1
|
Shetty S, Kouskouti C, Schoen U, Evangelatos N, Vishwanath S, Satyamoorthy K, Kainer F, Brand A. Diagnosis of Chlamydia trachomatis genital infections in the era of genomic medicine. Braz J Microbiol 2021; 52:1327-1339. [PMID: 34164797 PMCID: PMC8221097 DOI: 10.1007/s42770-021-00533-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 05/17/2021] [Indexed: 11/02/2022] Open
Abstract
PURPOSE Chlamydial genital infections constitute significant sexually transmitted infections worldwide. The often asymptomatic status of C. trachomatis (CT) infections leads to an increased burden on human reproductive health, especially in middle- and low-income settings. Early detection and management of these infections could play a decisive role in controlling this public health burden. The objective of this review is to provide an insight into the evolution of diagnostic methods for CT infections through the development of new molecular technologies, emphasizing on -omics' technologies and their significance as diagnostic tools both for effective patient management and control of disease transmission. METHODS Narrative review of the diagnostic methodologies of CT infections and the impact of the introduction of -omics' technologies on their diagnosis by review of the literature. RESULTS Various methodologies are discussed with respect to working principles, required specifications, advantages, and disadvantages. Implementing the most accurate methods in diagnosis is highlighted as the cornerstone in managing CT infections. CONCLUSION Diagnostics based on -omics' technologies are considered to be the most pertinent modalities in CT testing when compared to other available methods. There is a need to modify these effective and accurate diagnostic tools in order to render them more available and feasible in all settings, especially aiming on turning them to rapid point-of-care tests for effective patient management and disease control.
Collapse
Affiliation(s)
- Seema Shetty
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, Karnataka, India.
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands.
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
| | - Christina Kouskouti
- Department of Obstetrics and Perinatal Medicine, Klinik Hallerwiese, St. Johannis-Muhlgasse 19, 90419, Nuremberg, Germany
- Division of Maternal and Fetal Medicine Department of Obstetrics and Gynaecology, Mt. Sinai Hospital University of Toronto, Toronto, ON, Canada
| | - Uwe Schoen
- BioMedHeliX (Pty) Ltd., 3 Conifer Road, Cape Town, 8005, South Africa
| | - Nikolaos Evangelatos
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands
- Interdepartmental Division of Critical Care Medicine, University of Toronto, ON, Canada
- Dr. TMA Pai Endowment Chair in Research Policy in Biomedical Sciences and Public Health, Prasanna School of Public Health (PSPH), Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Shashidhar Vishwanath
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, Karnataka, India
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Franz Kainer
- Department of Obstetrics and Perinatal Medicine, Klinik Hallerwiese, St. Johannis-Muhlgasse 19, 90419, Nuremberg, Germany
| | - Angela Brand
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands
- Dr. TMA Pai Endowment Chair in Public Health Genomics, Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of International Health, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, 6229, GT, The Netherlands
| |
Collapse
|
2
|
Veličko I, Ploner A, Sparén P, Herrmann B, Marions L, Kühlmann-Berenzon S. Changes in the Trend of Sexually Acquired Chlamydia Infections in Sweden and the Role of Testing: A Time Series Analysis. Sex Transm Dis 2021; 48:329-334. [PMID: 33122597 PMCID: PMC8048723 DOI: 10.1097/olq.0000000000001318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/09/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND We investigated the notification trends of sexually acquired chlamydia (chlamydia) and its association with testing in Sweden before (1992-2004) and after (2009-2018) the discovery of a new variant of Chlamydia trachomatis (nvCT). METHODS We applied monthly time series analysis to study chlamydia trends and annual time series to study chlamydia rates adjusted for testing. We analyzed incidence nationally and by county group (based on able and unable to detect nvCT at time of discovery). RESULTS We present data on 606,000 cases of chlamydia and 9.9 million persons tested. We found a U-shaped chlamydia trend during the period 1992-2004, with an overall increase of 83.7% from 1996 onward. The period 2009-2018 began with a stable trend at a high incidence level followed by a decrease of 19.7% during the period 2015-2018. Peaks were seen in autumn and through during winter and summer. Similar results were observed by groups of county, although with varying levels of increase and decrease in both periods. Furthermore, increased testing volume was associated with increased chlamydia rates during the first period (P = 0.019) but not the second period. CONCLUSIONS Our results showed that chlamydia trends during the period 2009-2018 were not driven by testing, as they were during the period 1992-2004. This suggests less biased notified chlamydia rates and thus possibly a true decrease in chlamydia incidence rates. It is important to adjust case rates for testing intensity, and future research should target other potential factors influencing chlamydia rates.
Collapse
Affiliation(s)
- Inga Veličko
- From the Department of Medical Epidemiology and Biostatistics, Karolinska Institute
- Department of Public Health Analysis and Data Management, Public Health Agency of Sweden, Stockholm
| | - Alexander Ploner
- From the Department of Medical Epidemiology and Biostatistics, Karolinska Institute
| | - Pär Sparén
- From the Department of Medical Epidemiology and Biostatistics, Karolinska Institute
| | - Björn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lena Marions
- Department of Clinical Science and Education, Karolinska Institute
- Section of Obstetrics and Gynaecology, Stockholm South General Hospital, Stockholm, Sweden
| | - Sharon Kühlmann-Berenzon
- Department of Public Health Analysis and Data Management, Public Health Agency of Sweden, Stockholm
| |
Collapse
|
3
|
Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipsitch M, Grad YH. Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. eLife 2020; 9:e56367. [PMID: 32602459 PMCID: PMC7326491 DOI: 10.7554/elife.56367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/17/2020] [Indexed: 12/14/2022] Open
Abstract
Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require surveillance to ensure early detection of novel resistance variants, but efficient strategies to do so remain undefined. We evaluate the efficiency of targeted sampling approaches informed by patient and pathogen characteristics in detecting antibiotic resistance and diagnostic escape variants in Neisseria gonorrhoeae, a pathogen associated with a high burden of disease and antibiotic resistance and the development of genotype-based diagnostics. We show that patient characteristic-informed sampling is not a reliable strategy for efficient variant detection. In contrast, sampling informed by pathogen characteristics, such as genomic diversity and genomic background, is significantly more efficient than random sampling in identifying genetic variants associated with resistance and diagnostic escape.
Collapse
Affiliation(s)
- Allison L Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Melinda Ashcroft
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| |
Collapse
|
4
|
Hicks AL, Kissler SM, Lipsitch M, Grad YH. Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics. PLoS Biol 2019; 17:e3000547. [PMID: 31714937 PMCID: PMC6874359 DOI: 10.1371/journal.pbio.3000547] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/22/2019] [Accepted: 10/29/2019] [Indexed: 11/23/2022] Open
Abstract
The sensitivity of genotype-based diagnostics that predict antimicrobial susceptibility is limited by the extent to which they detect genes and alleles that lead to resistance. As novel resistance variants are expected to emerge, such sensitivity is expected to decline unless the new variants are detected and incorporated into the diagnostic. Here, we present a mathematical framework to define how many diagnostic failures may be expected under varying surveillance regimes and thus quantify the surveillance needed to maintain the sensitivity of genotype-based diagnostics.
Collapse
Affiliation(s)
- Allison L. Hicks
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Stephen M. Kissler
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|