1
|
Heideman DAM, Berkhof J, Verhoef L, Ouwerkerk C, Smit PW, Oštrbenk Valenčak A, Mlakar J, Poljak M, Steenbergen RDM, Bleeker MCG. Validation of the clinical performance and reproducibility of the NeuMoDx HPV assay self-sample workflow. J Clin Virol 2024; 171:105649. [PMID: 38335717 DOI: 10.1016/j.jcv.2024.105649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/15/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Human papillomavirus (HPV) testing on self-samples is a valid tool for cervical cancer screening. HPV self-sample workflows need to be clinically validated to ensure safe use in screening. OBJECTIVE This study evaluated the fully automated NeuMoDx HPV Assay self-sample workflow that is compiled of the NeuMoDx HPV assay and the NeuMoDx 96/288 Molecular Systems, for clinical performance and reproducibility on Evalyn Brush-collected self-samples. METHODS The clinical performance of the NeuMoDx HPV Assay self-sample workflow for cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and CIN3+ was evaluated on 987 self-samples obtained from women attending national organized HPV-based cervical cancer screening by a noninferiority analysis relative to reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR. Intra- and inter-laboratory reproducibility of the NeuMoDx HPV Assay self-sample workflow using both NeuMoDx 96 and 288 Molecular Systems was assessed on 520 self-samples in three laboratories. RESULTS The clinical sensitivity and specificity of the NeuMoDx HPV Assay self-sample workflow for the detection of CIN2+ and CIN3+ were found to be non-inferior to the reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR, with all p-values <0.034. The NeuMoDx HPV Assay self-sample workflow exhibited an intra-laboratory reproducibility of 94.4 % (95 %CI:92.5-96.1 %) with kappa value 0.86 (95 %CI:0.81-0.91). Inter-laboratory agreement was high (all ≥93.4 % and all kappa values ≥0.83). CONCLUSIONS The NeuMoDx HPV Assay self-sample workflow demonstrated high clinical accuracy for CIN2+/3+ and high reproducibility. The NeuMoDx HPV Assay self-sample workflow can be considered suitable for cervical cancer screening purposes.
Collapse
Affiliation(s)
- D A M Heideman
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands.
| | - J Berkhof
- Amsterdam UMC location Vrije Universiteit Amsterdam, Data Sciences, De Boelelaan 1117, Amsterdam, Netherlands
| | - L Verhoef
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - C Ouwerkerk
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - P W Smit
- Molecular Diagnostics Unit, Medical Microbiology, Maasstad Ziekenhuis, Rotterdam, Netherlands
| | - A Oštrbenk Valenčak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - J Mlakar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - R D M Steenbergen
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - M C G Bleeker
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, De Boelelaan 1117, Amsterdam, Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| |
Collapse
|
2
|
Poljak M, Oštrbenk Valenčak A, Gimpelj Domjanič G, Xu L, Arbyn M. Commercially available molecular tests for human papillomaviruses: a global overview. Clin Microbiol Infect 2020; 26:1144-1150. [DOI: 10.1016/j.cmi.2020.03.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 10/25/2022]
|
3
|
Maver Vodičar P, Oštrbenk Valenčak A, Zupan B, Avšič Županc T, Kurdija S, Korva M, Petrovec M, Demšar J, Knap N, Štrumbelj E, Vehovar V, Poljak M. Low prevalence of active COVID-19 in Slovenia: a nationwide population study of a probability-based sample. Clin Microbiol Infect 2020; 26:1514-1519. [PMID: 32688068 PMCID: PMC7367804 DOI: 10.1016/j.cmi.2020.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/03/2022]
Abstract
Objectives Accurate population-level assessment of the coronavirus disease 2019 (COVID-19) burden is fundamental for navigating the path forward during the ongoing pandemic, but current knowledge is scant. We conducted the first nationwide population study using a probability-based sample to assess active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, combined with a longitudinal follow-up of the entire cohort over the next 6 months. Baseline SARS-CoV-2 RNA testing results and the first 3-week follow-up results are presented. Methods A probability-based sample of the Slovenian population comprising data from 2.1 million people was selected from the Central Population Register (n = 3000). SARS-CoV-2 RNA was detected in nasopharyngeal samples using the cobas 6800 SARS-CoV-2 assay. Each participant filled in a detailed baseline questionnaire with basic sociodemographic data and detailed medical history compatible with COVID-19. After 3 weeks, participants were interviewed for the presence of COVID-19–compatible clinical symptoms and signs, including in household members, and offered immediate testing for SARS-CoV-2 RNA if indicated. Results A total of 1368 individuals (46%) consented to participate and completed the questionnaire. Two of 1366 participants tested positive for SARS-CoV-2 RNA (prevalence 0.15%; posterior mean 0.18%, 95% Bayesian confidence interval 0.03–0.47; 95% highest density region (HDR) 0.01–0.41). No newly diagnosed infections occurred in the cohort during the first 3-week follow-up round. Conclusions The low prevalence of active COVID-19 infections found in this study accurately predicted the dynamics of the epidemic in Slovenia over the subsequent month. Properly designed and timely executed studies using probability-based samples combined with routine target-testing figures provide reliable data that can be used to make informed decisions on relaxing or strengthening disease mitigation strategies.
Collapse
Affiliation(s)
- P Maver Vodičar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - A Oštrbenk Valenčak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - B Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - T Avšič Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - S Kurdija
- Faculty of Social Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - M Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - J Demšar
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - N Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - E Štrumbelj
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - V Vehovar
- Faculty of Social Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| |
Collapse
|
4
|
Branley J, O'Sullivan M, Polkinghorne A, Poljak M, Stephens D. Rapid deployment of pathology services to a remote Australian quarantine setting during the COVID-19 pandemic. Pathology 2020; 52:821-823. [PMID: 32798071 PMCID: PMC7351374 DOI: 10.1016/j.pathol.2020.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/23/2022]
Affiliation(s)
- James Branley
- Department of Microbiology and Infectious Diseases, New South Wales Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, Kingswood, NSW, Australia.
| | - Matthew O'Sullivan
- Centre for Infectious Diseases and Microbiology, Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Adam Polkinghorne
- Department of Microbiology and Infectious Diseases, New South Wales Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, Kingswood, NSW, Australia
| | | | - Dianne Stephens
- National Critical Care and Trauma Response Centre, Royal Darwin Hospital, Darwin, NT, Australia
| |
Collapse
|
5
|
Zidovec Lepej S, Poljak M. Portable molecular diagnostic instruments in microbiology: current status. Clin Microbiol Infect 2020; 26:411-420. [DOI: 10.1016/j.cmi.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
|
6
|
Sanguinetti M, Seme K, Poljak M. Mobile microbiology: an evolving concept in diagnosis of infectious diseases. Clin Microbiol Infect 2020; 26:409-410. [PMID: 31899335 DOI: 10.1016/j.cmi.2019.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Affiliation(s)
- M Sanguinetti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy; Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - K Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia.
| |
Collapse
|
7
|
Cambau E, Poljak M. Sniffing animals as a diagnostic tool in infectious diseases. Clin Microbiol Infect 2019; 26:431-435. [PMID: 31734357 DOI: 10.1016/j.cmi.2019.10.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Scents and odours characterize some microbes when grown in the laboratory, and experienced clinicians can diagnose patients with some infectious diseases based on their smell. Animal sniffing is an innate behaviour, and animals' olfactory acuity is used for detecting people, weapons, bombs, narcotics and food. OBJECTIVES We briefly summarized current knowledge regarding the use of sniffing animals to diagnose some infectious diseases and the potential use of scent-based diagnostic instruments in microbiology. SOURCES Information was sought through PubMed and extracted from peer-reviewed literature published between January 2000 and September 2019 and from reliable online news. The search terms 'odour', 'scent', 'bacteria', 'diagnostics', 'tuberculosis', 'malaria' and 'volatile compounds' were used. CONTENT Four major areas of using sniffing animals are summarized. Dogs have been used to reliably detect stool associated with toxigenic Clostridioides difficile and for surveillance. Dogs showed high sensitivity and moderate specificity for detecting urinary tract infections in comparison to culture, especially for Escherichia coli. African giant pouched rats showed superiority for diagnosing tuberculosis over microscopy, but inferiority to culture/molecular methods. Several approaches for detecting malaria by analysing host skin odour or exhaled breath have been explored successfully. Some microbial infections produce specific volatile organic compounds (VOCs), which can be analysed by spectrometry, metabolomics or other analytical approaches to replace animal sniffing. IMPLICATIONS The results of sniffing animal studies are fascinating, and animal sniffing can provide intermediate diagnostic solutions for some infectious diseases. Lack of reproducibility, and cost of animal training and housing are major drawbacks for wider implementation of sniffing animals. The ultimate goal is to understand the biological background of this animal ability and to characterize the specific VOCs that animals are recognizing. VOC identification, improvement of odour sampling methods and development of point-of-care instruments could allow implementation of scent-based tests for major human pathogens.
Collapse
Affiliation(s)
- E Cambau
- AP-HP, Groupe hospitalier Lariboisière - Fernand-Widal, Service de Bactériologie, Paris, France; Université de Paris, INSERM, IAME UMR1137, Paris, France.
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
8
|
Benoy I, Xu L, Vanden Broeck D, Poljak M, Oštrbenk Valenčak A, Arbyn M, Bogers J. Using the VALGENT-3 framework to assess the clinical and analytical performance of the RIATOL qPCR HPV genotyping assay. J Clin Virol 2019; 120:57-62. [DOI: 10.1016/j.jcv.2019.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/05/2019] [Accepted: 09/17/2019] [Indexed: 11/15/2022]
|
9
|
Ong DSY, Poljak M. Smartphones as mobile microbiological laboratories. Clin Microbiol Infect 2019; 26:421-424. [PMID: 31610301 DOI: 10.1016/j.cmi.2019.09.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/24/2019] [Accepted: 09/29/2019] [Indexed: 11/25/2022]
Abstract
BACKGROUND Point-of-care (POC) tests provide an alternative to traditional laboratory-based diagnostics due to reduced turnaround times, portability and no need for highly trained laboratory staff. Smartphones can be integrated into POC platforms because of their multifunctionality, enabled by high-quality digital cameras, computer processors, touchscreen interface and wireless data transfer. It is predicted that by 2020 about 80% of the world population will use smartphones. OBJECTIVES This review summarizes the current state of the art regarding smartphones as part of a mobile microbiological laboratory. SOURCES Selected peer-reviewed publications on smartphone-based microbiological testing published between January 2015 and August 2019. CONTENT Smartphones can be used as instrumental interfaces, dongles, microscopes or test result readers (brightfield, colorimetric and fluorescent measurements), or combined with amplification methods such as loop-mediated isothermal amplification (LAMP) tests in portable POC test platforms. Smartphone-based tests offer opportunities for microbiological diagnostics in remote areas and both resource-limited and resource-rich settings. Wireless connectivity may facilitate epidemiological studies and creation of spatiotemporal disease prevalence maps. However, the current analytical performance of many smartphone-based POC tests must be improved and carefully validated in clinical settings by comparison with current diagnostic standards. IMPLICATIONS Recent developments in smartphone-based POC tests for infectious diseases are promising, as evidenced by results from many proof-of-concept studies. Further progress will foster large-scale implementation of smartphone-based POC as mobile microbiological laboratories in the near future.
Collapse
Affiliation(s)
- D S Y Ong
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & Vlietland, Rotterdam, the Netherlands; Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
10
|
Poljak M, Šterbenc A. Use of drones in clinical microbiology and infectious diseases: current status, challenges and barriers. Clin Microbiol Infect 2019; 26:425-430. [PMID: 31574337 DOI: 10.1016/j.cmi.2019.09.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND Drones or unmanned aerial vehicles are autonomous or remotely controlled multipurpose aerial vehicles driven by aerodynamic forces and capable of carrying a payload. Whereas initially used exclusively for military purposes, the use of drones has gradually spread into other areas. Given their great flexibility and favourable costs, the use of drones has also been piloted in various healthcare settings. OBJECTIVES We briefly summarize current knowledge regarding the use of drones in healthcare, focusing on infectious diseases and/or microbiology when applicable. SOURCES Information was sought through PubMed and extracted from peer-reviewed literature published between January 2010 and August 2019 and from reliable online news sources. The search terms 'drones', 'unmanned aerial vehicles', 'microbiology' and 'medicine' were used. CONTENT Peer-reviewed literature on the use of drones in healthcare has steadily increased in recent years. Drones have been successfully evaluated in various pilot programmes and are already implemented in some settings for transporting samples and delivering blood, vaccines, medicines, organs, life-saving medical supplies and equipment. In addition, a promising proof-of-concept 'lab-on-a-drone' was recently presented, as well as several pilot studies showing the benefits of drone use in surveillance and epidemiology of infectious diseases. IMPLICATIONS The potential for drone use in clinical microbiology, infectious diseases and epidemiology is vast. Drones may help to increase access to healthcare for individuals that might otherwise not benefit from appropriate care due to remoteness and lack of infrastructure or funds. However, factors such as national airspace legislation and legal medical issues, differences in topography and climates, cost-effectiveness, and community attitudes and acceptance in different cultures and societies currently impede the widespread use of drones. Significant cost savings compared with ground transportation, speed and convenience of delivery, and the booming drone sector will probably drive drone implementation in various areas of medicine in the next 5 years.
Collapse
Affiliation(s)
- M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - A Šterbenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
11
|
Maver PJ, Poljak M. Primary HPV-based cervical cancer screening in Europe: implementation status, challenges, and future plans. Clin Microbiol Infect 2019; 26:579-583. [PMID: 31539637 DOI: 10.1016/j.cmi.2019.09.006] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/31/2019] [Accepted: 09/07/2019] [Indexed: 01/27/2023]
Abstract
BACKGROUND Cytology-based screening has been a cornerstone of cervical cancer prevention for decades. Following extensive evidence demonstrating higher sensitivity and accuracy, lower variability and better reproducibility of human papillomavirus (HPV)-based screening compared with conventional or liquid-based cytology, recent European guidelines strongly recommend primary HPV-based screening over standard cytology-based screening. In addition, HPV-based screening offers the possibility of self-sampling and makes possible longer screening intervals in women with negative screening results. OBJECTIVES We summarize the current status of implementation of HPV-based screening in Europe, describe the real-life experience and challenges from countries already performing HPV-based screening, and briefly review immediate and long-term plans for screening implementation in selected European countries. SOURCES Data were obtained from peer-reviewed literature, personal communication with experts and authorities involved in formulating national recommendations and practical guidelines, and relevant national websites. CONTENT As of July 2019, the Netherlands and Turkey are the only European countries with fully implemented national HPV-based cervical cancer screening. Italy, Sweden and Finland have already implemented HPV-based screening in several regions, and several other countries are at various stages of implementation. Some countries are considering transitioning from cytology-based to HPV-based screening, but are struggling with the suboptimal performance of current population-based programmes. Implementation of HPV-based screening has resulted in higher colposcopy referral rates, but also higher detection rates of CIN3+ lesions and cervical cancers requiring immediate treatment. Cytology is mostly used as a triage test, although other strategies are under consideration in some countries. IMPLICATIONS HPV-based screening is best suited in organized population-based screening settings. In 2019, cervical cancer screening policies across Europe vary greatly. Experience in countries with national and regional HPV-based screening already implemented is generally very positive. Urgent action is needed in many European countries, especially those with suboptimal opportunistic cytology-based cervical cancer screening.
Collapse
Affiliation(s)
- P J Maver
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia.
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia.
| |
Collapse
|
12
|
Scudeller L, Rodríguez-Baño J, Zinkernagel A, Tacconelli E, Akova M, Friedrich AW, Sanguinetti M, Paul M, Poljak M. ESCMID white paper: a guide on ESCMID guidance documents. Clin Microbiol Infect 2018; 25:155-162. [PMID: 30145398 DOI: 10.1016/j.cmi.2018.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND AND AIM The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) aims to further develop its role in international medical and scientific guidance in the field of Clinical Microbiology and Infectious Diseases, where many types of guidance documents exist. The ESCMID Executive Committee and the Clinical Microbiology and Infection (CMI) editorial board wish to clarify the terminology and format to be used in ESCMID guidance documents submitted for publication in CMI, and to highlight the principles behind ESCMID guidance documents. TYPES OF GUIDANCE DOCUMENTS There are five types of ESCMID guidance documents: White Papers, Clinical Practice Guidelines, Consensus Statements, State-of-the-Science Statements, and Position Papers. They differ in scope, methods of development, drafting group composition and preferred publication format. Guidance documents can be proposed, developed and published by ESCMID Study Groups, Committees and individual members; often, other scientific societies are involved. The full disclosure of potential conflicts of interest of all drafting group members is a requirement. FINAL REMARKS Guidance documents constitute a common cultural and scientific background to people in the same and related professions. Also, they are an important educational and training tool. Developing a guidance document is a scientific endeavour, where a sound and transparent development process is needed, requiring multidisciplinary and personal skills.
Collapse
Affiliation(s)
- L Scudeller
- IRCCS Policlinic San Matteo Foundation, Pavia, Italy.
| | - J Rodríguez-Baño
- Sección Enfermedades Infecciosas, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - A Zinkernagel
- FMH Innere Medizin und FMH Infektiologie, Universitätsspital Zürich, Zürich, Switzerland
| | | | - M Akova
- Department of Infectious Diseases, Hacettepe University, School of Medicine, Sihhiye, Ankara, Turkey
| | - A W Friedrich
- UMCG Medical Microbiology, Groningen, The Netherlands
| | | | - M Paul
- Infectious Diseases Institute, Rambam Health Care Campus, The Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel; CMI Editorial Office, Israel
| | - M Poljak
- Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
13
|
Arbyn M, Peeters E, Benoy I, Vanden Broeck D, Bogers J, De Sutter P, Donders G, Tjalma W, Weyers S, Cuschieri K, Poljak M, Bonde J, Cocuzza C, Zhao FH, Van Keer S, Vorsters A. VALHUDES: A protocol for validation of human papillomavirus assays and collection devices for HPV testing on self-samples and urine samples. J Clin Virol 2018; 107:52-56. [PMID: 30195193 DOI: 10.1016/j.jcv.2018.08.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/09/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
BACK GROUND Systematic reviews have concluded that hrHPV DNA testing using target-amplification tests is as accurate on vaginal self-samples as on clinician-taken specimens for the detection of cervical precancer. However, insufficient evidence is available for specific HPV assay/self-sample device combinations. OBJECTIVES The VALHUDES protocol is designed as a diagnostic test accuracy study that aims to compare the clinical sensitivity and specificity of particular hrHPV assay(s) on vaginal self-samples and first-void-urine, collected in agreement with standardized protocols, with hrHPV testing on matched clinician-taken samples. STUDY DESIGN Five hundred enrolled women referred to a colposcopy clinic are invited to collect a first-void urine sample and one or more vaginal self-samples with particular devices before collection of a cervical sample by a clinician. Sample sets are subsequently analysed in a laboratory accredited for HPV testing. Disease verification for all enrolled patients is provided by colposcopy combined with histological assessment of biopsies. RESULTS A first VALHUDES study has started in Belgium in December 2017 with enrolment from four colposcopy centres. The following assays are foreseen to be evaluated: RealTime High Risk HPV assay (Abbott), cobas-4800 and -6800 (Roche), Onclarity (BD), Xpert HPV (Cepheid) and Anyplex II HPV HR (Seegene). CONCLUSION Given empirical evidence that the relative accuracy of HPV-testing on self- vs clinician-samples is robust across clinical settings, the VALHUDES protocol offers a framework for validation of HPV assay/self-sample device combinations that can be translated to a primary screening setting.
Collapse
Affiliation(s)
- M Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium.
| | - E Peeters
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - I Benoy
- Laboratory of Molecular Pathology, AML Sonic Healthcare, Antwerp, Belgium; National Reference Centre for HPV, Brussels, Belgium; AMBIOR, Laboratory for Cell Biology & Histology, University of Antwerp, Antwerp, Belgium
| | - D Vanden Broeck
- Laboratory of Molecular Pathology, AML Sonic Healthcare, Antwerp, Belgium; National Reference Centre for HPV, Brussels, Belgium; AMBIOR, Laboratory for Cell Biology & Histology, University of Antwerp, Antwerp, Belgium; International Centre for Reproductive Health, Ghent University, Ghent, Belgium
| | - J Bogers
- Laboratory of Molecular Pathology, AML Sonic Healthcare, Antwerp, Belgium; National Reference Centre for HPV, Brussels, Belgium; AMBIOR, Laboratory for Cell Biology & Histology, University of Antwerp, Antwerp, Belgium; International Centre for Reproductive Health, Ghent University, Ghent, Belgium
| | - P De Sutter
- UZ Brussel - VUB, dept Gynaecology-Oncology, Brussels, Belgium
| | - G Donders
- Department of Obstetrics and Gynaecology of the General Regional Hospital Heilig Hart, Tienen, Belgium; Femicare vzw, Clinical Research for Women, Tienen, Belgium; Department of Obstetrics and Gynaecology University Hospital Antwerpen, Antwerp, Belgium
| | - W Tjalma
- Multidisciplinary Breast Clinic, Unit Gynaecologic Oncology, Department of Obstetrics and Gynaecology, Antwerp University Hospital (UZA), Edegem, Belgium; Molecular Imaging, Pathology, Radiotherapy, Oncology (MIPRO), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - S Weyers
- Department of Obstetrics and Gynecology, Ghent University Hospital, Ghent, Belgium
| | - K Cuschieri
- Scottish HPV Reference Laboratory, Department of Laboratory Medicine, NHS Lothian, Royal Infirmary of Edinburgh, United Kingdom
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - J Bonde
- Molecular Pathology Laboratory, Dept. Pathology, Copenhagen University Hospital, Hvidovre, Denmark
| | - C Cocuzza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - F H Zhao
- Department of Epidemiology, Cancer Institute of Chinese Academy of Medical Sciences, Peking Union Medical College, Department of Gynaecology and Obstetrics, Beijing Tongeren Hospital, Beijing, China
| | - S Van Keer
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk (Antwerp), Belgium
| | - A Vorsters
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk (Antwerp), Belgium
| |
Collapse
|
14
|
Mlakar J, Jakupi X, Lunar MM, Seme K, Rudhani I, Vince A, Poljak M. A40 Genotypic diversity of HCV in Kosovo with an emphasis on phylogenetic investigation of subtype 4D. Virus Evol 2018. [PMCID: PMC5905439 DOI: 10.1093/ve/vey010.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- J Mlakar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - X Jakupi
- Department of Microbiology, National Institute of Public Health of Kosovo, Prishtina, Kosovo
| | - M M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - K Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - I Rudhani
- Clinic for Nephrology, University Clinical Centre of Kosovo, Prishtina, Kosovo
| | - A Vince
- University Hospital for Infectious Diseases, “Dr Fran Mihaljević”, Zagreb, Croatia
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
15
|
Poljak M, Akova M, Friedrich A, Rodríguez-Baño J, Sanguinetti M, Tacconelli E, Zinkernagel A. ESCMID—an international Europe-based society committed to fostering cross-border collaboration and education to improve patient care. Clin Microbiol Infect 2018; 24:1-2. [DOI: 10.1016/j.cmi.2017.05.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 05/28/2017] [Indexed: 10/19/2022]
|
16
|
Cornall AM, Poljak M, Garland SM, Phillips S, Machalek DA, Tan JH, Quinn MA, Tabrizi SN. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples. Papillomavirus Res 2017; 4:79-84. [PMID: 29179874 PMCID: PMC5883236 DOI: 10.1016/j.pvr.2017.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 10/02/2017] [Accepted: 10/17/2017] [Indexed: 11/24/2022]
Abstract
Purpose To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene) and EuroArray HPV (EuroImmun), with Linear Array HPV (Roche). Methods DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic), from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Results Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 − 1.00) for most genotypes, and was almost perfect (κ = 0.81 – 0.98) for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497), HPV52 (Anyplex II; p = 0.039) and HPV61 (Anyplex II; p=0.047). EuroArray detected signficantly more HPV26 (p = 0.002) and Anyplex II detected more HPV42 (p = 0.035) than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively), but were in poor disagreement with each other (κ = −0.01). Conclusions EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52.
Collapse
Affiliation(s)
- Alyssa M Cornall
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville 3052, Victoria, Australia; Murdoch Childrens Research Institute, Parkville 3052, Victoria, Australia; Department of Obstetrics and Gynecology, University of Melbourne, Parkville 3052, Victoria, Australia.
| | - Marin Poljak
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville 3052, Victoria, Australia; Murdoch Childrens Research Institute, Parkville 3052, Victoria, Australia.
| | - Suzanne M Garland
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville 3052, Victoria, Australia; Murdoch Childrens Research Institute, Parkville 3052, Victoria, Australia; Department of Obstetrics and Gynecology, University of Melbourne, Parkville 3052, Victoria, Australia.
| | - Samuel Phillips
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville 3052, Victoria, Australia; Murdoch Childrens Research Institute, Parkville 3052, Victoria, Australia.
| | - Dorothy A Machalek
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville 3052, Victoria, Australia; Murdoch Childrens Research Institute, Parkville 3052, Victoria, Australia.
| | - Jeffrey H Tan
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville 3052, Victoria, Australia; Oncology and Dysplasia Unit, Royal Women's Hospital, Parkville 3052, Victoria, Australia.
| | - Michael A Quinn
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville 3052, Victoria, Australia; Oncology and Dysplasia Unit, Royal Women's Hospital, Parkville 3052, Victoria, Australia.
| | - Sepehr N Tabrizi
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville 3052, Victoria, Australia; Murdoch Childrens Research Institute, Parkville 3052, Victoria, Australia; Department of Obstetrics and Gynecology, University of Melbourne, Parkville 3052, Victoria, Australia.
| |
Collapse
|
17
|
Zorec TM, Hošnjak L, Kocjan B, Gale N, Zidar N, Strojan P, Poljak M. A32 Search for viral integration insertion sites into the human genome-strategy matters. Virus Evol 2017; 3:vew036.031. [PMID: 28845283 PMCID: PMC5565999 DOI: 10.1093/ve/vew036.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- T M Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - L Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - B Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - N Gale
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - N Zidar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - P Strojan
- Department of Radiation Oncology, Institute of Oncology, Ljubljana, Slovenia
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
18
|
Lunar MM, Mlakar J, Poljak M. A22 Increase in the numbers of HIV-1 non-B subtypes and potential recombinant forms circulating among Slovenian MSM in recent years. Virus Evol 2017; 3:vew036.021. [PMID: 28845249 PMCID: PMC5565932 DOI: 10.1093/ve/vew036.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- M M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - J Mlakar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
19
|
Mlakar J, Lunar MM, Abecasis AB, Vandamme AM, Tomažič J, Vovko TD, Pečavar B, Volčanšek G, Poljak M. A36 Prevalence of HIV-1 subtypes in Slovenia with an emphasis on molecular and phylogenetic investigation of subtype A. Virus Evol 2017; 3:vew036.035. [PMID: 28845276 PMCID: PMC5565990 DOI: 10.1093/ve/vew036.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- J Mlakar
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Maja M Lunar
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - A B Abecasis
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical Universidade Nova de Lisboa, Lisbon, Portugal
| | - A-M Vandamme
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical Universidade Nova de Lisboa, Lisbon, Portugal
| | - J Tomažič
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - T D Vovko
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - B Pečavar
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - G Volčanšek
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - M Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
20
|
Maraolo AE, Ong DSY, Cortez J, Dedić K, Dušek D, Martin-Quiros A, Maver PJ, Skevaki C, Yusuf E, Poljak M, Sanguinetti M, Tacconelli E. Personal life and working conditions of trainees and young specialists in clinical microbiology and infectious diseases in Europe: a questionnaire survey. Eur J Clin Microbiol Infect Dis 2017; 36:1287-1295. [PMID: 28233138 PMCID: PMC5495844 DOI: 10.1007/s10096-017-2937-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 11/25/2022]
Abstract
The purpose of this investigation was to assess the balance between the personal and professional lives of trainees and young European specialists in clinical microbiology (CM) and infectious diseases (ID), and determine differences according to gender, country of training, workplace and specialty. The Steering Committee of the Trainee Association of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) devised a questionnaire survey consisting, beyond the demographic questions, of nine yes/no questions, 11 Likert scale self-evaluations and one open-response item on parenthood, working conditions, quality of life, alcohol consumption and burnout. This anonymous survey in English was held between April and July 2015 among European CM/ID trainees and young specialists (<3 years after training completion). Responses from 416 participants with a mean age of 32 years [standard deviation (SD) 5 years] were analysed. Females and physicians from Northern/Western Europe (NWE) benefit more from paternity/maternity leaves even during training than their counterparts. Among all respondents, only half of breastfeeding mothers enjoyed the benefit of working hours flexibility. Only two-thirds of respondents found their working environment stimulating. In comparison to colleagues from other parts of Europe, trainees and young specialists from Southern/Eastern Europe (SEE) had less frequent regular meetings with mentors/supervisors and head of departments where trainees’ issues are discussed. Also, physicians from SEE were more frequently victims of workplace mobbing/bullying in comparison to those from other regions. Finally, multivariate analysis showed that female gender, SEE region and ID specialty were associated with burnout feelings. Female gender and country of work from SEE largely determine satisfactory working conditions, the possibility of parenthood leaves, amount of leisure time, mobbing experiences and burnout feelings among European CM/ID trainees and young specialists.
Collapse
Affiliation(s)
- A E Maraolo
- Department of Clinical Medicine and Surgery, Section of Infectious Diseases, University of Naples "Federico II", Naples, Italy
| | - D S Y Ong
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - J Cortez
- Infectious Diseases Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- CISA, Health Research Centre of Angola, Caxito, Angola
| | - K Dedić
- Microbiology Department, Cantonal Hospital "Dr. Irfan Ljubijankic", Bihac, Bosnia and Herzegovina
| | - D Dušek
- University Hospital for Infectious Diseases "Dr. Fran Mihaljevic", Zagreb, Croatia
| | - A Martin-Quiros
- Emergency Department, Instituto de Investigación del Hospital Universitario La Paz, Madrid, Spain
| | - P J Maver
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - C Skevaki
- University Hospital Giessen and Marburg GmbH, Philipps University, Marburg, Germany
| | - E Yusuf
- Department of Medical Microbiology, Universitair Ziekenhuis Antwerpen, University of Antwerp, Edegem, Belgium
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - E Tacconelli
- Infectious Diseases, University Hospital Tübingen, DZIF Center, Tübingen, Germany
| |
Collapse
|
21
|
Cornall AM, Poljak M, Garland SM, Phillips S, Tan JH, Machalek DA, Quinn MA, Tabrizi SN. Anyplex II HPV28 detection and Anyplex II HPV HR detection assays are highly concordant with other commercial assays for detection of high-risk HPV genotypes in women with high grade cervical abnormalities. Eur J Clin Microbiol Infect Dis 2016; 36:545-551. [PMID: 27822653 DOI: 10.1007/s10096-016-2831-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/23/2016] [Indexed: 11/25/2022]
Abstract
PURPOSE to evaluate the performance of Anyplex II HPV28 and HPV HR Detection assays against the EuroArray HPV, Cobas 4800 HPV (Cobas), HPV Amplicor (Amp), Linear Array HPV (LA) and Hybrid Capture 2 (HC2) in detection of high-risk HPV (HR-HPV) from liquid-based cervical cytology samples. METHODS cervical specimens from 404 women undergoing management of high-grade cytological abnormality were evaluated by Anyplex II HPV28 and HPV HR Detection assays for detection of HR-HPV genotypes and prediction of histologically-confirmed cervical intraepithelial neoplasia grade 2 or higher (≥CIN2). The results were compared to EuroArray, HC2, Cobas, Amp, and LA. RESULTS specimens were evaluated from 404 women with an average age of 30 years, including 336 with a histological diagnosis of ≥ CIN2 and 68 with ≤ CIN1. Concordance of HR-HPV detection between Anyplex II HPV28 and other genotyping assays was 94.79 % (κ = 0.84; EuroArray) and 97.27 % (κ = 0.91; LA); and between Anyplex II HPV HR and other HR-HPV detection assays was 86.35 % (κ = 0.62; HC2), 96.03 % (κ = 0.87; Cobas) and 96.77 % (κ = 0.89; Amp). Using HR-HPV detection for prediction of ≥ CIN2 by Anyplex II HPV28 and HPV HR, sensitivity (90.18, 95 % CI 86.48-93.14; 90.77, 95 % CI 87.16-93.65) and specificity (both 67.16, 95 % CI 54.60-78.15) were not significantly different to the other HPV assays tested, with one exception. Both Anyplex assays had significantly higher sensitivity than HC2 (p < 0.0001), with a specificity of 96 % (p > 0.05) of HC2 in this high-risk population. CONCLUSIONS both Anyplex II HPV detection assays were concordant with other commercial assays for HR-HPV detection, with comparable sensitivity and specificity for ≥ CIN2 detection.
Collapse
Affiliation(s)
- A M Cornall
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia.
- Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia.
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, 3052, Victoria, Australia.
| | - M Poljak
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - S M Garland
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, 3052, Victoria, Australia
| | - S Phillips
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - J H Tan
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, 3052, Victoria, Australia
- Oncology and Dysplasia Unit, Royal Women's Hospital, Parkville, 3052, Victoria, Australia
| | - D A Machalek
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - M A Quinn
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, 3052, Victoria, Australia
- Oncology and Dysplasia Unit, Royal Women's Hospital, Parkville, 3052, Victoria, Australia
| | - S N Tabrizi
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, 3052, Victoria, Australia
| |
Collapse
|
22
|
Komloš KF, Markocic P, Kušar B, Hošnjak L, Štamol T, Poljak M. Prospective evaluation of Cepheid Xpert HIV-1 Viral Load assay as a supplemental confirmatory HIV-1 test in the routine clinical laboratory setting. J Clin Virol 2016. [DOI: 10.1016/j.jcv.2016.08.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
23
|
Hošnjak L, Jelen M, Štunf Š, Zagožen A, Komloš KF, Markočič P, Seme K, Poljak M. Hepatitis D virus infection in Slovenian patients with chronic hepatitis B virus infection: A national prevalence study. J Clin Virol 2016. [DOI: 10.1016/j.jcv.2016.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
24
|
Tabrizi SN, Tan LY, Walker S, Twin J, Poljak M, Bradshaw CS, Fairley CK, Bissessor M, Mokany E, Todd AV, Garland SM. Multiplex Assay for Simultaneous Detection of Mycoplasma genitalium and Macrolide Resistance Using PlexZyme and PlexPrime Technology. PLoS One 2016; 11:e0156740. [PMID: 27271704 PMCID: PMC4894623 DOI: 10.1371/journal.pone.0156740] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/18/2016] [Indexed: 11/18/2022] Open
Abstract
Mycoplasma genitalium is a cause of non-gonoccocal urethritis (NGU) in men and cervicitis and pelvic inflammatory disease in women. Recent international data also indicated that the first line treatment, 1 gram stat azithromycin therapy, for M. genitalium is becoming less effective, with the corresponding emergence of macrolide resistant strains. Increasing failure rates of azithromycin for M. genitalium has significant implications for the presumptive treatment of NGU and international clinical treatment guidelines. Assays able to predict macrolide resistance along with detection of M. genitalium will be useful to enable appropriate selection of antimicrobials to which the organism is susceptible and facilitate high levels of rapid cure. One such assay recently developed is the MG 23S assay, which employs novel PlexZyme™ and PlexPrime™ technology. It is a multiplex assay for detection of M. genitalium and 5 mutations associated with macrolide resistance. The assay was evaluated in 400 samples from 254 (186 males and 68 females) consecutively infected participants, undergoing tests of cure. Using the MG 23S assay, 83% (331/440) of samples were positive, with 56% of positives carrying a macrolide resistance mutation. Comparison of the MG 23S assay to a reference qPCR method for M. genitalium detection and high resolution melt analysis (HRMA) and sequencing for detection of macrolide resistance mutations, resulted in a sensitivity and specificity for M. genitalium detection and for macrolide resistance of 99.1/98.5% and 97.4/100%, respectively. The MG 23S assay provides a considerable advantage in clinical settings through combined diagnosis and detection of macrolide resistance.
Collapse
Affiliation(s)
- Sepehr N. Tabrizi
- Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- * E-mail:
| | | | | | - Jimmy Twin
- Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Victoria, Australia
| | - Marin Poljak
- Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Victoria, Australia
| | - Catriona S. Bradshaw
- Melbourne Sexual Health Centre, Carlton, Victoria, Australia
- Central Clinical School, Monash University, Victoria, Australia
| | - Christopher K. Fairley
- Melbourne Sexual Health Centre, Carlton, Victoria, Australia
- Central Clinical School, Monash University, Victoria, Australia
| | | | | | | | - Suzanne M. Garland
- Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| |
Collapse
|
25
|
Cag Y, Erdem H, Leib S, Defres S, Kaya S, Larsen L, Poljak M, Ozturk-Engin D, Barsic B, Argemi X, Sørensen SM, Bohr AL, Tattevin P, Gunst JD, Baštáková L, Jereb M, Johansen IS, Karabay O, Pekok AU, Sipahi OR, Chehri M, Beraud G, Shehata G, Fontana R, Maresca M, Karsen H, Sengoz G, Sunbul M, Yilmaz G, Yilmaz H, Sharif-Yakan A, Kanj S, Parlak E, Pehlivanoglu F, Korkmaz F, Komur S, Kose S, Ulug M, Bolukcu S, Coskuner SA, Stahl JP, Ince N, Akkoyunlu Y, Halac G, Sahin-Horasan E, Tireli H, Kilicoglu G, Al-Mahdawi A, Nemli SA, Inan A, Senbayrak S, Vahaboglu H, Elaldi N. Managing atypical and typical herpetic central nervous system infections: results of a multinational study. Clin Microbiol Infect 2016; 22:568.e9-568.e17. [PMID: 27085724 DOI: 10.1016/j.cmi.2016.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 03/20/2016] [Accepted: 03/26/2016] [Indexed: 11/19/2022]
Abstract
There have been many studies pertaining to the management of herpetic meningoencephalitis (HME), but the majority of them have focussed on virologically unconfirmed cases or included only small sample sizes. We have conducted a multicentre study aimed at providing management strategies for HME. Overall, 501 adult patients with PCR-proven HME were included retrospectively from 35 referral centres in 10 countries; 496 patients were found to be eligible for the analysis. Cerebrospinal fluid (CSF) analysis using a PCR assay yielded herpes simplex virus (HSV)-1 DNA in 351 patients (70.8%), HSV-2 DNA in 83 patients (16.7%) and undefined HSV DNA type in 62 patients (12.5%). A total of 379 patients (76.4%) had at least one of the specified characteristics of encephalitis, and we placed these patients into the encephalitis presentation group. The remaining 117 patients (23.6%) had none of these findings, and these patients were placed in the nonencephalitis presentation group. Abnormalities suggestive of encephalitis were detected in magnetic resonance imaging (MRI) in 83.9% of the patients and in electroencephalography (EEG) in 91.0% of patients in the encephalitis presentation group. In the nonencephalitis presentation group, MRI and EEG data were suggestive of encephalitis in 33.3 and 61.9% of patients, respectively. However, the concomitant use of MRI and EEG indicated encephalitis in 96.3 and 87.5% of the cases with and without encephalitic clinical presentation, respectively. Considering the subtle nature of HME, CSF HSV PCR, EEG and MRI data should be collected for all patients with a central nervous system infection.
Collapse
Affiliation(s)
- Y Cag
- Dr Lütfi Kirdar Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - H Erdem
- Gulhane Medical Academy, Department of Infectious Diseases and Clinical Microbiology, Ankara, Turkey.
| | - S Leib
- Institute for Infectious Diseases, University of Bern, Switzerland
| | - S Defres
- Institute of Infection and Global Health, University of Liverpool, United Kingdom; Tropical Infections Diseases Unit In Royal Liverpool and Broadgreen University Hospitals NHS Trust, United Kingdom
| | - S Kaya
- Karadeniz Technical University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Trabzon, Turkey
| | - L Larsen
- Odense University Hospital, Department of Infectious Diseases Q, Odense, Denmark
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - D Ozturk-Engin
- Haydarpasa Numune Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - B Barsic
- Dr. Fran Mihaljevic University Hospital for Infectious Diseases, Department of Infectious Diseases, University of Zagreb School of Medicine, Zagreb, Croatia
| | - X Argemi
- Nouvel Hôpital Civil, Department of Infectious Diseases, Strasbourg, France
| | - S M Sørensen
- Aalborg University Hospital, Department of Infectious Diseases, Denmark
| | - A L Bohr
- Copenhagen University Hospital, Institute of Inflammation Research, Department of Infectious Diseases and Rheumatology, Rigshospitalet, Denmark
| | - P Tattevin
- University Hospital of Pontchaillou, Department of Infectious and Tropical Diseases, Rennes, France
| | - J D Gunst
- Aarhus University Hospital, Department of Infectious Diseases, Aarhus, Denmark
| | - L Baštáková
- Faculty Hospital Brno, Department of Infectious Diseases, Masaryk University, Faculty of Medicine, Brno, Czech Republic
| | - M Jereb
- University Medical Centre, Department of Infectious Diseases, Ljubljana, Slovenia
| | - I S Johansen
- Odense University Hospital, Department of Infectious Diseases Q, Odense, Denmark
| | - O Karabay
- Sakarya University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Sakarya, Turkey
| | - A U Pekok
- Private Erzurum Sifa Hospital, Department of Infectious Diseases and Clinical Microbiology, Erzurum, Turkey
| | - O R Sipahi
- Ege University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Izmir, Turkey
| | - M Chehri
- Hvidovre Hospital, Department of Infectious Diseases, Copenhagen, Denmark
| | - G Beraud
- Poitiers University Hospital, Department of Infectious Diseases, France
| | - G Shehata
- Assiut University Hospital, Department of Neurology and Psychiatry, Assiut, Egypt
| | - R Fontana
- University of Catania, Section of Infectious Diseases, Department of Clinical and Molecular Biomedicine, Catania, Italy
| | - M Maresca
- University of Catania, Section of Infectious Diseases, Department of Clinical and Molecular Biomedicine, Catania, Italy
| | - H Karsen
- Harran University, School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Sanliurfa, Turkey
| | - G Sengoz
- Haseki Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - M Sunbul
- Ondokuz Mayis University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Samsun, Turkey
| | - G Yilmaz
- Ankara University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Ankara, Turkey
| | - H Yilmaz
- Ondokuz Mayis University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Samsun, Turkey
| | - A Sharif-Yakan
- American University of Beirut Medical Center, Beirut, Lebanon
| | - S Kanj
- American University of Beirut Medical Center, Beirut, Lebanon
| | - E Parlak
- Ataturk University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Erzurum, Turkey
| | - F Pehlivanoglu
- Haseki Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - F Korkmaz
- Konya Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Konya, Turkey
| | - S Komur
- Cukurova University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Adana, Turkey
| | - S Kose
- Tepecik Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Izmir, Turkey
| | - M Ulug
- Private Umit Hospital, Department of Infectious Diseases and Clinical Microbiology, Eskisehir, Turkey
| | - S Bolukcu
- Haydarpasa Numune Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - S A Coskuner
- Izmir Bozyaka Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Izmir, Turkey
| | - J P Stahl
- Joseph Fourier University and University Hospital of Grenoble, Department of Infectious Diseases, Grenoble, France
| | - N Ince
- Duzce University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Konuralp, Duzce, Turkey
| | - Y Akkoyunlu
- Bezmi Alem Vakif University, School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - G Halac
- Bezmi Alem Vakif University, School of Medicine, Department of Neurology, Istanbul, Turkey
| | - E Sahin-Horasan
- Mersin University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Mersin, Turkey
| | - H Tireli
- Haydarpasa Numune Training and Research Hospital, Department of Neurology, Turkey
| | - G Kilicoglu
- Haydarpasa Numune Training and Research Hospital, Department of Radiology, Turkey
| | - A Al-Mahdawi
- Department of Neurology, Baghdad Teaching Hospital, Iraq
| | - S A Nemli
- Katip Celebi University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Izmir, Turkey
| | - A Inan
- Haydarpasa Numune Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - S Senbayrak
- Haydarpasa Numune Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - H Vahaboglu
- Medeniyet University, Goztepe Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology, Istanbul, Turkey
| | - N Elaldi
- Cumhuriyet University School of Medicine, Department of Infectious Diseases and Clinical Microbiology, Sivas, Turkey
| |
Collapse
|
26
|
Cornall AM, Poljak M, Garland SM, Phillips S, Machalek DA, Tan JH, Quinn MA, Tabrizi SN. EUROarray human papillomavirus (HPV) assay is highly concordant with other commercial assays for detection of high-risk HPV genotypes in women with high grade cervical abnormalities. Eur J Clin Microbiol Infect Dis 2016; 35:1033-6. [PMID: 27048314 DOI: 10.1007/s10096-016-2634-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
Abstract
The purpose of this study was to evaluate the performance of the EUROIMMUN EUROArray HPV genotyping assay against the Roche Cobas 4800, Roche HPV Amplicor, Roche Linear Array and Qiagen Hybrid Capture 2 assays in the detection of high-risk HPV (HR-HPV) from liquid based cervical cytology samples collected from women undergoing follow-up for abnormal cervical cytology results. Cervical specimens from 404 women undergoing management of high-grade cytological abnormality were evaluated by EUROarray HPV for detection of HR-HPV genotypes and prediction of histologically-confirmed cervical intraepithelial neoplasia grade 2 or higher (≥CIN2). The results were compared to Hybrid Capture 2, Cobas 4800 HPV, Amplicor and Linear Array HPV. Positivity for 14 HR-HPV types was 80.0 % for EUROarray (95 % CI; 75.7-83.8 %). Agreement (κ, 95 % CI) between the EUROarray and other HPV tests for detection of HR-HPV was good to very good [Hybrid Capture κ = 0.62 (0.54-0.71); Cobas κ = 0.81 (0.74-0.88); Amplicor κ = 0.68 (0.60-0.77); Linear Array κ = 0.77 (0.70-0.85)]. For detection of HR-HPV, agreement with EUROarray was 87.90 % (Hybrid Capture), 93.58 % (Cobas), 92.84 % (Amplicor) and 92.59 % (Linear Array). Detection of HR-HPV was not significantly different between EUROarray and any other test (p < 0.001). EUROarray was concordant with other assays evaluated for detection of high-risk HPV and showed sensitivity and specificity for detection of ≥ CIN2 of 86 % and 71 %, respectively.
Collapse
Affiliation(s)
- A M Cornall
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia. .,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia.
| | - M Poljak
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia.,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - S M Garland
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia.,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, 3052, Victoria, Australia
| | - S Phillips
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia.,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - D A Machalek
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia.,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia
| | - J H Tan
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, 3052, Victoria, Australia.,Oncology and Dysplasia Unit, Royal Women's Hospital, Parkville, 3052, Victoria, Australia
| | - M A Quinn
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, 3052, Victoria, Australia.,Oncology and Dysplasia Unit, Royal Women's Hospital, Parkville, 3052, Victoria, Australia
| | - S N Tabrizi
- Regional HPV Lab Net Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, 3052, Victoria, Australia.,Murdoch Childrens Research Institute, Parkville, 3052, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, 3052, Victoria, Australia
| |
Collapse
|
27
|
Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, Van de Vijver DAMC, Åsjö B, Beshkov D, Coughlan S, Descamps D, Griskevicius A, Hamouda O, Horban A, Van Kasteren M, Kolupajeva T, Kostrikis LG, Liitsola K, Linka M, Mor O, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Staneková D, Stanojevic M, Van Laethem K, Zazzi M, Zidovec Lepej S, Boucher CAB, Schmit JC, Wensing AMJ, Puchhammer-Stockl E, Sarcletti M, Schmied B, Geit M, Balluch G, Vandamme AM, Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Vandekerckhove LPR, Van den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Van Laethem K, Beshkov D, Alexiev I, Lepej SZ, Begovac J, Kostrikis L, Demetriades I, Kousiappa I, Demetriou V, Hezka J, Linka M, Maly M, Machala L, Nielsen C, Jørgensen LB, Gerstoft J, Mathiesen L, Pedersen C, Nielsen H, Laursen A, Kvinesdal B, Liitsola K, Ristola M, Suni J, Sutinen J, Descamps D, Assoumou L, Castor G, Grude M, Flandre P, Storto A, Hamouda O, Kücherer C, Berg T, Braun P, Poggensee G, Däumer M, Eberle J, Heiken H, Kaiser R, Knechten H, Korn K, Müller H, Neifer S, Schmidt B, Walter H, Gunsenheimer-Bartmeyer B, Harrer T, Paraskevis D, Hatzakis A, Zavitsanou A, Vassilakis A, Lazanas M, Chini M, Lioni A, Sakka V, Kourkounti S, Paparizos V, Antoniadou A, Papadopoulos A, Poulakou G, Katsarolis I, Protopapas K, Chryssos G, Drimis S, Gargalianos P, Xylomenos G, Lourida G, Psichogiou M, Daikos GL, Sipsas NV, Kontos A, Gamaletsou MN, Koratzanis G, Sambatakou H, Mariolis H, Skoutelis A, Papastamopoulos V, Georgiou O, Panagopoulos P, Maltezos E, Coughlan S, De Gascun C, Byrne C, Duffy M, Bergin C, Reidy D, Farrell G, Lambert J, O'Connor E, Rochford A, Low J, Coakely P, O'Dea S, Hall W, Mor O, Levi I, Chemtob D, Grossman Z, Zazzi M, de Luca A, Balotta C, Riva C, Mussini C, Caramma I, Capetti A, Colombo MC, Rossi C, Prati F, Tramuto F, Vitale F, Ciccozzi M, Angarano G, Rezza G, Kolupajeva T, Vasins O, Griskevicius A, Lipnickiene V, Schmit JC, Struck D, Sauvageot N, Hemmer R, Arendt V, Michaux C, Staub T, Sequin-Devaux C, Wensing AMJ, Boucher CAB, van de Vijver DAMC, van Kessel A, van Bentum PHM, Brinkman K, Connell BJ, van der Ende ME, Hoepelman IM, van Kasteren M, Kuipers M, Langebeek N, Richter C, Santegoets RMWJ, Schrijnders-Gudde L, Schuurman R, van de Ven BJM, Åsjö B, Kran AMB, Ormaasen V, Aavitsland P, Horban A, Stanczak JJ, Stanczak GP, Firlag-Burkacka E, Wiercinska-Drapalo A, Jablonowska E, Maolepsza E, Leszczyszyn-Pynka M, Szata W, Camacho R, Palma C, Borges F, Paixão T, Duque V, Araújo F, Otelea D, Paraschiv S, Tudor AM, Cernat R, Chiriac C, Dumitrescu F, Prisecariu LJ, Stanojevic M, Jevtovic D, Salemovic D, Stanekova D, Habekova M, Chabadová Z, Drobkova T, Bukovinova P, Shunnar A, Truska P, Poljak M, Lunar M, Babic D, Tomazic J, Vidmar L, Vovko T, Karner P, Garcia F, Paredes R, Monge S, Moreno S, Del Amo J, Asensi V, Sirvent JL, de Mendoza C, Delgado R, Gutiérrez F, Berenguer J, Garcia-Bujalance S, Stella N, de Los Santos I, Blanco JR, Dalmau D, Rivero M, Segura F, Elías MJP, Alvarez M, Chueca N, Rodríguez-Martín C, Vidal C, Palomares JC, Viciana I, Viciana P, Cordoba J, Aguilera A, Domingo P, Galindo MJ, Miralles C, Del Pozo MA, Ribera E, Iribarren JA, Ruiz L, de la Torre J, Vidal F, Clotet B, Albert J, Heidarian A, Aperia-Peipke K, Axelsson M, Mild M, Karlsson A, Sönnerborg A, Thalme A, Navér L, Bratt G, Karlsson A, Blaxhult A, Gisslén M, Svennerholm B, Bergbrant I, Björkman P, Säll C, Mellgren Å, Lindholm A, Kuylenstierna N, Montelius R, Azimi F, Johansson B, Carlsson M, Johansson E, Ljungberg B, Ekvall H, Strand A, Mäkitalo S, Öberg S, Holmblad P, Höfer M, Holmberg H, Josefson P, Ryding U. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis 2015; 62:655-663. [PMID: 26620652 PMCID: PMC4741360 DOI: 10.1093/cid/civ963] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors. Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.
Collapse
Affiliation(s)
- L Marije Hofstra
- Luxembourg Institute of Health, Luxembourg.,Department of Virology, University Medical Center Utrecht, The Netherlands
| | | | - Jan Albert
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Federico Garcia
- Complejo Hospitalario Universitario de Granada, Instituto de Investigación IBS Granada; on behalf of Cohorte de Adultos de la Red de Investigación en SIDA, Spain
| | | | | | | | - Danail Beshkov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Diane Descamps
- AP-HP Groupe hospitalier Bichat-Claude Bernard, IAME INSERM UMR 1137, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | | | | | | | | | | | | | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - Orna Mor
- National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. dr. Matei Bals", Bucharest, Romania
| | | | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia
| | | | - Anders Sönnerborg
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Tabrizi SN, Tan LY, Walker S, Poljak M, Twin J, Garland SM, Bradshaw CS, Fairley CK, Mokany E. 005.4 Multiplex assay for simultaneous detection ofmycoplasma genitaliumand macrolide resistance using pass mnazyme QPCR. Sex Transm Infect 2015. [DOI: 10.1136/sextrans-2015-052270.106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
29
|
Kristina FK, Popovic M, Kocjan J, Zivanovic M, Seme K, Poljak M. Detection of human polyomaviruses JC and BK in brain tissues from patients with progressive multifocal leukoencephalopathy using in situ hybridization and polymerase chain reaction. J Clin Virol 2015. [DOI: 10.1016/j.jcv.2015.07.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
30
|
Bissessor M, Tabrizi SN, Bradshaw CS, Fairley CK, Twin J, Poljak M, Peel J, Hocking JS, Garland SM, Chen MY. 003.2 The contribution of mycoplasma genitaliumto the aetiology of sexually acquired proctitis in men who have sex with men. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.92] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
31
|
Casadellà M, van Ham PM, Noguera-Julian M, van Kessel A, Pou C, Hofstra LM, Santos JR, Garcia F, Struck D, Alexiev I, Bakken Kran AM, Hoepelman AI, Kostrikis LG, Somogyi S, Liitsola K, Linka M, Nielsen C, Otelea D, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Staneková D, Stanojevic M, Van Laethem K, Zidovec Lepej S, Clotet B, Boucher CAB, Paredes R, Wensing AMJ. Primary resistance to integrase strand-transfer inhibitors in Europe. J Antimicrob Chemother 2015; 70:2885-8. [PMID: 26188038 DOI: 10.1093/jac/dkv202] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/16/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. METHODS This was a multicentre, cross-sectional study within the European SPREAD HIV resistance surveillance programme. A representative set of 300 samples was selected from 1950 naive HIV-positive subjects newly diagnosed in 2006-07. The prevalence of InSTI resistance was evaluated using quality-controlled baseline population sequencing of integrase. Signature raltegravir, elvitegravir and dolutegravir resistance mutations were defined according to the IAS-USA 2014 list. In addition, all integrase substitutions relative to HXB2 were identified, including those with a Stanford HIVdb score ≥ 10 to at least one InSTI. To rule out circulation of minority InSTI-resistant HIV, 65 samples were selected for 454 integrase sequencing. RESULTS For the population sequencing analysis, 278 samples were retrieved and successfully analysed. No signature resistance mutations to any of the InSTIs were detected. Eleven (4%) subjects had mutations at resistance-associated positions with an HIVdb score ≥ 10. Of the 56 samples successfully analysed with 454 sequencing, no InSTI signature mutations were detected, whereas integrase substitutions with an HIVdb score ≥ 10 were found in 8 (14.3%) individuals. CONCLUSIONS No signature InSTI-resistant variants were circulating in Europe before the introduction of InSTIs. However, polymorphisms contributing to InSTI resistance were not rare. As InSTI use becomes more widespread, continuous surveillance of primary InSTI resistance is warranted. These data will be key to modelling the kinetics of InSTI resistance transmission in Europe in the coming years.
Collapse
Affiliation(s)
- M Casadellà
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - P M van Ham
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | - M Noguera-Julian
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - A van Kessel
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | - C Pou
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - L M Hofstra
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - J R Santos
- HIV Unit, Hospital Universitari Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - F Garcia
- Complejo Hospitalario Univeristario de Granada, Instituto de Investigación IBS, Granada, Cohorte de Adultos de la Red de Investigación en SIDA (CoRIS) Spain
| | - D Struck
- Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - I Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - A I Hoepelman
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | | | - S Somogyi
- Robert Koch-Institute, Berlin, Germany
| | - K Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - M Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - C Nielsen
- Statens Serum Institut, Copenhagen, Denmark
| | - D Otelea
- National Institute for Infectious Diseases 'Prof. Dr. Matei Bals', Bucharest, Romania
| | - D Paraskevis
- National Retrovirus Reference Center, University of Athens, Athens, Greece
| | - M Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | - D Staneková
- Slovak Medical University, Bratislava, Slovakia
| | - M Stanojevic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - K Van Laethem
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium
| | - S Zidovec Lepej
- University Hospital for Infectious Diseases 'Dr. Fran Mihaljevic', Zagreb, Croatia
| | - B Clotet
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - C A B Boucher
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - R Paredes
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - A M J Wensing
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | | |
Collapse
|
32
|
Kopilović B, Poljak M, Seme K, Klavs I. Hepatitis C virus infection among pregnant women in Slovenia: study on 31,849 samples obtained in four screening rounds during 1999, 2003, 2009 and 2013. ACTA ACUST UNITED AC 2015; 20:21144. [PMID: 26062646 DOI: 10.2807/1560-7917.es2015.20.22.21144] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The majority of people infected with hepatitis C virus (HCV) are unaware of their infection. Assessment of the prevalence of HCV infection in the general population and in key populations at increased risk is needed for evidence-based testing policies. Our objectives were to estimate the prevalence of antibodies to HCV (anti-HCV), the prevalence of HCV viraemia (HCV RNA), and to describe HCV genotype distribution among pregnant women in Slovenia. Unlinked anonymous testing was performed on residual sera obtained from 31,849 pregnant women for routine syphilis screening during 1999, 2003, 2009, and 2013. Anti-HCV reactive specimens were tested for HCV RNA and HCV genotypes were determined. Annual prevalence of anti-HCV ranged between 0.09% (95% confidence interval (CI): 0.03–0.18) in 2009 and 0.21% (95% CI: 0.12–0.34) in 2003 and HCV RNA positivity between 0.06% (95% CI: 0.02–0.14) in 2009 and 0.14% (95% CI: 0.07–0.25) in 2003. We observed no statistically significant differences in anti-HCV or HCV RNA prevalence between age groups (<20, 20–29 and ≥30 years) in any year and no trend in time. Of 29 HCV active infections, 19 were with genotype 1 and 10 with genotype 3. HCV infection among pregnant women was rare suggesting a low burden in the Slovenian general population. Antenatal screening for HCV in Slovenia could not be recommended.
Collapse
Affiliation(s)
- B Kopilović
- National Institute of Public Health, Ljubljana, Slovenia
| | | | | | | |
Collapse
|
33
|
Kocjan BJ, Bzhalava D, Forslund O, Dillner J, Poljak M. Molecular methods for identification and characterization of novel papillomaviruses. Clin Microbiol Infect 2015; 21:808-16. [PMID: 26003284 DOI: 10.1016/j.cmi.2015.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/27/2015] [Accepted: 05/12/2015] [Indexed: 02/02/2023]
Abstract
Papillomaviruses (PV) are a remarkably heterogeneous family of small DNA viruses that infect a wide variety of vertebrate species and are aetiologically linked with the development of various neoplastic changes of the skin and mucosal epithelia. Based on nucleotide similarity, PVs are hierarchically classified into genera, species and types. Novel human PV (HPV) types are given a unique number only after the whole genome has been cloned and deposited with the International HPV Reference Center. As of 9 March 2015, 200 different HPV types, belonging to 49 species, had been recognized by the International HPV Reference Center. In addition, 131 animal PV types identified from 66 different animal species exist. Recent advances in molecular techniques have resulted in an explosive increase in the identification of novel HPV types and novel subgenomic HPV sequences in the last few years. Among PV genera, the γ-PV genus has been growing most rapidly in recent years with 80 completely sequenced HPV types, followed by α-PV and β-PV genera that have 65 and 51 recognized HPV types, respectively. We reviewed in detail the contemporary molecular methods most often used for identification and characterization of novel PV types, including PCR, rolling circle amplification and next-generation sequencing. Furthermore, we present a short overview of 12 and 10 novel HPV types recently identified in Sweden and Slovenia, respectively. Finally, an update on the International Human Papillomavirus Reference Center is provided.
Collapse
Affiliation(s)
- B J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - D Bzhalava
- International Human Papillomavirus Reference Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - O Forslund
- Department of Laboratory Medicine, Lund University, Malmö, Sweden
| | - J Dillner
- International Human Papillomavirus Reference Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia.
| |
Collapse
|
34
|
Boštjančič E, Bandelj E, Luzar B, Poljak M, Glavač D. Hepatic expression of miR-122, miR-126, miR-136 and miR-181a and their correlation to histopathological and clinical characteristics of patients with hepatitis C. J Viral Hepat 2015; 22:146-57. [PMID: 25065618 DOI: 10.1111/jvh.12266] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 04/03/2014] [Indexed: 12/13/2022]
Abstract
It has been shown for hepatitis C virus (HCV) infection that host miRNAs contribute to the replication of the viral RNA genome. However, the clinical impact of these and many other cellular miRNAs on HCV in humans is still largely unclear. We therefore analysed the expression of miR-122, miR-126, miR-181a and miR-136 in HCV-infected patients. The study included liver biopsies of 65 patients infected with HCV of different genotypes (gt 1, gt 1a, gt 1b, gt 3 and gt 4) and nine noninfected individuals. Expression analysis of miRNAs was performed by qPCR, and they were analysed for differences between patient gender and age, genotypes, stage of fibrosis, grade of inflammation, serum level of liver enzymes, serum viral load, the presence of steatosis and mode of transmission. Different target prediction algorithms were used to search for targets of analyzed miRNAs. Statistical analysis revealed significant up-regulation of miR-136 and down-regulation of miR-126 and miR-181a in patients infected with HCV of different genotypes compared with noninfected individuals. The same expression pattern was observed in different stages and grades of liver disease. miR-122 was up-regulated in women relative to men and associated to portal inflammation, miR-122 and miR-126 correlated with serum HCV load and miR-136 and miR-122 correlated with the presence of steatosis. miR-126 and miR-136 were differentially expressed between different modes of HCV transmission. There were approximately 2000 different targets predicted for all four miRNAs and each of the analyzed miRNAs could be involved in more than a 100 different biochemical pathways. miR-122, miR-126, miR-136 and miR-181a have been shown to be involved in HCV infection with different genotypes. Their expression has been associated with the gender, stage and grade of liver disease, mode of transmission, serum HCV load and the presence of steatosis. Numerous target genes and biochemical pathways are predicted for each of the analyzed miRNAs. All these results suggest their role in HCV-infected liver disease.
Collapse
Affiliation(s)
- E Boštjančič
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | | |
Collapse
|
35
|
Affiliation(s)
- M Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia.
| | | |
Collapse
|
36
|
Poljak M, Lim R, Barker G, Lappas M. Class I to III histone deacetylases differentially regulate inflammation-induced matrix metalloproteinase 9 expression in primary amnion cells. Reprod Sci 2014; 21:804-13. [PMID: 24429678 DOI: 10.1177/1933719113518990] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Matrix metalloproteinase (MMP) 9 plays an important role in the degradation of the extracellular matrix in fetal membranes, and pathological activation of MMP-9 can lead to preterm birth. In nongestational tissues, modulation of histone deacetylases (HDACs) regulates MMP-9 expression. The aim of this study was to determine whether class I to III HDACs regulate MMP-9 expression and activity in primary amnion cells. Class I and II HDAC regulation of MMP-9 was assessed using the general class I and II HDAC inhibitors (HDACi) trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA), the class I HDACi MS-275, and the class II HDACi MC1568. Class III HDAC regulation of MMP-9 was assessed using the SIRT1 activators resveratrol and SRT1720 as well as SIRT1 small interfering RNA (siRNA). Primary amnion epithelial cells were incubated with 1 ng/mL interleukin (IL) 1β in the absence or presence of 0.3 μmol/L TSA, 5 μmol/L SAHA, 2.5 μmol/L MS-275, 2.5 μmol/L MC1568, 50 μmol/L resveratrol, or 10 μmol/L SRT1720 for 20 hours. We found that the class I and II HDACi TSA and SAHA and the class II HDACi MC1568 significantly decreased IL-β-induced MMP-9 gene and pro-MMP-9 expression in primary amnion cells. There was, however, no effect of the class I HDACi MS-275 on IL-β-induced MMP-9 expression. On the other hand, inhibition of class III HDAC SIRT1 using siRNA significantly augmented IL-1β-induced MMP-9, and SIRT1 activation using resveratrol and SRT1720 inhibited IL-1β-induced MMP-9 expression. In summary, class I to III HDACs differentially regulate inflammation-induced MMP-9 expression in primary amnion cells.
Collapse
Affiliation(s)
- Marin Poljak
- 1Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia
| | | | | | | |
Collapse
|
37
|
Klavs I, Kastelic Z, Kustec T, Poljak M. P3.320 Unlinked Anonymous Testing For Monitoring HIV Prevalence in Sentinel Groups in Slovenia, 2002–2011. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
38
|
Klavs I, Učakar V, Jelen MM, Faust H, Dillner J, Poljak M. O16.6 Pre-Vaccination Seroprevalence of 15 Human Papillomavirus (HPV) Types Among Slovenian Women Screened For Cervical Cancer. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
39
|
Učakar V, Poljak M, Oštrbenk A, Klavs I. P3.051 Pre-Vaccination Prevalence of Infections with 25 Low-Risk Human Papillomavirus (HPV) Types Among 1000 Slovenian Women Screened For Cervical Cancer in 2010. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
40
|
Poljak M. Prophylactic human papillomavirus vaccination and primary prevention of cervical cancer: issues and challenges. Clin Microbiol Infect 2012; 18 Suppl 5:64-9. [DOI: 10.1111/j.1469-0691.2012.03946.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
41
|
Burk RD, Chen Z, Harari A, Smith BC, Kocjan BJ, Maver PJ, Poljak M. Classification and nomenclature system for human Alphapapillomavirus variants: general features, nucleotide landmarks and assignment of HPV6 and HPV11 isolates to variant lineages. Acta Dermatovenerol Alp Pannonica Adriat 2011; 20:113-123. [PMID: 22131111 PMCID: PMC3690374] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND Papillomaviruses constitute a family of viruses that can be classified into genera, species and types based on their viral genome heterogeneity. Currently circulating infectious human Alphapapillomaviruses (alpha-PVs) constitute a set of viral genomes that have evolved from archaic times and display features of host co-speciation. Viral variants are more recently evolved genomes that require a standardized classification and nomenclature. OBJECTIVES To describe a system for the classification and nomenclature of HPV viral variants and provide landmarks for the numbering of nucleotide positions. METHODS The complete 8 kb genomes of the alpha-9 species group and HPV6 and 11 types, collected from isolates throughout the world were obtained from published reports and GenBank. Complete genomes for each HPV type were aligned using the E1 start codon and sequence divergence was calculated by global and pairwise alignments using the MUSCLE program. Phylogenetic trees were constructed from the aligned sequences using a maximum likelihood method (RAxML). RESULTS Pairwise comparisons of nucleotide differences between complete genomes of each type from alpha-9 HPV isolates (HPV16, 31, 33, 35, 52, 58 and 67) revealed a trimodal distribution. Maximum heterogeneity for variants within a type varied from 0.6%-2.3%. Nucleotide differences of approximately 1.0%-10.0% and 0.5%-1.0% of the complete genomes were used to define variant lineages and sublineages, respectively. Analysis of 43 HPV6 complete genomes indicated the presence of 2 variant lineages, whereas 32 HPV11 isolates were highly similar and clustered into 2 sublineages. A table was constructed of the human alpha-PV landmark nucleotide sequences for future reference and alignments. CONCLUSIONS A proposed nomenclature system for viral variants and coordination of nucleotide positions will facilitate the comparison of variants across geographic regions and amongst different populations. In addition, this system will facilitate study of pathogenic, tissue tropism and functional differences amongst variant lineages of and polymorphisms within HPV variants.
Collapse
Affiliation(s)
- R. D. Burk
- Departments Pediatrics, Microbiology and addresses Immunology, Epidemiology and Population Health, and Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, New York, 10461, United States of America
| | - Z. Chen
- Department of Pediatrics, Albert Einstein College of Medicine, same address.
| | - A. Harari
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, same address. ariana.harari@phd. einstien.yu.edu
| | - B. C. Smith
- Department of Pediatrics, Albert Einstein College of Medicine, same address.
| | - B. J. Kocjan
- University of Ljubljana, Institute of Microbiology and Immunology, Faculty of Medicine, Zaloška 4, 1105 Ljubljana, Slovenia.
| | - P. J. Maver
- University of Ljubljana, Institute of Microbiology and Immunology, Faculty of Medicine, same address.
| | - M. Poljak
- University of Ljubljana, Institute of Microbiology and Immunology, Faculty of Medicine, same address.
| |
Collapse
|
42
|
Klavs I, Ucakar V, Poljak M. P1-S1.54 High-risk Human Papilloma Virus (HPV) types prevalence in 20-64-years-old Women; Slovenian National HPV Prevalence Study, 2010. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050108.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
43
|
van de Vijver DAMC, Wensing AMJ, Åsjö B, Bruckova M, Jorgensen LB, Camacho R, Horban A, Linka M, Lazanas M, Loveday C, MacRae E, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Ruiz L, Schmit JC, Stanczak G, Stanojevic M, Vandamme AM, Vercauteren J, Zazzi M, Bacheler L, Lecocq P, Villacian J, Boucher CAB. HIV-1 drug-resistance patterns among patients on failing treatment in a large number of European countries. Acta Dermatovenerol Alp Pannonica Adriat 2010; 19:3-9. [PMID: 21390473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
BACKGROUND Information about patterns of HIV-1 drug resistance among treatment-exposed patients is crucial for the development of novel effective drugs. Currently no system exists that monitors patterns of resistance in patients failing therapy. METHODS The study included 1,988 HIV-1 sequences from patients experiencing therapy failure collected between 2000 and 2004 in 15 European countries. Genotypic resistance was interpreted using the ANRS algorithm. Phenotypic resistance was predicted using the Virco geno- to phenotype system. RESULTS 80.7% of the sequences included at least one drug-resistance mutation. Mutations were found for NRTIs (73.5%), NNRTIs (48.5%), and protease inhibitors (35.8%). Ninety percent of sequences with genotypic resistance harbored M184V, M41L, K103N, D67N, and/or T215Y. Among NRTIs, resistance was most frequently predicted for lamivudine. About half of all sequences had reduced susceptibility for NNRTIs. Resistance to most boosted protease inhibitors was found in < 25%. No sequence had resistance to all currently available drugs. CONCLUSION Levels of resistance among patients with therapy failure were high. The patterns of resistance reflect resistance to drugs available for a longer time. Fully suppressive regimens can be designed even for the most mutated HIV because boosted protease inhibitors have remained active against most circulating viruses and new drug classes have become available.
Collapse
Affiliation(s)
- D A M C van de Vijver
- Dept. of Virology, Erasmus MC, Rotterdam University Medical Centre, Rotterdam, the Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Poljak M, Barlic J, Seme K, Avsic-Zupanc T, Zore A. Isolation of DNA from archival Papanicolaou stained cytological smears using a simple salting-out procedure. Mol Pathol 2010; 48:M55-6. [PMID: 16695977 PMCID: PMC407921 DOI: 10.1136/mp.48.1.m55] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
DNA from archival Papanicolaou stained and unstained cytological smears was successfully isolated using a simple, rapid and inexpensive salting-out procedure. The quality of DNA was controlled by polymerase chain reaction (PCR) amplification of segments of the human beta-globin, human beta-actin and human papillomavirus L1 genes. Only negligible differences in amplification efficiency were observed between DNA isolated from stained and unstained smears. The salting-out procedure is a more rapid method for the isolation of DNA than phenol-chloroform extraction and may be used in instances where fresh or cryopreserved clinical specimens are not available.
Collapse
Affiliation(s)
- M Poljak
- Institute of Microbiology, Medical Faculty of Ljubljana, Zaloska 4, 61105 Ljubljana, Slovenia
| | | | | | | | | |
Collapse
|
45
|
Takač I, Arko D, Kodrič T, Poljak M, Zagorac A, Erjavec-Škerget A, Kokalj-Vokač N. P1111 Human telomerase gene amplification does not correlate with the grade of cervical intraepithelial neoplasia. Int J Gynaecol Obstet 2009. [DOI: 10.1016/s0020-7292(09)62595-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
46
|
Takač I, Arko D, Kodrič T, Poljak M, Zagorac A, Erjavec-Škerget A, Kokalj-Vokač N. Human Telomerase Gene Amplification and High-Risk Human Papillomavirus Infection in Women with Cervical Intra-Epithelial Neoplasia. J Int Med Res 2009; 37:1588-95. [DOI: 10.1177/147323000903700537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This study was designed to investigate whether a correlation exists between amplification of the human telomerase gene (human telomerase RNA component [ TERC]) and high-risk human papillomavirus (HR-HPV) infection in 101 women with cervical intra-epithelial neoplasia (CIN). Eight patients (7.9%) had CIN 1, 24 (23.8%) had CIN 2 and 69 (68.3%) had CIN 3. TERC was amplified in 31.7% of all CIN patients. The difference in frequency of TERC amplification between patients with low-grade CIN (CIN 1) and those with high-grade CIN (CIN 2 and CIN 3) was not significant. HR-HPV infection was detected in 88.1% of all CIN cases and was significantly more frequent in patients with CIN 2 and CIN 3 than in patients with CIN 1. There was no significant difference in the frequency of HR-HPV infection between groups of patients with and without TERC amplification. In conclusion, this study found no correlation between TERC amplification and HR-HPV infection in patients with CIN.
Collapse
Affiliation(s)
- I Takač
- Department of Gynaecological and Breast Oncology, Maribor University Hospital, Maribor, Slovenia
| | - D Arko
- Department of Gynaecological and Breast Oncology, Maribor University Hospital, Maribor, Slovenia
| | - T Kodrič
- Department of Gynaecological and Breast Oncology, Maribor University Hospital, Maribor, Slovenia
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - A Zagorac
- Laboratory of Medical Genetics, University Department of Gynaecology and Perinatology, Maribor University Hospital, Maribor, Slovenia
| | - A Erjavec-Škerget
- Laboratory of Medical Genetics, University Department of Gynaecology and Perinatology, Maribor University Hospital, Maribor, Slovenia
| | - N Kokalj-Vokač
- Laboratory of Medical Genetics, University Department of Gynaecology and Perinatology, Maribor University Hospital, Maribor, Slovenia
| |
Collapse
|
47
|
Kovanda A, Juvan U, Sterbenc A, Kocjan BJ, Seme K, Jancar N, Vrtacnik-Bokal E, Poljak M. Pre-vaccination distribution of human papillomavirus (HPV) genotypes in women with cervical intraepithelial neoplasia grade 3 (CIN 3) lesions in Slovenia. Acta Dermatovenerol Alp Pannonica Adriat 2009; 18:47-52. [PMID: 19588057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
BACKGROUND High-risk human papillomaviruses (HPV) are the main etiological factor of cervical cancer. Cervical intraepithelial neoplasia grade 3 (CIN 3) is the latest pre-invasive stage of cervical cancer, with an approximately 20% progression rate to invasive cervical carcinoma. OBJECTIVE To establish the pre-vaccination distribution of HPV genotypes in Slovenian women with CIN 3 lesions, in order to assess the potential benefit of prophylactic HPV vaccination in Slovenia, and to provide baseline data for monitoring the potential replacement of HPV genotypes under selective pressure of HPV vaccines. METHODS AND RESULTS A total of 261 cervical swabs collected from women with histologically confirmed CIN 3 lesions were analyzed using four genotyping methods: the Abbott RealTime High Risk HPV Assay, the Innogenetics INNO-LiPA HPV Genotyping Extra Test, and the in-house PGMY09/11, and CPI/CPIIg polymerase chain reaction (PCR) and sequencing. Of 261 samples, 253 (96.9%) were HPV positive. The most common HPV genotype in CIN 3 lesions in the Slovenian samples was HPV-16 (59.0%), followed by HPV-31 (7.5%), HPV-33 (7.1%), HPV-58 (5.0%), and HPV-51 (4.0%). The presence of more than one HPV genotype was detected in 49/253 (19.4%) samples. Together, HPV-16 and HPV- 18 accounted for 67.4% of CIN 3 lesions in this Slovenian population. CONCLUSION The high proportion of CIN 3 lesions caused by HPV-16 and HPV-18 should further support the recent decision to include the prophylactic vaccination against HPV in the national vaccination program in Slovenia.
Collapse
Affiliation(s)
- A Kovanda
- Institute of Microbiology and Immunology, Faculty of Medicine, Zaloska 4, 1000 Ljubljana, Slovenia
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
Testing for HIV is one of the cornerstones in the combat against HIV infection. The 2008 European Guideline on HIV Testing provides advice on testing for HIV infection in individuals aged 16 years and older who have sought evaluation and treatment at sexually transmitted infection services for dermatovenereology clinics across Europe. Its aim is to provide practical guidance to clinicians in these settings who undertake HIV testing and suggest appropriate standards for the audit of service provision.
Collapse
Affiliation(s)
- M Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Liubljana, Zatos̄ka 4, 1000, Ljubljana, Slovenia
| | - E Smit
- Birmingham Heartlands and Solihull NHS Trust, Birmingham
| | - J Ross
- Whitall Street Clinic, Birmingham, UK
| |
Collapse
|
49
|
Jancar N, Kocjan BJ, Poljak M, Bokal EV. Comparison of paired cervical scrape and tumor tissue samples for detection of human papillomaviruses in patients with cervical cancer. EUR J GYNAECOL ONCOL 2009; 30:675-678. [PMID: 20099503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
PURPOSE OF INVESTIGATION To compare the detection and distribution of HPV genotypes in paired cervical scrape samples and tumor tissue samples in patients with cervical cancer. METHODS Forty cervical scrape samples and 40 paired archival or fresh frozen tissue samples were collected from women with cervical cancer. Polymerase chain reaction with GP5+ and GP6+ primers was performed in all samples for HPV DNA detection. All GP5+/GP6+ negative samples were additionally tested using INNO-LiPA HPV Genotyping Extra Test. RESULTS Overall, 39/40 (97.5%) of CC samples were HPV DNA positive. HPV 16 was found in 24/40 samples, HPV 18 in 5/40 samples. A co-infection with two different HPV genotypes was identified in one cervical scrape specimen, while in tissue samples only single infections were detected. Overall agreement between paired samples was 98.75%. CONCLUSION The present study has shown that cervical scrape samples are equally useful for HPV genotype determination as tumor tissue samples in patients with cervical cancer. They can be used as accurate clinical samples for detection of HPV genotype causing cervical cancer or for epidemiological molecular studies.
Collapse
Affiliation(s)
- N Jancar
- Department of Obstetrics and Gynecology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | | | | |
Collapse
|
50
|
Maticic M, Poljak M, Lunder T, Rener-Sitar K, Stojanovic L. Lichen planus and other cutaneous manifestations in chronic hepatitis C: pre- and post-interferon-based treatment prevalence vary in a cohort of patients from low hepatitis C virus endemic area. J Eur Acad Dermatol Venereol 2008; 22:779-88. [DOI: 10.1111/j.1468-3083.2008.02676.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|