive CMV serostatuses were less likely to have drug-resistant mutations (Fisher's exact test, p < 0.05). CONCLUSION Newly and previously detected CMV mutations in UL97 and UL54 may be associated with the development of drug-resistant CMV infection. The detection of these mutations may provide guidance for the management of post-transplant CMV infections.
Collapse
Affiliation(s)
- Uet Yu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Xiaodong Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Xiaoling Zhang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Chunjing Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Chunlan Yang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Xiaohui Zhou
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Yue Li
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Xiaochan Huang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Jing Wen
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Feiqiu Wen
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China
| | - Sixi Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Yitian Road No. 7019, Futian, Shenzhen, 518038, China.
| |
Collapse
|
21
|
Jiang H, Duan K, Han X, Wang J, Liu X, Yan M, Wang Y, Liu H, Shi H, Gao X, Ouyang C, Fu X, Zhang X, Liu C. Detection of Mitochondrial Mutations Through Isothermal Nucleic Acid Amplification Coupled With Clustered Regularly Interspaced Short Palindromic Repeat-Associated Endonuclease Cas13a. Front Genet 2021; 11:622671. [PMID: 33510775 PMCID: PMC7835798 DOI: 10.3389/fgene.2020.622671] [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: 10/29/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated endonuclease Cas13a can specifically bind and cleave RNA. After nucleic acid pre-amplification, bacterial Cas13a has been used to detect genetic mutations. In our study, using a transcription-mediated amplification together with Cas13a, we can isothermally amplify and detect mitochondrial point mutations under non-denaturing conditions from human genomic DNA. Unlike previous reports, we prepared CRISPR DNA with T7 promoter sequences and generated CRISPR RNA via transcription-mediated amplification instead of synthesizing and adding CRISPR RNA in a separate step. As a proof-of-concept, we showed that both m.1494C > T and m.1555A > G mutations were detected within 90 min. In addition, we explored various designs of CRISPR DNA to improve assay specificity, including the location and number of nucleotide mismatches, length of protospacer sequence, and different buffering conditions. We also confirmed the possibility of a “one-step single-tube” reaction for mutation detection. This assay can robustly distinguish circular DNA templates that differ by a single nucleotide. It has the potential to be adapted for automated applications, such as the screening of mitochondrial diseases.
Collapse
Affiliation(s)
- Hua Jiang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Duan
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Xu Han
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Jun Wang
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Xiao Liu
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maoxiao Yan
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunxiu Wang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongyan Liu
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huiling Shi
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Xiaoqing Gao
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Chuan Ouyang
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Xue Fu
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Xinxin Zhang
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Chao Liu
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| |
Collapse
|
22
|
Douglas CM, Barnard R, Holder D, Leavitt R, Levitan D, Maguire M, Nickle D, Teal V, Wan H, van Alewijk DCJG, van Doorn LJ, Chou S, Strizki J. Letermovir Resistance Analysis in a Clinical Trial of Cytomegalovirus Prophylaxis for Hematopoietic Stem Cell Transplant Recipients. J Infect Dis 2021; 221:1117-1126. [PMID: 31781762 DOI: 10.1093/infdis/jiz577] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Letermovir (LET), a cytomegalovirus (CMV) deoxyribonucleic acid (DNA) terminase inhibitor, was recently approved for prophylaxis of CMV infection in adult CMV-seropositive recipients of allogeneic hematopoietic stem cell transplantation. Cytomegalovirus genotyping was performed to identify LET-resistance-associated variants (RAVs) among subjects in a Phase 3 trial. METHODS The CMV UL56 and UL89 genes, encoding subunits of CMV DNA terminase, were sequenced from plasma collected from subjects with clinically significant CMV infection (CS-CMVi). Novel variants were evaluated by recombinant phenotyping to assess their potential to confer resistance to LET. RESULTS Genotyping was successful for 50 of 79 LET subjects with CS-CMVi. Resistance-associated variants (encoding pUL56 V236M and C325W) were detected independently in subjects 1 and 3 who experienced CS-CMVi while receiving LET prophylaxis, and 2 other variants (encoding pUL56 E237G and R369T) were detected >3 weeks after subjects 2 and 3, respectively, had discontinued LET prophylaxis and received preemptive therapy with ganciclovir. CONCLUSIONS The detected incidence of CMV resistance among subjects who received LET as prophylaxis in this Phase 3 trial was low. The LET RAVs that were detected mapped to the CMV UL56 gene at positions associated with reduced susceptibility to LET based on resistance selections in cell culture.
Collapse
Affiliation(s)
- Cameron M Douglas
- Infectious Disease Research, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Richard Barnard
- Infectious Disease Research, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Daniel Holder
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Randi Leavitt
- Clinical Research, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Diane Levitan
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Maureen Maguire
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - David Nickle
- Pharmacogenomics and Genetics, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Valerie Teal
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Hong Wan
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | | | - Sunwen Chou
- Department of Veterans Affairs Medical Center, Oregon Health and Science University, Portland, Oregon, USA
| | - Julie Strizki
- Infectious Disease Research, Merck & Co., Inc., Kenilworth, New Jersey, USA
| |
Collapse
|
23
|
Limaye AP, Babu TM, Boeckh M. Progress and Challenges in the Prevention, Diagnosis, and Management of Cytomegalovirus Infection in Transplantation. Clin Microbiol Rev 2020; 34:34/1/e00043-19. [PMID: 33115722 PMCID: PMC7920732 DOI: 10.1128/cmr.00043-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hosts with compromised or naive immune systems, such as individuals living with HIV/AIDS, transplant recipients, and fetuses, are at the highest risk for complications from cytomegalovirus (CMV) infection. Despite substantial progress in prevention, diagnostics, and treatment, CMV continues to negatively impact both solid-organ transplant (SOT) and hematologic cell transplant (HCT) recipients. In this article, we summarize important developments in the field over the past 10 years and highlight new approaches and remaining challenges to the optimal control of CMV infection and disease in transplant settings.
Collapse
Affiliation(s)
- Ajit P Limaye
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Tara M Babu
- Division of Infectious Diseases, University of Rochester Medical Center, Rochester, New York, USA
- Department of Infectious Diseases, Overlake Medical Center, Bellevue, Washington, USA
| | - Michael Boeckh
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| |
Collapse
|
24
|
Prevention and Management of CMV Infections after Liver Transplantation: Current Practice in German Transplant Centers. J Clin Med 2020; 9:jcm9082352. [PMID: 32717978 PMCID: PMC7465768 DOI: 10.3390/jcm9082352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
Human cytomegalovirus (CMV) remains a major cause of mortality and morbidity in human liver transplant recipients. Anti-CMV therapeutics can be used to prevent or treat CMV in liver transplant recipients, but their toxicity needs to be balanced against the benefits. The choice of prevention strategy (prophylaxis or preemptive treatment) depends on the donor/recipient sero-status but may vary between institutions. We conducted a series of consultations and roundtable discussions with German liver transplant center representatives. Based on 20 out of 22 centers, we herein summarize the current approaches to CMV prevention and treatment in the context of liver transplantation in Germany. In 90% of centers, transient prophylaxis with ganciclovir or valganciclovir was standard of care in high-risk (donor CMV positive, recipient CMV naive) settings, while preemptive therapy (based on CMV viremia detected during (bi) weekly PCR testing for circulating CMV-DNA) was preferred in moderate- and low-risk settings. Duration of prophylaxis or intense surveillance was 3-6 months. In the case of CMV infection, immunosuppression was adapted. In most centers, antiviral treatment was initiated based on PCR results (median threshold value of 1000 copies/mL) with or without symptoms. Therefore, German transplant centers report similar approaches to the prevention and management of CMV infection in liver transplantation.
Collapse
|
25
|
Mitchell SL, Simner PJ. Next-Generation Sequencing in Clinical Microbiology: Are We There Yet? Clin Lab Med 2020; 39:405-418. [PMID: 31383265 DOI: 10.1016/j.cll.2019.05.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Next-generation sequencing (NGS) applications have been transitioning from research tools to diagnostic methods and are becoming more commonplace in clinical microbiology laboratories. These applications include (1) whole-genome sequencing, (2) targeted next-generation sequencing methods, and (3) metagenomic next-generation sequencing. The introduction of these methods into the clinical microbiology laboratory has led to the theoretic question of "Will NGS-based methods supplant traditional methods for strain typing, identification, and antimicrobial susceptibility prediction?" The authors address this question and discuss where we are at now with clinical NGS applications for infectious diseases, what does the future hold, and at what cost?
Collapse
Affiliation(s)
- Stephanie L Mitchell
- Department of Pathology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, 4401 Penn Avenue, Main Hospital, Floor B, #269, Pittsburgh, PA 15224, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
| |
Collapse
|
26
|
Lu IN, Muller CP, He FQ. Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies. Virus Res 2020; 283:197963. [PMID: 32278821 PMCID: PMC7144618 DOI: 10.1016/j.virusres.2020.197963] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the scale and depth of biomedical sciences. Because of its unique ability for the detection of sub-clonal variants within genetically diverse populations, NGS has been successfully applied to analyze and quantify the exceptionally-high diversity within viral quasispecies, and many low-frequency drug- or vaccine-resistant mutations of therapeutic importance have been discovered. Although many works have intensively discussed the latest NGS approaches and applications in general, none of them has focused on applying NGS in viral quasispecies studies, mostly due to the limited ability of current NGS technologies to accurately detect and quantify rare viral variants. Here, we summarize several error-correction strategies that have been developed to enhance the detection accuracy of minority variants. We also discuss critical considerations for preparing a sequencing library from viral RNAs and for analyzing NGS data to unravel the mutational landscape.
Collapse
Affiliation(s)
- I-Na Lu
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, D-45147 Essen, Germany; Department of Infectious Diseases, Aarhus University Hospital, DK-8200 Aarhus N, Denmark.
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Laboratoire National de Santé, L-3583 Dudelange, Luxembourg
| | - Feng Q He
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| |
Collapse
|
27
|
Chemaly RF, Chou S, Einsele H, Griffiths P, Avery R, Razonable RR, Mullane KM, Kotton C, Lundgren J, Komatsu TE, Lischka P, Josephson F, Douglas CM, Umeh O, Miller V, Ljungman P. Definitions of Resistant and Refractory Cytomegalovirus Infection and Disease in Transplant Recipients for Use in Clinical Trials. Clin Infect Dis 2020; 68:1420-1426. [PMID: 30137245 DOI: 10.1093/cid/ciy696] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022] Open
Abstract
Despite advances in preventive strategies, cytomegalovirus (CMV) infection remains a major complication in solid organ and hematopoietic cell transplant recipients. CMV infection may fail to respond to commercially available antiviral therapies, with or without demonstrating genotypic mutation(s) known to be associated with resistance to these therapies. This lack of response has been termed "resistant/refractory CMV" and is a key focus of clinical trials of some investigational antiviral agents. To provide consistent criteria for future clinical trials and outcomes research, the CMV Resistance Working Group of the CMV Drug Development Forum (consisting of scientists, clinicians, regulatory officials, and industry representatives from the United States, Canada, and Europe) has undertaken establishing standardized consensus definitions of "resistant" and "refractory" CMV. These definitions have emerged from the Working Group's review of the available virologic and clinical literature and will be subject to reassessment and modification based on results of future studies.
Collapse
Affiliation(s)
- Roy F Chemaly
- Department of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston
| | - Sunwen Chou
- Division of Infectious Diseases, Oregon Health and Science University, and Research and Development Service, Veterans Affairs Portland Health Care System
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Wuerzburg, Germany
| | - Paul Griffiths
- Institute for Immunity and Transplantation, University College London Medical School, United Kingdom
| | - Robin Avery
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Raymund R Razonable
- Division of Infectious Diseases, Department of Medicine, William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, Minnesota
| | - Kathleen M Mullane
- Section of Infectious Diseases and Global Health, Department of Medicine, University of Chicago, Illinois
| | - Camille Kotton
- Infectious Diseases Division, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Jens Lundgren
- Centre for Health and Infectious Disease Research, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Takashi E Komatsu
- Division of Antiviral Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland
| | - Peter Lischka
- AiCuris Anti-infective Cures GmbH, Wuppertal, Germany
| | | | | | - Obi Umeh
- Shire Global Clinical Development (Immunology Therapeutic Area), Lexington, Massachusetts
| | - Veronica Miller
- Forum for Collaborative Research, University of California, Berkeley
| | - Per Ljungman
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation, Karolinska University Hospital.,Division of Hematology, Department of Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | | |
Collapse
|
28
|
Suárez NM, Blyth E, Li K, Ganzenmueller T, Camiolo S, Avdic S, Withers B, Linnenweber-Held S, Gwinner W, Dhingra A, Heim A, Schulz TF, Gunson R, Gottlieb D, Slobedman B, Davison AJ. Whole-Genome Approach to Assessing Human Cytomegalovirus Dynamics in Transplant Patients Undergoing Antiviral Therapy. Front Cell Infect Microbiol 2020; 10:267. [PMID: 32612959 PMCID: PMC7308726 DOI: 10.3389/fcimb.2020.00267] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Human cytomegalovirus (HCMV) is the most frequent cause of opportunistic viral infection following transplantation. Viral factors of potential clinical importance include the selection of mutants resistant to antiviral drugs and the occurrence of infections involving multiple HCMV strains. These factors are typically addressed by analyzing relevant HCMV genes by PCR and Sanger sequencing, which involves independent assays of limited sensitivity. To assess the dynamics of viral populations with high sensitivity, we applied high-throughput sequencing coupled with HCMV-adapted target enrichment to samples collected longitudinally from 11 transplant recipients (solid organ, n = 9, and allogeneic hematopoietic stem cell, n = 2). Only the latter presented multiple-strain infections. Four cases presented resistance mutations (n = 6), two (A594V and L595S) at high (100%) and four (V715M, V781I, A809V, and T838A) at low (<25%) frequency. One allogeneic hematopoietic stem cell transplant recipient presented up to four resistance mutations, each at low frequency. The use of high-throughput sequencing to monitor mutations and strain composition in people at risk of HCMV disease is of potential value in helping clinicians implement the most appropriate therapy.
Collapse
Affiliation(s)
- Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Emily Blyth
- Westmead Institute for Medical Research, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Blood and Bone Marrow Transplant Unit, Westmead Hospital, Sydney, NSW, Australia.,Sydney Cellular Therapies Laboratory, Westmead Hospital, Sydney, NSW, Australia
| | - Kathy Li
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Tina Ganzenmueller
- Institute for Medical Virology, University Hospital Tübingen, Tübingen, Germany.,Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Salvatore Camiolo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Selmir Avdic
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Barbara Withers
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Silvia Linnenweber-Held
- Department of Nephrology, Hannover Medical School, Hanover, Germany.,Public Health Agency of Lower Saxony, Hanover, Germany
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hanover, Germany
| | - Akshay Dhingra
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, Hanover, Germany.,German Center for Infection Research, Hanover, Germany
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - David Gottlieb
- Westmead Institute for Medical Research, Sydney, NSW, Australia.,Blood and Bone Marrow Transplant Unit, Westmead Hospital, Sydney, NSW, Australia
| | - Barry Slobedman
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| |
Collapse
|
29
|
The Value of Combined Radial Endobronchial Ultrasound-Guided Transbronchial Lung Biopsy and Metagenomic Next-Generation Sequencing for Peripheral Pulmonary Infectious Lesions. Can Respir J 2020; 2020:2367505. [PMID: 32322324 PMCID: PMC7165338 DOI: 10.1155/2020/2367505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 11/18/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a new technology that allows for unbiased detection of pathogens. However, there are few reports on mNGS of lung biopsy tissues for pulmonary infection diagnosis. In addition, radial endobronchial ultrasound (R-EBUS) is widely used to detect peripheral pulmonary lesions (PPLs), but it is rarely used in the diagnosis of peripheral lung infection. Objective The present study aims to evaluate the combined application of R-EBUS-guided transbronchial lung biopsy (TBLB) and mNGS for the diagnosis of peripheral pulmonary infectious lesions. Methods From July 2018 to April 2019, 121 patients from Tianjin Medical University General Hospital diagnosed with PPLs and lung infection were enrolled in this prospective randomized study . Once the lesion was located, either TBLB or R-EBUS-guided-TBLB was performed in randomly selected patients, and mNGS was applied for pathogen detection in lung biopsy tissues. The results of mNGS were compared between the TBLB group and R-EBUS-guided TBLB group. In addition, the clinical characteristics and EBUS images from 61 patients receiving bronchoscopy for peripheral lung infectious detection were analyzed and compared with the results of mNGS. Results The positivity rate of mNGS in R-EBUS-guided TBLB was (78.7%, 48/61) that was significantly higher than (60.0%, 36/60) in the TBLB group. Difference in the position of R-EBUS probe and image characteristics of peripheral lung infectious lesions affected the positivity rate of mNGS. Tissue collected by R-EBUS within the lesion produced higher positivity rate than samples collected adjacent to the lesion (P=0.030, odds ratio 17.742; 95% confidence interval, from 1.325 to 237.645). Anechoic areas and luminant areas of ultrasonic image characteristics were correlated with lower positivity rate of mNGS (respectively, P=0.019, odds ratio 17.878; 95% confidence interval, from 1.595 to 200.399; P=0.042, odds ratio 16.745; 95% confidence interval, from 1.106 to 253.479). Conclusions R-EBUS-guided TBLB is a safe and effective technique in the diagnosis of peripheral lung infectious lesions. R-EBUS significantly facilitates the accurate insertion of bronchoscope into the lesions, which improves positivity rate of mNGS analysis in pathogen detection. The R-EBUS probe position within lesion produced a higher positivity rate of mNGS analysis. Nevertheless, the presence of anechoic and luminant areas on ultrasonic image was correlated with poor mNGS positivity rate.
Collapse
|
30
|
Mullane KM. Human Cytomegalovirus Prophylaxis and Treatment in Lung Transplantation in the Current Era. CURRENT PULMONOLOGY REPORTS 2020. [DOI: 10.1007/s13665-020-00246-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
31
|
Délye C, Michel S, Pernin F, Gautier V, Gislard M, Poncet C, Le Corre V. Harnessing the power of next-generation sequencing technologies to the purpose of high-throughput pesticide resistance diagnosis. PEST MANAGEMENT SCIENCE 2020; 76:543-552. [PMID: 31270924 DOI: 10.1002/ps.5543] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Next Generation Sequencing (NGS) technologies offer tremendous possibilities for high-throughput pesticide resistance diagnosis via massive genotyping-by-sequencing. Herein, we used Illumina sequencing combined with a simple, non-commercial bioinformatics pipe-line to seek mutations involved in herbicide resistance in two weeds. RESULTS DNA was extracted from 96 pools of 50 plants for each species. Three amplicons encompassing 15 ALS (acetolactate-synthase) codons crucial for herbicide resistance were amplified from each DNA extract. Above 18 and 20 million quality 250-nucleotide sequence reads were obtained for groundsel (Senecio vulgaris, tetraploid) and ragweed (Ambrosia artemisiifolia, diploid), respectively. Herbicide resistance-endowing mutations were identified in 45 groundsel and in eight ragweed field populations. The mutations detected and their frequencies assessed by NGS were checked by individual plant genotyping or Sanger sequencing. NGS results were fully confirmed, except in three instances out of 12 where mutations present at a frequency of 1% were detected below the threshold set for reliable mutation detection. CONCLUSION Analyzing 9600 plants requested 192 DNA extractions followed by 1728 PCRs and two Illumina runs. Equivalent results obtained by individual analysis would have necessitated 9600 individual DNA extractions followed by 216 000 genotyping PCRs, or by 121 500 PCRs and 40 500 Sanger sequence runs. This clearly demonstrates the interest and power of NGS-based detection of pesticide resistance from pools of individuals for diagnosing resistance in massive numbers of individuals. © 2019 Society of Chemical Industry.
Collapse
Affiliation(s)
| | | | | | - Véronique Gautier
- INRA, UMR1095 Génétique, Diversité et Écophysiologie des Céréales, Clermont-Ferrand, France
| | | | - Charles Poncet
- INRA, UMR1095 Génétique, Diversité et Écophysiologie des Céréales, Clermont-Ferrand, France
| | | |
Collapse
|
32
|
Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
Collapse
Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| |
Collapse
|
33
|
Advances in the genotypic diagnosis of cytomegalovirus antiviral drug resistance. Antiviral Res 2020; 176:104711. [PMID: 31940472 DOI: 10.1016/j.antiviral.2020.104711] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/22/2019] [Accepted: 01/09/2020] [Indexed: 12/20/2022]
Abstract
Cytomegalovirus (CMV) drug resistance mutation maps are updated with recent information for polymerase inhibitors, the terminase inhibitor letermovir and the UL97 kinase inhibitor maribavir. Newly mapped mutations and their phenotypes provide more detail on cross-resistance properties and suggest the need to expand the CMV gene regions covered in diagnostic testing. Next-generation deep sequencing technology offers a more sensitive, higher resolution view of emerging antiviral resistance and is recommended for use in clinical trials. Issues of standardization and diagnostic utility in comparison with traditional Sanger sequencing remain unresolved. Quality control is important for the accurate and reproducible detection of mutant viral populations in clinical specimens.
Collapse
|
34
|
Luo J, Shi X, Lin Y, Cheng N, Shi Y, Wang Y, Wu BQ. Cytomegalovirus Infection in an Adult Patient With Neuromyelitis Optica and Acute Hemorrhagic Rectal Ulcer: Case Report and Literature Review. Front Immunol 2020; 11:1634. [PMID: 32849558 PMCID: PMC7417347 DOI: 10.3389/fimmu.2020.01634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Previous infectious or inflammatory events may be involved in the pathogenesis of neuromyelitis optica (NMO), potentially by triggering an autoimmune response. Cytomegalovirus (CMV)-related NMO (CMV-NMO) is rarely reported. Acute hemorrhagic rectal ulcer (AHRU) is a rare disease with a largely unknown pathogenesis. Herein, we reported a co-NMO and AHRU case associated with CMV infection. In addition, we review previously reported cases of CMV-NMO and CMV-AHRU. Case presentation: A 40-year-old female diagnosed with aquaporin4 (AQP4)-IgG+ NMO and a poor response to high-dose intravenous methylprednisolone and immunoglobulin, followed by three rounds of plasma exchange was transferred to Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China. She developed repeated acute lower gastrointestinal hemorrhage from the third day of admission. Abdominal computed tomography angiography (CTA) and interventional angiography did not detect any bleeding vessel. Bedside colonoscopy revealed a large ulcer-like lesion at 10 cm above the anus. Rectal biopsy pathology confirmed a CMV infection on day 23 post-admission, and cerebrospinal fluid (CSF) pathogen gene sequencing detected CMV gene copies on day 25 post-admission. After 2 weeks of treatment with ganciclovir and sodium phosphinate, the patient's lower gastrointestinal bleeding stopped, and her limb muscle strength and visual acuity gradually improved. After 4 weeks of antiviral therapy, colonoscopy showed that the intestinal wall of the original lesion was smooth. Hematoxylin and eosin (HE) staining and immunohistochemistry (IHC) of a biopsy specimen was negative for CMV, her right eye vision was normal, and limb muscle strength had recovered. Serum AQP4-IgG was negative, and lesions on brain magnetic resonance imaging (MRI) manifested shrinkage. Conclusions: The benefits of antiviral therapy remain unclear; however, clinicians should be aware of the possibility of CMV-related NMO, if NMO was refractory to high-dose intravenous methylprednisolone, immunoglobulin, and plasma exchange. Moreover, clinicians should consider the possibility of CMV-related AHRU when recurrent acute lower gastrointestinal bleeding occurs in a patient.
Collapse
Affiliation(s)
- Jinmei Luo
- Medical Intensive Care Unit and Division of Respiratory Diseases, Department of Internal Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaowei Shi
- Medical Intensive Care Unit and Division of Respiratory Diseases, Department of Internal Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ying Lin
- Department of Gastroenterology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Na Cheng
- Department of Pathology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yunfeng Shi
- Medical Intensive Care Unit and Division of Respiratory Diseases, Department of Internal Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanhong Wang
- Medical Intensive Care Unit and Division of Respiratory Diseases, Department of Internal Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ben-Quan Wu
- Medical Intensive Care Unit and Division of Respiratory Diseases, Department of Internal Medicine, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Ben-Quan Wu
| |
Collapse
|
35
|
Improvement in detecting cytomegalovirus drug resistance mutations in solid organ transplant recipients with suspected resistance using next generation sequencing. PLoS One 2019; 14:e0219701. [PMID: 31318908 PMCID: PMC6638921 DOI: 10.1371/journal.pone.0219701] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022] Open
Abstract
OBJETIVES The aim of this study was to identify CMV drug resistance mutations (DRM) in solid organ transplant (SOT) recipients with suspected resistance comparing next-generation sequencing (NGS) with Sanger sequencing and assessing risk factors and the clinical impact of resistance. METHODS Using Sanger sequencing as the reference method, we prospectively assessed the ability of NGS to detect CMV DRM in the UL97 and UL54 genes in a nationwide observational study from September 2013 to August 2016. RESULTS Among 44 patients recruited, 14 DRM were detected by Sanger in 12 patients (27%) and 20 DRM were detected by NGS, in 16 (36%). NGS confirmed all the DRM detected by Sanger. The additional six mutations detected by NGS were present in <20% of the sequenced population, being located in the UL97 gene and conferring high-level resistance to ganciclovir. The presence of DRM by NGS was associated with lung transplantation (p = 0.050), the administration of prophylaxis (p = 0.039), a higher mean time between transplantation and suspicion of resistance (p = 0.038) and longer antiviral treatment duration before suspicion (p = 0.024). However, the latter was the only factor independently associated with the presence of DRM by NGS in the multivariate analysis (OR 2.24, 95% CI 1.03 to 4.87). CONCLUSIONS NGS showed a higher yield than Sanger sequencing for detecting CMV resistance mutations in SOT recipients. The presence of DRM detected by NGS was independently associated with longer antiviral treatment.
Collapse
|
36
|
Andrei G, Van Loon E, Lerut E, Victoor J, Meijers B, Bammens B, Sprangers B, Gillemot S, Fiten P, Opdenakker G, Lagrou K, Kuypers D, Snoeck R, Naesens M. Persistent primary cytomegalovirus infection in a kidney transplant recipient: Multi-drug resistant and compartmentalized infection leading to graft loss. Antiviral Res 2019; 168:203-209. [PMID: 31212020 DOI: 10.1016/j.antiviral.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
Abstract
Cytomegalovirus (CMV) is one of the most common opportunistic infections after transplantation. To prevent CMV infections, universal prophylaxis and pre-emptive therapy with ganciclovir or its prodrug valganciclovir is applied. However, prolonged antiviral therapy may result in drug-resistance emergence. We describe a case of a 43-year-old CMV-seronegative patient who underwent kidney transplantation from a CMV-seropositive donor and developed CMV disease despite valganciclovir prophylaxis. CMV viral load increased even though valgangiclovir dose was augmented and immunosuppressive therapy reduced. CMV genotyping revealed mutations in the viral UL97 protein kinase, explaining ganciclovir-resistant CMV infection. The viral load failed to respond to foscavir, cidofovir and CMV-neutralizing immunoglobulins. Kidney allograft dysfunction developed 3 months post-transplantation with a histopathologic diagnosis of CMV nephropathy and potentially concomitant T-cell mediated rejection. A transplantectomy was performed on day 164 post-transplantation since the patient had uncontrollable CMV disease associated with a circulating multidrug-resistant DNA polymerase-mutant virus. Detailed monitoring in this patient demonstrated hallmarks of complicated CMV disease: (i) relatively rapid evolution of drug-resistant CMV mutants in the setting of persistent high blood viral loads, (ii) emergence of viral drug-resistance linked to acute graft rejection, (iii) transient and, thereafter, lack of response to various anti-CMV treatments, (iv) compartmentalization and heterogeneity of CMV viral populations, (v) possible differential ability of viral mutants to cause disease in the graft, and (vi) detection of minor viral variants by next generation sequencing. Translational research platforms that provide rapid molecular genotyping for detection of CMV drug-resistance are essential in guiding CMV disease management in high-risk transplant recipients.
Collapse
Affiliation(s)
| | - Elisabet Van Loon
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| | - Evelyne Lerut
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| | - Jasper Victoor
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| | - Björn Meijers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| | - Bert Bammens
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| | - Ben Sprangers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| | | | - Pierre Fiten
- Rega Institute for Medical Research, KU Leuven, Belgium
| | | | - Katrien Lagrou
- Laboratory of Clinical Bacteriology and Mycology University Hospitals Leuven, Leuven, Belgium
| | - Dirk Kuypers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, Belgium
| | - Maarten Naesens
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Belgium
| |
Collapse
|
37
|
Ma L, Jakobiec FA, Dryja TP. A Review of Next-Generation Sequencing (NGS): Applications to the Diagnosis of Ocular Infectious Diseases. Semin Ophthalmol 2019; 34:223-231. [PMID: 31170015 DOI: 10.1080/08820538.2019.1620800] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: To review the value of next-generation sequencing (NGS) in identifying the pathogens which cause ocular infections, thereby facilitating prompt initiation of treatment with an optimal anti-microbial regimen. Both contemporary and futuristic approaches to identifying pathogens in ocular infections are covered in this brief overview. Methods: Review of the peer reviewed literature on conventional and advanced methods as applied to the diagnosis of infectious diseases of the eye. Conclusion: NGS is a novel technology for identifying the pathogens responsible for ocular infections with the potential to improve the accuracy and speed of diagnosis and hastening the selection of the best therapy.
Collapse
Affiliation(s)
- Lina Ma
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
| | - Frederick A Jakobiec
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
| | - Thaddeus P Dryja
- a David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary , Harvard Medical School , Boston , MA , USA
| |
Collapse
|
38
|
Mercier-Darty M, Boutolleau D, Rodriguez C, Burrel S. Added value of ultra-deep sequencing (UDS) approach for detection of genotypic antiviral resistance of herpes simplex virus (HSV). Antiviral Res 2019; 168:128-133. [PMID: 31158412 DOI: 10.1016/j.antiviral.2019.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/03/2019] [Accepted: 05/30/2019] [Indexed: 11/16/2022]
Abstract
Classically, Sanger sequencing is considered the gold standard for detection of HSV drug resistance mutations (DRMs). As a complementary method, ultra-deep sequencing (UDS) has an improved ability to detect minor variants and mixed populations. The aim of this work was to apply UDS performed on MiSeq® Illumina platform to the detection of HSV DRMs and to the evaluation of the subpopulation diversity in clinical samples in comparison with Sanger sequencing. A total of 59 HSV-positive clinical samples (31 HSV-1 and 28 HSV-2) recovered from 50 patients mainly immunocompromised (70%) were retrospectively analyzed. Remarkably, UDS analysis revealed significant differences of relative abundance according to the type of DRMs within TK and Pol: natural polymorphisms and amino acid changes associated with resistance to antivirals were identified as high-abundant mutations (>96%), whereas TK frameshifts conferring resistance to ACV were systematically detected at lower abundance (≈80%). This work also revealed that UDS can detect low-frequency DRMs and provides extensive information on viral population composition.
Collapse
Affiliation(s)
- Mélanie Mercier-Darty
- INSERM U955 Eq18, IMRB, UPEC, AP-HP, Virology Department, Hospital Henri Mondor, Créteil, France
| | - David Boutolleau
- Sorbonne Université, INSERM, Institut Pierre Louis D'Epidémiologie et de Santé Publique (iPLESP), AP-HP, University Hospital Pitié-Salpêtrière - Charles Foix, National Reference Center for Herpesviruses, Virology Department, Paris, France
| | - Christophe Rodriguez
- INSERM U955 Eq18, IMRB, UPEC, AP-HP, Virology Department, Hospital Henri Mondor, Créteil, France
| | - Sonia Burrel
- Sorbonne Université, INSERM, Institut Pierre Louis D'Epidémiologie et de Santé Publique (iPLESP), AP-HP, University Hospital Pitié-Salpêtrière - Charles Foix, National Reference Center for Herpesviruses, Virology Department, Paris, France.
| |
Collapse
|
39
|
Martí-Carreras J, Maes P. Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges. Virus Genes 2019; 55:138-164. [PMID: 30604286 PMCID: PMC6458973 DOI: 10.1007/s11262-018-1627-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
The human cytomegalovirus (HCMV) genome was sequenced by hierarchical shotgun almost 30 years ago. Over these years, low and high passaged strains have been sequenced, improving, albeit still far from complete, the understanding of the coding potential, expression dynamics and diversity of wild-type HCMV strains. Next-generation sequencing (NGS) platforms have enabled a huge advancement, facilitating the comparison of differentially passaged strains, challenging diagnostics and research based on a single or reduced gene set genotyping. In addition, it allowed to link genetic features to different viral phenotypes as for example, correlating large genomic re-arrangements to viral attenuation or different mutations to antiviral resistance and cell tropism. NGS platforms provided the first high-resolution experiments to HCMV dynamics, allowing the study of intra-host viral population structures and the description of rare transcriptional events. Long-read sequencing has recently become available, helping to identify new genomic re-arrangements, partially accounting for the genetic variability displayed in clinical isolates, as well as, in changing the understanding of the HCMV transcriptome. Better knowledge of the transcriptome resulted in a vast number of new splicing events and alternative transcripts, although most of them still need additional validation. This review summarizes the sequencing efforts reached so far, discussing its approaches and providing a revision and new nuances on HCMV sequence variability in the sequencing field.
Collapse
Affiliation(s)
- Joan Martí-Carreras
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium.
| |
Collapse
|
40
|
Razonable RR, Humar A. Cytomegalovirus in solid organ transplant recipients-Guidelines of the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant 2019; 33:e13512. [PMID: 30817026 DOI: 10.1111/ctr.13512] [Citation(s) in RCA: 379] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/11/2019] [Indexed: 12/11/2022]
Abstract
Cytomegalovirus (CMV) is one of the most common opportunistic infections that affect the outcome of solid organ transplantation. This updated guideline from the American Society of Transplantation Infectious Diseases Community of Practice provides evidence-based and expert recommendations for screening, diagnosis, prevention, and treatment of CMV in solid organ transplant recipients. CMV serology to detect immunoglobulin G remains as the standard method for pretransplant screening of donors and transplant candidates. Antiviral prophylaxis and preemptive therapy are the mainstays of CMV prevention. The lack of a widely applicable viral load threshold for diagnosis and preemptive therapy is highlighted, as a result of variability of CMV nucleic acid testing, even in the contemporary era when calibrators are standardized. Valganciclovir and intravenous ganciclovir remain as drugs of choice for CMV management. Strategies for managing drug-resistant CMV infection are presented. There is an increasing use of CMV-specific cell-mediated immune assays to stratify the risk of CMV infection after solid organ transplantation, but their role in optimizing CMV prevention and treatment efforts has yet to be demonstrated. Specific issues related to pediatric transplant recipients are discussed.
Collapse
Affiliation(s)
| | - Atul Humar
- University Health Network, Toronto, Ontario, Canada.,Transplant Institute, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
41
|
The Third International Consensus Guidelines on the Management of Cytomegalovirus in Solid-organ Transplantation. Transplantation 2019; 102:900-931. [PMID: 29596116 DOI: 10.1097/tp.0000000000002191] [Citation(s) in RCA: 699] [Impact Index Per Article: 139.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite recent advances, cytomegalovirus (CMV) infections remain one of the most common complications affecting solid organ transplant recipients, conveying higher risks of complications, graft loss, morbidity, and mortality. Research in the field and development of prior consensus guidelines supported by The Transplantation Society has allowed a more standardized approach to CMV management. An international multidisciplinary panel of experts was convened to expand and revise evidence and expert opinion-based consensus guidelines on CMV management including prevention, treatment, diagnostics, immunology, drug resistance, and pediatric issues. Highlights include advances in molecular and immunologic diagnostics, improved understanding of diagnostic thresholds, optimized methods of prevention, advances in the use of novel antiviral therapies and certain immunosuppressive agents, and more savvy approaches to treatment resistant/refractory disease. The following report summarizes the updated recommendations.
Collapse
|
42
|
Gu W, Miller S, Chiu CY. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:319-338. [PMID: 30355154 DOI: 10.1146/annurev-pathmechdis-012418-012751] [Citation(s) in RCA: 667] [Impact Index Per Article: 111.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers ( a) next-generation sequencing technologies and common platforms, ( b) next-generation sequencing assay workflows in the clinical microbiology laboratory, ( c) bioinformatics analysis of metagenomic next-generation sequencing data, ( d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and ( e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.
Collapse
Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA; .,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California 94107, USA
| |
Collapse
|
43
|
ViroFind: A novel target-enrichment deep-sequencing platform reveals a complex JC virus population in the brain of PML patients. PLoS One 2018; 13:e0186945. [PMID: 29360822 PMCID: PMC5779639 DOI: 10.1371/journal.pone.0186945] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022] Open
Abstract
Deep nucleotide sequencing enables the unbiased, broad-spectrum detection of viruses in clinical samples without requiring an a priori hypothesis for the source of infection. However, its use in clinical research applications is limited by low cost-effectiveness given that most of the sequencing information from clinical samples is related to the human genome, which renders the analysis of viral genomes challenging. To overcome this limitation we developed ViroFind, an in-solution target-enrichment platform for virus detection and discovery in clinical samples. ViroFind comprises 165,433 viral probes that cover the genomes of 535 selected DNA and RNA viruses that infect humans or could cause zoonosis. The ViroFind probes are used in a hybridization reaction to enrich viral sequences and therefore enhance the detection of viral genomes via deep sequencing. We used ViroFind to detect and analyze all viral populations in the brain of 5 patients with progressive multifocal leukoencephalopathy (PML) and of 18 control subjects with no known neurological disease. Compared to direct deep sequencing, by using ViroFind we enriched viral sequences present in the clinical samples up to 127-fold. We discovered highly complex polyoma virus JC populations in the PML brain samples with a remarkable degree of genetic divergence among the JC virus variants of each PML brain sample. Specifically for the viral capsid protein VP1 gene, we identified 24 single nucleotide substitutions, 12 of which were associated with amino acid changes. The most frequent (4 of 5 samples, 80%) amino acid change was D66H, which is associated with enhanced tissue tropism, and hence likely a viral fitness advantage, compared to other variants. Lastly, we also detected sparse JC virus sequences in 10 of 18 (55.5%) of control samples and sparse human herpes virus 6B (HHV6B) sequences in the brain of 11 of 18 (61.1%) control subjects. In sum, ViroFind enabled the in-depth analysis of all viral genomes in PML and control brain samples and allowed us to demonstrate a high degree of JC virus genetic divergence in vivo that has been previously underappreciated. ViroFind can be used to investigate the structure of the virome with unprecedented depth in health and disease state.
Collapse
|
44
|
Antiviral resistance in herpes simplex virus and varicella-zoster virus infections: diagnosis and management. Curr Opin Infect Dis 2018; 29:654-662. [PMID: 27306564 DOI: 10.1097/qco.0000000000000288] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Aciclovir (ACV) is the first-line drug for the management of herpes simplex virus (HSV) and varicella-zoster virus (VZV) infections. Long-term administration of ACV for the treatment of severe infections in immunocompromised patients can lead to the development of drug resistance. Furthermore, the emergence of isolates resistant to ACV is increasingly recognized in immunocompetent individuals with herpetic keratitis. This review describes the mechanisms involved in drug resistance for HSV and VZV, the laboratory diagnosis and management of patients with infections refractory to ACV therapy. RECENT FINDINGS Genotypic testing is more frequently performed for the diagnosis of infections caused by drug-resistant HSV or VZV isolates. Molecular biology-based systems for the generation of recombinant viruses have been developed to link unknown mutations with their drug phenotypes. Fast and sensitive methods based on next-generation sequencing will improve the detection of heterogeneous viral populations of drug-resistant viruses and their temporal changes during antiviral therapy, which could allow better patient management. Novel promising compounds acting on targets that differ from the viral DNA polymerase are under clinical development. SUMMARY Antiviral drug resistance monitoring for HSV and VZV is required for a rational use of antiviral therapy in high-risk populations.
Collapse
|
45
|
Hancer VS, Yarimcan FS, Buyukdogan M, Aki SZ, Oksuz B, Acar K, Acar M, Bulut P. A novel ganciclovir resistance mutation in the UL97 gene of the HHV-5 in an adult hematopoietic stem cell transplant recipient. Future Virol 2017. [DOI: 10.2217/fvl-2017-0085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Therapeutic management of cytomegalovirus (CMV) disease in hematopoietic stem cell transplantation patients can become a challenge because of the emergence of anti-CMV drug resistance. This case report presents a patient with clinical ganciclovir resistance due to a new mutation: histidine-to-asparagine change at residue 393 of UL97. This mutation, which is located in the nonfunctional region of the UL97 gene, is very unusual. Having more information about the mutations leading to drug resistance in CMV is important for both improved clinical management and development of new diagnostic tests and drugs.
Collapse
Affiliation(s)
- Veysel Sabri Hancer
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul
| | - Filiz Saglam Yarimcan
- Department of Medical Microbiology, Faculty of Medicine, Istinye University, Istanbul
| | - Murat Buyukdogan
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul
| | - Sahika Zeynep Aki
- Division of Hematology, Department of Internal Medicine, Bahcesehir University, Istanbul
| | - Burcu Oksuz
- Istinye University Genetic Diagnosis Center, Istanbul
| | - Kadir Acar
- Division of Hematology, Department of Internal Medicine, Altinbas University, Istanbul
| | - Muradiye Acar
- Istinye University Genetic Diagnosis Center, Istanbul
| | - Pelin Bulut
- Istinye University Genetic Diagnosis Center, Istanbul
| |
Collapse
|
46
|
Fujii H, Kakiuchi S, Tsuji M, Nishimura H, Yoshikawa T, Yamada S, Omura N, Inagaki T, Shibamura M, Harada S, Taniguchi S, Saijo M. Application of next-generation sequencing to detect acyclovir-resistant herpes simplex virus type 1 variants at low frequency in thymidine kinase gene of the isolates recovered from patients with hematopoietic stem cell transplantation. J Virol Methods 2017; 251:123-128. [PMID: 29074089 DOI: 10.1016/j.jviromet.2017.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/25/2022]
Abstract
Ion Torrent next-generation sequencing (NGS) technology was applied to study the mode of emergence of acyclovir (ACV)-resistant (ACVr) herpes simplex virus type 1 (HSV-1) in patients with hematopoietic stem cell transplantation (HSCT) by quantitatively detecting mutations in the viral thymidine kinase (vTK) gene in the HSV-1 isolates recovered from HSCT patients. All of the mutations detected with the Sanger sequencing method in the vTK genes of HSV-1 isolates were also detected with the NGS assay. Furthermore, different mutations, which conferred ACV resistance and were not detected with the Sanger sequencing method, were also detected in a quantitative manner by using the NGS assay. The approach described here is applicable to studying the emergence process of vTK gene mutation-associated ACVr HSV-1 more in detail than the Sanger method. The NGS assay makes it possible to make a diagnosis of vTK gene mutation-associated ACVr HSV-1 infections at the early stage, which the ratio of ACVr HSV-1 is much lower than that of ACV-sensitive (ACVs) HSV-1.
Collapse
Affiliation(s)
- Hikaru Fujii
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Satsuki Kakiuchi
- Department of Pediatrics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Masanori Tsuji
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-8470, Japan
| | - Hidekazu Nishimura
- Virus Research Center, Sendai Medical Center, 2-8-8 Miyagino, Miyagino-ku, Sendai-shi, Miyagi, 983-8520, Japan
| | - Tomoki Yoshikawa
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Souichi Yamada
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Natsumi Omura
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Takuya Inagaki
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Miho Shibamura
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan; Department of Pediatrics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shizuko Harada
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minato-ku, Tokyo, 105-8470, Japan
| | - Masayuki Saijo
- Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
| |
Collapse
|
47
|
Deak E, Marlowe EM. Right-Sizing Technology in the Era of Consumer-Driven Health Care. CLINICAL MICROBIOLOGY NEWSLETTER 2017; 39:115-123. [PMID: 32287687 PMCID: PMC7132510 DOI: 10.1016/j.clinmicnews.2017.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Technology for modern clinical and public health microbiology laboratories has evolved at an impressive rate over the last two decades. Contemporary diagnostics can rapidly provide powerful data that can impact patient lives and support infectious disease outbreak investigations. At the same time, dramatic changes to health care delivery are putting new pressures on a system that is now focusing on patient-centric, value-driven, convenient care. For laboratories, balancing all these demands in a cost-contained environment remains a challenge. This article explores the current and future directions of diagnostics in our dynamic health care environment.
Collapse
Affiliation(s)
- Eszter Deak
- The Permanente Medical Group, Regional Laboratories, Berkeley, California
| | | |
Collapse
|
48
|
Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, Budvytiene I, Cevallos V, Zhong L, Zhou Z, Lietman TM, DeRisi JL. Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections. Ophthalmology 2017; 124:1247-1248. [PMID: 28526549 DOI: 10.1016/j.ophtha.2017.03.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 03/22/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022] Open
Affiliation(s)
- Thuy Doan
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California
| | - Nisha R Acharya
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, California
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Vicky Cevallos
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Zhaoxia Zhou
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California
| | - Thomas M Lietman
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California; Department of Ophthalmology, University of California, San Francisco, California
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, California; Chan Zuckerberg Biohub, San Francisco, California.
| |
Collapse
|
49
|
Detection of Emerging Vaccine-Related Polioviruses by Deep Sequencing. J Clin Microbiol 2017; 55:2162-2171. [PMID: 28468861 PMCID: PMC5483918 DOI: 10.1128/jcm.00144-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/19/2017] [Indexed: 12/13/2022] Open
Abstract
Oral poliovirus vaccine can mutate to regain neurovirulence. To date, evaluation of these mutations has been performed primarily on culture-enriched isolates by using conventional Sanger sequencing. We therefore developed a culture-independent, deep-sequencing method targeting the 5′ untranslated region (UTR) and P1 genomic region to characterize vaccine-related poliovirus variants. Error analysis of the deep-sequencing method demonstrated reliable detection of poliovirus mutations at levels of <1%, depending on read depth. Sequencing of viral nucleic acids from the stool of vaccinated, asymptomatic children and their close contacts collected during a prospective cohort study in Veracruz, Mexico, revealed no vaccine-derived polioviruses. This was expected given that the longest duration between sequenced sample collection and the end of the most recent national immunization week was 66 days. However, we identified many low-level variants (<5%) distributed across the 5′ UTR and P1 genomic region in all three Sabin serotypes, as well as vaccine-related viruses with multiple canonical mutations associated with phenotypic reversion present at high levels (>90%). These results suggest that monitoring emerging vaccine-related poliovirus variants by deep sequencing may aid in the poliovirus endgame and efforts to ensure global polio eradication.
Collapse
|
50
|
Parker J, Chen J. Application of next generation sequencing for the detection of human viral pathogens in clinical specimens. J Clin Virol 2016; 86:20-26. [PMID: 27902961 DOI: 10.1016/j.jcv.2016.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/02/2016] [Accepted: 11/21/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) is a new technology that can be used for broad detection of infectious pathogens and is rapidly becoming an essential platform in clinical laboratories. It is not known how NGS will displace or enhance gold standard methodologies in infectious disease diagnosis. OBJECTIVES To investigate the feasibility and application of NGS technology in public health laboratories and compare NGS technology with conventional methods. STUDY DESIGN Illumina MiSeq system was used to detect viral pathogens alongside other conventional virology methods using typical clinical specimen matrices. Sixteen clinical specimens and two CDC proficiency panels containing seventeen specimens were analyzed. RESULTS Known pathogenic viral nucleic acid was positively identified in all clinical specimens, correlating and building upon results obtained by more conventional laboratory methods. Sequencing depths ranged from 0.008X to 319 and genome coverage ranged from 0.6% to 99.9%. To substantiate the described methods used to analyze data derived from clinical specimens, the results of a clinical proficiency panel are also presented. DISCUSSION Our results reveal true scarcity of known pathogenic viral nucleic acids in clinical specimens. NGS outperforms more conventional detection methods in this study by turnaround time as well as the improved depth of knowledge in regards to serotyping and drug resistance.
Collapse
Affiliation(s)
- Jayme Parker
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA; Alaska State Public Health Virology Laboratory, Fairbanks, AK 99775, USA
| | - Jack Chen
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA; Alaska State Public Health Virology Laboratory, Fairbanks, AK 99775, USA.
| |
Collapse
|