1
|
Eamsakulrat P, Santanirand P, Phuphuakrat A. Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens. Microbiol Spectr 2022; 10:e0209422. [PMID: 36374024 PMCID: PMC9769669 DOI: 10.1128/spectrum.02094-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a "gold standard," the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.
Collapse
Affiliation(s)
- Pruke Eamsakulrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
2
|
Bladder Microbiome in the Context of Urological Disorders—Is There a Biomarker Potential for Interstitial Cystitis? Diagnostics (Basel) 2022; 12:diagnostics12020281. [PMID: 35204374 PMCID: PMC8870776 DOI: 10.3390/diagnostics12020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/23/2022] Open
Abstract
Since the development of modern cultivation and sequencing techniques, the human microbiome has increasingly become the focus of scientific attention. Even in the bladder, long considered to be a sterile niche, a highly variable and complex microbial colonization has now been demonstrated. Especially in the context of diseases such as interstitial cystitis, whose etiopathogenesis is largely unknown, and whose diagnosis is based on a process of exclusion of confusable diseases, science hopes to gain far-reaching insights for etiology and diagnosis, including the identification of potential biomarkers. While for functional disorders such as urge urinary incontinence and overactive bladder syndrome, initial associations have been demonstrated between reduced microbial diversity and increased symptomatology, as well as shifts in the abundance of specific microorganisms such as Lactobacillus or Proteus, studies in interstitial cystitis show conflicting results and have failed to identify a putative organism or urotype that clearly distinguishes the urinary microbiome of patients with IC/BPS from that of healthy controls. At the present time, therefore, the new insights into the bladder microbiome and its potential influence on urologic disease cannot yet be used in the context of elucidating possible etiopathogenetic causes, as well as in the use of a biomarker for diagnostic or prognostic purposes. Further studies should focus primarily on uniform procedures and detection methods to achieve better comparability of results and increase the likelihood of detecting hidden patterns.
Collapse
|
3
|
Abstract
The introduction of next generation sequencing techniques has enabled the characterization of the urinary tract microbiome, which resulted in the rejection of the long-held notion of urinary bladder sterility. Since the discovery and confirmation of the human bladder microbiome, an increasing number of studies have defined this microbial community and understand better its relationship to urinary pathologies. The composition of microbial communities in the urinary tract is linked to a variety of urinary diseases. The purpose of this review is to provide an overview of current information about the urinary microbiome and diseases as well as the development of novel treatment methods.
Collapse
|
4
|
Perez-Carrasco V, Soriano-Lerma A, Soriano M, Gutiérrez-Fernández J, Garcia-Salcedo JA. Urinary Microbiome: Yin and Yang of the Urinary Tract. Front Cell Infect Microbiol 2021; 11:617002. [PMID: 34084752 PMCID: PMC8167034 DOI: 10.3389/fcimb.2021.617002] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
The application of next generation sequencing techniques has allowed the characterization of the urinary tract microbiome and has led to the rejection of the pre-established concept of sterility in the urinary bladder. Not only have microbial communities in the urinary tract been implicated in the maintenance of health but alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections (UTI). Therefore, the study of the urinary microbiome in healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis and treatment strategies for urinary pathologies. In this review we present an overview of the current state of knowledge about the urinary microbiome in health and disease, as well as its involvement in the development of new therapeutic strategies.
Collapse
Affiliation(s)
- Virginia Perez-Carrasco
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
| | - Ana Soriano-Lerma
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Department of Physiology, Faculty of Pharmacy, Institute of Nutrition and Food Technology "Jose' Mataix", University of Granada, Granada, Spain
| | - Miguel Soriano
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, Almeria, Spain
| | - José Gutiérrez-Fernández
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
| | - Jose A Garcia-Salcedo
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
| |
Collapse
|
5
|
Men X, Zhao G, Zhao W, Zhang J, Yang Y, Chen C. Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:2427-2438. [PMID: 33042356 PMCID: PMC7539889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Antimicrobial therapy necessitates fast and accurate detection of pathogens in purulent meningitis (PM) diagnosis. Although considered a gold standard, the traditional bacterial detection and identification methods based on routine bacterial culture are time-consuming and show low sensitivity and specificity. In order to reduce PM-related deaths and improve the treatment efficiency, we employed trace DNA extraction technology and combined it with Next-Generation Sequencing technology for bacteria identification. We extracted DNA from 31 cerebrospinal fluid (CSF) samples from people with PM. The samples were collected by lumbar puncture at Xi'an Children Hospital under a stringent protocol. Ion PGMTM System Next-Generation Sequencing was used to screen for pathogens in the CSF samples based on their 16S ribosomal RNA (rRNA) genes. Of the 31 CSF samples, 29 were culture negative. Streptococcus was detected in 2 samples by culture-based methods. The species identified by Next-Generation Sequencing showed a diverse bacterial population that included Streptococcus (22.6%), Escherichia (15.9%), Peptostreptococcus (10.7%), Pseudomonas (10.5%), Rothia (8.8%), Acinetobacter (4.9%), Prevotella (4.1%), Bacillus (3.3%), Neisseria (2.5%), Catonella (2.4%), Acitinomyces (2.0%), and Citrobacter (2.0%). Clustering analysis revealed three major bacterial groups, namely Streptococcus, Escherichia and Acinetobacter, each group with a different proportion of bacterial species. The results indicated that PM may result from infections by multiple bacterial species as opposed to a single species, with infectivity determined by abundance of the dominant species. Furthermore, Next-Generation Sequencing allowed a sensitive and specific etiological basis for identification of pathogens not only in the cerebrospinal fluid specimens, but also in other clinical samples.
Collapse
Affiliation(s)
- Xin Men
- College of Life Science, Northwest University229 North Taibai Road, Xi’an 710069, Shaanxi, P. R. China
- Microbiology Institute of ShaanxiXi’an, Shaanxi, P. R. China
| | - Guige Zhao
- College of Life Science, Northwest University229 North Taibai Road, Xi’an 710069, Shaanxi, P. R. China
| | - Wei Zhao
- Lifegen Co. Ltd.Xi’an, Shaanxi, P. R. China
| | | | - Yuan Yang
- Lifegen Co. Ltd.Xi’an, Shaanxi, P. R. China
| | - Chao Chen
- College of Life Science, Northwest University229 North Taibai Road, Xi’an 710069, Shaanxi, P. R. China
| |
Collapse
|
6
|
Talebi Bezmin Abadi A, Yamaoka Y. Helicobacter pylori therapy and clinical perspective. J Glob Antimicrob Resist 2018; 14:111-117. [DOI: 10.1016/j.jgar.2018.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
|
7
|
Aguilera-Arreola MG, Ostria-Hernández ML, Albarrán-Fernández E, Juárez-Enriquez SR, Majalca-Martínez C, Rico-Verdín B, Ruiz EA, Ruiz-Palma MDS, Morales-García MR, Contreras-Rodríguez A. Correct Identification of Ochrobactrum anthropi From Blood Culture Using 16rRNA Sequencing: A First Case Report in an Immunocompromised Patient in Mexico. Front Med (Lausanne) 2018; 5:205. [PMID: 30079338 PMCID: PMC6062634 DOI: 10.3389/fmed.2018.00205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/29/2018] [Indexed: 11/23/2022] Open
Abstract
The present report describes the misidentification of Brucella spp. from a positive blood culture using traditional microbiology tests. A molecular test identified the bacterium as Ochrobactrum anthropi. According to the information available, this report is the first to include this type of case in Mexico.
Collapse
Affiliation(s)
- Ma G Aguilera-Arreola
- Medical Bacteriology Laboratory, Department of Microbiology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico
| | - Martha L Ostria-Hernández
- Medical Bacteriology Laboratory, Department of Microbiology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico
| | - Enrique Albarrán-Fernández
- Department of Epidemiology, Centro Médico Nacional, 20 de Noviembre del Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - Sara R Juárez-Enriquez
- Special Test Laboratory, Centro Médico Nacional, 20 de Noviembre - Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - Cristina Majalca-Martínez
- Special Test Laboratory, Centro Médico Nacional, 20 de Noviembre - Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - Beatríz Rico-Verdín
- Department of Epidemiology, Centro Médico Nacional, 20 de Noviembre del Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City, Mexico
| | - Enrico A Ruiz
- Ecology Laboratory, Department of Zoology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico
| | - María Del Socorro Ruiz-Palma
- Medical Bacteriology Laboratory, Department of Microbiology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico.,General Microbiology Laboratory, Department of Microbiology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico
| | - María R Morales-García
- General Microbiology Laboratory, Department of Microbiology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico.,Biotechnology Area, Instituto Politécnico Nacional, Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Querétaro, Mexico
| | - Araceli Contreras-Rodríguez
- General Microbiology Laboratory, Department of Microbiology, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City, Mexico
| |
Collapse
|
8
|
Fritzenwanker M, Imirzalioglu C, Chakraborty T, Wagenlehner FM. Modern diagnostic methods for urinary tract infections. Expert Rev Anti Infect Ther 2016; 14:1047-1063. [DOI: 10.1080/14787210.2016.1236685] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|