1
|
Poulsen SH, Søgaard KK, Fuursted K, Nielsen HL. Evaluating the diagnostic accuracy and clinical utility of 16S and 18S rRNA gene targeted next-generation sequencing based on five years of clinical experience. Infect Dis (Lond) 2023; 55:767-775. [PMID: 37535652 DOI: 10.1080/23744235.2023.2241550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The use of 16S/18S rRNA targeted next-generation sequencing (tNGS) has improved microbial diagnostics, however, the use of tNGS in a routine clinical setting requires further elucidation. We retrospectively evaluated the diagnostic accuracy and clinical utility of 16S/18S tNGS, routinely used in the North Denmark Region between 2017 and 2021. METHODS We retrieved 544 tNGS results from 491 patients hospitalised with suspected infection (e.g. meningitis, pneumonia, intraabdominal abscess, osteomyelitis and joint infection). The tNGS assays was performed using the Illumina MiSeq desktop sequencer, and BION software for annotation. The patients' diagnosis and clinical management was evaluated by medical chart review. We calculated sensitivity and specificity, and determined the diagnostic accuracy of tNGS by defining results as true positive, true negative, false positive, and false negative. RESULTS Overall, tNGS had a sensitivity of 56% and a specificity of 97%. tNGS was more frequently true positive compared to culture (32% vs 18%), and tNGS detected a greater variety of bacteria and fungi, and was more frequently polymicrobial. However, the total diagnostic turnaround time was 16 days, and although 73% of tNGS results were true positive or true negative, only 4.4% of results led to changes in clinical management. CONCLUSIONS As a supplement to culture, tNGS improves identification of pathogenic microorganisms in a broad range of clinical specimens. However, the long turnaround time of tNGS in our setting may have contributed to a limited clinical utility. An improved turnaround time can be the key to improved clinical utility in a future setting.
Collapse
Affiliation(s)
| | - Kirstine Kobberøe Søgaard
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| |
Collapse
|
2
|
Laimon W, El-Ziny M, El-Hawary A, Elsharkawy A, Salem NAB, Aboelenin HM, Awad MH, Flanagan SE, De Franco E. Genetic and clinical heterogeneity of permanent neonatal diabetes mellitus: a single tertiary centre experience. Acta Diabetol 2021; 58:1689-1700. [PMID: 34426871 DOI: 10.1007/s00592-021-01788-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/13/2021] [Indexed: 11/25/2022]
Abstract
AIMS Neonatal diabetes mellitus (NDM) is a rare disease where diabetes presents during the first six months of life. There are two types of this disorder: permanent neonatal diabetes (PNDM) and transient neonatal diabetes mellitus (TNDM). PNDM occurs due to mutations in genes involved in either beta-cell survival, insulin regulation, and secretion. This study aims to define the genetic aetiology and clinical phenotypes of PNDM in a large Egyptian cohort from a single centre. METHODS Patients with PNDM who were diagnosed, treated, or referred for follow-up between January 2002 and January 2021 were identified and clinically phenotyped. All patients were tested for mutations in EIF2AK3, KCNJ11, ABCC8, INS, FOXP3, GATA4, GATA6, GCK, GLIS3, HNF1B, IER3IP1, PDX1, PTF1A, NEUROD1, NEUROG3, NKX2-2, RFX6, SLC2A2, SLC19A2, STAT3, WFS1, ZFP57 using targeted next-generation sequencing (NGS) panel. INSR gene mutation was tested in one patient who showed clinical features of insulin resistance. RESULTS Twenty-nine patients from twenty-six families were diagnosed with PNDM. Pathogenic variants were identified in 17/29 patients (59%). EIF2AK3, INS, and KATP channel mutations were the commonest causes with frequency of 17%, 17%, and 14%, respectively. Patients with ABBC8 and KCNJ11 mutations were successfully shifted to sulfonylureas (SU). Paired data of glycosylated haemoglobin before and after SU transfer showed improved glycaemic control; 9.6% versus 7.1%, P = 0.041. CONCLUSIONS PNDM is a heterogenous disease with variable genotypes and clinical phenotypes among Egyptian patients. EIF2AK3, INS, ABCC8, and KCNJ11 mutations were the commonest causes of PNDM in the study cohort. All patients with KATP channel mutations were effectively treated with glyburide, reflecting the fact that genetic testing for patients with NDM is not only important for diagnosis but also for treatment plan and prognosis.
Collapse
Affiliation(s)
- Wafaa Laimon
- Pediatric Endocrinology and Diabetes Unit, Department of Pediatrics, Mansoura Faculty of Medicine, Mansoura University, Mansoura University Children's Hospital, Gomhoria Street, Mansoura, Dakhlia, 35516, Egypt.
| | - Magdy El-Ziny
- Pediatric Endocrinology and Diabetes Unit, Department of Pediatrics, Mansoura Faculty of Medicine, Mansoura University, Mansoura University Children's Hospital, Gomhoria Street, Mansoura, Dakhlia, 35516, Egypt
| | - Amany El-Hawary
- Pediatric Endocrinology and Diabetes Unit, Department of Pediatrics, Mansoura Faculty of Medicine, Mansoura University, Mansoura University Children's Hospital, Gomhoria Street, Mansoura, Dakhlia, 35516, Egypt
| | - Ashraf Elsharkawy
- Pediatric Endocrinology and Diabetes Unit, Department of Pediatrics, Mansoura Faculty of Medicine, Mansoura University, Mansoura University Children's Hospital, Gomhoria Street, Mansoura, Dakhlia, 35516, Egypt
| | - Nanees Abdel-Badie Salem
- Pediatric Endocrinology and Diabetes Unit, Department of Pediatrics, Mansoura Faculty of Medicine, Mansoura University, Mansoura University Children's Hospital, Gomhoria Street, Mansoura, Dakhlia, 35516, Egypt
| | - Hadil Mohamed Aboelenin
- Pediatric Endocrinology and Diabetes Unit, Department of Pediatrics, Mansoura Faculty of Medicine, Mansoura University, Mansoura University Children's Hospital, Gomhoria Street, Mansoura, Dakhlia, 35516, Egypt
| | - Mohammad Hosny Awad
- Pediatric Endocrinology and Diabetes Unit, Department of Pediatrics, Mansoura Faculty of Medicine, Mansoura University, Mansoura University Children's Hospital, Gomhoria Street, Mansoura, Dakhlia, 35516, Egypt
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| |
Collapse
|
3
|
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
|