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Vrbová E, Mikalová L, Grillová L, Pospíšilová P, Strnadel R, Dastychová E, Kojanová M, Kreidlová M, Vaňousová D, Rob F, Procházka P, Krchňáková A, Vašků V, Woznicová V, Dvořáková Heroldová M, Kuklová I, Zákoucká H, Šmajs D. A retrospective study on nested PCR detection of syphilis treponemes in clinical samples: PCR detection contributes to the diagnosis of syphilis in patients with seronegative and serodiscrepant results. PLoS One 2020; 15:e0237949. [PMID: 32817658 PMCID: PMC7446855 DOI: 10.1371/journal.pone.0237949] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/05/2020] [Indexed: 11/19/2022] Open
Abstract
Syphilis, caused by Treponema pallidum ssp. pallidum (TPA), is a persisting global health problem. Although syphilis diagnostics relies mainly on serology, serological tests have some limitations, and it is recommended that the final diagnosis be supported by additional tests. The purpose of this study was to analyze the relationship between serology and PCR in syphilis diagnostics. From the year 2004 to May 2019, a total of 941 samples were taken from 833 patients suspected of having syphilis, in Czech Republic. In all these samples, both nested PCR detection of TPA and serology testing were performed. Of the 941 samples, 126 were seronegative, 651 were seropositive, and 164 were serodiscrepant. Among seronegative samples (n = 126), 11 were PCR-positive (8.7%). Among seropositive samples (n = 651; i.e., samples positive for both non-treponemal and treponemal serology tests), 368 samples were PCR-positive (56.5%). The remaining 164 serodiscrepant samples included RPR negative and treponemal serological test-positive samples (n = 154) and a set of 10 RPR-positive samples negative in treponemal serological tests. While the first group revealed 73 PCR-positive samples (47.4%), the second revealed 5 PCR positive samples (50.0%). PCR detection rates were highest in primary syphilis, with lower rates in the secondary and undetermined syphilis stages. As shown here, the nested PCR can improve diagnostics of syphilis, especially in seronegative patients and in patients with discrepant serology.
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Affiliation(s)
- Eliška Vrbová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Radim Strnadel
- Department of Dermatovenerology, Faculty Hospital Brno, Brno, Czech Republic
| | - Eliška Dastychová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Martina Kojanová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Miluše Kreidlová
- Institute of Medical Biochemistry and Laboratory Diagnostics of the General University Hospital and of The First Faculty of Medicine of Charles University in Prague, Prague, Czech Republic
| | - Daniela Vaňousová
- Department of Dermatovenerology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Filip Rob
- Department of Dermatovenerology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | - Alena Krchňáková
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Vladimír Vašků
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Vladana Woznicová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Monika Dvořáková Heroldová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne’s Hospital and Masaryk University, Brno, Czech Republic
| | - Ivana Kuklová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Hana Zákoucká
- National Reference Laboratory for Diagnostics of the Syphilis, National Institute for Public Health, Prague, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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Grillová L, Oppelt J, Mikalová L, Nováková M, Giacani L, Niesnerová A, Noda AA, Mechaly AE, Pospíšilová P, Čejková D, Grange PA, Dupin N, Strnadel R, Chen M, Denham I, Arora N, Picardeau M, Weston C, Forsyth RA, Šmajs D. Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens. Front Microbiol 2019; 10:1691. [PMID: 31417509 PMCID: PMC6685089 DOI: 10.3389/fmicb.2019.01691] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 02/28/2019] [Accepted: 07/09/2019] [Indexed: 11/13/2022] Open
Abstract
Syphilis, caused by Treponema pallidum subsp. pallidum (TPA), remains an important public health problem with an increasing worldwide prevalence. Despite recent advances in in vitro cultivation, genetic variability of this pathogen during infection is poorly understood. Here, we present contemporary and geographically diverse complete treponemal genome sequences isolated directly from patients using a methyl-directed enrichment prior to sequencing. This approach reveals that approximately 50% of the genetic diversity found in TPA is driven by inter- and/or intra-strain recombination events, particularly in strains belonging to one of the defined genetic groups of syphilis treponemes: Nichols-like strains. Recombinant loci were found to encode putative outer-membrane proteins and the recombination variability was almost exclusively found in regions predicted to be at the host-pathogen interface. Genetic recombination has been considered to be a rare event in treponemes, yet our study unexpectedly showed that it occurs at a significant level and may have important impacts in the biology of this pathogen, especially as these events occur primarily in the outer membrane proteins. This study reveals the existence of strains with different repertoires of surface-exposed antigens circulating in the current human population, which should be taken into account during syphilis vaccine development.
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Affiliation(s)
- Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia.,Biology of Spirochetes Unit, Institut Pasteur, Paris, France
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Markéta Nováková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States.,Department of Global Health, Harborview Medical Center, University of Washington, Seattle, WA, United States
| | - Anežka Niesnerová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Angel A Noda
- Department of Mycology-Bacteriology, Instituto de Medicina Tropical "Pedro Kourí", Havana, Cuba
| | - Ariel E Mechaly
- Plateforme de Cristallographie, Institut Pasteur, Paris, France
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czechia
| | - Philippe A Grange
- Faculté de Médecine, Laboratoire de Dermatologie-CNR IST Bactériennes, Institut Cochin U1016, Université Sorbonne Paris Descartes, Paris, France
| | - Nicolas Dupin
- Faculté de Médecine, Laboratoire de Dermatologie-CNR IST Bactériennes, Institut Cochin U1016, Université Sorbonne Paris Descartes, Paris, France.,AP-HP, Service de Dermatologie et Vénéréologie, Groupe Hospitalier Paris Centre Cochin-Hôtel Dieu-Broca, Paris, France
| | - Radim Strnadel
- Department of Dermatovenerology, University Hospital Brno, Brno, Czechia
| | - Marcus Chen
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia.,Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Ian Denham
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | | | - R Allyn Forsyth
- GeneticPrime Dx, Inc., La Jolla, CA, United States.,Department of Biology, San Diego State University, San Diego, CA, United States
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
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Vrbová E, Grillová L, Mikalová L, Pospíšilová P, Strnadel R, Dastychová E, Kojanová M, Kreidlová M, Vaňousová D, Rob F, Procházka P, Krchňáková A, Vašků V, Woznicová V, Dvořáková Heroldová M, Kuklová I, Zákoucká H, Šmajs D. MLST typing of Treponema pallidum subsp. pallidum in the Czech Republic during 2004-2017: Clinical isolates belonged to 25 allelic profiles and harbored 8 novel allelic variants. PLoS One 2019; 14:e0217611. [PMID: 31150464 PMCID: PMC6544256 DOI: 10.1371/journal.pone.0217611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 03/04/2019] [Accepted: 05/16/2019] [Indexed: 11/18/2022] Open
Abstract
A recently introduced Multilocus Sequence Typing scheme for Treponema pallidum subsp. pallidum was applied to clinical samples collected from 2004 to 2017 from the two largest cities (Prague and Brno) in the Czech Republic. Altogether, a total of 675 samples were tested in this study and 281 of them were found PCR-positive for treponemal DNA and typeable. Most of the typed samples (n = 281) were swabs from primary or secondary syphilis lesions (n = 231), and only a minority were whole blood or tissue samples (n = 50). Swab samples from patients with rapid plasma regain (RPR) values of 1–1024 were more frequently PCR-positive (84.6%) compared to samples from patients with non-reactive RPR test (46.5%; p-value = 0.0001). Out of 281 typeable samples, 136 were fully-typed at all TP0136, TP0548, and TP0705 loci. Among the fully and partially typed samples, 25 different allelic profiles were identified. Altogether, eight novel allelic variants were found among fully (n = 5) and partially (n = 3) typed samples. The distribution of TPA allelic profiles identified in the Czech Republic from 2004 to 2017 revealed a dynamic character with allelic profiles disappearing and emerging over time. While the number of samples with the A2058G mutation was seen to increase (86.7% in 2016/2017), the number of samples harboring the A2059G mutation was found to have decreased over time (3.3% in 2016/2017). In addition, we found several allelic profile associations with macrolide resistance or susceptibility, the gender of patients, as well as patient residence.
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Affiliation(s)
- Eliška Vrbová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Radim Strnadel
- Department of Dermatovenerology, Faculty Hospital Brno, Brno, Czech Republic
| | - Eliška Dastychová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne's Hospital and Masaryk University, Brno, Czech Republic
| | - Martina Kojanová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Miluše Kreidlová
- Institute of Medical Biochemistry and Laboratory Diagnostics of the General University Hospital, The First Faculty of Medicine of Charles University in Prague, Prague, Czech Republic
| | - Daniela Vaňousová
- Department of Dermatovenerology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Filip Rob
- Department of Dermatovenerology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | - Alena Krchňáková
- Department of Medical Microbiology, Faculty of Medicine, St. Anne's Hospital and Masaryk University, Brno, Czech Republic
| | - Vladimír Vašků
- Department of Medical Microbiology, Faculty of Medicine, St. Anne's Hospital and Masaryk University, Brno, Czech Republic
| | - Vladana Woznicová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne's Hospital and Masaryk University, Brno, Czech Republic
| | - Monika Dvořáková Heroldová
- Department of Medical Microbiology, Faculty of Medicine, St. Anne's Hospital and Masaryk University, Brno, Czech Republic
| | - Ivana Kuklová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Hana Zákoucká
- National Reference Laboratory for Diagnostics of the Syphilis, National Institute for Public Health, Prague, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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Grillová L, Giacani L, Mikalová L, Strouhal M, Strnadel R, Marra C, Centurion-Lara A, Poveda L, Russo G, Čejková D, Vašků V, Oppelt J, Šmajs D. Sequencing of Treponema pallidum subsp. pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material. PLoS One 2018; 13:e0202619. [PMID: 30130365 PMCID: PMC6103504 DOI: 10.1371/journal.pone.0202619] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/07/2018] [Indexed: 12/11/2022] Open
Abstract
Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis, a disease that infects more than 5 million people annually. Since TPA is an uncultivable bacterium, most of the information on TPA genetics comes from genome sequencing and molecular typing studies. This study presents the first complete TPA genome (without sequencing gaps) of clinical isolate (UZ1974), which was obtained directly from clinical material, without multiplication in rabbits. Whole genome sequencing was performed using a newly developed Anti-Treponemal Antibody Enrichment technique combined with previously reported Pooled Segment Genome Sequencing. We identified the UW074B genome, isolated from a sample previously propagated in rabbits, to be the closest relative of the UZ1974 genome and calculated the TPA mutation rate as 2.8 x 10(-10) per site per generation.
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Affiliation(s)
- Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Radim Strnadel
- Department of Dermatovenerology, University Hospital Brno, Brno, Czech Republic
| | - Christina Marra
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Arturo Centurion-Lara
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, United States of America
| | - Lucy Poveda
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Vladimír Vašků
- 1 Dermatovenereological Clinic St. Anne´s University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Grillova L, Strnadel R, Smajs D. 009.5 Isolation and amplification of treponemal dna for whole genome sequencing directly from the patient sample. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.131] [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]
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Nechvátal L, Pětrošová H, Grillová L, Pospíšilová P, Mikalová L, Strnadel R, Kuklová I, Kojanová M, Kreidlová M, Vaňousová D, Procházka P, Zákoucká H, Krchňáková A, Šmajs D. Syphilis-causing strains belong to separate SS14-like or Nichols-like groups as defined by multilocus analysis of 19 Treponema pallidum strains. Int J Med Microbiol 2014; 304:645-53. [DOI: 10.1016/j.ijmm.2014.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/14/2014] [Accepted: 04/21/2014] [Indexed: 11/24/2022] Open
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Flasarová M, Pospíšilová P, Mikalová L, Vališová Z, Dastychová E, Strnadel R, Kuklová I, Woznicová V, Zákoucká H, Šmajs D. Sequencing-based molecular typing of treponema pallidum strains in the Czech Republic: all identified genotypes are related to the sequence of the SS14 strain. Acta Derm Venereol 2012; 92:669-74. [PMID: 22434073 DOI: 10.2340/00015555-1335] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A set of 415 clinical samples isolated from 294 patients suspected of having syphilis collected in the Czech Republic between 2004 and 2010 was tested for the presence of treponemal DNA. Standard serological tests showed that 197 patients were syphilis-seropositive and 97 patients were syphilis-seronegative. In each sample, PCR tests for polA (TP0105), tmpC (TP0319), TP0136, TP0548 and 23S rRNA genes were performed. Samples taken from 91 patients were PCR-positive. Molecular typing of treponemal DNA was based on the sequencing of TP0136, TP0548 and 23S rRNA genes. Treponemal DNA was typeable in samples taken from 64 PCR-positive patients and 9 different genotypes were found. The proportion of treponemal strains resistant to macrolide antibiotics was 37.3%. In the DNA samples taken from 39 patients, a parallel treponemal typing approved by Centers for Disease Control and Prevention was performed. The variants of arp and tpr genes appear to combine independently with sequence variants of TP0136, TP0548 and 23S rRNA genes.
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Affiliation(s)
- Magdalena Flasarová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
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