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Harte AJ, Ghasemian E, Pickering H, Houghton J, Chernet A, Sata E, Yismaw G, Zeru T, Tadesse Z, Callahan EK, Nash SD, Holland MJ. Unravelling Chlamydia trachomatis diversity in Amhara, Ethiopia: MLVA-ompA sequencing as a molecular typing tool for trachoma. PLoS Negl Trop Dis 2024; 18:e0012143. [PMID: 38662795 DOI: 10.1371/journal.pntd.0012143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/07/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Trachoma is the leading infectious cause of blindness worldwide and is now largely confined to around 40 low- and middle-income countries. It is caused by Chlamydia trachomatis (Ct), a contagious intracellular bacterium. The World Health Organization recommends mass drug administration (MDA) with azithromycin for treatment and control of ocular Ct infections, alongside improving facial cleanliness and environmental conditions to reduce transmission. To understand the molecular epidemiology of trachoma, especially in the context of MDA and transmission dynamics, the identification of Ct genotypes could be useful. While many studies have used the Ct major outer membrane protein gene (ompA) for genotyping, it has limitations. Our study applies a typing system novel to trachoma, Multiple Loci Variable Number Tandem Repeat Analysis combined with ompA (MLVA-ompA). Ocular swabs were collected post-MDA from four trachoma-endemic zones in Ethiopia between 2011-2017. DNA from 300 children with high Ct polymerase chain reaction (PCR) loads was typed using MLVA-ompA, utilizing 3 variable number tandem repeat (VNTR) loci within the Ct genome. Results show that MLVA-ompA exhibited high discriminatory power (0.981) surpassing the recommended threshold for epidemiological studies. We identified 87 MLVA-ompA variants across 26 districts. No significant associations were found between variants and clinical signs or chlamydial load. Notably, overall Ct diversity significantly decreased after additional MDA rounds, with a higher proportion of serovar A post-MDA. Despite challenges in sequencing one VNTR locus (CT1299), MLVA-ompA demonstrated cost-effectiveness and efficiency relative to whole genome sequencing, providing valuable information for trachoma control programs on local epidemiology. The findings suggest the potential of MLVA-ompA as a reliable tool for typing ocular Ct and understanding transmission dynamics, aiding in the development of targeted interventions for trachoma control.
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Affiliation(s)
- Anna J Harte
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ehsan Ghasemian
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harry Pickering
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Joanna Houghton
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | | | - Taye Zeru
- The Amhara Regional Health Bureau, Bahir Dar, Ethiopia
| | | | | | - Scott D Nash
- The Carter Center, Atlanta, Georgia, United States of America
| | - Martin J Holland
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
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Ghasemian E, Faal N, Pickering H, Sillah A, Breuer J, Bailey RL, Mabey D, Holland MJ. Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages. Microb Genom 2024; 10:001210. [PMID: 38445851 PMCID: PMC10999739 DOI: 10.1099/mgen.0.001210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Trachoma, a neglected tropical disease caused by Chlamydia trachomatis (Ct) serovars A-C, is the leading infectious cause of blindness worldwide. Africa bears the highest burden, accounting for over 86 % of global trachoma cases. We investigated Ct serovar A (SvA) and B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors contributing to Ct strain diversification and the implications for Ct evolution within the context of ocular infection. A cohort study in 2002-2003 collected ocular swabs across nine Gambian villages during a 6 month follow-up study. To explore the genetic diversity of Ct within and between individuals, we conducted whole-genome sequencing (WGS) on a limited number (n=43) of Ct-positive samples with an omcB load ≥10 from four villages. WGS was performed using target enrichment with SureSelect and Illumina paired-end sequencing. Out of 43 WGS samples, 41 provided sufficient quality for further analysis. ompA analysis revealed that 11 samples had highest identity to ompA from strain A/HAR13 (NC_007429) and 30 had highest identity to ompA from strain B/Jali20 (NC_012686). While SvB genome sequences formed two distinct village-driven subclades, the heterogeneity of SvA sequences led to the formation of many individual branches within the Gambian SvA subclade. Comparing the Gambian SvA and SvB sequences with their reference strains, Ct A/HAR13 and Ct B/Jali20, indicated an single nucleotide polymorphism accumulation rate of 2.4×10-5 per site per year for the Gambian SvA and 1.3×10-5 per site per year for SvB variants (P<0.0001). Variant calling resulted in a total of 1371 single nucleotide variants (SNVs) with a frequency >25 % in SvA sequences, and 438 SNVs in SvB sequences. Of note, in SvA variants, highest evolutionary pressure was recorded on genes responsible for host cell modulation and intracellular survival mechanisms, whereas in SvB variants this pressure was mainly on genes essential for DNA replication/repair mechanisms and protein synthesis. A comparison of the sequences between observed separate infection events (4-20 weeks between infections) suggested that the majority of the variations accumulated in genes responsible for host-pathogen interaction such as CTA_0166 (phospholipase D-like protein), CTA_0498 (TarP) and CTA_0948 (deubiquitinase). This comparison of Ct SvA and SvB variants within a trachoma endemic population focused on their local evolutionary adaptation. We found a different variation accumulation pattern in the Gambian SvA chromosomal genes compared with SvB, hinting at the potential of Ct serovar-specific variation in diversification and evolutionary fitness. These findings may have implications for optimizing trachoma control and prevention strategies.
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Affiliation(s)
- Ehsan Ghasemian
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Nkoyo Faal
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Harry Pickering
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Ansumana Sillah
- National Eye Health Programme, Ministry of Health, Kanifing, Gambia
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Robin L. Bailey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - David Mabey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Martin J. Holland
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
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Dichtl K, Osterman A, Forster J, Jakob L, Suerbaum S, Flaig MJ, Schubert S, Wagener J. A retrospective evaluation of the Euroarray STI-11 multiplex system for the detection of eight STI causing agents. Sci Rep 2023; 13:11382. [PMID: 37452127 PMCID: PMC10349140 DOI: 10.1038/s41598-023-38121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
With an incidence of more than > 1,000,000/day, sexually transmitted diseases remain a major challenge for health care systems worldwide. To reduce disease burden, complications, and spread, rapid diagnosis permitting early therapy is pivotal. The range of pathogens is wide and co-infections are common. This complicates pre-analytics, which are based on different laboratory techniques with potentially long turnaround times, e.g., cultivation and multistep serologies. Multiplex PCR provides the opportunity to overcome these limitations. In this study, we evaluated a novel assay, the Euroarray STI-11 microarray (EA; Euroimmun Medizinische Labordiagnostika), for the detection of eight obligate or facultative pathogens. Three-hundred-thirteen clinical specimens, which had been tested and pre-characterized for STI causing agents as part of routine diagnostics, were used as cases and controls in this retrospective study. The EA detected 34/44 Chlamydia trachomatis, 48/50 HSV-1, 50/50 HSV-2, 48/48 Mycoplasma hominis, 45/47 Neisseria gonorrhoeae, 9/11 Treponema pallidum, 46/46 Ureaplasma parvum, and 49/49 Ureaplasma urealyticum infections, respectively. 293 samples were EA positive, with polymicrobial infections (positive for two to six microbial or viral agents) detected in 130/293 cases. Specificities were 100% in the respective control groups (n = 18-48 depending on targeted pathogen) except for N. gonorrhoeae (25/26) and U. urealyticum (44/45). The broad spectrum of obligate and facultative pathogens targeted by the EA makes it a valuable tool in the setting of STI diagnostics and surveillance. The test has the potential to diagnose diseases neglected or overlooked in routine clinical practice. Besides a low sensitivity for C. trachomatis, the EA demonstrated high performance for all analyzed parameters. Further studies are warranted in order to capture a larger variety of the tested pathogens.
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Affiliation(s)
- Karl Dichtl
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Osterman
- Lehrstuhl für Virologie, Max von Pettenkofer-Institut, LMU München, Medizinische Fakultät, Munich, Germany
| | - Johannes Forster
- Institut für Hygiene und Mikrobiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lena Jakob
- Klinik und Poliklinik für Dermatologie und Allergologie, Klinikum der Universität München, LMU München, Munich, Germany
| | - Sebastian Suerbaum
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany
| | - Michael J Flaig
- Klinik und Poliklinik für Dermatologie und Allergologie, Klinikum der Universität München, LMU München, Munich, Germany
| | - Sören Schubert
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany
| | - Johannes Wagener
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany.
- Institut für Hygiene und Mikrobiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, the University of Dublin, St. James's Hospital Campus, Dublin, Ireland.
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Kasimov V, White RT, Foxwell J, Jenkins C, Gedye K, Pannekoek Y, Jelocnik M. Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers. Microb Genom 2023; 9:mgen001072. [PMID: 37486739 PMCID: PMC10438822 DOI: 10.1099/mgen.0.001072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. psittaci infections have been reported in various hosts, isolation and culture of Chlamydia is challenging, hampering efforts to produce contemporary global C. psittaci genomes. This is particularly evident in the lack of avian C. psittaci genomes from Australia and New Zealand. In this study, we used culture-independent probe-based whole-genome sequencing to expand the global C. psittaci genome catalogue. Here, we provide new C. psittaci genomes from two pigeons, six psittacines, and novel hosts such as the Australian bustard (Ardeotis australis) and sooty shearwater (Ardenna grisea) from Australia and New Zealand. We also evaluated C. psittaci genetic diversity using multilocus sequence typing (MLST) and major outer membrane protein (ompA) genotyping on additional C. psittaci-positive samples from various captive avian hosts and field isolates from Australasia. We showed that the first C. psittaci genomes sequenced from New Zealand parrots and pigeons belong to the clonal sequence type (ST)24 and diverse 'pigeon-type' ST27 clade, respectively. Australian parrot-derived strains also clustered in the ST24 group, whereas the novel ST332 strain from the Australian bustard clustered in a genetically diverse clade of strains from a fulmar, parrot, and livestock. MLST and ompA genotyping revealed ST24/ompA genotype A in wild and captive parrots and a sooty shearwater, whilst 'pigeon-types' (ST27/35 and ompA genotypes B/E) were found in pigeons and other atypical hosts, such as captive parrots, a little blue penguin/Kororā (Eudyptula minor) and a zebra finch (Taeniopygia guttata castanotis) from Australia and New Zealand. This study provides new insights into the global phylogenomic diversity of C. psittaci and further demonstrates the multi-host generalist capacity of this pathogen.
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Affiliation(s)
- Vasilli Kasimov
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
| | - Rhys T. White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia
- The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, 66 Ward Street, Upper Hutt 5018, New Zealand
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Kristene Gedye
- Massey University, School of Veterinary Science, Palmerston North 4442, New Zealand
| | - Yvonne Pannekoek
- University of Amsterdam, Amsterdam UMC, Department of Medical Microbiology and Infection Prevention, Amsterdam 1105, Netherlands
| | - Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia
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Monteiro IP, Azzi CFG, Bilibio JP, Monteiro PS, Braga GC, Nitz N. Prevalence of sexually transmissible infections in adolescents treated in a family planning outpatient clinic for adolescents in the western Amazon. PLoS One 2023; 18:e0287633. [PMID: 37352297 PMCID: PMC10289307 DOI: 10.1371/journal.pone.0287633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/09/2023] [Indexed: 06/25/2023] Open
Abstract
Sexually transmitted infections (STIs) are among the most common public health problems worldwide, especially among adolescents and young adults, who account for almost 50% of all STI patients. Studies on the subject in the western Amazon are limited. This study aimed to evaluate the prevalence of STIs (chlamydia, gonorrhea, trichomoniasis, herpes simplex virus, syphilis, human immunodeficiency virus [HIV], hepatitis B, and hepatitis C) in adolescents treated at a family planning outpatient clinic in the western Amazon: Porto Velho, Rondônia, Brazil. A total of 196 adolescents were enrolled. During the gynecological examination, endocervical samples were collected to test for four STIs (chlamydia, gonorrhea, trichomoniasis, and herpes simplex virus), and blood samples were collected for the detection of HIV, syphilis, and hepatitis B and C. The mean age was 17.3 ± 1.5 years, the age at sexarche was 14.4 ± 1.6 years, and 54.6% of participants had their first sexual intercourse at 14 years or younger. Only 1.0% of the adolescents used condoms in all sexual relations, and 19.9% had casual partner(s) in the last year. In the evaluation of prevalence, we found that 32% of the adolescents had at least one STI, with the most prevalent being chlamydia (23%), followed by trichomoniasis (5.6%), herpes simplex (4.6%), and gonorrhea (3.1%). No positive cases of hepatitis B, hepatitis C, or HIV were detected, but 1% of the adolescents tested positive for syphilis. These indicators will support more effective health care strategies aimed at improving the quality of life of populations in this region of the western Amazon. In conclusion, our findings demonstrated high rates of STIs in the studied patients, reinforcing the need to expand epidemiological studies to implement more appropriate public policies and intervention strategies to prevent STIs in adolescents and other vulnerable populations in the western Amazon.
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Affiliation(s)
- Ida Peréa Monteiro
- Municipal Health Department, Mãe Esperança Municipal Maternity, Porto Velho, Rondônia, Brazil
| | - Camila Flávia Gomes Azzi
- Molecular Biology Laboratory, Central Laboratory of Public Health of Rondônia, Porto Velho, Rondônia, Brazil
| | - João Paolo Bilibio
- Faculty of Medicine, Centro Universitário de Brusque–UNIFEBE, Brusque, Santa Catarina, Brazil
| | | | - Giordana Campos Braga
- Department of Social Medicine, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Nadjar Nitz
- Faculty of Medicine, Interdisciplinary Laboratory of Biosciences, University of Brasília, Brasília, Brazil
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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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Martínez-García L, González-Alba JM, Puerta T, Comunión A, Rodríguez-Jiménez MC, Orviz E, Sánchez-Conde M, Rodríguez-Domínguez M, Cantón R, Galán JC. Specific high-resolution scheme to improve understanding of the spatio-temporal dispersion of lymphogranuloma venereum epidemic. Front Microbiol 2022; 13:1056216. [PMID: 36605505 PMCID: PMC9808035 DOI: 10.3389/fmicb.2022.1056216] [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: 09/29/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Lymphogranuloma venereum (LGV) is already endemic in vulnerable populations in several European countries; however, molecular epidemiology data with improved accuracy are necessary to better understand LGV epidemic in these countries. Current strategies to study the molecular epidemiology of LGV cases involve schemes based on a few genetic fragments of Chlamydia trachomatis, which have demonstrated limited discriminatory power for LGV. Therefore, this study aimed to propose a new combination of molecular markers based on the most variable genes of L-genotype genomes to improve the characterization of the current LGV epidemic in Madrid, Spain. Methods Four genes were selected according to their diversity index (CTLon_0054, CTLon_0087, CTLon_0243 and CTLon_0301) for use in combination with ompA. In silico and experimental studies were performed to compare the previously described multilocus sequence typing (MLST) schemes with our proposal. Moreover, the proposed scheme was applied (n = 68) to analyze the spatio-temporal spread of the LGV cases. Results Our proposal demonstrated higher diversity allowing the identification of three main groups compared to the previously published MLST based on hypervariable genes wherein only a single sequence type was identified. The temporal analysis showed that the major cluster was progressively diversifying, revealing a very active transmission chain. Furthermore, an L2b genome identical to that of the origin of the epidemic was detected, suggesting reintroductions or a low screening rate in vulnerable populations. The spatial distribution suggests that the selection and spread of new variants occurs from the central district to the peripheral regions. Discussion The scheme proposed in this study has proven to be useful for appropriate discrimination of LGV strains. This study, to our knowledge for the first time, demonstrates a spatio-temporal spread that increases our understanding and identifies areas with special susceptibility for maintenance of the endemic situation of LGV.
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Affiliation(s)
- Laura Martínez-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - José María González-Alba
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Teresa Puerta
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | | | - María Concepción Rodríguez-Jiménez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Eva Orviz
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Matilde Sánchez-Conde
- Servicio de Enfermedades Infecciosas. Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Mario Rodríguez-Domínguez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain,*Correspondence: Juan Carlos Galán,
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9
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Suchland RJ, Carrell SJ, Ramsey SA, Hybiske K, Debrine AM, Sanchez J, Celum C, Rockey DD. Genomic Analysis of MSM Rectal Chlamydia trachomatis Isolates Identifies Predicted Tissue-Tropic Lineages Generated by Intraspecies Lateral Gene Transfer-Mediated Evolution. Infect Immun 2022; 90:e0026522. [PMID: 36214558 PMCID: PMC9670952 DOI: 10.1128/iai.00265-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Chlamydia trachomatis is an obligate intracellular bacterium that causes serious diseases in humans. Rectal infection and disease caused by this pathogen are important yet understudied aspects of C. trachomatis natural history. The University of Washington Chlamydia Repository has a large collection of male-rectal-sourced strains (MSM rectal strains) isolated in Seattle, USA and Lima, Peru. Initial characterization of strains collected over 30 years in both Seattle and Lima led to an association of serovars G and J with male rectal infections. Serovar D, E, and F strains were also collected from MSM patients. Genome sequence analysis of a subset of MSM rectal strains identified a clade of serovar G and J strains that had high overall genomic identity. A genome-wide association study was then used to identify genomic loci that were correlated with tissue tropism in a collection of serovar-matched male rectal and female cervical strains. The polymorphic membrane protein PmpE had the strongest correlation, and amino acid sequence alignments identified a set of PmpE variable regions (VRs) that were correlated with host or tissue tropism. Examination of the positions of VRs by the protein structure-predicting Alphafold2 algorithm demonstrated that the VRs were often present in predicted surface-exposed loops in both PmpE and PmpH protein structure. Collectively, these studies identify possible tropism-predictive loci for MSM rectal C. trachomatis infections and identify predicted surface-exposed variable regions of Pmp proteins that may function in MSM rectal versus cervical tropism differences.
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Affiliation(s)
- Robert J. Suchland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Steven J. Carrell
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Stephen A. Ramsey
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Abigail M. Debrine
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Jorge Sanchez
- Centro de Investigaciones Tecnológicas, Universidad Nacional Mayor San Marcos, Lima, Peru
| | - Connie Celum
- Departments of Global Health and Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel D. Rockey
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
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10
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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: 0] [Impact Index Per Article: 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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11
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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: 0] [Impact Index Per Article: 0] [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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12
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Thapa J, Yoshiiri G, Ito K, Okubo T, Nakamura S, Furuta Y, Higashi H, Yamaguchi H. Chlamydia trachomatis Requires Functional Host-Cell Mitochondria and NADPH Oxidase 4/p38MAPK Signaling for Growth in Normoxia. Front Cell Infect Microbiol 2022; 12:902492. [PMID: 35719337 PMCID: PMC9199516 DOI: 10.3389/fcimb.2022.902492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydia trachomatis (Ct) is an intracellular energy-parasitic bacterium that requires ATP derived from infected cells for its growth. Meanwhile, depending on the O2 concentration, the host cells change their mode of ATP production between oxidative phosphorylation in mitochondria (Mt) and glycolysis; this change depends on signaling via reactive oxygen species (ROS) produced by NADPH oxidases (NOXs) as well as Mt. It has been proposed that Ct correspondingly switches its source of acquisition of ATP between host-cell Mt and glycolysis, but this has not been verified experimentally. In the present study, we assessed the roles of host-cell NOXs and Mt in the intracellular growth of CtL2 (L2 434/Bu) under normoxia (21% O2) and hypoxia (2% O2) by using several inhibitors of NOXs (or the downstream molecule) and Mt-dysfunctional (Mtd) HEp-2 cells. Under normoxia, diphenyleneiodonium, an inhibitor of ROS diffusion, abolished the growth of CtL2 and other Chlamydiae (CtD and C. pneumoniae). Both ML171 (a pan-NOX inhibitor) and GLX351322 (a NOX4-specific inhibitor) impaired the growth of CtL2 under normoxia, but not hypoxia. NOX4-knockdown cells diminished the bacterial growth. SB203580, an inhibitor of the NOX4-downstream molecule p38MAPK, also inhibited the growth of CtL2 under normoxia but not hypoxia. Furthermore, CtL2 failed to grow in Mtd cells under normoxia, but no effect was observed under hypoxia. We conclude that under normoxia, Ct requires functional Mt in its host cells as an ATP source, and that this process requires NOX4/p38MAPK signaling in the host cells. In contrast to hypoxia, crosstalk between NOX4 and Mt via p38MAPK may be crucial for the growth of Ct under normoxia.
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Affiliation(s)
- Jeewan Thapa
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Gen Yoshiiri
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Koki Ito
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Shinji Nakamura
- Laboratory of Morphology and Image Analysis, Research Support Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoshikazu Furuta
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hideaki Higashi
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
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13
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A Review of Next Generation Sequencing Methods and its Applications in Laboratory Diagnosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) is a new technology used to detect the sequence of DNA and RNA and to detect mutations or variations of significance. NGS generates large quantities of sequence data within a short time duration. The various types of sequencing includes Sanger Sequencing, Pyrosequencing, Sequencing by Synthesis (Illumina), Ligation (SoLID), Single molecule Fluorescent Sequencing (Helicos), Single molecule Real time Sequencing (Pacbio), Semiconductor sequencing (Ion torrent technology), Nanopore sequencing and fourth generation sequencing. These methods of sequencing have been modified and improved over the years such that it has become cost effective and accessible to diagnostic laboratories. Management of Outbreaks, rapid identification of bacteria, molecular case finding, taxonomy, detection of the zoonotic agents and guiding prevention strategies in HIV outbreaks are just a few of the many applications of Next Generation sequencing in clinical microbiology.
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14
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Abstract
Trachoma is a neglected tropical disease caused by infection with conjunctival strains of Chlamydia trachomatis. It can result in blindness. Pathophysiologically, trachoma is a disease complex composed of two linked chronic processes: a recurrent, generally subclinical infectious-inflammatory disease that mostly affects children, and a non-communicable, cicatricial and, owing to trichiasis, eventually blinding disease that supervenes in some individuals later in life. At least 150 infection episodes over an individual's lifetime are needed to precipitate trichiasis; thus, opportunity exists for a just global health system to intervene to prevent trachomatous blindness. Trachoma is found at highest prevalence in the poorest communities of low-income countries, particularly in sub-Saharan Africa; in June 2021, 1.8 million people worldwide were going blind from the disease. Blindness attributable to trachoma can appear in communities many years after conjunctival C. trachomatis transmission has waned or ceased; therefore, the two linked disease processes require distinct clinical and public health responses. Surgery is offered to individuals with trichiasis and antibiotic mass drug administration and interventions to stimulate facial cleanliness and environmental improvement are designed to reduce infection prevalence and transmission. Together, these interventions comprise the SAFE strategy, which is achieving considerable success. Although much work remains, a continuing public health problem from trachoma in the year 2030 will be difficult for the world to excuse.
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15
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López-Pintor JM, Martínez-García L, Maruri A, Menéndez B, Puerta T, Rodríguez C, González-Alba JM, Rodríguez-Domínguez M, Galán JC. Quantification of plasmid copy number as surrogate marker of virulence among different invasive and non-invasive genotypes of Chlamydia trachomatis. Diagn Microbiol Infect Dis 2022; 102:115610. [DOI: 10.1016/j.diagmicrobio.2021.115610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 02/04/2023]
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16
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Pitt R, Doyle R, Theilgaard Christiansen M, Horner P, Hathorn E, Alexander S, Woodford N, Cole M, Breuer J. Whole-genome sequencing of Chlamydia trachomatis isolates from persistently infected patients. Int J STD AIDS 2022; 33:442-446. [PMID: 35239412 DOI: 10.1177/09564624211048662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Current understanding of the causes of treatment failure in Chlamydia trachomatis is poor and antimicrobial susceptibility data are lacking. We used genome sequencing to seek evidence of antimicrobial resistance in isolates sourced from patients who were persistently infected. METHODS Genomic DNA was extracted from C. trachomatis isolates cultured in McCoy cell monolayers. Sequencing libraries were prepared using the SureSelectXT Illumina paired-end protocol. Paired reads were mapped against a reference genome and single nucleotide variants (SNVs) were identified. RESULTS Seven isolates from persistently infected patients and five isolates from successfully treated patients were sequenced. No previously reported SNVs associated with antimicrobial resistance were found. A unique SNV was identified in the gyrA gene of one treatment failure isolate but was located outside of the quinolone resistance determining region; this SNV has been previously reported in other members of the Chlamydiaceae family. CONCLUSION No genomic evidence was found to explain the differences in clinical outcome for our two groups of patients. A mutation unrelated to antimicrobial susceptibility was found in an isolate from a persistently infected patient. The cause of these persistent infections with C. trachomatis remains unclear.
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Affiliation(s)
- Rachel Pitt
- National Infection Service, Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI), 372064Public Health England, London, UK
| | - Ronan Doyle
- Division of Infection and Immunity, 4919University College London, London, UK
| | | | - Paddy Horner
- Population Health Sciences, 1980University of Bristol, Bristol, UK.,Unity Sexual Health, 1984University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Emma Hathorn
- Whittal Street Clinic, 1732University Hospitals Birmingham, Birmingham, UK
| | - Sarah Alexander
- Sexually Transmitted Bacteria Reference Unit, 371011Public Health England, London, UK
| | - Neil Woodford
- National Infection Service, Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI), 372064Public Health England, London, UK
| | - Michelle Cole
- National Infection Service, Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI), 372064Public Health England, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, 4919University College London, London, UK
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17
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Marti H, Suchland RJ, Rockey DD. The Impact of Lateral Gene Transfer in Chlamydia. Front Cell Infect Microbiol 2022; 12:861899. [PMID: 35321311 PMCID: PMC8936141 DOI: 10.3389/fcimb.2022.861899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
Lateral gene transfer (LGT) facilitates many processes in bacterial ecology and pathogenesis, especially regarding pathogen evolution and the spread of antibiotic resistance across species. The obligate intracellular chlamydiae, which cause a range of diseases in humans and animals, were historically thought to be highly deficient in this process. However, research over the past few decades has demonstrated that this was not the case. The first reports of homologous recombination in the Chlamydiaceae family were published in the early 1990s. Later, the advent of whole-genome sequencing uncovered clear evidence for LGT in the evolution of the Chlamydiaceae, although the acquisition of tetracycline resistance in Chlamydia (C.) suis is the only recent instance of interphylum LGT. In contrast, genome and in vitro studies have shown that intraspecies DNA exchange occurs frequently and can even cross species barriers between closely related chlamydiae, such as between C. trachomatis, C. muridarum, and C. suis. Additionally, whole-genome analysis led to the identification of various DNA repair and recombination systems in C. trachomatis, but the exact machinery of DNA uptake and homologous recombination in the chlamydiae has yet to be fully elucidated. Here, we reviewed the current state of knowledge concerning LGT in Chlamydia by focusing on the effect of homologous recombination on the chlamydial genome, the recombination machinery, and its potential as a genetic tool for Chlamydia.
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Affiliation(s)
- Hanna Marti
- Institute of Veterinary Pathology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Hanna Marti,
| | - Robert J. Suchland
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Daniel D. Rockey
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
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18
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Call for consensus in Chlamydia trachomatis nomenclature: moving from biovars, serovars and serotypes to genovariants and genotypes. Clin Microbiol Infect 2022; 28:761-763. [PMID: 35202789 DOI: 10.1016/j.cmi.2022.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/29/2022] [Accepted: 02/07/2022] [Indexed: 11/21/2022]
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19
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Emergence of Novel Chlamydia trachomatis Sequence Types among Chlamydia Patients in the Republic of Belarus. Microorganisms 2022; 10:microorganisms10020478. [PMID: 35208932 PMCID: PMC8876968 DOI: 10.3390/microorganisms10020478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Chlamydia trachomatis (CT) is a major cause of sexually transmitted diseases worldwide. The multilocus sequence typing (MLST) of clinical samples from random heterosexual chlamydia patients who were either asymptomatic or reported clinical manifestations of genital chlamydiosis (n = 63) in each of the seven major regions of the Republic of Belarus in 2017–2018 revealed 12 different CT sequence types (STs). We found seven known STs, ST4, ST6, ST9, ST13, ST38, ST95 and ST110, and five novel variants, namely ST271–ST275, which have not been detected elsewhere thus far. The ST4 variant was predominant (27/63, 42.9%) and detected in six out of seven regions. The two most common STs, ST9 and ST13, were regularly seen in four out of seven regions. In contrast, the remaining STs, ST6, ST38, ST95, ST110, and novel STs271-275, surfaced randomly in different parts of the country. The emergence of novel STs was registered in two regions, namely Minsk (ST271 and ST275) and Brest (ST271, ST272, ST273, and ST274). All the STs of detected CT strains were clustered into two Groups, I and III, which are characteristic of CT urogenital strains. No STs typical for Group II, specific to the LGV strains, were revealed. Our study contributes to better understanding the genetic diversity and molecular evolution of CT, one of the most important pathogens in public health worldwide.
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20
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Brunham RC. Problems with Understanding Chlamydia trachomatis Immunology. J Infect Dis 2021; 225:2043-2049. [DOI: 10.1093/infdis/jiab610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
The pay off for understanding Chlamydia. trachomatis (CT) immunology is the development of a vaccine. Two lines of research have contributed to our current understanding of CT immunology. The first is the Grayston model of type specific immunity and genus specific pathology which was elaborated by Caldwell and Morrison as the major outer membrane protein (MOMP) and heat shock protein 60 (HSP60) paradigm. The second is the murine model of C. muridarum (CM) infection which established the essential role of major histocompatibility complex class II and CD4 T cells in immunity. However neither approach has yielded a vaccine. I review these two lines of research and conclude with six problem areas in human CT immunology whose resolution may result in a vaccine.(122 words)
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Affiliation(s)
- Robert C Brunham
- Department of Medicine, University of British Columbia, Vaccine Research Laboratory, British Columbia Centre for Disease Control Vancouver, Canada
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21
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Garvin L, Vande Voorde R, Dickinson M, Carrell S, Hybiske K, Rockey D. A broad-spectrum cloning vector that exists as both an integrated element and a free plasmid in Chlamydia trachomatis. PLoS One 2021; 16:e0261088. [PMID: 34914750 PMCID: PMC8675754 DOI: 10.1371/journal.pone.0261088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
Plasmid transformation of chlamydiae has created new opportunities to investigate host-microbe interactions during chlamydial infections; however, there are still limitations. Plasmid transformation requires a replicon derived from the native Chlamydia plasmid, and these transformations are species-specific. We explored the utility of a broad host-range plasmid, pBBR1MCS-4, to transform chlamydiae, with a goal of simplifying the transformation process. The plasmid was modified to contain chromosomal DNA from C. trachomatis to facilitate homologous recombination. Sequences flanking incA were cloned into the pBBR1MCS-4 vector along with the GFP:CAT cassette from the pSW2-GFP chlamydial shuttle vector. The final plasmid construct, pBVR2, was successfully transformed into C. trachomatis strain L2-434. Chlamydial transformants were analyzed by immunofluorescence microscopy and positive clones were sequentially purified using limiting dilution. PCR and PacBio-based whole genome sequencing were used to determine if the plasmid was maintained within the chromosome or as an episome. PacBio sequencing of the cloned transformants revealed allelic exchange events between the chromosome and plasmid pBVR2 that replaced chromosomal incA with the plasmid GFP:CAT cassette. The data also showed evidence of full integration of the plasmid into the bacterial chromosome. While some plasmids were fully integrated, some were maintained as episomes and could be purified and retransformed into E. coli. Thus, the plasmid can be successfully transformed into chlamydia without a chlamydial origin of replication and can exist in multiple states within a transformed population.
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Affiliation(s)
- Lotisha Garvin
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - Rebecca Vande Voorde
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - Mary Dickinson
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Disease (CERID), University of Washington, Seattle, WA, United States of America
| | - Steven Carrell
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Disease (CERID), University of Washington, Seattle, WA, United States of America
| | - Daniel Rockey
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
- * E-mail:
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22
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White RT, Legione AR, Taylor-Brown A, Fernandez CM, Higgins DP, Timms P, Jelocnik M. Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala ( Phascolarctos cinereus) Pathogen. Pathogens 2021; 10:1543. [PMID: 34959498 PMCID: PMC8703710 DOI: 10.3390/pathogens10121543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety of C. pecorum molecular studies, to date, only four complete and 16 draft genomes have been published. Of those, only five draft genomes are from koalas. Here, using whole-genome sequencing and a comparative genomics approach, we describe the first two complete C. pecorum genomes collected from diseased koalas. A de novo assembly of DBDeUG_2018 and MC/MarsBar_2018 resolved the chromosomes and chlamydial plasmids each as single, circular contigs. Robust phylogenomic analyses indicate biogeographical separation between strains from northern and southern koala populations, and between strains infecting koala and livestock hosts. Comparative genomics between koala strains identified new, unique, and shared loci that accumulate single-nucleotide polymorphisms and separate between northern and southern, and within northern koala strains. Furthermore, we predicted novel type III secretion system effectors. This investigation constitutes a comprehensive genome-wide comparison between C. pecorum from koalas and provides improvements to annotations of a C. pecorum reference genome. These findings lay the foundations for identifying and understanding host specificity and adaptation behind chlamydial infections affecting koalas.
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Affiliation(s)
- Rhys T. White
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
| | - Alistair R. Legione
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Alyce Taylor-Brown
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Cristina M. Fernandez
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; (C.M.F.); (D.P.H.)
| | - Damien P. Higgins
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; (C.M.F.); (D.P.H.)
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
| | - Martina Jelocnik
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia; (R.T.W.); (A.T.-B.); (P.T.)
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23
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Shetty S, Kouskouti C, Schoen U, Evangelatos N, Vishwanath S, Satyamoorthy K, Kainer F, Brand A. Diagnosis of Chlamydia trachomatis genital infections in the era of genomic medicine. Braz J Microbiol 2021; 52:1327-1339. [PMID: 34164797 PMCID: PMC8221097 DOI: 10.1007/s42770-021-00533-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 05/17/2021] [Indexed: 11/02/2022] Open
Abstract
PURPOSE Chlamydial genital infections constitute significant sexually transmitted infections worldwide. The often asymptomatic status of C. trachomatis (CT) infections leads to an increased burden on human reproductive health, especially in middle- and low-income settings. Early detection and management of these infections could play a decisive role in controlling this public health burden. The objective of this review is to provide an insight into the evolution of diagnostic methods for CT infections through the development of new molecular technologies, emphasizing on -omics' technologies and their significance as diagnostic tools both for effective patient management and control of disease transmission. METHODS Narrative review of the diagnostic methodologies of CT infections and the impact of the introduction of -omics' technologies on their diagnosis by review of the literature. RESULTS Various methodologies are discussed with respect to working principles, required specifications, advantages, and disadvantages. Implementing the most accurate methods in diagnosis is highlighted as the cornerstone in managing CT infections. CONCLUSION Diagnostics based on -omics' technologies are considered to be the most pertinent modalities in CT testing when compared to other available methods. There is a need to modify these effective and accurate diagnostic tools in order to render them more available and feasible in all settings, especially aiming on turning them to rapid point-of-care tests for effective patient management and disease control.
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Affiliation(s)
- Seema Shetty
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, Karnataka, India.
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands.
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
| | - Christina Kouskouti
- Department of Obstetrics and Perinatal Medicine, Klinik Hallerwiese, St. Johannis-Muhlgasse 19, 90419, Nuremberg, Germany
- Division of Maternal and Fetal Medicine Department of Obstetrics and Gynaecology, Mt. Sinai Hospital University of Toronto, Toronto, ON, Canada
| | - Uwe Schoen
- BioMedHeliX (Pty) Ltd., 3 Conifer Road, Cape Town, 8005, South Africa
| | - Nikolaos Evangelatos
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands
- Interdepartmental Division of Critical Care Medicine, University of Toronto, ON, Canada
- Dr. TMA Pai Endowment Chair in Research Policy in Biomedical Sciences and Public Health, Prasanna School of Public Health (PSPH), Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Shashidhar Vishwanath
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, Karnataka, India
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Franz Kainer
- Department of Obstetrics and Perinatal Medicine, Klinik Hallerwiese, St. Johannis-Muhlgasse 19, 90419, Nuremberg, Germany
| | - Angela Brand
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands
- Dr. TMA Pai Endowment Chair in Public Health Genomics, Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of International Health, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, 6229, GT, The Netherlands
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24
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Ghasemian E, Inic-Kanada A, Collingro A, Mejdoubi L, Alchalabi H, Keše D, Elshafie BE, Hammou J, Barisani-Asenbauer T. Comparison of genovars and Chlamydia trachomatis infection loads in ocular samples from children in two distinct cohorts in Sudan and Morocco. PLoS Negl Trop Dis 2021; 15:e0009655. [PMID: 34370735 PMCID: PMC8376198 DOI: 10.1371/journal.pntd.0009655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/19/2021] [Accepted: 07/16/2021] [Indexed: 11/30/2022] Open
Abstract
Trachoma is a blinding disease caused by repeated conjunctival infection with different Chlamydia trachomatis (Ct) genovars. Ct B genovars have been associated with more severe trachoma symptoms. Here, we investigated associations between Ct genovars and bacterial loads in ocular samples from two distinct geographical locations in Africa, which are currently unclear. We tested ocular swabs from 77 Moroccan children (28 with trachomatous inflammation-follicular (TF) and 49 healthy controls), and 96 Sudanese children (54 with TF and 42 healthy controls) with a Ct-specific real-time polymerase chain reaction (PCR) assay. To estimate bacterial loads, Ct-positive samples were further processed by multiplex real-time qPCR to amplify the chromosomal outer membrane complex B and plasmid open reading frame 2 of Ct. Genotyping was performed by PCR-based amplification of the outer membrane protein A gene (~1120 base pairs) of Ct and Sanger sequencing. Ct-positivities among the Moroccan and Sudanese patient groups were 60·7% and 31·5%, respectively. Significantly more Sudanese patients than Moroccan patients were genovar A-positive. In contrast, B genovars were significantly more prevalent in Moroccan patients than in Sudanese patients. Significantly higher Ct loads were found in samples positive for B genovars (598596) than A genovar (51005). Geographical differences contributed to the distributions of different ocular Ct genovars. B genovars may induce a higher bacterial load than A genovars in trachoma patients. Our findings emphasize the importance of conducting broader studies to elucidate if the noted difference in multiplication abilities are genovar and/or endemicity level dependent. We investigated the association between different Ct genovars, the approximate load of infection, and the distribution of Chlamydia genovars by comparing samples from one trachoma-endemic area (i.e., the city of El-Gadaref in Al Qadarif, Sudan) and one previously endemic area (i.e., the Zagora Province in Morocco), currently considered as non-endemic. This study is the first to reveal a significant difference between the genome copy numbers of Ct genovar A and B/Ba in children with TF. Evidence that Ct is still circulating in rural foci of countries like Morocco that are no longer considered endemic implies that the continuation of the trachoma surveillance must be warranted in future to avoid further spreading of Ct. The clinical significance of different infectious loads in the development of sequelae has to be determined as well as whether these differences are genovar specific or related to the given endemicity level.
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Affiliation(s)
- Ehsan Ghasemian
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Aleksandra Inic-Kanada
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Lamiss Mejdoubi
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Hadeel Alchalabi
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Darja Keše
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Jaouad Hammou
- Medicine and Pharmacy Faculty, Mohammed V University, Rabat, Morocco
| | - Talin Barisani-Asenbauer
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- * E-mail:
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25
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Manning C, O’Neill C, Clarke IN, Rebec M, Cliff PR, Marsh P. High-resolution genotyping of Lymphogranuloma Venereum (LGV) strains of Chlamydia trachomatis in London using multi-locus VNTR analysis-ompA genotyping (MLVA-ompA). PLoS One 2021; 16:e0254233. [PMID: 34237111 PMCID: PMC8266103 DOI: 10.1371/journal.pone.0254233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background Lymphogranuloma venereum (LGV) is caused by Chlamydia trachomatis strains with ompA genotypes L1 to L3. An LGV epidemic associated with the L2b genotype has emerged in the past few decades amongst men who have sex with men (MSM). C. trachomatis genotypes can be discriminated by outer membrane protein A gene (ompA) sequencing, however this method has limited resolution. This study employed a high-resolution genotyping method, namely, multi-locus tandem repeat (VNTR) analysis with ompA sequencing (MLVA-ompA), to assess the distribution of LGV MLVA-ompA genotypes amongst individuals attending genitourinary medicine (GUM) clinics in London. Methods Clinical specimens were collected from individuals attending eight London-based GUM clinics. Specimens that tested positive for C. trachomatis by commercial nucleic acid amplification test (NAAT) were confirmed as LGV by pmpH real-time PCR. LGV-positive DNA extracts were subsequently genotyped using MLVA-ompA. Results Two hundred and thirty DNA extracts were confirmed as LGV, and 162 (70%) yielded complete MLVA-ompA genotypes. Six LGV MLVA-ompA genotypes were identified: 1.9.2b-L2, 1.9.3b-L2b, 1.9.2b-L2b, 1.9.2b-L2b/D, 1.4a.2b-L2b, and 5.9.2b-L1. The following LGV ompA genotypes were identified (in descending order of abundance): L2, L2b, L2b/D, and L1. Eight ompA sequences with the hybrid L2b/D profile were detected. The hybrid sequence was identical to the ompA of a recombinant L2b/D strain detected in Portugal in 2017. Conclusions The L2 ompA genotype was found to predominate in the London study population. The study detected an unusual hybrid L2b/D ompA profile that was previously reported in Portugal. We recommend further monitoring and surveillance of LGV strains within the UK population.
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Affiliation(s)
- Chloe Manning
- Department of Molecular Microbiology, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- * E-mail:
| | - Colette O’Neill
- Department of Molecular Microbiology, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ian N. Clarke
- Department of Molecular Microbiology, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, United Kingdom
| | - Penelope R. Cliff
- Department of Infection Sciences, St Thomas’ Hospital, London, United Kingdom
| | - Peter Marsh
- Public Health England, Porton Down, Salisbury, United Kingdom
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26
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Seth-Smith HMB, Bénard A, Bruisten SM, Versteeg B, Herrmann B, Kok J, Carter I, Peuchant O, Bébéar C, Lewis DA, Puerta T, Keše D, Balla E, Zákoucká H, Rob F, Morré SA, de Barbeyrac B, Galán JC, de Vries HJC, Thomson NR, Goldenberger D, Egli A. Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains. Microb Genom 2021; 7. [PMID: 34184981 PMCID: PMC8461462 DOI: 10.1099/mgen.0.000599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) Chlamydia trachomatis, is caused by strains from the LGV biovar, most commonly represented by ompA-genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using typing and genome sequencing. LGV-positive samples (n=321) from eight countries collected between 2011 and 2017 (Spain n=97, Netherlands n=67, Switzerland n=64, Australia n=53, Sweden n=37, Hungary n=31, Czechia n=30, Slovenia n=10) were genotyped for pmpH and ompA variants. All were found to contain the 9 bp insertion in the pmpH gene, previously associated with ompA-genotype L2b. However, analysis of the ompA gene shows ompA-genotype L2b (n=83), ompA-genotype L2 (n=180) and several variants of these (n=52; 12 variant types), as well as other/mixed ompA-genotypes (n=6). To elucidate the genomic diversity, whole genome sequencing (WGS) was performed from selected samples using SureSelect target enrichment, resulting in 42 genomes, covering a diversity of ompA-genotypes and representing most of the countries sampled. A phylogeny of these data clearly shows that these ompA-genotypes derive from an ompA-genotype L2b ancestor, carrying up to eight SNPs per isolate. SNPs within ompA are overrepresented among genomic changes in these samples, each of which results in an amino acid change in the variable domains of OmpA (major outer membrane protein, MOMP). A reversion to ompA-genotype L2 with the L2b genomic backbone is commonly seen. The wide diversity of ompA-genotypes found in these recent LGV samples indicates that this gene is under immunological selection. Our results suggest that the ompA-genotype L2b genomic backbone is the dominant strain circulating and evolving particularly in men who have sex with men (MSM) populations.
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Affiliation(s)
- Helena M B Seth-Smith
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Angèle Bénard
- Present address: Healthcare Systems Research Group, VHIR, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sylvia M Bruisten
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Bart Versteeg
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Björn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Olivia Peuchant
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Cécile Bébéar
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - David A Lewis
- Western Sydney Sexual Health Centre, Western Sydney Local Health District, Parramatta, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Teresa Puerta
- Unidad de ITS/VIH, Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Darja Keše
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | - Eszter Balla
- Bacterial STI Reference Laboratory, National Public Health Center (former National Center for Epidemiology), Budapest, Hungary
| | - Hana Zákoucká
- National Reference Laboratory for Diagnostics of Syphilis and Chlamydia Infections, National Institute of Public Health, Srobarova 48, 100 42, Prague 10, Czech Republic
| | - Filip Rob
- Department of Dermatovenereology, Second Faculty of Medicine, Charles University and Hospital Bulovka, Budinova 2, 180 81, Prague 8, Czech Republic
| | - Servaas A Morré
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.,Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research Institute GROW, University of Maastricht, Maastricht, The Netherlands
| | - Bertille de Barbeyrac
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. CIBER en Epidemiología y Salud Pública (CIBERESP)
| | - Henry J C de Vries
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Cambridge, UK.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Daniel Goldenberger
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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27
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Brunham RC, Paavonen J. Reproductive system infections in women: lower genital tract syndromes. Pathog Dis 2021; 78:5848196. [PMID: 32463432 DOI: 10.1093/femspd/ftaa022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Gynecological and obstetrical infectious diseases are an important component of women's health. A system approach to gynecological and obstetrical infection helps unify and classify microbial etiology and pathogenesis within a clinical anatomical framework of lower and upper genital tract syndromes. The reproductive system of women includes the vulva, vagina, cervix, uterus, fallopian tubes and ovaries. During pregnancy, additional tissues include the chorioamnion and placenta together with the fetus and amniotic fluid. We review in two parts reproductive system infection syndromes in women using selected research results to illustrate the clinical utility of the system approach in terms of diagnosis, treatment and prevention. We conclude that a reproductive system perspective will lead to improvements in understanding, management and prevention of these diseases.
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Affiliation(s)
- Robert C Brunham
- Department of Medicine, University of British Columbia, BC V5Z 4R4, Vancouver, Canada
| | - Jorma Paavonen
- Department of Obstetrics and Gynecology, University of Helsinki, Helsinki, 00014 Finland
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28
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Banerjee A, Nelson DE. The growing repertoire of genetic tools for dissecting chlamydial pathogenesis. Pathog Dis 2021; 79:ftab025. [PMID: 33930127 PMCID: PMC8112481 DOI: 10.1093/femspd/ftab025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/28/2021] [Indexed: 01/29/2023] Open
Abstract
Multiple species of obligate intracellular bacteria in the genus Chlamydia are important veterinary and/or human pathogens. These pathogens all share similar biphasic developmental cycles and transition between intracellular vegetative reticulate bodies and infectious elementary forms, but vary substantially in their host preferences and pathogenic potential. A lack of tools for genetic engineering of these organisms has long been an impediment to the study of their biology and pathogenesis. However, the refinement of approaches developed in C. trachomatis over the last 10 years, and adaptation of some of these approaches to other Chlamydia spp. in just the last few years, has opened exciting new possibilities for studying this ubiquitous group of important pathogens.
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Affiliation(s)
- Arkaprabha Banerjee
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - David E Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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29
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Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. mBio 2021; 12:mBio.00605-21. [PMID: 33975934 PMCID: PMC8262981 DOI: 10.1128/mbio.00605-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted infections and blindness globally. To date, Ct urogenital strains are considered tryptophan prototrophs, utilizing indole for tryptophan synthesis within a closed-conformation tetramer comprised of two α (TrpA)- and two β (TrpB)-subunits. In contrast, ocular strains are auxotrophs due to mutations in TrpA, relying on host tryptophan pools for survival. It has been speculated that there is strong selective pressure for urogenital strains to maintain a functional operon. Here, we performed genetic, phylogenetic, and novel functional modeling analyses of 595 geographically diverse Ct ocular, urethral, vaginal, and rectal strains with complete operon sequences. We found that ocular and urogenital, but not lymphogranuloma venereum, TrpA-coding sequences were under positive selection. However, vaginal and urethral strains exhibited greater nucleotide diversity and a higher ratio of nonsynonymous to synonymous substitutions [Pi(a)/Pi(s)] than ocular strains, suggesting a more rapid evolution of beneficial mutations. We also identified nonsynonymous amino acid changes for an ocular isolate with a urogenital backbone in the intergenic region between TrpR and TrpB at the exact binding site for YtgR-the only known iron-dependent transcription factor in Chlamydia-indicating that selective pressure has disabled the response to fluctuating iron levels. In silico effects on protein stability, ligand-binding affinity, and tryptophan repressor (TrpR) affinity for single-stranded DNA (ssDNA) measured by calculating free energy changes (ΔΔG) between Ct reference and mutant tryptophan operon proteins were also analyzed. We found that tryptophan synthase function was likely suboptimal compared to other bacterial tryptophan prototrophs and that a diversity of urogenital strain mutations rendered the synthase nonfunctional or inefficient. The novel mutations identified here affected active sites in an orthosteric manner but also hindered α- and β-subunit allosteric interactions from distant sites, reducing efficiency of the tryptophan synthase. Importantly, strains with mutant proteins were inclined toward energy conservation by exhibiting an altered affinity for their respective ligands compared to reference strains, indicating greater fitness. This is not surprising as l-tryptophan is one of the most energetically costly amino acids to synthesize. Mutations in the tryptophan repressor gene (trpR) among urogenital strains were similarly detrimental to function. Our findings indicate that urogenital strains are evolving more rapidly than previously recognized with mutations that impact tryptophan operon function in a manner that is energetically beneficial, providing a novel host-pathogen evolutionary mechanism for intracellular survival.IMPORTANCE Chlamydia trachomatis (Ct) is a major global public health concern causing sexually transmitted and ocular infections affecting over 130 million and 260 million people, respectively. Sequelae include infertility, preterm birth, ectopic pregnancy, and blindness. Ct relies on available host tryptophan pools and/or substrates to synthesize tryptophan to survive. Urogenital strains synthesize tryptophan from indole using their intact tryptophan synthase (TS). Ocular strains contain a trpA frameshift mutation that encodes a truncated TrpA with loss of TS function. We found that TS function is likely suboptimal compared to other tryptophan prototrophs and that urogenital stains contain diverse mutations that render TS nonfunctional/inefficient, evolve more rapidly than previously recognized, and impact operon function in a manner that is energetically beneficial, providing an alternative host-pathogen evolutionary mechanism for intracellular survival. Our research has broad scientific appeal since our approach can be applied to other bacteria that may explain evolution/survival in host-pathogen interactions.
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Mlaga KD, Mathieu A, Beauparlant CJ, Ott A, Khodr A, Perin O, Droit A. HCK and ABAA: A Newly Designed Pipeline to Improve Fungi Metabarcoding Analysis. Front Microbiol 2021; 12:640693. [PMID: 34025601 PMCID: PMC8134036 DOI: 10.3389/fmicb.2021.640693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction The fungi ITS sequence length dissimilarity, non-specific amplicons, including chimaera formed during Polymerase Chain Reaction (PCR), added to sequencing errors, create bias during similarity clustering and abundance estimation in the downstream analysis. To overcome these challenges, we present a novel approach, Hierarchical Clustering with Kraken (HCK), to classify ITS1 amplicons and Abundance-Base Alternative Approach (ABAA) pipeline to detect and filter non-specific amplicons in fungi metabarcoding sequencing datasets. Materials and Methods We compared the performances of both pipelines against QIIME, KRAKEN, and DADA2 using publicly available fungi ITS mock community datasets and using BLASTn as a reference. We calculated the Precision, Recall, F-score using the True-Positive, False-positive, and False-negative estimation. Alpha diversity (Chao1 and Shannon metrics) was also used to evaluate the diversity estimation of our method. Results The analysis shows that ABAA reduced the number of false-positive with all metabarcoding methods tested, and HCK increases precision and recall. HCK, coupled with ABAA, improves the F-score and bring alpha diversity metric value close to that of the BLASTn alpha diversity values when compared to QIIME, KRAKEN, and DADA2. Conclusion The developed HCK-ABAA approach allows better identification of the fungi community structures while avoiding use of a reference database for non-specific amplicons filtration. It results in a more robust and stable methodology over time. The software can be downloaded on the following link: https://bitbucket.org/GottySG36/hck/src/master/.
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Affiliation(s)
- Kodjovi D Mlaga
- Department of Molecular Medicine, Laval University, Quebec, QC, Canada
| | - Alban Mathieu
- Department of Molecular Medicine, Laval University, Quebec, QC, Canada.,Centre de Recherche du CHU de Québec, Quebec, QC, Canada
| | - Charles Joly Beauparlant
- Department of Molecular Medicine, Laval University, Quebec, QC, Canada.,Centre de Recherche du CHU de Québec, Quebec, QC, Canada
| | - Alban Ott
- Research and Innovation, L'Oreal, Paris, France
| | - Ahmad Khodr
- Research and Innovation, L'Oreal, Paris, France
| | | | - Arnaud Droit
- Department of Molecular Medicine, Laval University, Quebec, QC, Canada.,Centre de Recherche du CHU de Québec, Quebec, QC, Canada
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Kacerovsky M, Romero R, Pliskova L, Bolehovska R, Hornychova H, Matejkova A, Vosmikova H, Andrys C, Kolackova M, Laudański P, Pelantova V, Jacobsson B, Musilova I. Presence of Chlamydia trachomatis DNA in the amniotic fluid in women with preterm prelabor rupture of membranes. J Matern Fetal Neonatal Med 2021; 34:1586-1597. [PMID: 31272257 PMCID: PMC7062296 DOI: 10.1080/14767058.2019.1640676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The primary aim of this study was to assess the rate and load of amniotic fluid Chlamydia trachomatis DNA and their associations with intra-amniotic infection and intra-uterine inflammatory complications in women with preterm prelabor rupture of membranes (PPROM). The secondary aim was to assess the short-term morbidity of newborns from PPROM pregnancies complicated by amniotic fluid C. trachomatis DNA. METHODS A retrospective study of 788 women with singleton pregnancies complicated by PPROM between 24 + 0 and 36 + 6 weeks of gestation was performed. Transabdominal amniocenteses were performed at the time of admission. C. trachomatis DNA in the amniotic fluid was assessed by real-time polymerase chain reaction using a commercial AmpliSens® C. trachomatis/Ureaplasma/Mycoplasma hominis-FRT kit, and the level of Ct DNA was quantified. RESULTS Amniotic fluid C. trachomatis DNA complicated 2% (16/788) of the PPROM pregnancies and was present in very low loads (median 57 copies DNA/mL). In addition to amniotic fluid C. trachomatis DNA, other bacteria were detected in 62% (10/16) of the C. trachomatis DNA-complicated PPROM pregnancies. Amniotic fluid C. trachomatis DNA was associated with intra-amniotic infection, histologic chorioamnionitis (HCA), and funisitis in 31%, 47%, and 33%, respectively. The presence of C. trachomatis DNA accompanied by Ureaplasma species in the amniotic fluid was associated with a higher rate of HCA than the presence of amniotic fluid C. trachomatis DNA alone. The composite neonatal morbidity in newborns from PPROM pregnancies with amniotic fluid C. trachomatis DNA was 31%. CONCLUSION The presence of C. trachomatis DNA in the amniotic fluid is a relatively rare condition in PPROM. Amniotic fluid C. trachomatis DNA in PPROM is not related to intensive intra-amniotic and intr-auterine inflammatory responses or adverse short-term neonatal outcomes.
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Affiliation(s)
- Marian Kacerovsky
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
| | - Lenka Pliskova
- Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Radka Bolehovska
- Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Helena Hornychova
- The Fingerland Department of Pathology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Adela Matejkova
- The Fingerland Department of Pathology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Hana Vosmikova
- The Fingerland Department of Pathology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ctirad Andrys
- Department of Clinical immunology and Allergy, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove
| | - Martina Kolackova
- Department of Clinical immunology and Allergy, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove
| | - Piotr Laudański
- 1 Department of Obstetrics and Gynecology, Medical University of Warsaw, Poland
| | - Vera Pelantova
- Department of Infectious Diseases, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Ivana Musilova
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Charles University, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
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Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs. mSphere 2021; 6:6/2/e01302-20. [PMID: 33658279 PMCID: PMC8546720 DOI: 10.1128/msphere.01302-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlamydia trachomatis, an obligately intracellular bacterium, is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. Numbers of U.S. infections of the urogenital tract and rectum have increased annually. Because C. trachomatis is not easily cultured, comparative genomic studies are limited, restricting our understanding of strain diversity and emergence among populations globally. While Agilent SureSelectXT target enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal samples, public access to these libraries is not available. We therefore designed an RNA bait library (34,795 120-mer probes based on 85 genomes, versus 33,619 probes using 74 genomes in a previous one) to augment organism sequencing from clinical samples that can be shared with the scientific community, enabling comparison studies. We describe the library and limit of detection for genome copy input, and we present results of 100% efficiency and high-resolution determination of recombination and identical genomes within vaginal-rectal specimen pairs in women. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men.IMPORTANCE Chlamydia trachomatis is an obligate intracellular bacterium that is not easily cultured, which limits our understanding of urogenital and rectal C. trachomatis transmission and impact on morbidity. To provide a publicly available workflow for whole-genome target enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal specimens, we developed and report on an RNA bait library to enrich the organism from clinical samples for sequencing. We demonstrate an increased efficiency in the percentage of reads mapping to C. trachomatis and identified recombinant and identical C. trachomatis genomes in paired vaginal-rectal samples from women. Our workflow provides a robust genomic epidemiologic approach to advance our understanding of C. trachomatis strains causing ocular, urogenital, and rectal infections and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.
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Valiente-Mullor C, Beamud B, Ansari I, Francés-Cuesta C, García-González N, Mejía L, Ruiz-Hueso P, González-Candelas F. One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. PLoS Comput Biol 2021; 17:e1008678. [PMID: 33503026 PMCID: PMC7870062 DOI: 10.1371/journal.pcbi.1008678] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 02/08/2021] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended. Mapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the ‘reference genome’ of a species—a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. It is known that genetic differences between the reference genome and the read sequences may produce incorrect alignments during mapping. Eventually, these errors could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). To our knowledge, this is the first work to systematically examine the effect of different references for mapping on the inference of tree topology as well as the impact on recombination and natural selection inferences. Furthermore, the novelty of this work relies on a procedure that guarantees that we are evaluating only the effect of the reference. This effect has proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.
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Affiliation(s)
- Carlos Valiente-Mullor
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Beatriz Beamud
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- * E-mail: (BB); (FG-C)
| | - Iván Ansari
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Carlos Francés-Cuesta
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Neris García-González
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Lorena Mejía
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paula Ruiz-Hueso
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER in Epidemiology and Public Health, Valencia, Spain
- * E-mail: (BB); (FG-C)
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Pilo S, Zizelski Valenci G, Rubinstein M, Pichadze L, Scharf Y, Dveyrin Z, Rorman E, Nissan I. High-resolution multilocus sequence typing for Chlamydia trachomatis: improved results for clinical samples with low amounts of C. trachomatis DNA. BMC Microbiol 2021; 21:28. [PMID: 33461496 PMCID: PMC7814548 DOI: 10.1186/s12866-020-02077-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/20/2020] [Indexed: 11/17/2022] Open
Abstract
Background Several Multilocus Sequence Typing (MLST) schemes have been developed for Chlamydia trachomatis. Bom’s MLST scheme for MLST is based on nested PCR amplification and sequencing of five hypervariable genes and ompA. In contrast to other Chlamydia MLST schemes, Bom’s MLST scheme gives higher resolution and phylogenetic trees that are comparable to those from whole genome sequencing. However, poor results have been obtained with Bom’s MLST scheme in clinical samples with low concentrations of Chlamydia DNA. Results In this work, we present an improved version of the scheme that is based on the same genes and MLST database as Bom’s MLST scheme, but with newly designed primers for nested-1 and nested-2 steps under stringent conditions. Furthermore, we introduce a third primer set for the sequencing step, which considerably improves the performance of the assay. The improved primers were tested in-silico using a dataset of 141 Whole Genome Sequences (WGS) and in a comparative analysis of 32 clinical samples. Based on cycle threshold and melting curve analysis values obtained during Real-Time PCR of nested-1 & 2 steps, we developed a simple scoring scheme and flow chart that allow identification of reaction inhibitors as well as to predict with high accuracy amplification success. The improved MLST version was used to obtain a genovars distribution in patients attending an STI clinic in Tel Aviv. Conclusions The newly developed MLST version showed great improvement of assay results for samples with very low concentrations of Chlamydia DNA. A similar concept could be applicable to other MLST schemes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02077-y.
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Affiliation(s)
- Shlomo Pilo
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | | | - Mor Rubinstein
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Lea Pichadze
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Yael Scharf
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Zeev Dveyrin
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Efrat Rorman
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Israel Nissan
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel.
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Arif ED, Saeed NM, Rachid SK. Isolation and Identification of Chlamydia abortus from Aborted Ewes in Sulaimani Province, Northern Iraq. Pol J Microbiol 2020; 69:1-7. [PMID: 32108450 PMCID: PMC7256821 DOI: 10.33073/pjm-2020-009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/20/2020] [Accepted: 01/30/2020] [Indexed: 11/21/2022] Open
Abstract
Abortion in small ruminants is a significant problem in Iraq and causes severe economic losses in sheep farms. Chlamydia abortus causes enzootic abortion in ewes and is associated with reproductive problems in sheep in Sulaimani province – Northern Iraq. During a lambing season in 2017, abortion was widespread among several sheep flocks in different regions of Sulaimani (Kalar, Said Sadiq, and Chamchamal), and C. abortus was one of the causes. Accordingly, we carried out this study to isolate and identify C. abortus in aborted ewes in these regions. We collected 30 samples of aborted fetuses from five herds in which abortions had been observed. The pathogen isolation was done by inoculation into embryonated chicken eggs and conventional PCR was used to identify C. abortus in clinical specimens. C. abortus was identified in one of the 30 aborted fetuses (3.33%) from the Kalar district, and all the remaining 29 samples (96.66%) were found positive to Brucella abortus. The gene ompA encoding the outer membrane protein of C. abortus was sequenced and got the accession number MK643153 in NCBI GenBank. The sequence was named C. abortus strain Sul/2017. Our isolate showed 99.79% homology with Sul/014 (accession No. KY399850) and differed from the latter by two amino acid substitutions at E115K and K259N. The topology of the phylogenetic tree based on the ompA gene showed that the isolate belongs to C. abortus and has a common ancestor with isolates of sheep in Iraq and Tunisia with accession numbers KY399850 and HQ62243, respectively.
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Affiliation(s)
- Eman Dhahir Arif
- Department of Microbiology, College of Veterinary Medicine, University of Sulaimani , New Sulaimani, Sulaymaniyah, Kurdistan Region , Northern Iraq
| | - Nahla Muhammad Saeed
- Department of Microbiology, College of Veterinary Medicine, University of Sulaimani , New Sulaimani, Sulaymaniyah, Kurdistan Region , Northern Iraq
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Abstract
This paper provides an overview of the current knowledge of chlamydiae. These intracellular microorganisms belonging to the Chlamydiaceae family are widely distributed throughout the world. Constant development of culture-independent approaches for characterisation of microbial genomes enables new discoveries in the field of Chlamydia. The number of new taxa is continuously increasing as well as the range of hosts. New species and genotypes are constantly being discovered, particularly new avian and reptilian agents, which are discussed in this article. Interestingly, wild animals are the main hosts for new Chlamydia species including different species of bird, turtle and snake. The availability of next-generation sequencing opens up a new prospect for research and leads to deeper knowledge of these interesting microorganisms about which much is still to discover.
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Pickering H, Chernet A, Sata E, Zerihun M, Williams CA, Breuer J, Nute AW, Haile M, Zeru T, Tadesse Z, Bailey RL, Callahan EK, Holland MJ, Nash SD. Genomics of Ocular Chlamydia trachomatis after 5 years of SAFE interventions for trachoma in Amhara, Ethiopia. J Infect Dis 2020; 225:994-1004. [PMID: 33034349 PMCID: PMC8922003 DOI: 10.1093/infdis/jiaa615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
To eliminate trachoma as a public health problem, the WHO recommends the SAFE (Surgery, Antibiotics, Facial cleanliness, and Environmental improvement) strategy. As part of the SAFE strategy in the Amhara Region, Ethiopia, the Trachoma Control Program distributed over 124 million doses of antibiotic between 2007 and 2015. Despite this, trachoma remained hyperendemic in many districts and a considerable level of Chlamydia trachomatis (Ct) infection was evident. We utilised residual material from Abbott m2000 Ct diagnostic tests to sequence 99 ocular Ct samples from Amhara and investigated the role of Ct genomic variation in continued transmission of Ct. Sequences were typical of ocular Ct, at the whole-genome level and in tissue tropism-associated genes. There was no evidence of macrolide-resistance in this population. Polymorphism around ompA gene was associated with village-level trachomatous inflammation-follicular prevalence. Greater ompA diversity at the district-level was associated with increased Ct infection prevalence. We found no evidence for Ct genomic variation contributing to continued transmission of Ct after treatment, adding to evidence that azithromycin does not drive acquisition of macrolide resistance in Ct. Increased Ct infection in areas with more ompA variants requires longitudinal investigation to understand what impact this may have on treatment success and host immunity.
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Affiliation(s)
- Harry Pickering
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, UK
| | | | | | | | | | - Judith Breuer
- Division of Infection and Immunity, University College London, UK
| | | | | | - Taye Zeru
- Amhara Public Health Institute Bahir Dar, Ethiopia
| | | | - Robin L Bailey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, UK
| | | | - Martin J Holland
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, UK
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Solomon AW, Kello AB, Bangert M, West SK, Taylor HR, Tekeraoi R, Foster A. The simplified trachoma grading system, amended. Bull World Health Organ 2020; 98:698-705. [PMID: 33177759 PMCID: PMC7652564 DOI: 10.2471/blt.19.248708] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/27/2022] Open
Abstract
A simplified grading system for trachoma was published by the World Health Organization (WHO) in 1987. Intended for use by non-specialist personnel working at community level, the system includes five signs, each of which can be present or absent in any eye: (i) trachomatous trichiasis; (ii) corneal opacity; (iii) trachomatous inflammation—follicular; (iv) trachomatous inflammation—intense; and (v) trachomatous scarring. Though neither perfectly sensitive nor perfectly specific for trachoma, these signs have been essential tools for identifying populations that need interventions to eliminate trachoma as a public health problem. In 2018, at WHO’s 4th global scientific meeting on trachoma, the definition of one of the signs, trachomatous trichiasis, was amended to exclude trichiasis that affects only the lower eyelid. This paper presents the amended system, updates its presentation, offers notes on its use and identifies areas of ongoing debate.
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Affiliation(s)
- Anthony W Solomon
- Department of Control of Neglected Tropical Diseases, World Health Organization, Avenue Appia 20, 1211 Geneva 27, Switzerland
| | - Amir B Kello
- World Health Organization Regional Office for Africa, Brazzaville, Congo
| | - Mathieu Bangert
- Department of Control of Neglected Tropical Diseases, World Health Organization, Avenue Appia 20, 1211 Geneva 27, Switzerland
| | - Sheila K West
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, United States of America
| | - Hugh R Taylor
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Rabebe Tekeraoi
- Eye Department, Ministry of Health and Medical Services, South Tarawa, Kiribati
| | - Allen Foster
- International Centre for Eye Health, London School of Hygiene & Tropical Medicine, London, England
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Greub G, Palagi PM, Dylus D, Egli A, Pillonel T, Rossen JWA, Seth-Smith HMB, Lebrand A. Clinical bioinformatics for microbial genomics and metagenomics: an ESCMID Postgraduate Technical Workshop. Microbes Infect 2020; 22:626-634. [PMID: 32841729 DOI: 10.1016/j.micinf.2020.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Gilbert Greub
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Patricia M Palagi
- Training, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Dylus
- University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - John W A Rossen
- Department of Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Aitana Lebrand
- Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
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Yu X, Zheng B, Xiao F, Jin Y, Guo L, Xu H, Luo Q, Xiao Y. Effect of Short-Term Antimicrobial Therapy on the Tolerance and Antibiotic Resistance of Multidrug-Resistant Staphylococcus capitis. Infect Drug Resist 2020; 13:2017-2026. [PMID: 32636655 PMCID: PMC7335296 DOI: 10.2147/idr.s254141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022] Open
Abstract
Background Bacteria undergo adaptive mutation in the host. However, the specific effect of antimicrobial use on bacterial evolution and genome mutations related to bacterial survival within a patient is unclear. Materials and Methods Three S. capitis strains were sequentially isolated from cerebrospinal fluid of a clinical inpatient. Antimicrobial susceptibility, growth rate, biofilm formation and whole blood survival of these strains were measured. Relative fitness was calculated. The virulence was examined in the Galleria mellonella model. Whole-genome sequencing and in silico analysis were performed to explore the genetic mechanisms of the changes in antimicrobial resistance phenotype. Hypothetical proteins are cloned, expressed and characterized by detection the susceptibility to gentamycin. Results The first isolate was susceptible to rifampin (MIC=0.25 μg/mL), resistant to gentamicin (MIC=16 μg/mL), while the later two isolates were resistant to rifampin (MIC >64 μg/mL), susceptible to gentamicin (MIC=4 μg/mL). For the latter two strains, compared to the first, frameshift mutation in a hypothetical protein encoding gene and base substitutions (in genes saeR, moaA and rpoB) were discovered. The mutation of rpoB gene caused rifampicin resistance. Mutations in saeR, moaA and hypothetical gene are associated with changes in other biological traits. Amino acid sequence-based structure and function identification of the hypothetical protein indicated that a mutation in the encoding gene might be associated with altered aminoglycoside susceptibility. Growth curve showed that the later two isolates grew faster than the first isolate with a positive fitness advantage of 13.5%, and 14.8%, accordingly. Biofilm form ability and whole blood survival of the derivative mutants were also enhanced. No significant differences of virulence in the G. mellonella model were observed. Conclusion We report here for the first time that short-term clinical antibiotic use was associated with resistance mutations, collateral sensitivity, and positive in vivo fitness advantages to S. capitis during infection.
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Affiliation(s)
- Xiao Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Feng Xiao
- Neurosurgery Department, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Ye Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Lihua Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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Chlamydiae in the Environment. Trends Microbiol 2020; 28:877-888. [PMID: 32591108 DOI: 10.1016/j.tim.2020.05.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria.
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Brancaccio M, Mennitti C, Laneri S, Franco A, De Biasi MG, Cesaro A, Fimiani F, Moscarella E, Gragnano F, Mazzaccara C, Limongelli G, Frisso G, Lombardo B, Pagliuca C, Colicchio R, Salvatore P, Calabrò P, Pero R, Scudiero O. Methicillin-Resistant Staphylococcus aureus: Risk for General Infection and Endocarditis Among Athletes. Antibiotics (Basel) 2020; 9:E332. [PMID: 32570705 PMCID: PMC7345113 DOI: 10.3390/antibiotics9060332] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/23/2022] Open
Abstract
The first studies on Staphylococcus aureus (SA) infections in athletes were conducted in the 1980s, and examined athletes that perform in close physical contact, with particular attention to damaged or infected skin. Recent studies have used molecular epidemiology to shed light on the transmission of SA in professional athletes. These studies have shown that contact between athletes is prolonged and constant, and that these factors influence the appearance of infections caused by SA. These results support the need to use sanitary measures designed to prevent the appearance of SA infections. The factors triggering the establishment of SA within professional sports groups are the nasal colonization of SA, contact between athletes and sweating. Hence, there is a need to use the most modern molecular typing methods to evaluate the appearance of cutaneous SA disease. This review aims to summarize both the current SA infections known in athletes and the diagnostic methods employed for recognition, pointing to possible preventive strategies and the factors that can act as a springboard for the appearance of SA and subsequent transmission between athletes.
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Affiliation(s)
- Mariarita Brancaccio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Cristina Mennitti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
| | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (S.L.); (A.F.); (M.G.D.B.)
| | - Adelaide Franco
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (S.L.); (A.F.); (M.G.D.B.)
| | - Margherita G. De Biasi
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (S.L.); (A.F.); (M.G.D.B.)
| | - Arturo Cesaro
- Department of Cardio-Thoracic and Respiratory Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.C.); (G.L.)
| | - Fabio Fimiani
- Center of Excellence for Research on Cardiovascular Diseases Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy;
| | - Elisabetta Moscarella
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (E.M.); (P.C.)
| | - Felice Gragnano
- Division of Cardiology, Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy;
| | - Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Giuseppe Limongelli
- Department of Cardio-Thoracic and Respiratory Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.C.); (G.L.)
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Barbara Lombardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Chiara Pagliuca
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
| | - Roberta Colicchio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
| | - Paola Salvatore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy
| | - Paolo Calabrò
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (E.M.); (P.C.)
| | - Raffaela Pero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy
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Unemo M, Hansen M, Hadad R, Puolakkainen M, Westh H, Rantakokko-Jalava K, Thilesen C, Cole MJ, Boiko I, Lan PT, Golparian D, Ito S, Sundqvist M. Sensitivity, specificity, inclusivity and exclusivity of the updated Aptima Combo 2 assay, which provides detection coverage of the new diagnostic-escape Chlamydia trachomatis variants. BMC Infect Dis 2020; 20:419. [PMID: 32546213 PMCID: PMC7298785 DOI: 10.1186/s12879-020-05148-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/11/2020] [Indexed: 01/30/2023] Open
Abstract
Background Four new variants of Chlamydia trachomatis (nvCTs), detected in several countries, cause false-negative or equivocal results using the Aptima Combo 2 assay (AC2; Hologic). We evaluated the clinical sensitivity and specificity, as well as the analytical inclusivity and exclusivity of the updated AC2 for the detection of CT and Neisseria gonorrhoeae (NG) on the automated Panther system (Hologic). Methods We examined 1004 clinical AC2 samples and 225 analytical samples spiked with phenotypically and/or genetically diverse NG and CT strains, and other potentially cross-reacting microbial species. The clinical AC2 samples included CT wild type (WT)-positive (n = 488), all four described AC2 diagnostic-escape nvCTs (n = 170), NG-positive (n = 214), and CT/NG-negative (n = 202) specimens. Results All nvCT-positive samples (100%) and 486 (99.6%) of the CT WT-positive samples were positive in the updated AC2. All NG-positive, CT/NG-negative, Trichomonas vaginalis (TV)-positive, bacterial vaginosis-positive, and Candida-positive AC2 specimens gave correct results. The clinical sensitivity and specificity of the updated AC2 for CT detection was 99.7 and 100%, respectively, and for NG detection was 100% for both. Examining spiked samples, the analytical inclusivity and exclusivity were 100%, i.e., in clinically relevant concentrations of spiked microbe. Conclusions The updated AC2, including two CT targets and one NG target, showed a high sensitivity, specificity, inclusivity and exclusivity for the detection of CT WT, nvCTs, and NG. The updated AC2 on the fully automated Panther system offers a simple, rapid, high-throughput, sensitive, and specific diagnosis of CT and NG, which can easily be combined with detection of Mycoplasma genitalium and TV.
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Affiliation(s)
- Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden.
| | - Marit Hansen
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | - Ronza Hadad
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | - Mirja Puolakkainen
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Henrik Westh
- Department of Clinical Medicine, Faculty of Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | | | - Carina Thilesen
- Department of Microbiology, Unilabs Laboratory Medicine, Skien, Norway
| | - Michelle J Cole
- National Infection Service, Public Health England, London, UK
| | - Iryna Boiko
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden.,Department of Functional and Laboratory Diagnostics, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Pham T Lan
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Daniel Golparian
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | | | - Martin Sundqvist
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
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Khan AA, A Abuderman A, Ashraf MT, Khan Z. Protein-protein interactions of HPV- Chlamydia trachomatis-human and their potential in cervical cancer. Future Microbiol 2020; 15:509-520. [PMID: 32476479 DOI: 10.2217/fmb-2019-0242] [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] [Indexed: 01/09/2023] Open
Abstract
Aim: HPV is an important cause of cervical cancer, but Chlamydia trachomatis (CT) is suspiciously involved in this disease ranging from direct to its involvement as a cofactor with HPV. We performed this study to understand the interaction of HPV and C. trachomatis with humans and its contribution to cervical cancer. Materials & methods: Host-pathogen and pathogen-pathogen protein-protein interaction maps of HPV/CT/human were prepared and compared to analyze interactions during single/coinfection of C. trachomatis and HPV. The interacting human proteins were detected by their involvement in cervical cancer. Results: C. trachomatis may interact with several cancer associated proteins while HPV and C. trachomatis largely interact with different human proteins, suggesting different pathogenesis. Conclusion: C. trachomatis coinfection with HPV may modulate cervical cancer development.
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Affiliation(s)
- Abdul Arif Khan
- Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdulwahab A Abuderman
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Mohd Tashfeen Ashraf
- School of Biotechnology, Gautam Buddha University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh, 201312, India
| | - Zakir Khan
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Baverly Blvd., Los Angeles, CA 90048, USA
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Szabo KV, O’Neill CE, Clarke IN. Diversity in Chlamydial plasmids. PLoS One 2020; 15:e0233298. [PMID: 32469898 PMCID: PMC7259575 DOI: 10.1371/journal.pone.0233298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/01/2020] [Indexed: 11/30/2022] Open
Abstract
Background Evolutionary studies have been conducted that have investigated the chromosomal variance in the genus of Chlamydia. However, no all-encompassing genus-wide comparison has been performed on the plasmid. Therefore, there is a gap in the current knowledge on Chlamydia plasmid diversity. Aims This project is aimed to investigate and establish the nature and extent of diversity across the entire genus of Chlamydia, by comparing the sequences of all currently available plasmid carrying strains. Methods The PUBMED database was used to identify plasmid sequences from all available strains that met the set quality criteria for their inclusion in the study. Alignments were performed on the 51 strains that fulfilled the criteria using MEGA X software. Following that Maximum Likelihood estimation was used to construct 11 phylogenetic trees of the whole plasmid sequence, the individual 8 coding sequences, the iteron and a chromosomal gene ompA as a comparator. Results The genus-wide plasmid phylogeny produced three distinct lineages labelled as alpha, beta and gamma. Nineteen genotypes were found in the initial whole plasmid analysis. Their distribution was allocated as six C. pecorum, two C. pneumoniae, one C. gallinacea, one C. avium, one C. caviae, one C. felis, two C. psittaci, one C. trachomatis, one C. muridarum, and two C. suis. The chromosomal comparative gene ompA supported this distribution, with the same number of primary clades with the same species distribution. However, ompA sequence comparison resulted in fewer genotypes due to a reduced amount of available sequences (33 out of 51). All results were statistically significant. Conclusion The results of this study indicate that the common bacterial ancestor of all the species had a plasmid, which has diverged over time. Moreover, it suggests that there is a strong evolutionary selection towards these species retaining their plasmids due to its high level of conservation across the genus, with the notable exception of C. pneumoniae. Furthermore, the evolutionary analysis showed that the plasmid and the chromosome have co-evolved.
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Affiliation(s)
- Kolos V. Szabo
- Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom
- * E-mail:
| | - Colette E. O’Neill
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Ian N. Clarke
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
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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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Lin Y, Ali Abuderman AW, Aldakheel FM, Ahmad M. Bioinformatics approach to understand the mode of microbial pathogenesis of Chlamydia trachomatis and their implications in gynecologic malignancy. J Reprod Immunol 2020; 140:103127. [PMID: 32311665 DOI: 10.1016/j.jri.2020.103127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 11/18/2022]
Abstract
Chlamydia trachomatis has a say on the target gene i.e., modulating the expression of target gene in the host so that it is given protection from the immune cells and so its survival and replication are not arrested by the host. The current study reports a wide range of C. trachomatis proteins that target the cellular as well as sub-cellular components of the host in gynecologic malignancy. Various bioinformatics tools was used to conduct an in-depth analysis on nuclear and eukaryotic sub cellular localization signal to find the sequences of the predicted proteins of C. trachomatis strain G. A total of 411 proteins was identified with 79.54% maximum expected accuracy and 51.02% least expected accuracy. There were uneven prediction of proteins along with redundancies between BaCeILo and HSLpred in the determination of sub-cellular localization of the CT proteins. The highest molecular weight proteins (>80 kDa) were observed to be the targeted proteins to nucleus of host cell. There was no constant patterns observed in the values of isoelectric point (pI) in case of mitochondrial targeting. The expression of eight proteins were significant with different fold changes. The in-silico study provided much detailed insights for further research in gynecological cancer. However, further experiments should be conducted to validate the specificity and confirmatory roles played by these predicted proteins in carcinogenesis.
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Affiliation(s)
- Yanyan Lin
- Faculty of Basic Medicine, Zhangzhou Health Vocational College, Synergistic innovation center of transformation medical testing application technology of Zhangzhou Health Vocational College (TMTSIC), Zhangzhou City, Fujian Province, China.
| | - Abdul Wahab Ali Abuderman
- Department of Basic Medical Science, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia.
| | - Fahad M Aldakheel
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
| | - Mohammad Ahmad
- Medical Surgical Department, College of Nursing, King Saud University, P.O. Box 642, Riyadh, 11421, Saudi Arabia.
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Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a nonmutagenic approach, we can capture all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
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Jones CA, Hadfield J, Thomson NR, Cleary DW, Marsh P, Clarke IN, O’Neill CE. The Nature and Extent of Plasmid Variation in Chlamydia trachomatis. Microorganisms 2020; 8:microorganisms8030373. [PMID: 32155798 PMCID: PMC7143637 DOI: 10.3390/microorganisms8030373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 01/03/2023] Open
Abstract
Chlamydia trachomatis is an obligate intracellular pathogen of humans, causing both the sexually transmitted infection, chlamydia, and the most common cause of infectious blindness, trachoma. The majority of sequenced C. trachomatis clinical isolates carry a 7.5-Kb plasmid, and it is becoming increasingly evident that this is a key determinant of pathogenicity. The discovery of the Swedish New Variant and the more recent Finnish variant highlight the importance of understanding the natural extent of variation in the plasmid. In this study we analysed 524 plasmid sequences from publicly available whole-genome sequence data. Single nucleotide polymorphisms (SNP) in each of the eight coding sequences (CDS) were identified and analysed. There were 224 base positions out of a total 7550 bp that carried a SNP, which equates to a SNP rate of 2.97%, nearly three times what was previously calculated. After normalising for CDS size, CDS8 had the highest SNP rate at 3.97% (i.e., number of SNPs per total number of nucleotides), whilst CDS6 had the lowest at 1.94%. CDS5 had the highest total number of SNPs across the 524 sequences analysed (2267 SNPs), whereas CDS6 had the least SNPs with only 85 SNPs. Calculation of the genetic distances identified CDS6 as the least variable gene at the nucleotide level (d = 0.001), and CDS5 as the most variable (d = 0.007); however, at the amino acid level CDS2 was the least variable (d = 0.001), whilst CDS5 remained the most variable (d = 0.013). This study describes the largest in-depth analysis of the C. trachomatis plasmid to date, through the analysis of plasmid sequence data mined from whole genome sequences spanning 50 years and from a worldwide distribution, providing insights into the nature and extent of existing variation within the plasmid as well as guidance for the design of future diagnostic assays. This is crucial at a time when single-target diagnostic assays are failing to detect natural mutants, putting those infected at risk of a serious long-term and life-changing illness.
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Affiliation(s)
- Charlotte A. Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA;
| | - Nicholas R. Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK;
| | - David W. Cleary
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
| | - Peter Marsh
- Public Health England, Porton Down, Wiltshire SP40JG, UK;
| | - Ian N. Clarke
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
| | - Colette E. O’Neill
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
- Correspondence:
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Jin Y, Zhou J, Zhou J, Hu M, Zhang Q, Kong N, Ren H, Liang L, Yue J. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biol Direct 2020; 15:6. [PMID: 32131884 PMCID: PMC7057466 DOI: 10.1186/s13062-020-0258-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer This article was reviewed by Dr. Xianwen Ren.
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Affiliation(s)
- Yuan Jin
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jianglin Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jing Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Qi Zhang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Na Kong
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,Anhui University, Hefei, 230039, Anhui, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| | - Long Liang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,Anhui University, Hefei, 230039, Anhui, China.
| | - Junjie Yue
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
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