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Luu LDW, Kasimov V, Phillips S, Myers GSA, Jelocnik M. Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny. Front Cell Infect Microbiol 2023; 13:1178736. [PMID: 37287464 PMCID: PMC10242142 DOI: 10.3389/fcimb.2023.1178736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023] Open
Abstract
The genus Chlamydia contains important obligate intracellular bacterial pathogens to humans and animals, including C. trachomatis and C. pneumoniae. Since 1998, when the first Chlamydia genome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge in Chlamydia genomics and how whole genome sequencing has revolutionised our understanding of Chlamydia virulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge of Chlamydia pathogenesis and future directions for chlamydial genomics.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Vasilli Kasimov
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Samuel Phillips
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Garry S. A. Myers
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Martina Jelocnik
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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Piñeiro L, Villa L, Salmerón P, Maciá MD, Otero L, Vall-Mayans M, Milagro A, Bernal S, Manzanal A, Ansa I, Cilla G. Genetic Characterization of Non- Lymphogranuloma venereum Chlamydia trachomatis Indicates Distinct Infection Transmission Networks in Spain. Int J Mol Sci 2023; 24:ijms24086941. [PMID: 37108105 PMCID: PMC10138622 DOI: 10.3390/ijms24086941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Chlamydia trachomatis infection is an important public health problem. Our objective was to assess the dynamics of the transmission of this infection, analysing the distribution of circulating ompA genotypes and multilocus sequence types of C. trachomatis in Spain as a function of clinical and epidemiological variables. During 2018 and 2019, we genetically characterized C. trachomatis in tertiary hospitals in six areas in Spain (Asturias, Barcelona, Gipuzkoa, Mallorca, Seville and Zaragoza), with a catchment population of 3.050 million people. Genotypes and sequence types were obtained using polymerase chain reaction techniques that amplify a fragment of the ompA gene, and five highly variable genes (hctB, CT058, CT144, CT172 and pbpB), respectively. Amplicons were sequenced and phylogenetic analysis was conducted. We obtained genotypes in 636/698 cases (91.1%). Overall and by area, genotype E was the most common (35%). Stratifying by sex, genotypes D and G were more common among men, and genotypes F and I among women (p < 0.05). Genotypes D, G and J were more common in men who have sex with men (MSM) than in men who have sex with women (MSW), in whom the most common genotypes were E and F. The diversity index was higher in sequence typing (0.981) than in genotyping (0.791), and the most common sequence types were ST52 and ST108 in MSM, and ST30, ST148, ST276 and ST327 in MSW. Differences in genotype distribution between geographical areas were attributable to differences in population characteristics. The transmission dynamics varied with sexual behaviour: the predominant genotypes and most frequent sequence types found in MSM were different to those detected in MSW and women.
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Affiliation(s)
- Luis Piñeiro
- Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
| | - Laura Villa
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
- Microbiology Department, Central University Hospital of Asturias, 33011 Oviedo, Spain
| | - Paula Salmerón
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
- Microbiology Department, Vall d'Hebrón University Hospital, 08035 Barcelona, Spain
| | - Maria Dolores Maciá
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
- Microbiology Department, Son Espases University Hospital, 07120 Palma de Mallorca, Spain
| | - Luis Otero
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
- Microbiology Department, Cabueñes University Hospital, 33394 Gijón, Spain
| | - Martí Vall-Mayans
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
- Vall'Hebron-Drassanes STI Unit, Infectious Diseases Department, Vall d'Hebrón University Hospital, 08035 Barcelona, Spain
| | - Ana Milagro
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
- Microbiology Department, Miguel Servet University Hospital, 50009 Zaragoza, Spain
| | - Samuel Bernal
- Sexually Transmitted Infections Study Group of the Infectious Diseases and Clinical Microbiology Spanish Society (GEITS-SEIMC), 28003 Madrid, Spain
- Infectious Diseases and Microbiology Unit, Valme University Hospital, 41014 Seville, Spain
| | - Ayla Manzanal
- Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain
| | - Iñigo Ansa
- Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain
| | - Gustavo Cilla
- Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, 20014 San Sebastian, Spain
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Zhao J, Shui J, Luo L, Ao C, Lin H, Liang Y, Wang L, Wang H, Chen H, Tang S. Identification and characterization of mixed infections of Chlamydia trachomatis via high-throughput sequencing. Front Microbiol 2022; 13:1041789. [PMID: 36439830 PMCID: PMC9687396 DOI: 10.3389/fmicb.2022.1041789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Precise genotyping is necessary to understand epidemiology and clinical manifestations of Chlamydia trachomatis infection with different genotypes. Next-generation high-throughput sequencing (NGHTS) has opened new frontiers in microbial genotyping, but has been clinically characterized in only a few settings. This study aimed to determine C. trachomatis genotypes in particular mixed-genotype infections and their association with clinical manifestations and to characterize the sensitivity and accuracy of NGHTS. Cervical specimens were collected from 8,087 subjects from physical examination center (PEC), assisted reproductive technology center (ART) and gynecology clinics (GC) of Chenzhou Hospital of China. The overall prevalence of C. trachomatis was 3.8% (311/8087) whereas a prevalence of 2.8, 3.7 and 4.8% was found in PEC, ART and GC, respectively. The most frequent three C. trachomatis genotypes were E (27.4%, 83/303), F (21.5%, 65/303) and J (18.2%, 55/303). Moreover, NGHTS identified 20 (6.6%, 20/303) mixed-genotype infections of C. trachomatis. Genotype G was more often observed in the subjects with pelvic inflammatory disease than genotype E (adjusted OR = 3.61, 95%CI, 1.02–12.8, p = 0.046). Mixed-genotype infection was associated with severe vaginal cleanliness (degree IV) with an adjusted OR of 5.17 (95%CI 1.03–25.9, p = 0.046) whereas mixed-genotype infection with large proportion of minor genotypes was associated with cervical squamous intraepithelial lesion (SIL) with an adjusted OR of 5.51 (95%CI 1.17–26.01, p = 0.031). Our results indicated that NGHTS is a feasible tool to identity C. trachomatis mixed-genotype infections, which may be associated with worse vaginal cleanliness and cervical SIL.
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Affiliation(s)
- Jianhui Zhao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jingwei Shui
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Lipei Luo
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Cailing Ao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Hongqing Lin
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuanhao Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Li Wang
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Haiying Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Hongliang Chen
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
- *Correspondence: Hongliang Chen, ; Shixing Tang,
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- *Correspondence: Hongliang Chen, ; Shixing Tang,
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Tang Y, Yang X, Duan L, Zhan W, Chen K, Chai H, Liu P, Chen M, Zhao H, Liang L, Wei M, Luo M. Genetic and clinical characteristics of genital Chlamydia trachomatis infection in Guangzhou, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105285. [PMID: 35447370 DOI: 10.1016/j.meegid.2022.105285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Genital Chlamydia trachomatis (CT) is one of the most common agents of sexually transmitted infections and can cause severe disorders. This study aimed to analyse the genetic and clinical characteristics of genital CT infection among women in Guangzhou, China. METHODS From September 2020 to August 2021, a total of 8955 female patients were enrolled in this study. The presence of genital CT was detected by real-time PCR, and 273 positive samples were randomly selected for further genetic and clinical characteristics analysis. RESULTS The positive rate of genital CT infection was 7.5% (670/8955), with the highest rate in women aged 21-30 years. A total of 8 genotypes were identified: DH, J, K, and recombinant genotype Ba/D. The predominant genotype was J (n = 78, 28.6%), followed by E (n = 63, 23.1%), F (n = 48, 17.6%), and D (n = 38, 13.9%). Abnormal vaginal discharge (n = 165, 61.8%), cervical columnar epithelial ectopy (n = 124, 46.4%), vaginal itching (n = 77, 28.8%), and lower abdominal pain (n = 61, 22.8%) were the predominant symptoms. Additionally, genotype G infection exhibited a significantly higher rate of abnormal vaginal discharge (P = 0.03) and genotype D infection exhibited a higher white blood cell count (P = 0.01) than the other genotypes. Phylogenetic analysis revealed a total of 20 variants with 25 mutation positions and the H2 variant in four patients was first discovered in our study. CONCLUSIONS Genotypes J, E, F, and D were the major genotypes of genital CT in Guangzhou, and they manifested as abnormal vaginal discharge, cervical columnar epithelial ectopy, vaginal itching, and lower abdominal pain. The present study provides guidance for future integrated interventions to reduce the burden of genital CT infection and accelerate the development of vaccines.
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Affiliation(s)
- Yuan Tang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China
| | - Xiaohan Yang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Lei Duan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China
| | - Wenli Zhan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Keyi Chen
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Huiying Chai
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Pan Liu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Minchai Chen
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Hongyu Zhao
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Lihua Liang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China
| | - Mengru Wei
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China
| | - Mingyong Luo
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, Guangzhou 511442, People's Republic of China; Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou 511442, People's Republic of China.
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Carossino M, Nevarez JG, Sakaguchi K, Paulsen DB, Langohr IM, Strother K, Ferracone J, Roy A, Crossland NA, Del Piero F. An outbreak of systemic chlamydiosis in farmed American alligators ( Alligator mississippiensis). Vet Pathol 2022; 59:860-868. [PMID: 35502797 DOI: 10.1177/03009858221095269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Chlamydia spp are reported to causes systemic disease in a variety of hosts worldwide including few reports in crocodilians. Disease presentations vary from asymptomatic to fulminant disease, some of which are zoonotic. The aim of this study was to describe the pathological, immunohistochemical, and molecular findings associated with the occurrence of a previously unreported Chlamydia sp infection causing a major mortality event in farmed American alligators (Alligator mississippiensis). The outbreak presented with sudden death in juvenile alligators mainly associated with necrotizing hepatitis and myocarditis, followed by the occurrence of conjunctivitis after the initial high mortality event. The widespread inflammatory lesions in multiple organs correlated with intralesional chlamydial organisms identified via immunohistochemistry and confirmed by 23S rRNA-specific real-time quantitative polymerase chain reaction (qPCR) for Chlamydiaceae bacteria. By sequencing and phylogenetic analysis of the OmpA gene, this uncultured Chlamydia sp grouped closely with Chlamydia poikilothermis recently described in snakes. This study highlights the significance of such outbreaks in farmed populations. Enhanced epidemiological monitoring is needed to gain further insight into the biology of Chlamydia sp in alligators, disease dynamics, risk factors, and role of carrier animals.
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Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Javier G Nevarez
- Veterinary Teaching Hospital & Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | | | - Daniel B Paulsen
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Ingeborg M Langohr
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Keith Strother
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | | | - Alma Roy
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Nicholas A Crossland
- Department of Pathology & National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA
| | - Fabio Del Piero
- Louisiana Animal Disease Diagnostic Laboratory & Department of Pathobiological Sciences, School of Veteterinary Medicine, Louisiana State University, Baton Rouge, LA
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Tufa TB, Wölfel S, Zubriková D, Víchová B, Andersson M, Rieß R, Rutaihwa L, Fuchs A, Orth HM, Häussinger D, Feldt T, Poppert S, Dobler G, Bakkes DK, Chitimia-Dobler L. Tick species from cattle in the Adama Region of Ethiopia and pathogens detected. EXPERIMENTAL & APPLIED ACAROLOGY 2021; 84:459-471. [PMID: 33909190 PMCID: PMC8190025 DOI: 10.1007/s10493-021-00623-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/21/2021] [Indexed: 06/01/2023]
Abstract
Ticks will diminish productivity among farm animals and transmit zoonotic diseases. We conducted a study to identify tick species infesting slaughter bulls from Adama City and to screen them for tick-borne pathogens. In 2016, 291 ticks were collected from 37 bulls in Adama, which were ready for slaughter. Ticks were identified morphologically. Total genomic DNA was extracted from ticks and used to test for Rickettsia spp. with real-time PCR. Species identification was done by phylogenetic analysis using sequencing that targeted the 23S-5S intergenic spacer region and ompA genes. Four tick species from two genera, Amblyomma and Rhipicephalus, were identified. Amblyomma cohaerens was the dominant species (n = 241, 82.8%), followed by Amblyomma variegatum (n = 22, 7.5%), Rhipicephalus pulchellus (n = 19, 6.5%), and Rhipicephalus decoloratus (n = 9, 3.0%). Among all ticks, 32 (11%) were positive for Rickettsia spp. and 15 (5.2%) of these were identified as R. africae comprising at least two genetic clades, occurring in A. variegatum (n = 10) and A. cohaerens (n = 5). The remainder of Rickettsia-positive samples could not be amplified due to low DNA yield. Furthermore, another 15 (5.2%) samples carried other pathogenic bacteria: Ehrlichia ruminantium (n = 9; 3.1%) in A. cohaerens, Ehrlichia sp. (n = 3; 1%) in Rh. pulchellus and A. cohaerens, Anaplasma sp. (n = 1; 0.5%) in A. cohaerens, and Neoehrlichia mikurensis (n = 2; 0.7%) in A. cohaerens. All ticks were negative for Bartonella spp., Babesia spp., Theileria spp., and Hepatozoon spp. We reported for the first time E. ruminatium, N. mikurensis, Ehrlichia sp., and Anaplasma sp. in A. cohaerens. Medically and veterinarily important pathogens were mostly detected from A. variegatum and A. cohaerens. These data are relevant for a One-health approach for monitoring and prevention of tick-borne disease transmission.
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Affiliation(s)
- Tafese Beyene Tufa
- College of Health Science, Arsi University, Asella, Ethiopia.
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University, Düsseldorf, Germany.
| | - Silke Wölfel
- Bundeswehr Institute of Microbiology, Munich, Germany
- Amedes MVZ for Laboratory Medicine and Microbiology, Fürstenfeldbruck, Germany
| | - Dana Zubriková
- Institute of Parasitology, Slovak Academy of Sciences, Kosice, Slovakia
| | | | | | - Ramona Rieß
- Bundeswehr Institute of Microbiology, Munich, Germany
| | | | - André Fuchs
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University, Düsseldorf, Germany
| | - Hans Martin Orth
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University, Düsseldorf, Germany
| | - Dieter Häussinger
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University, Düsseldorf, Germany
| | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University, Düsseldorf, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University Basel, Basel, Switzerland
| | | | - Deon K Bakkes
- Gertrud Theiler Tick Museum, Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria, South Africa
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
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Neves JM, Ramos Pinheiro R, Côrte-Real R, Borrego MJ, Rodrigues A, Fernandes C. Lymphogranuloma venereum: a retrospective analysis of an emerging sexually transmitted disease in a Lisbon Tertiary Center. J Eur Acad Dermatol Venereol 2021; 35:1712-1716. [PMID: 33896044 DOI: 10.1111/jdv.17302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/08/2021] [Accepted: 04/02/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND Lymphogranuloma venereum (LGV) is a sexual transmitted infection (STI), currently endemic within the population of men who have sex with men (MSM) of Western Countries. L2B variant has been reported as the predominant strain in the current LGV epidemics, although a shift towards L2-434 has been observed in some European countries. OBJECTIVES To evaluate and characterize the population with LGV infection diagnosed in Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal. METHODS A retrospective analysis of all LGV diagnoses between 2016 and 2019 was performed. The diagnosis was established through ompA-genotyping of samples yielding a positive result to Chlamydia trachomatis (CT). All considered samples were retrieved from the clinician activity, through swabbing and urine analysis and CT infection diagnosis was obtained using real-time PCR. RESULTS During the period studied 16 279 CT diagnostics tests were employed, with a striking increase from 2016 (n = 467) to 2019 (n = 9362). A total of 1602 diagnoses of CT were established, from which 168 (10.5%) corresponded to LGV, with both infections showing a rising evolution, between 2016 and 2019, of 2.9 and 2.7 times, respectively. The majority of the LGV strains were genotyped as L2/434 (67.3%; n = 113). LGV predominantly affected MSM and men who have sex with men and women (97.0%; n = 163). Anorectal infection was the most prevalent one (90.5%; n = 152), being proctitis the main clinical presentation (76.2%; n = 128). Absence of symptoms was reported in almost 15% of the cases (n = 24). The presence of concomitant infection with human immunodeficiency virus was dominant (73.2%; n = 123) and the prevalence of one or more STI co-infections was about 60.1% (n = 99). CONCLUSIONS An increasing evolution of CT and LGV testing and diagnosing was observable throughout the studied period. Characteristics of the population are similar with those described within LGV epidemics. In accordance with recent European studies, predominance towards L2 genotype was identified.
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Affiliation(s)
- J M Neves
- Dermatology Department, Hospital Santo António dos Capuchos, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - R Ramos Pinheiro
- Dermatology Department, Hospital Santo António dos Capuchos, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - R Côrte-Real
- Laboratory of Molecular Biology, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - M J Borrego
- National Health Institute Dr. Ricardo Jorge, Lisbon, Portugal
| | - A Rodrigues
- Dermatology Department, Hospital Santo António dos Capuchos, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - C Fernandes
- Dermatology Department, Hospital Santo António dos Capuchos, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
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Dimond ZE, Hefty PS. Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors. Pathog Dis 2020; 79:5868767. [PMID: 32639528 DOI: 10.1093/femspd/ftaa035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Chlamydia suis, a ubiquitous swine pathogen, has the potential for zoonotic transmission to humans and often encodes for resistance to the primary treatment antibiotic, tetracycline. Because of this emerging threat, comparative genomics for swine isolate R19 with inter- and intra-species genomes was performed. A 1.094 Mb genome was determined through de novo assembly of Illumina high throughput sequencing reads. Annotation and subsystem analyses were conducted, revealing 986 putative genes (Chls_###) that are predominantly orthologs to other known Chlamydia genes. Subsequent comparative genomics revealed a high level of genomic synteny and overall sequence identity with other Chlamydia while 92 unique C. suis open reading frames were annotated. Direct comparison of Chlamydia-specific gene families that included the plasticity zone, inclusion membrane proteins, polymorphic membrane proteins and the major outer membrane protein, demonstrated high gene content identity with C. trachomatis and C. muridarum. These comparisons also identified diverse components that potentially could contribute to host-specificity. This study constitutes the first genome-wide comparative analysis for C. suis, generating a fully annotated reference genome. These studies will enable focused efforts on factors that provide key species specificity and adaptation to cognate hosts that are attributed to chlamydial infections, including humans.
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Affiliation(s)
- Zoe E Dimond
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave. Lawrence KS 66044
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave. Lawrence KS 66044
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9
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Borges V, Cordeiro D, Salas AI, Lodhia Z, Correia C, Isidro J, Fernandes C, Rodrigues AM, Azevedo J, Alves J, Roxo J, Rocha M, Côrte-Real R, Vieira L, Borrego MJ, Gomes JP. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microb Genom 2020; 5. [PMID: 31697227 PMCID: PMC6927300 DOI: 10.1099/mgen.0.000313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Dora Cordeiro
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Ana Isabel Salas
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Zohra Lodhia
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Cristina Correia
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Cândida Fernandes
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Ana Maria Rodrigues
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Jacinta Azevedo
- Sexually Transmitted Diseases Clinic, Lapa Health Centre, Lisbon, Portugal
| | - João Alves
- Sexually Transmitted Diseases Clinic, Lapa Health Centre, Lisbon, Portugal
| | - João Roxo
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisboa, Portugal
| | - Miguel Rocha
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisboa, Portugal
| | - Rita Côrte-Real
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Maria José Borrego
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
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10
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Kumar S, Caimano MJ, Anand A, Dey A, Hawley KL, LeDoyt ME, La Vake CJ, Cruz AR, Ramirez LG, Paštěková L, Bezsonova I, Šmajs D, Salazar JC, Radolf JD. Sequence Variation of Rare Outer Membrane Protein β-Barrel Domains in Clinical Strains Provides Insights into the Evolution of Treponema pallidum subsp. pallidum, the Syphilis Spirochete. mBio 2018; 9:e01006-18. [PMID: 29895642 PMCID: PMC6016234 DOI: 10.1128/mbio.01006-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 02/07/2023] Open
Abstract
In recent years, considerable progress has been made in topologically and functionally characterizing integral outer membrane proteins (OMPs) of Treponema pallidum subspecies pallidum, the syphilis spirochete, and identifying its surface-exposed β-barrel domains. Extracellular loops in OMPs of Gram-negative bacteria are known to be highly variable. We examined the sequence diversity of β-barrel-encoding regions of tprC, tprD, and bamA in 31 specimens from Cali, Colombia; San Francisco, California; and the Czech Republic and compared them to allelic variants in the 41 reference genomes in the NCBI database. To establish a phylogenetic framework, we used T. pallidum 0548 (tp0548) genotyping and tp0558 sequences to assign strains to the Nichols or SS14 clades. We found that (i) β-barrels in clinical strains could be grouped according to allelic variants in T. pallidum subsp. pallidum reference genomes; (ii) for all three OMP loci, clinical strains within the Nichols or SS14 clades often harbored β-barrel variants that differed from the Nichols and SS14 reference strains; and (iii) OMP variable regions often reside in predicted extracellular loops containing B-cell epitopes. On the basis of structural models, nonconservative amino acid substitutions in predicted transmembrane β-strands of T. pallidum repeat C (TprC) and TprD2 could give rise to functional differences in their porin channels. OMP profiles of some clinical strains were mosaics of different reference strains and did not correlate with results from enhanced molecular typing. Our observations suggest that human host selection pressures drive T. pallidum subsp. pallidum OMP diversity and that genetic exchange contributes to the evolutionary biology of T. pallidum subsp. pallidum They also set the stage for topology-based analysis of antibody responses to OMPs and help frame strategies for syphilis vaccine development.IMPORTANCE Despite recent progress characterizing outer membrane proteins (OMPs) of Treponema pallidum, little is known about how their surface-exposed, β-barrel-forming domains vary among strains circulating within high-risk populations. In this study, sequences for the β-barrel-encoding regions of three OMP loci, tprC, tprD, and bamA, in T. pallidum subsp. pallidum isolates from a large number of patient specimens from geographically disparate sites were examined. Structural models predict that sequence variation within β-barrel domains occurs predominantly within predicted extracellular loops. Amino acid substitutions in predicted transmembrane strands that could potentially affect porin channel function were also noted. Our findings suggest that selection pressures exerted within human populations drive T. pallidum subsp. pallidum OMP diversity and that recombination at OMP loci contributes to the evolutionary biology of syphilis spirochetes. These results also set the stage for topology-based analysis of antibody responses that promote clearance of T. pallidum subsp. pallidum and frame strategies for vaccine development based upon conserved OMP extracellular loops.
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Affiliation(s)
- Sanjiv Kumar
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Melissa J Caimano
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Arvind Anand
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Abhishek Dey
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Kelly L Hawley
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Pediatric Infectious Diseases, Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - Morgan E LeDoyt
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Carson J La Vake
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
| | - Adriana R Cruz
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
| | - Lady G Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
| | - Lenka Paštěková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Juan C Salazar
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Pediatric Infectious Diseases, Connecticut Children's Medical Center, Hartford, Connecticut, USA
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Justin D Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
- Department of Genetic and Genome Sciences, UConn Health, Farmington, Connecticut, USA
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11
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Madden D, Whaite A, Jones E, Belov K, Timms P, Polkinghorne A. Koala immunology and infectious diseases: How much can the koala bear? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 82:177-185. [PMID: 29382557 DOI: 10.1016/j.dci.2018.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/24/2018] [Accepted: 01/24/2018] [Indexed: 06/07/2023]
Abstract
Infectious diseases are contributing to the decline of the iconic Australian marsupial, the koala (Phascolarctos cinereus). Infections with the obligate intracellular bacteria, Chlamydia pecorum, cause debilitating ocular and urogenital-tract disease while the koala-retrovirus (KoRV) has been implicated in host immunosuppression and exacerbation of chlamydial pathogenesis. Although histological studies have provided insight into the basic architecture of koala immune tissues, our understanding of the koala immune response to infectious disease has been limited, until recently, by a lack of species-specific immune reagents. Recent advances in the characterisation of key immune genes have focused on advancing our understanding of the immune response to Chlamydia infection, revealing commonalities in disease pathologies and immunity between koalas and other hosts and paving the way for the development of a koala Chlamydia vaccine. This review summarises these recent findings and highlights key aspects of the koala immune system requiring further attention with particular regard to their most prominent infectious diseases.
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Affiliation(s)
- Danielle Madden
- Animal Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs 4556, Australia.
| | - Alessandra Whaite
- Animal Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs 4556, Australia.
| | - Elizabeth Jones
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, NSW 2006, Australia.
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, NSW 2006, Australia.
| | - Peter Timms
- Animal Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs 4556, Australia.
| | - Adam Polkinghorne
- Animal Research Centre, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs 4556, Australia.
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12
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Urogenital Chlamydia trachomatis multilocus sequence types and genovar distribution in chlamydia infected patients in a multi-ethnic region of Saratov, Russia. PLoS One 2018; 13:e0195386. [PMID: 29641543 PMCID: PMC5895025 DOI: 10.1371/journal.pone.0195386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
Background This is the first report to characterize the prevalence and genovar distribution of genital chlamydial infections among random heterosexual patients in the multi-ethnic Saratov Region, located in Southeast Russia. Methods Sixty-one clinical samples (cervical or urethral swabs) collected from a random cohort of 856 patients (7.1%) were C. trachomatis (CT) positive in commercial nucleic acid amplification tests (NAATs) and duplex TaqMan PCRs. Results Sequence analysis of the VDII region of the ompA gene revealed seven genovars of C. trachomatis in PCR-positive patients. The overall genovars were distributed as E (41.9%), G (21.6%), F (13.5%), K (9.5%), D (6.8%), J (4.1%), and H (2.7%). CT-positive samples were from males (n = 12, 19.7%), females (n = 42, 68.8%), and anonymous (n = 7, 11.5%) patients, with an age range of 19 to 45 years (average 26.4), including 12 different ethnic groups representative of this region. Most patients were infected with a single genovar (82%), while 18% were co-infected with either two or three genovars. The 1156 bp-fragment of the ompA gene was sequenced in 46 samples to determine single nucleotide polymorphisms (SNP) among isolates. SNP-based subtyping and phylogenetic reconstruction revealed the presence of 13 variants of the ompA gene, such as E (E1, E2, E6), G (G1, G2, G3, G5), F1, K, D (D1, Da2), J1, and H2. Differing genovar distribution was identified among urban (E>G>F) and rural (E>K) populations, and in Slavic (E>G>D) and non-Slavic (E>G>K) ethnic groups. Multilocus sequence typing (MLST) determined five sequences types (STs), such as ST4 (56%, 95% confidence interval, CI, 70.0 to 41.3), ST6 (10%, 95% CI 21.8 to 3.3), ST9 (22%, 95% CI 35.9 to 11.5), ST10 (2%, 95% CI 10.7 to 0.05) and ST38 (10%, 95% CI 21.8 to 3.3). Thus, the most common STs were ST4 and ST9. Conclusion C. trachomatis is a significant cause of morbidity among random heterosexual patients with genital chlamydial infections in the Saratov Region. Further studies should extend this investigation by describing trends in a larger population, both inside and outside of the Saratov Region to clarify some aspects for the actual application of C. trachomatis genotype analysis for disease control.
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13
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Piñeiro L, Isaksson J, Zapico M, Cilla G, Herrmann B. Chlamydia trachomatis genotypes A and B from urogenital specimens of patients in Spain: molecular characterization. Clin Microbiol Infect 2018; 24:910.e5-910.e8. [PMID: 29427803 DOI: 10.1016/j.cmi.2018.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/11/2018] [Accepted: 01/23/2018] [Indexed: 01/10/2023]
Abstract
OBJECTIVES Chlamydia trachomatis ompA genotypes A and B, primarily associated with trachoma, were unexpectedly detected in urogenital samples of patients in Spain, a trachoma-free country. In this study, we aimed to explain this finding using analysis of organotropism-related genes and a multilocus sequence typing (MLST) technique. METHODS C. trachomatis genotypes A or B were detected in 8/930 (0.9%) infection episodes between 2006 and 2012. In these strains, organotropism-related genes (polymorphic membrane protein gene H, tryptophan synthase gene A, CTA0934, and cytotoxin) were studied. Further, the strains were analysed by MLST, using a polymerase chain reaction that amplifies five highly variable genomic loci (hctB, CT058, CT144, CT172, and pbpB). Amplicons were sequenced and phylogenetic analysis was conducted. RESULTS Seven strains were detected in the eight infection episodes (in one patient, an identical strain being found in two episodes). Analysis of organotropism-related genes showed that these strains shared genetic features characteristic of genitotropic genotypes but not of trachoma strains. Three strains of genotype A showed a unique and new MLST-sequence type (ST551, allele profile 8-8-2-27-69). The four strains of genotype B belonged to ST138. CONCLUSIONS C. trachomatis ompA genotypes A and B associated with trachoma, but detected sporadically in urogenital samples in trachoma-free countries, may be the result of recombination between strains adapted to trachoma and strains adapted to sexual transmission.
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Affiliation(s)
- L Piñeiro
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain.
| | - J Isaksson
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - M Zapico
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
| | - G Cilla
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain; Biomedical Research Centre Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - B Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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14
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Gharsallah H, Frikha-Gargouri O, Bom RJ, Hammami A, Bruisten SM. Comparison of reverse hybridization and ompA sequencing methods applied on Chlamydia trachomatis strains from Tunisia. Microbiologyopen 2017; 7:e00549. [PMID: 29282889 PMCID: PMC5911986 DOI: 10.1002/mbo3.549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/22/2017] [Accepted: 09/04/2017] [Indexed: 12/14/2022] Open
Abstract
Two techniques based on ompA amplification of Chlamydia trachomatis were compared, being reverse hybridization (RHM) and ompA sequencing (OSA), to investigate the concordance between them and to study the epidemiological relevance of each method. In addition, phylogenetic analysis was performed on the ompA sequences. One hundred and seven C. trachomatis positive samples from Tunisian patients and female sex workers were analyzed using both the RHM and ompA sequencing. The overall genovar distribution obtained with both techniques was very similar. The RHM identified nine genovars, being B, D, E, F, G, H, I, J and K, where B, I, J, and K were only found in mixed infections versus 7 types for the OSA being D, E, F, G, H, I, and K. The agreement between both typing techniques was 87.8%. Both methods showed that genovar E was the most predominant type. In 24.3% of the analyzed samples, mixed infections were detected. In 96.1% of these, the genovar identified by OSA was also detected using the RHM. OmpA sequencing allowed determination of six genovar types that could not be typed using RHM. The analyses of ompA nucleotide variation in the 107 clinical specimens detected ompA genovar variants with distinct ompA mutational patterns for types D2, G1, G2, and H1. In conclusion, RHM and OSA showed a high agreement in C. trachomatis genotyping results with each having their specific benefits.
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Affiliation(s)
- Houda Gharsallah
- Department of Microbiology and research laboratory "Microorganismes et Pathologies Humaines", Habib Bourguiba university hospital, Medical School of Sfax, University of Sfax, Sfax, Tunisia
| | - Olfa Frikha-Gargouri
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Reinier J Bom
- Public Health Laboratory, The Netherlands Condomerie, Cluster Infectious Diseases, Public Health Service Amsterdam, Amsterdam, The Netherlands
| | - Adnene Hammami
- Department of Microbiology and research laboratory "Microorganismes et Pathologies Humaines", Habib Bourguiba university hospital, Medical School of Sfax, University of Sfax, Sfax, Tunisia
| | - Sylvia M Bruisten
- Public Health Laboratory, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, the Netherlands
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15
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Pickering H, Teng A, Faal N, Joof H, Makalo P, Cassama E, Nabicassa M, Last AR, Burr SE, Rowland-Jones SL, Thomson NR, Roberts CH, Mabey DCW, Bailey RL, Hayward RD, de la Maza LM, Holland MJ. Genome-wide profiling of humoral immunity and pathogen genes under selection identifies immune evasion tactics of Chlamydia trachomatis during ocular infection. Sci Rep 2017; 7:9634. [PMID: 28851925 PMCID: PMC5575166 DOI: 10.1038/s41598-017-09193-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022] Open
Abstract
The frequency and duration of Chlamydia trachomatis (Ct) ocular infections decrease with age, suggesting development of partial immunity. However, there is a lack of clear correlates of immunity to Ct infection in humans. We screened sera from a cohort of Gambian children followed for six-months against a Ct-proteome microarray. At genome sequence level, we detected signatures of selection from a population of ocular Ct isolates from Guinea-Bissau. Together these approaches allowed us to highlight the focus of humoral responses and hypothesise new modes of pathogen immune evasion. Children who were susceptible to frequent and/or prolonged Ct infection had a less focussed antibody response, including preferential recognition of forty-two antigens. There was evidence of positive and purifying selection across the genome, but little balancing selection. In contrast, most antigens that were associated with susceptibility were under neutral selection. These data suggest an evasion strategy in which Ct presents a large panel of irrelevant antigens to the immune system to block or misdirect protective responses. Development of a focused immune response, possibly induced through vaccination, may be an effective strategy to promote protection to Ct infection.
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Affiliation(s)
- Harry Pickering
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.
| | - Andy Teng
- ImmPORT Therapeutics, Inc./Antigen Discovery Inc., 1 Technology Dr., Suite E309, Irvine, CA, 92618, United States
| | - Nkoyo Faal
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Hassan Joof
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Pateh Makalo
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Eunice Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - Meno Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - Anna R Last
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Sarah E Burr
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.,Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Sarah L Rowland-Jones
- Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
| | - Nicholas R Thomson
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.,Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Chrissy H Roberts
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - David C W Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Robin L Bailey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | - Richard D Hayward
- Institute of Structural and Molecular Biology, Birkbeck & University College London, Malet Street, London, WC1E 7HX, United Kingdom
| | - Luis M de la Maza
- Department of Pathology and Laboratory Medicine, Medical Sciences I, Room D440, University of California, Irvine, CA, 92697-4800, United States
| | - Martin J Holland
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.,Disease Control and Elimination Theme, Medical Research Council The Gambia Unit, Fajara, Banjul, The Gambia
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16
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Ferreira R, Borges V, Borrego MJ, Gomes JP. Global survey of mRNA levels and decay rates of Chlamydia trachomatis trachoma and lymphogranuloma venereum biovars. Heliyon 2017; 3:e00364. [PMID: 28795162 PMCID: PMC5541142 DOI: 10.1016/j.heliyon.2017.e00364] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/18/2017] [Indexed: 12/15/2022] Open
Abstract
Interpreting the intricate bacterial transcriptomics implies understanding the dynamic relationship established between de novo transcription and the degradation of transcripts. Here, we performed a comparative overview of gene expression levels and mRNA decay rates for different-biovar (trachoma and lymphogranuloma venereum) strains of the obligate intracellular bacterium Chlamydia trachomatis. By using RNA-sequencing to measure gene expression levels at mid developmental stage and mRNA decay rates upon rifampicin-based transcription blockage, we observed that: i) 60-70% of the top-50 expressed genes encode proteins with unknown function and proteins involved in "Translation, ribosomal structure and biogenesis" for all strains; ii) the expression ranking by genes' functional categories was in general concordant among different-biovar strains; iii) the median of the half-life time (t1/2) values of transcripts were 15-17 min, indicating that the degree of transcripts' stability seems to correlate with the bacterial intracellular life-style, as these values are considerably higher than the ones observed in other studies for facultative intracellular and free-living bacteria; iv) transcript decay rates were highly heterogeneous within each C. trachomatis strain and did not correlate with steady-state expression levels; v) only at very few instances (essentially at gene functional category level) was possible to unveil dissimilarities potentially underlying phenotypic differences between biovars. In summary, the unveiled transcriptomic scenario, marked by a general lack of correlation between transcript production and degradation and a huge inter-transcript heterogeneity in decay rates, likely reflects the challenges underlying the unique biphasic developmental cycle of C. trachomatis and its intricate interactions with the human host, which probably exacerbate the complexity of the bacterial transcription regulation.
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Affiliation(s)
- Rita Ferreira
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Vítor Borges
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.,Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Maria José Borrego
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal.,Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
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Frati ER, Fasoli E, Martinelli M, Colzani D, Bianchi S, Carnelli L, Amendola A, Olivani P, Tanzi E. Sexually Transmitted Infections: A Novel Screening Strategy for Improving Women's Health in Vulnerable Populations. Int J Mol Sci 2017. [PMID: 28632191 PMCID: PMC5486132 DOI: 10.3390/ijms18061311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background: Migrant women are one of the most vulnerable population to health problems and well-being. This study aimed at implementing a counseling and preventive strategy for sexually transmitted infections (STIs) in undocumented migrant women in Milan, Italy. Methods: Women (ages 18–65) were enrolled at the NAGA Centre (2012–2013) and asked for a urine sample in order to carry out molecular detection of Human papillomavirus (HPV), Chlamydia trachomatis (Ct), Trichomonas vaginalis (Tv), Neisseria gonorrhoeae (Ng)-DNA. Socio-demographic and sexual behavior information were collected. All HPV/Ct+ women were offered Pap tests and/or were prescribed antibiotic treatment. Results: 537/757 women participated in the study (acceptability rate: 70.9%). Most of the women were from Latin America (45.6%) and Eastern Europe (30.7%); >60% of them had stable partners, did not use contraception and had had at least one pregnancy. The prevalence rates of HPV, Ct, Tv and Ng infections were 24.2%, 7.8%, 4.8% and 0%, respectively. In all, 43.2% of the positive women agreed to undergo a gynecological examination and accepted suitable treatment. Conclusions: This study shows an overall high prevalence of STIs in undocumented migrant women in Milan. The screening strategy based on counseling and urine testing contributed to the successfully high acceptability rate. More appropriate health services that adequately address all aspects of women’s health are required.
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Affiliation(s)
- Elena R Frati
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
| | - Ester Fasoli
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
| | - Marianna Martinelli
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
| | - Daniela Colzani
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
| | - Silvia Bianchi
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
| | - Luciana Carnelli
- Lega Italiana per la Lotta contro i Tumori (LILT), Section of Milan, Viale Molise 5, 20137 Milan, Italy.
| | - Antonella Amendola
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
- Coordinated Research Center "EpiSoMI", University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
- CIRI-IV, Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16100 Genoa, Italy.
| | - Pierfranco Olivani
- NAGA Centre, Associazione Volontaria di Assistenza Socio-Sanitaria e per i Diritti di Cittadini Stranieri, Rom e Sinti, Via L. L. Zamenhof 7/A, 20136 Milan, Italy.
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for Health, University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
- Coordinated Research Center "EpiSoMI", University of Milan, Via C. Pascal 36, 20133 Milan, Italy.
- CIRI-IV, Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16100 Genoa, Italy.
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Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits. mSystems 2017; 2:mSystems00001-17. [PMID: 28293680 PMCID: PMC5347184 DOI: 10.1128/msystems.00001-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/30/2017] [Indexed: 01/30/2023] Open
Abstract
Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.
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BIANCHI S, FRATI E, CANUTI M, COLZANI D, FASOLI E, AMENDOLA A, TANZI E. Molecular epidemiology and genotyping of Chlamydia trachomatis infection in a cohort of young asymptomatic sexually active women (18-25 years) in Milan, Italy. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2016; 57:E128-E134. [PMID: 27980376 PMCID: PMC5139607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Chlamydia trachomatis (Ct) is the most common bacterial cause of sexually transmitted infections (STI) and is associated with severe long-term sequelae in female populations. In Italy Ct infections are not submitted to a screening programme, and its epidemiological profile is understudied. Even scarcer information is available about the genetic diversity on ompA gene, whose sequence defines 18 different genovars. This study aims at evaluating the prevalence of Ct infection in young sexually active asymptomatic women aged 18-25, and characterizing the molecular epidemiology of the different circulating genovars in this population. METHODS Cervical samples collected from 909 sexually-activeyoung women (mean age 21.5 years) were analyzed through molecular assay for the detection of Ct infection. Phylogenetic analysis on the ompA gene was performed on Ct positive samples to identify the circulating genovars. RESULTS The overall prevalence of Ct-infection was 4.4% (95%CI: 3.2-5.9%): 5.3% among women aged 18-21 years and 3.5% among those aged 22-25 years. Phylogenetic analysis has identified 5 different genovars: D, E, F, G, and H. The most common genovar was the E (46%), followed by genovar F and G (18.9% each), D (13.5%), and H (2.7%). CONCLUSIONS This study underlines the high prevalence of asymptomatic Ct-infections among young women. Overall, about half of the asymptomatic infections is sustained by genovar E. The introduction in Italy of a systematic screening program should be considered to allow a better understanding of Ct spreading and providing women with an opportunity for early treatment to protect their sexual and reproductive health.
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Affiliation(s)
- S. BIANCHI
- Department of Biomedical Sciences for Health, University of Milan, Italy;,Correspondence: Silvia Bianchi, Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal 36, 20133 Milan, Italy - Tel. +39 02 50315122 - Fax +39 02 50315120 -
| | - E.R. FRATI
- Department of Biomedical Sciences for Health, University of Milan, Italy
| | - M. CANUTI
- Department of Biology, Memorial University of Newfoundland, Canada
| | - D. COLZANI
- Department of Biomedical Sciences for Health, University of Milan, Italy
| | - E. FASOLI
- Department of Biomedical Sciences for Health, University of Milan, Italy
| | - A. AMENDOLA
- Department of Biomedical Sciences for Health, University of Milan, Italy;, CIRI-IT, Department of Health Sciences, University of Genoa, Italy;, Coordinated Research Center "EpiSoMI", University of Milan, Italy
| | - E. TANZI
- Department of Biomedical Sciences for Health, University of Milan, Italy;, CIRI-IT, Department of Health Sciences, University of Genoa, Italy;, Coordinated Research Center "EpiSoMI", University of Milan, Italy
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Stenkova AM, Bystritskaya EP, Guzev KV, Rakin AV, Isaeva MP. Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC). Evol Bioinform Online 2016; 12:185-91. [PMID: 27578962 PMCID: PMC4993215 DOI: 10.4137/ebo.s40346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 01/06/2023] Open
Abstract
The genus Yersinia includes species with a wide range of eukaryotic hosts (from fish, insects, and plants to mammals and humans). One of the major outer membrane proteins, the porin OmpC, is preferentially expressed in the host gut, where osmotic pressure, temperature, and the concentrations of nutrients and toxic products are relatively high. We consider here the molecular evolution and phylogeny of Yersinia ompC. The maximum likelihood gene tree reflects the macroevolution processes occurring within the genus Yersinia. Positive selection and horizontal gene transfer are the key factors of ompC diversification, and intraspecies recombination was revealed in two Yersinia species. The impact of recombination on ompC evolution was different from that of another major porin gene, ompF, possibly due to the emergence of additional functions and conservation of the basic transport function. The predicted antigenic determinants of OmpC were located in rapidly evolving regions, which may indicate the evolutionary mechanisms of Yersinia adaptation to the host immune system.
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Affiliation(s)
- Anna M. Stenkova
- Far Eastern Federal University, Vladivostok, Russia
- Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia
| | - Evgeniya P. Bystritskaya
- Far Eastern Federal University, Vladivostok, Russia
- Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia
| | | | - Alexander V. Rakin
- Max von Pettenkofer Institute for Hygiene and Clinical Microbiology, Ludwig Maximilian University, Munich, Germany
| | - Marina P. Isaeva
- Far Eastern Federal University, Vladivostok, Russia
- Pacific Institute of Bioorganic Chemistry, Vladivostok, Russia
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Li X, Zhang S, Liang Q, Wang M, Hu A, Li X, Yang B, Zhang M, Wang N, Lu X. Molecular characteristics of the ompA gene of serotype B Chlamydia trachomatis in Qinghai Tibetan primary school students. SCIENCE CHINA-LIFE SCIENCES 2016; 59:561-70. [PMID: 27225260 DOI: 10.1007/s11427-016-5059-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 04/15/2016] [Indexed: 11/30/2022]
Abstract
To study the molecular characteristics of Chlamydia trachomatis, the major outer membrane protein gene (ompA) of C. trachomatis from primary school students with trachoma residing in the Qinghai Tibetan area was sequenced and compared with the same serotype in GenBank. In Jianshetang Primary School and Galeng Central Primary School in the Galeng Tibetan Township of Qinghai Haidong Sala Autonomous County, scraped samples were collected from the upper tarsal conjunctiva and lower conjunctival sac of both eyes of 45 students with trachoma, stored at 4°C, and transported to Beijing Tongren Hospital by air within 24 h. The samples were screened for C. trachomatis by real-time PCR. The ompA gene from the C. trachomatis-positive samples was amplified by nested PCR. The serotype was confirmed by National Center for Biotechnology Information (NCBI) BLAST search and homology analysis. The entire ompA gene sequence was compared with the corresponding gene sequences of serotype B strains available in GenBank. Of the 45 students aged 6-13 years with trachoma, 26 C. trachomatis-positive students were identified by the initial real-time PCR screening (average age, (9.09±1.63) years; sex ratio, 1.0), accounting for 57.78% (26/45). The cycle threshold values for real-time PCR were 16.79-37.77. Half (13/26) of C. trachomatis-positive students had a bacterial copy number of >10(5). The compliance rate of the ompA gene sequences with the C. trachomatis serotype B strains in GenBank was up to 99%. Two novel genetic mutations were found when the ompA gene was compared with those of the 11 serotype B strains in GenBank. The two non-synonymous mutations were located at (i) position 271 in the second constant domain, an adenine (A) to guanine (G) substitution (ACT→GCT), changing the amino acid at position 91 from threonine to alanine (Thr→Ala) in all 26 strains; and (ii) position 887 in the fourth variable domain, a cytosine (C) to thymine (T) substitution (GCA→GTA), changing the amino acid at residue 296 from alanine to valine (Ala→Val) in four of the 26 strains. Six mutations were identified relative to ATCC VR-573. The strains could be divided into two gene clusters according to the mutation at nucleotide position 887: CQZ-1 (China Qinghai Tibetan-1) and CQZ-2 (China Qinghai Tibetan-2). We thus detected two novel serotype B mutant strains of C. trachomatis among study subjects with trachoma.
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Affiliation(s)
- Xue Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Shaoya Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Qingfeng Liang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
| | - Mei Wang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Ailian Hu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
| | - Xiuyuan Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Benshan Yang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Mingxin Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Ningli Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
| | - Xinxin Lu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
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Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors. PLoS One 2015. [PMID: 26207372 PMCID: PMC4514472 DOI: 10.1371/journal.pone.0133420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Research on the obligate intracellular bacterium Chlamydia trachomatis demands culture in cell-lines, but the adaptive process behind the in vivo to in vitro transition is not understood. We assessed the genomic and transcriptomic dynamics underlying C. trachomatis in vitro adaptation of strains representing the three disease groups (ocular, epithelial-genital and lymphogranuloma venereum) propagated in epithelial cells over multiple passages. We found genetic features potentially underlying phase variation mechanisms mediating the regulation of a lipid A biosynthesis enzyme (CT533/LpxC), and the functionality of the cytotoxin (CT166) through an ON/OFF mechanism. We detected inactivating mutations in CT713/porB, a scenario suggesting metabolic adaptation to the available carbon source. CT135 was inactivated in a tropism-specific manner, with CT135-negative clones emerging for all epithelial-genital populations (but not for LGV and ocular populations) and rapidly increasing in frequency (~23% mutants per 10 passages). RNA-sequencing analyses revealed that a deletion event involving CT135 impacted the expression of multiple virulence factors, namely effectors known to play a role in the C. trachomatis host-cell invasion or subversion (e.g., CT456/Tarp, CT694, CT875/TepP and CT868/ChlaDub1). This reflects a scenario of attenuation of C. trachomatis virulence in vitro, which may take place independently or in a cumulative fashion with the also observed down-regulation of plasmid-related virulence factors. This issue may be relevant on behalf of the recent advances in Chlamydia mutagenesis and transformation where culture propagation for selecting mutants/transformants is mandatory. Finally, there was an increase in the growth rate for all strains, reflecting gradual fitness enhancement over time. In general, these data shed light on the adaptive process underlying the C. trachomatis in vivo to in vitro transition, and indicates that it would be prudent to restrict culture propagation to minimal passages and check the status of the CT135 genotype in order to avoid the selection of CT135-negative mutants, likely originating less virulent strains.
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Defining species-specific immunodominant B cell epitopes for molecular serology of Chlamydia species. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2015; 22:539-52. [PMID: 25761461 DOI: 10.1128/cvi.00102-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/09/2015] [Indexed: 11/20/2022]
Abstract
Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens.
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Borges V, Gomes JP. Deep comparative genomics among Chlamydia trachomatis lymphogranuloma venereum isolates highlights genes potentially involved in pathoadaptation. INFECTION GENETICS AND EVOLUTION 2015; 32:74-88. [PMID: 25745888 DOI: 10.1016/j.meegid.2015.02.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/23/2015] [Accepted: 02/26/2015] [Indexed: 11/19/2022]
Abstract
Lymphogranuloma venereum (LGV) is a human sexually transmitted disease caused by the obligate intracellular bacterium Chlamydia trachomatis (serovars L1-L3). LGV clinical manifestations range from severe ulcerative proctitis (anorectal syndrome), primarily caused by the epidemic L2b strains, to painful inguinal lymphadenopathy (the typical LGV bubonic form). Besides potential host-related factors, the differential disease severity and tissue tropism among LGV strains is likely a function of the genetic backbone of the strains. We aimed to characterize the genetic variability among LGV strains as strain- or serovar-specific mutations may underlie phenotypic signatures, and to investigate the mutational events that occurred throughout the pathoadaptation of the epidemic L2b lineage. By analyzing 20 previously published genomes from L1, L2, L2b and L3 strains and two new genomes from L2b strains, we detected 1497 variant sites and about 100 indels, affecting 453 genes and 144 intergenic regions, with 34 genes displaying a clear overrepresentation of nonsynonymous mutations. Effectors and/or type III secretion substrates (almost all of those described in the literature) and inclusion membrane proteins showed amino acid changes that were about fivefold more frequent than silent changes. More than 120 variant sites occurred in plasmid-regulated virulence genes, and 66% yielded amino acid changes. The identified serovar-specific variant sites revealed that the L2b-specific mutations are likely associated with higher fitness and pointed out potential targets for future highly discriminatory diagnostic/typing tests. By evaluating the evolutionary pathway beyond the L2b clonal radiation, we observed that 90.2% of the intra-L2b variant sites occurring in coding regions involve nonsynonymous mutations, where CT456/tarp has been the main target. Considering the progress on C. trachomatis genetic manipulation, this study may constitute an important contribution for prioritizing study targets for functional genomics aiming to dissect the impact of the identified intra-LGV polymorphisms on virulence or tropism dissimilarities among LGV strains.
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Affiliation(s)
- Vítor Borges
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal; Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal; Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal.
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Martínez MA, Ovalle A, Camponovo R, Vidal R. Chlamydia trachomatis genovars causing urogenital infections in Santiago, Chile. Infect Dis (Lond) 2015; 47:156-60. [PMID: 25622941 DOI: 10.3109/00365548.2014.977341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Chlamydia trachomatis is a common sexually transmitted infection in Chile, but little is known about the genovar distribution in genital infections. Thus, the objective of this study was to determine the distribution of C. trachomatis genovars in such cases. METHODS A total of 522 urogenital specimens, 403 from women and 119 from men, were analyzed for C. trachomatis by nested polymerase chain reaction (PCR) targeting of the ompA gene. Positive specimens were genotyped by DNA sequencing of the amplicons. RESULTS Sixty-two (11.9%) specimens were positive. Of these, 43 (69.4%) were collected from men and 19 (30.6%) from women (p < 0.0001). Eight genovars were identified in men and seven in women. Genovar E was the most common in both men and women, followed by genovar Da in men, and F in women. Together these three genovars accounted for 84% of infections. Genovar D was the third most common genovar (n = 4). Genovar G was detected in two samples, and sequences of genovars Ba, H, and Ja were each found in single samples. One sample (1.6%) contained mixed sequences. No association was found between gender and specific genovars. Fifty-six (92%) sequences were identical to those reported for the respective reference genovars and the other two have been described in several regions. CONCLUSIONS Our findings add to the results of most studies, which indicate that genovars E, F, and D/Da are the most frequent. No association was found between gender and specific genovars. Despite the heterogeneous population of genovars, most ompA sequences were conserved.
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Affiliation(s)
- María A Martínez
- Programa de Microbiología y Micología, Facultad de Medicina, Universidad de Chile , Santiago
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26
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Bachmann NL, Polkinghorne A, Timms P. Chlamydia genomics: providing novel insights into chlamydial biology. Trends Microbiol 2014; 22:464-72. [PMID: 24882432 DOI: 10.1016/j.tim.2014.04.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 12/12/2022]
Abstract
Chlamydiaceae are obligate intracellular pathogens that have successfully evolved to colonize a diverse range of hosts. There are currently 11 described species of Chlamydia, most of which have a significant impact on the health of humans or animals. Expanding chlamydial genome sequence information has revolutionized our understanding of chlamydial biology, including aspects of their unique lifecycle, host-pathogen interactions, and genetic differences between Chlamydia strains associated with different host and tissue tropisms. This review summarizes the major highlights of chlamydial genomics and reflects on the considerable impact these have had on understanding the biology of chlamydial pathogens and the changing nature of genomics tools in the 'post-genomics' era.
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Affiliation(s)
- Nathan L Bachmann
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia.
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Kollipara A, Polkinghorne A, Wan C, Kanyoka P, Hanger J, Loader J, Callaghan J, Bell A, Ellis W, Fitzgibbon S, Melzer A, Beagley K, Timms P. Genetic diversity of Chlamydia pecorum strains in wild koala locations across Australia and the implications for a recombinant C. pecorum major outer membrane protein based vaccine. Vet Microbiol 2013; 167:513-22. [DOI: 10.1016/j.vetmic.2013.08.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 11/29/2022]
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Abdelsamed H, Peters J, Byrne GI. Genetic variation in Chlamydia trachomatis and their hosts: impact on disease severity and tissue tropism. Future Microbiol 2013; 8:1129-1146. [PMID: 24020741 PMCID: PMC4009991 DOI: 10.2217/fmb.13.80] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chlamydia trachomatis infections are a global health problem. This obligate intracellular bacterial pathogen comprises lymphogranuloma venereum (L1-L3), ocular (A-C) and genital (D-K) serovars. Although genetically similar, each serovar group differs in disease severity and tissue tropism through mechanisms that are not well understood. It is clear that host genetic differences also play a role in chlamydial disease outcome and key host polymorphisms are beginning to emerge from both human and experimental animal studies. In this review, we will highlight pathogen and host genes that link genetic diversity, disease severity and tissue tropism. We will also use this information to provide new insights that may be helpful in developing improved management strategies for these important pathogens.
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Affiliation(s)
- Hossam Abdelsamed
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Jan Peters
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Gerald I Byrne
- Department of Microbiology, Immunology & Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Sciences Center, Memphis, TN, USA
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Nunes A, Borrego MJ, Gomes JP. Genomic features beyond Chlamydia trachomatis phenotypes: what do we think we know? INFECTION GENETICS AND EVOLUTION 2013; 16:392-400. [PMID: 23523596 DOI: 10.1016/j.meegid.2013.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/25/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
Abstract
The obligate intracellular pathogen Chlamydia trachomatis is the causative agent of the blinding trachoma and the world's leading cause of bacterial sexually transmitted infections. Despite aggressive antibacterial control measures, C. trachomatis infections have been increasing, constituting a serious public health concern due to its morbidity and socioeconomic burden. Still, very little is known about the molecular basis underlying the phenotypic disparities observed among C. trachomatis serovars in terms of tissue tropism (ocular conjunctiva, epithelial-genitalia and lymph nodes), virulence (disease outcomes) and ecological success. This is in part due to the inexistence of straightforward tools to genetically manipulate Chlamydiae and host cell-free growth systems, hampering the elucidation of the biological role of loci. The recent release of tenths of full-genome C. trachomatis sequences depict a strains clustering scenario reflecting the organ/cell-type that they preferentially infect. However, the high degree of genomic conservation implies that few genetic features are involved in phenotypic dissimilarities. The purpose of this review is to gather the most relevant data dispersed throughout the literature concerning the genotypic evidences that support niche-specific phenotypes. This review focus on chromosomal dynamics phenomena like recombination and point-mutations, essentially involving outer and inclusion membrane proteins, type III secretion effectors, and hypothetical proteins with unknown function. The scrutiny of C. trachomatis loci involved in tissue tropism, pathogenesis and ecological success is crucial for the development of disease-specific prophylaxis.
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Affiliation(s)
- Alexandra Nunes
- Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal.
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Zocevic A, Vorimore F, Marhold C, Horvatek D, Wang D, Slavec B, Prentza Z, Stavianis G, Prukner-Radovcic E, Dovc A, Siarkou VI, Laroucau K. Molecular characterization of atypical Chlamydia and evidence of their dissemination in different European and Asian chicken flocks by specific real-time PCR. Environ Microbiol 2012; 14:2212-22. [DOI: 10.1111/j.1462-2920.2012.02800.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Harris SR, Clarke IN, Seth-Smith HMB, Solomon AW, Cutcliffe LT, Marsh P, Skilton RJ, Holland MJ, Mabey D, Peeling RW, Lewis DA, Spratt BG, Unemo M, Persson K, Bjartling C, Brunham R, de Vries HJC, Morré SA, Speksnijder A, Bébéar CM, Clerc M, de Barbeyrac B, Parkhill J, Thomson NR. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet 2012; 44:413-9, S1. [PMID: 22406642 PMCID: PMC3378690 DOI: 10.1038/ng.2214] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 02/06/2012] [Indexed: 11/16/2022]
Abstract
Chlamydia trachomatis is responsible for both trachoma and sexually transmitted infections causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed whole genome phylogeny from representative strains of both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis demonstrates that predicting phylogenetic structure using the ompA gene, traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks true relationships. We show that in many instances ompA is a chimera that can be exchanged in part or whole, both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, another important diagnostic target. We have used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b.
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Affiliation(s)
- Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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Peuchant O, Le Roy C, Herrmann B, Clerc M, Bébéar C, de Barbeyrac B. MLVA subtyping of genovar E Chlamydia trachomatis individualizes the Swedish variant and anorectal isolates from men who have sex with men. PLoS One 2012; 7:e31538. [PMID: 22363667 PMCID: PMC3283677 DOI: 10.1371/journal.pone.0031538] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/12/2012] [Indexed: 01/22/2023] Open
Abstract
This study describes a new multilocus variable number tandem-repeat (VNTR) analysis (MLVA) typing system for the discrimination of Chlamydia trachomatis genovar D to K isolates or specimens. We focused our MLVA scheme on genovar E which predominates in most populations worldwide. This system does not require culture and therefore can be performed directly on DNA extracted from positive clinical specimens. Our method was based on GeneScan analysis of five VNTR loci labelled with fluorescent dyes by multiplex PCR and capillary electrophoresis. This MLVA, called MLVA-5, was applied to a collection of 220 genovar E and 94 non-E genovar C. trachomatis isolates and specimens obtained from 251 patients and resulted in 38 MLVA-5 types. The genetic stability of the MLVA-5 scheme was assessed for results obtained both in vitro by serial passage culturing and in vivo using concomitant and sequential isolates and specimens. All anorectal genovar E isolates from men who have sex with men exhibited the same MLVA-5 type, suggesting clonal spread. In the same way, we confirmed the clonal origin of the Swedish new variant of C. trachomatis. The MLVA-5 assay was compared to three other molecular typing methods, ompA gene sequencing, multilocus sequence typing (MLST) and a previous MLVA method called MLVA-3, on 43 genovar E isolates. The discriminatory index was 0.913 for MLVA-5, 0.860 for MLST and 0.622 for MLVA-3. Among all of these genotyping methods, MLVA-5 displayed the highest discriminatory power and does not require a time-consuming sequencing step. The results indicate that MLVA-5 enables high-resolution molecular epidemiological characterisation of C. trachomatis genovars D to K infections directly from specimens.
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Affiliation(s)
- Olivia Peuchant
- Université de Bordeaux, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- INRA, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- CHU de Bordeaux, Laboratoire de Bactériologie, Bordeaux, France
| | - Chloé Le Roy
- Université de Bordeaux, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- INRA, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
| | - Björn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Maithé Clerc
- Université de Bordeaux, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- INRA, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
| | - Cécile Bébéar
- Université de Bordeaux, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- INRA, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- CHU de Bordeaux, Laboratoire de Bactériologie, Bordeaux, France
| | - Bertille de Barbeyrac
- Université de Bordeaux, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- INRA, USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Centre for Chlamydial Infections, Bordeaux, France
- CHU de Bordeaux, Laboratoire de Bactériologie, Bordeaux, France
- * E-mail:
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Santo I, Azevedo J, Nunes B, Gomes JP, Borrego MJ. Partner notification for Chlamydia trachomatis urogenital infections: eight years of patient referral experience in the major Portuguese sexually transmitted infections clinic, 2000–07. Int J STD AIDS 2011; 22:548-51. [DOI: 10.1258/ijsa.2011.010268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of this study was to perform a retrospective evaluation of the success of patient referral for partner notification of chlamydial infections to the major Portuguese sexually transmitted infection (STI) clinic. A total of 8277 patients were screened for Chlamydia trachomatis during 2000–2007, and 695 (8.4%) tested positive. The sexual partners of 34% of these index cases attended the clinic as contacts following partner referral. In univariate analysis, heterosexual men referred partners more frequently than men who have sex with men (MSM) and HIV-negative index cases referred partners four-fold more frequently than HIV-positives; however, these associations were non-significant after multivariate analysis (adjusted odds ratio [OR] 1.4, 95% confidence interval [CI] 0.7–2.6; adjusted OR 4.2, 95% CI 0.9–18.7, respectively). Index patients who reported lower numbers of partners referred more frequently, and this association remained significant after multivariate analysis. One-third of the referred individuals tested C. trachomatis-positive; the risk for infection was three-fold higher for referred partners from symptomatic index cases ( P < 0.001, adjusted OR, 95% CI 1.8–6.3). In conclusion, the results of the present study concerning sexual behaviour, HIV status and clinical signs highlight the need for further evaluations that may shape future partner notification strategies in order to reduce the chlamydial disease burden.
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Affiliation(s)
- I Santo
- Lapa Health Centre, Sexually Transmitted Diseases Clinic, Lisbon
| | - J Azevedo
- Lapa Health Centre, Sexually Transmitted Diseases Clinic, Lisbon
| | - B Nunes
- Infectious Diseases Department, National Institute of Health, Lisbon, Portugal
| | - J P Gomes
- Infectious Diseases Department, National Institute of Health, Lisbon, Portugal
| | - M J Borrego
- Infectious Diseases Department, National Institute of Health, Lisbon, Portugal
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Joseph SJ, Didelot X, Gandhi K, Dean D, Read TD. Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biol Direct 2011; 6:28. [PMID: 21615910 PMCID: PMC3126793 DOI: 10.1186/1745-6150-6-28] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 05/26/2011] [Indexed: 02/02/2023] Open
Abstract
Background Chlamydia trachomatis is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published C. trachomatis genomes to assess the contribution of recombination and selection in this pathogen and to understand the major evolutionary forces acting on the genome of this bacterium. Results The conserved core genes of C. trachomatis are a large proportion of the pan-genome: we identified 836 core genes in C. trachomatis out of a range of 874-927 total genes in each genome. The ratio of recombination events compared to mutation (ρ/θ) was 0.07 based on ancestral reconstructions using the ClonalFrame tool, but recombination had a significant effect on genetic diversification (r/m = 0.71). The distance-dependent decay of linkage disequilibrium also indicated that C. trachomatis populations behaved intermediately between sexual and clonal extremes. Fifty-five genes were identified as having a history of recombination and 92 were under positive selection based on statistical tests. Twenty-three genes showed evidence of being under both positive selection and recombination, which included genes with a known role in virulence and pathogencity (e.g., ompA, pmps, tarp). Analysis of inter-clade recombination flux indicated non-uniform currents of recombination between clades, which suggests the possibility of spatial population structure in C. trachomatis infections. Conclusions C. trachomatis is the archetype of a bacterial species where recombination is relatively frequent yet gene gains by horizontal gene transfer (HGT) and losses (by deletion) are rare. Gene conversion occurs at sites across the whole C. trachomatis genome but may be more often fixed in genes that are under diversifying selection. Furthermore, genome sequencing will reveal patterns of serotype specific gene exchange and selection that will generate important research questions for understanding C. trachomatis pathogenesis. Reviewers This article was reviewed by Dr. Jeremy Selengut, Dr. Lee S. Katz (nominated by Dr. I. King Jordan) and Dr. Arcady Mushegian.
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Affiliation(s)
- Sandeep J Joseph
- Department of Medicine, Division of Infectious, Diseases Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
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Chlamydia trachomatis genotypes and the Swedish new variant among urogenital Chlamydia trachomatis strains in Finland. Infect Dis Obstet Gynecol 2011; 2011:481890. [PMID: 21747641 PMCID: PMC3124027 DOI: 10.1155/2011/481890] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 02/15/2011] [Accepted: 03/03/2011] [Indexed: 01/06/2023] Open
Abstract
Our aims were to genotype Chlamydia trachomatis strains present in urogenital samples and to investigate the occurrence of the Swedish new variant of C. trachomatis in Finland. We genotyped 160 C. trachomatis positive samples with ompA real-time PCR and analyzed 495 samples for the new variant. The three most prevalent genotypes were E (40%), F (28%), and G (13%). Only two specimens containing bacteria with the variant plasmid were detected. It seems that in Finland the percentage of infections due to genotypes F and G has slightly increased during the last 20 years. Genotypes E and G appear to be more common, and genotypes J/Ja and I/Ia appear to be less common in Europe than in the USA. Although the genotype E was the most common genotype among C. trachomatis strains, the new variant was rarely found in Finland.
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Nunes A, Nogueira PJ, Borrego MJ, Gomes JP. Adaptive evolution of the Chlamydia trachomatis dominant antigen reveals distinct evolutionary scenarios for B- and T-cell epitopes: worldwide survey. PLoS One 2010; 5. [PMID: 20957150 PMCID: PMC2950151 DOI: 10.1371/journal.pone.0013171] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/14/2010] [Indexed: 11/23/2022] Open
Abstract
Background Chlamydia trachomatis is one of the most disseminated human pathogens, for which no vaccine is available yet. Understanding the impact of the host pressure on pathogen antigens is crucial, but so far it was only assessed for highly-restricted geographic areas. We aimed to evaluate the evolutionary picture of the chlamydial key antigen (MOMP), which is one of the leading multi-subunit vaccine candidates, in a worldwide basis. Methodology/Principal Findings Using genetics, molecular evolution methods and mathematical modelling, we analyzed all MOMP sequences reported worldwide, composed by 5026 strains from 33 geographic regions of five continents. Overall, 35.9% of variants were detected. The evolutionary pattern of MOMP amino acid gains/losses was found to differ from the remaining chromosome, reflecting the demanding constraints of this porin, adhesin and dominant antigen. Amino acid changes were 4.3-fold more frequent in host-interacting domains (P<10−12), specifically within B-cell epitopes (P<10−5), where 25% of them are at fixation (P<10−5). According to the typical pathogen-host arms race, this rampant B-cell antigenic variation likely represents neutralization escape mutants, as some mutations were previously shown to abrogate neutralization of chlamydial infectivity in vitro. In contrast, T-cell clusters of diverse HLA specificities are under purifying selection, suggesting a strategy that may lead to immune subversion. Moreover, several silent mutations are at fixation, generating preferential codons that may influence expression, and may also reflect recombination-derived ‘hitchhiking-effect’ from favourable nonsilent changes. Interestingly, the most prevalent C. trachomatis genotypes, E and F, showed a mutation rate 22.3-fold lower than that of the remainder (P<10−20), suggesting more fitted antigenic profiles. Conclusions/Significance Globally, the adaptive evolution of the C. trachomatis dominant antigen is likely driven by its complex pathogenesis-related function and reflects distinct evolutionary antigenic scenarios that may benefit the pathogen, and thus should be taking into account in the development of a MOMP-based vaccine.
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Affiliation(s)
- Alexandra Nunes
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Paulo J. Nogueira
- Department of Epidemiology, National Institute of Health, Lisbon, Portugal
| | - Maria J. Borrego
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João P. Gomes
- Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
- * E-mail:
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Touzain F, Denamur E, Médigue C, Barbe V, El Karoui M, Petit MA. Small variable segments constitute a major type of diversity of bacterial genomes at the species level. Genome Biol 2010; 11:R45. [PMID: 20433696 PMCID: PMC2884548 DOI: 10.1186/gb-2010-11-4-r45] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 03/15/2010] [Accepted: 04/30/2010] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. RESULTS We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed. CONCLUSIONS This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes.
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Affiliation(s)
- Fabrice Touzain
- INRA, UMR1319, Micalis, Bat 222, Jouy en Josas, 78350, France
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