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Lawrence LA, Vidal P, Varughese RS, Tiger Li ZR, Chen TD, Tuske SC, Jimenez AR, Lowen AC, Shafer WM, Swaims-Kohlmeier A. Murine modeling of menstruation identifies immune correlates of protection during Chlamydia muridarum challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595090. [PMID: 38826233 PMCID: PMC11142139 DOI: 10.1101/2024.05.21.595090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The menstrual cycle influences the risk of acquiring sexually transmitted infections (STIs), including Chlamydia trachomatis (C. trachomatis), although the underlying immune contributions are poorly defined. A mouse model simulating the immune-mediated process of menstruation could provide valuable insights into tissue-specific determinants of protection against chlamydial infection within the cervicovaginal and uterine mucosae comprising the female reproductive tract (FRT). Here, we used the pseudopregnancy approach in naïve C57Bl/6 mice and performed vaginal challenge with Chlamydia muridarum (C. muridarum) at decidualization, endometrial tissue remodeling, or uterine repair. This strategy identified that the time frame comprising uterine repair correlated with robust infection and greater bacterial burden as compared with mice on hormonal contraception, while challenges during endometrial remodeling were least likely to result in a productive infection. By comparing the infection site at early time points following chlamydial challenge, we found that a greater abundance of innate effector populations and proinflammatory signaling, including IFNγ correlated with protection. FRT immune profiling in uninfected mice over pseudopregnancy or in pig-tailed macaques over the menstrual cycle identified NK cell infiltration into the cervicovaginal tissues and lumen over the course of endometrial remodeling. Notably, NK cell depletion over this time frame reversed protection, with mice now productively infected with C. muridarum following challenge. This study shows that the pseudopregnancy murine menstruation model recapitulates immune changes in the FRT as a result of endometrial remodeling and identifies NK cell localization at the FRT as essential for immune protection against primary C. muridarum infection.
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Affiliation(s)
- Laurel A Lawrence
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Paola Vidal
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Richa S Varughese
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Zheng-Rong Tiger Li
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Thien Duy Chen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Steven C Tuske
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Ariana R Jimenez
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
| | - William M Shafer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Laboratories of Bacterial Pathogenesis, Atlanta Veterans Affairs Medical Center, Decatur, Georgia
| | - Alison Swaims-Kohlmeier
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Department of GYNOB, Emory University School of Medicine, Atlanta, Georgia
- Division of HIV Prevention Centers for Disease Control and Prevention, Atlanta, Georgia (previous affiliation)
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2
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Favacho JDFR, Leite KK, Jacomasso T, Farias AB, Franco Filho LC, Gomes STM, dos Reis HS, Mota GD, Schluga PHDC, Tassi WS, Rampazzo RDCP, West SK, Gaydos CA, da Cunha AJLA, Costa ADT. Validation of a New Duplex Real-Time Polymerase Chain Reaction for Chlamydia trachomatis DNA Detection in Ocular Swab Samples. Diagnostics (Basel) 2024; 14:892. [PMID: 38732307 PMCID: PMC11083659 DOI: 10.3390/diagnostics14090892] [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: 01/26/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 05/13/2024] Open
Abstract
Trachoma is the world-leading infectious cause of preventable blindness and is caused by the bacteria Chlamydia trachomatis. In developing countries, diagnosis is usually based on clinical evaluation. Serological-based tests are cheaper than molecular-based ones, but the latter are more sensitive and specific. The present study developed a new duplex qPCR which concomitantly detects the C. trachomatis cryptic plasmid and the human 18S rRNA gene, with an LOD95% for C. trachomatis DNA of 13.04 genome equivalents per reaction. The new qPCR was tested using 50 samples from an endemic area and 12 from a non-endemic area that were previously characterized using direct immunofluorescence assay (DFA) and clinical evaluation. Among the 50 endemic samples, 3 were found to be positive by clinical evaluation (6%), 18 were found to be positive by DFA (36%), and 48 were found to be positive by qPCR (96%). Next, the new duplex qPCR was validated using 50 samples previously characterized by qPCR. Validation was carried out on a benchtop instrument (ABI7500) or on a portable point-of-care instrument (Q3-Plus), showing 95% specificity and 100% sensitivity. The ubiquitous presence of C. trachomatis DNA in samples from the endemic region confirms that constant monitoring is of paramount importance for the effective measurement of the elimination of trachoma. The newly developed duplex qPCR presented in this study, along with its validation in a portable qPCR system, constitutes important tools toward achieving this goal.
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Affiliation(s)
- Joana da Felicidade Ribeiro Favacho
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Keren Kariene Leite
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Thiago Jacomasso
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Aline Burda Farias
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Luciano Chaves Franco Filho
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Samara Tatielle Monteiro Gomes
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Herald Souza dos Reis
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Gardene Dourado Mota
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | | | - Walleyd Sami Tassi
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | | | - Sheila Kay West
- Dana Center for Preventative Ophthalmology, Johns Hopkins University, Baltimore, MD 21287, USA;
| | - Charlotte Ann Gaydos
- International Sexually Transmitted Disease Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD 21218, USA
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3
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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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Galogahi FM, Christie M, Yadav AS, An H, Stratton H, Nguyen NT. Microfluidic encapsulation of DNAs in liquid beads for digital PCR application. Analyst 2023; 148:4064-4071. [PMID: 37469285 DOI: 10.1039/d3an00868a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Droplet-based microfluidics and digital polymerase chain reaction (PCR) hold significant promise for accurately detecting and quantifying pathogens. However, existing droplet-based digital PCR (ddPCR) applications have been relying exclusively on single emulsion droplets. Single emulsion droplets may not be suitable for applications such as identifying the source and pathways of water contamination where the templates must be protected against harsh environmental conditions. In this study, we developed a core-shell particle to serve as a protective framework for DNAs, with potential applications in digital PCR. We employed a high-throughput and facile flow-focusing microfluidic device to generate liquid beads, core-shell particles with liquid cores, which provided precise control over process parameters and consequently particle characteristics. Notably, the interfacial interaction between the core and shell liquids could be adjusted without adding surfactants to either phase. As maintaining stability is essential for ensuring the accuracy of digital PCR (dPCR), we investigated parameters that affect the stability of core-shell droplets, including surfactants in the continuous phase and core density. As a proof of concept, we encapsulated a series of human faecal DNA samples in the core-shell droplets and the subsequent liquid beads. The core-shell particles ensure contamination-free encapsulation of DNA in the core. The volume of the core droplets containing the PCR mixture is only 0.12 nL. Our experimental results indicate that the liquid beads formulated using our technique can amplify the encapsulated DNA and be used for digital PCR without interfering with the fluorescence signal. We successfully demonstrated the ability to detect and quantify DNA under varying concentrations. These findings provide new insights and a step change in digital PCR that could benefit various applications, including the detection and tracking of environmental pollution.
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Affiliation(s)
- Fariba Malekpour Galogahi
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Melody Christie
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Ajeet Singh Yadav
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Hongjie An
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Helen Stratton
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Nathan, Queensland 4111, Australia.
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5
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Murthy S, Suresh A, Dandasena D, Singh S, Subudhi M, Bhandari V, Bhanot V, Arora JS, Sharma P. Multiplex ddPCR: A Promising Diagnostic Assay for Early Detection and Drug Monitoring in Bovine Theileriosis. Pathogens 2023; 12:pathogens12020296. [PMID: 36839568 PMCID: PMC9965958 DOI: 10.3390/pathogens12020296] [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: 10/22/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 02/16/2023] Open
Abstract
Accurate quantification based on nucleic acid amplification is necessary to avoid the spread of pathogens, making early diagnosis essential. Droplet digital PCR (ddPCR) stands out for absolute parasite quantification because it combines microfluidics with the TaqMan test. This helps deliver maximum accuracy without needing a reference curve. This study assessed the efficacy of ddPCR as a detection tool for the bovine theileriosis (BT) caused by Theileria parasites. We developed and validated a duplex ddPCR method that detects and quantifies the Theileria genus (18S rRNA) and identifies clinically significant Theileria annulata parasites (TaSP) in experimental and clinical samples. ddPCR was shown to be as effective as qPCR throughout a 10-fold sample dilution range. However, ddPCR was more sensitive than qPCR at lower parasite DNA concentrations and reliably assessed up to 8.5 copies/µL of the TaSP gene in the infected DNA (0.01 ng) samples. The ddPCR was very accurate and reproducible, and it could follow therapeutic success in clinical cases of theileriosis. In conclusion, our ddPCR assays were highly sensitive and precise, providing a valuable resource for the study of absolute parasite quantification, drug treatment monitoring, epidemiological research, large-scale screening, and the identification of asymptomatic parasite reservoirs in the pursuit of BT eradication.
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Affiliation(s)
- Shweta Murthy
- National Institute of Animal Biotechnology, Hyderabad 500032, India
| | - Akash Suresh
- National Institute of Animal Biotechnology, Hyderabad 500032, India
| | - Debabrata Dandasena
- National Institute of Animal Biotechnology, Hyderabad 500032, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad 121001, India
| | - Sakshi Singh
- National Institute of Animal Biotechnology, Hyderabad 500032, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad 121001, India
| | - Madhusmita Subudhi
- National Institute of Animal Biotechnology, Hyderabad 500032, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad 121001, India
| | - Vasundhra Bhandari
- National Institute of Animal Biotechnology, Hyderabad 500032, India
- Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad 121001, India
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500037, India
| | - Vandna Bhanot
- Disease Investigation Laboratory, LUVAS (Hisar), Haryana 125011, India
| | | | - Paresh Sharma
- National Institute of Animal Biotechnology, Hyderabad 500032, India
- Correspondence:
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Pickering H, Ramadhani AM, Massae P, Mafuru E, Malisa A, Mbuya K, Makupa W, Mtuy T, Derrick T, Houghton J, Bailey RL, Mabey DCW, Burton MJ, Holland MJ. The conjunctival microbiome before and after azithromycin mass drug administration for trachoma control in a cohort of Tanzanian children. Front Public Health 2022; 10:1015714. [PMID: 36324475 PMCID: PMC9619060 DOI: 10.3389/fpubh.2022.1015714] [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: 08/10/2022] [Accepted: 09/30/2022] [Indexed: 01/27/2023] Open
Abstract
Background Trachoma, caused by ocular infection with Chlamydia trachomatis, is a neglected tropical disease that can lead to blinding pathology. Current trachoma control programmes have successfully used mass drug administration (MDA) with azithromycin to clear C. trachomatis infection and reduce transmission, alongside promoting facial cleanliness for better personal hygiene and environmental improvement. In areas of low-trachoma endemicity, the relationship between C. trachomatis infection and trachomatous disease weakens, and non-chlamydial bacteria have been associated with disease signs. Methods We enrolled a cohort of children aged 6-10 years from three adjacent trachoma endemic villages in Kilimanjaro and Arusha regions, Northern Tanzania. Children were divided into four clinical groups based on the presence or absence of ocular C. trachomatis infection and clinical signs of trachomatous papillary inflammation (TP). To determine the impact of treatment on the ocular microbiome in these clinical groups, we performed V4-16S rRNA sequencing of conjunctival DNA from children 3-9 months pre-MDA (n = 269) and 3 months post-MDA (n = 79). Results Chlamydia trachomatis PCR-negative, no TP children had the highest pre-MDA ocular microbiome alpha diversity, which was reduced in C. trachomatis infected children and further decreased in those with TP. Pre-MDA, Haemophilus and Staphylococcus were associated with C. trachomatis infection with and without concurrent TP, while Helicobacter was increased in those with TP in the absence of current C. trachomatis infection. Post-MDA, none of the studied children had ocular C. trachomatis infection or TP. MDA increased ocular microbiome diversity in all clinical groups, the change was of greater magnitude in children with pre-MDA TP. MDA effectively reduced the prevalence of disease causing pathogenic non-chlamydial bacteria, and promoted restoration of a normal, healthy conjunctival microbiome. Conclusion We identified Helicobacter as a non-chlamydial bacterium associated with the clinical signs of TP. Further investigation to determine its relevance in other low-endemicity communities is required. MDA was shown to be effective at clearing C. trachomatis infection and other non-chlamydial ocular pathogens, without any detrimental longitudinal effects on the ocular microbiome. These findings suggest that azithromycin MDA may be valuable in trachoma control even in populations where the relationship between clinical signs of trachoma and the prevalence of current ocular C. trachomatis infection has become dissociated.
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Affiliation(s)
- Harry Pickering
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom,*Correspondence: Harry Pickering
| | | | | | - Elias Mafuru
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Aiweda Malisa
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Kelvin Mbuya
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | - Tara Mtuy
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Tamsyn Derrick
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Joanna Houghton
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Robin L. Bailey
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David C. W. Mabey
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew J. Burton
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom,National Institute for Health Research (NIHR) Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Martin J. Holland
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom,Kilimanjaro Christian Medical Centre, Moshi, Tanzania
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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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Shin J, Shin S, Jung SH, Park C, Cho SY, Lee DG, Chung YJ. Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach. J Microbiol Biotechnol 2021; 31:1481-1489. [PMID: 34528911 PMCID: PMC9705831 DOI: 10.4014/jmb.2103.03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsiscausing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.
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Affiliation(s)
- Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biochemistry, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Corresponding author Phone: +82-2-2258-7343 Fax: +82-2-537-0572 E-mail:
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9
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Sahu R, Vishnuraj MR, Srinivas C, Dadimi B, Megha GK, Pollumahanti N, Malik SS, Vaithiyanathan S, Rawool DB, Barbuddhe SB. Development and comparative evaluation of droplet digital PCR and quantitative PCR for the detection and quantification of Chlamydia psittaci. J Microbiol Methods 2021; 190:106318. [PMID: 34592374 DOI: 10.1016/j.mimet.2021.106318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Chlamydia psittaci is a zoonotic pathogen mainly transmitted by psittacine birds and poultry. The low shedding rate of the pathogen in the apparently healthy birds and human clinical cases may result in false-negative results. In the present study, a droplet digital PCR (ddPCR) assay was developed and compared with optimized quantitative PCR (qPCR) for the detection of C. psittaci from the clinical samples. The ddPCR assay was found to be comparatively more sensitive than the qPCR, wherein the limit of detection (LOD) of ddPCR was upto 2.4 copies of the DNA template, whereas, the qPCR could detect upto 38 copies of the DNA template in the reaction mixture. Overall, the developed ddPCR assay was found to be robust, specific, and could reliably quantify up to 17.8 copies of the DNA template. Finally, the applicability of the developed ddPCR assay was tested by screening the field samples (n = 124), comprising lung tissues from dead poultry and feral birds; pooled faecal samples from the free-living birds, commercial and backyard poultry farms; pharyngeal and cloacal swabs collected from the duck farms. Of these, a total of seven samples were found to be positive by the ddPCR, whereas, three samples could be detected as positive using the qPCR. The developed ddPCR could serve as a reliable screening tool, particularly in those clinical samples wherein the shedding of C. psittaci is substantially very low.
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Affiliation(s)
- Radhakrishna Sahu
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India; Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - M R Vishnuraj
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Ch Srinivas
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Bhargavi Dadimi
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - G K Megha
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | | | - Satyaveer S Malik
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - S Vaithiyanathan
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Deepak B Rawool
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
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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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11
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Lei S, Chen S, Zhong Q. Digital PCR for accurate quantification of pathogens: Principles, applications, challenges and future prospects. Int J Biol Macromol 2021; 184:750-759. [PMID: 34171259 DOI: 10.1016/j.ijbiomac.2021.06.132] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022]
Abstract
Pathogens pose a severe threat to food safety and human health. The traditional methods for pathogen detection can't meet the growing diagnosis and control need. Digital PCR (dPCR) attracts a considerable attention for its ability to absolutely quantify pathogens with features of high selectivity, simplicity, accuracy and rapidity. The dPCR technique that achieves absolute quantification based on end-point measurement without standard curve offers a guideline for further genetic analysis and molecular diagnosis. It could contribute to the quantification of low level of nucleic acid, early detection and timely prevention of pathogenic diseases. In this review, 1442 publications about dPCR were selected and the detections of various pathogens by dPCR were reviewed comprehensively, including viruses, bacteria, parasites and fungi. A number of examples are cited to illustrate that dPCR is a new powerful tool with desired accuracy, sensitivity, and reproducibility for quantification of different types of pathogens. Moreover, the benefits, challenges and future prospects of the dPCR were also highlighted in this review.
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Affiliation(s)
- Shuwen Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Song Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qingping Zhong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China.
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12
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Macleod CK, Butcher R, Javati S, Gwyn S, Jonduo M, Abdad MY, Roberts CH, Keys D, Koim SP, Ko R, Garap J, Pahau D, Houinei W, Martin DL, Pomat WS, Solomon AW. Trachoma, Anti-Pgp3 Serology, and Ocular Chlamydia trachomatis Infection in Papua New Guinea. Clin Infect Dis 2021; 72:423-430. [PMID: 31965155 PMCID: PMC7850549 DOI: 10.1093/cid/ciaa042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/19/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND In Melanesia, the prevalence of trachomatous inflammation-follicular (TF) suggests that public health-level interventions against active trachoma are needed. However, the prevalence of trachomatous trichiasis is below the threshold for elimination as a public health problem and evidence of conjunctival infection with trachoma's causative organism (Chlamydia trachomatis [CT]) is rare. Here, we examine the prevalence of ocular infection with CT and previous exposure to CT in three evaluation units (EUs) of Papua New Guinea. METHODS All individuals aged 1-9 years who were examined for clinical signs of trachoma in 3 Global Trachoma Mapping Project EUs were eligible to take part in this study (N = 3181). Conjunctival swabs were collected from 349 children with TF and tested by polymerase chain reaction to assess for ocular CT infection. Dried blood spots were collected from 2572 children and tested for anti-Pgp3 antibodies using a multiplex assay. RESULTS The proportion of children with TF who had CT infection was low across all 3 EUs (overall 2%). Anti-Pgp3 seroprevalence was 5.2% overall and there was no association between anti-Pgp3 antibody level and presence of TF. In 2 EUs, age-specific seroprevalence did not increase significantly with increasing age in the 1- to 9-year-old population. In the third EU, there was a statistically significant change with age but the overall seroprevalence and peak age-specific seroprevalence was very low. CONCLUSIONS Based on these results, together with similar findings from the Solomon Islands and Vanuatu, the use of TF to guide antibiotic mass drug administration decisions in Melanesia should be reviewed.
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Affiliation(s)
- Colin K Macleod
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Robert Butcher
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sarah Javati
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Sarah Gwyn
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marinjho Jonduo
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Mohammad Yazid Abdad
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
- National Centre for Infectious Diseases, Singapore
| | - Chrissy H Roberts
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Drew Keys
- Brien Holden Vision Institute Foundation, Sydney, Australia
| | | | - Robert Ko
- Department of Ophthalmology, Port Moresby General Hospital, Port Moresby, Papua New Guinea
| | - Jambi Garap
- Department of Ophthalmology, Port Moresby General Hospital, Port Moresby, Papua New Guinea
| | - David Pahau
- Department of Ophthalmology, Boram General Hospital, Wewak, Papua New Guinea
| | - Wendy Houinei
- Neglected Tropical Diseases, National Department of Health, Port Moresby, Papua New Guinea
| | - Diana L Martin
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - William S Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Anthony W Solomon
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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13
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Cheng YY, Yuen ML, Rath EM, Johnson B, Zhuang L, Yu TK, Aleksova V, Linton A, Kao S, Clarke CJ, McCaughan BC, Takahashi K, Lee K. CDKN2A and MTAP Are Useful Biomarkers Detectable by Droplet Digital PCR in Malignant Pleural Mesothelioma: A Potential Alternative Method in Diagnosis Compared to Fluorescence In Situ Hybridisation. Front Oncol 2020; 10:579327. [PMID: 33304846 PMCID: PMC7693432 DOI: 10.3389/fonc.2020.579327] [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: 07/02/2020] [Accepted: 10/12/2020] [Indexed: 01/22/2023] Open
Abstract
Background The diagnosis of malignant pleural mesothelioma (MPM) can be difficult, in part due to the difficulty in distinguishing between MPM and reactive mesothelial hyperplasia (RMH). The tumor suppressor gene, CDKN2A, is frequently silenced by epigenetic mechanisms in many cancers; in the case of MPM it is mostly silenced via genomic deletion. Co-deletion of the CDKN2A and methylthioadenosine phosphorylase (MTAP) genes has been researched extensively and discovered to be a highly specific characteristic of MPM. Most studies have used FISH to detect the deletion of CDKN2A and IHC for MTAP as a surrogate for this. In this study, we aim to investigate and validate droplet digital PCR (ddPCR) as an emerging alternative and efficient testing method in diagnosing MPM, by particularly emphasizing on the loss of MTAP and CDKN2A. Methods This study included 75 formalin fixed paraffin embedded (FFPE) MPM tissue, and 12 normal pleural tissue and 10 RMH as control. Additionally, primary MPM cell lines and normal pleural samples were used as biomarker detection controls, as established in our previous publication. All FFPE specimens were processed to isolate the DNA, that was subsequently used for ddPCR detection of CDKN2A and MTAP. FFPE samples were also analyzed by fluorescence in situ hybridization (FISH) for CDKN2A and MTAP deletion, and for MTAP IHC expression. Concordance of IHC and ddPCR with FISH were studied in these samples. Results 95% and 82% of cases showed co-deletion of both MTAP and CDKN2A when determined by FISH and ddPCR respectively. ddPCR has a sensitivity of 72% and specificity of 100% in detecting CDKN2A homozygous loss in MPM. ddPCR also has a concordance rate of 92% with FISH in detecting homozygous loss of CDKN2A. MTAP IHC was 68% sensitive and 100% specific for detecting CDKN2A homozygous loss in MPM when these losses were determined by ddPCR. Conclusion Our study confirms that MTAP is often co-deleted with CDKN2A in MPM. Our in-house designed ddPCR assays for MTAP and CDKN2A are useful in differentiating MPM from RMH, and is highly concordant with FISH that is currently used in diagnosing MPM. ddPCR detection of these genetic losses can potentially be utilized as an alternative method in the diagnosis of MPM and for the future development of a less-invasive MPM-specific detection technique on MPM tumor tissue DNA.
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Affiliation(s)
- Yuen Yee Cheng
- Asbestos Diseases Research Institute, Concord, NSW, Australia
| | - Man Lee Yuen
- Asbestos Diseases Research Institute, Concord, NSW, Australia
| | - Emma M Rath
- Giannoulatou Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Ben Johnson
- Asbestos Diseases Research Institute, Concord, NSW, Australia
| | - Ling Zhuang
- Asbestos Diseases Research Institute, Concord, NSW, Australia
| | - Ta-Kun Yu
- Asbestos Diseases Research Institute, Concord, NSW, Australia
| | - Vesna Aleksova
- Asbestos Diseases Research Institute, Concord, NSW, Australia
| | - Anthony Linton
- Asbestos Diseases Research Institute, Concord, NSW, Australia.,Concord Repatriation General Hospital, School of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Steven Kao
- Asbestos Diseases Research Institute, Concord, NSW, Australia.,Chris O'Brien Life House, School of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Candice Julie Clarke
- Anatomical Pathology Department, NSW Health Pathology, Concord Repatriation General Hospital, Sydney, NSW, Australia
| | - Brian C McCaughan
- Sydney Cardiothoracic Surgeons, RPA Medical Centre, Sydney, NSW, Australia
| | - Ken Takahashi
- Asbestos Diseases Research Institute, Concord, NSW, Australia
| | - Kenneth Lee
- Asbestos Diseases Research Institute, Concord, NSW, Australia.,Concord Repatriation General Hospital, School of Medicine, University of Sydney, Sydney, NSW, Australia.,Anatomical Pathology Department, NSW Health Pathology, Concord Repatriation General Hospital, Sydney, NSW, Australia
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14
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Kathrada AI, Wei SC, Xu Y, Cheow, LF, Chen CH. Microfluidic compartmentalization to identify gene biomarkers of infection. BIOMICROFLUIDICS 2020; 14:061502. [PMID: 33312326 PMCID: PMC7717927 DOI: 10.1063/5.0032849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/09/2020] [Indexed: 05/20/2023]
Abstract
Infectious diseases caused by pathogens, such as SARS-COV, H7N9, severe fever with thrombocytopenia syndrome virus, and human immunodeficiency virus, have fatal outcomes with common features of severe fever and subsequent bacterial invasion progressing to multiorgan failure. Gene biomarkers are promising to distinguish specific infections from others with similar presenting symptoms for the prescription of correct therapeutics, preventing pandemics. While routine laboratory methods based on polymerase chain reaction (PCR) to measure gene biomarkers have provided highly sensitive and specific viral detection techniques over the years, they are still hampered by their precision and resource intensity precluding their point-of-care use. Recently, there has been growing interest in employing microfluidic technologies to advance current methods for infectious disease determination via gene biomarker measurements. Here, based on the requirement of infection detection, we will review three microfluidic approaches to compartmentalize gene biomarkers: (1) microwell-based PCR platforms; (2) droplet-based PCR; and (3) point-of-care devices including centrifugal chip, SlipChip, and self-powered integrated microfluidic point-of-care low-cost enabling chip. By capturing target genes in microwells with a small sample volume (∼μl), sensitivity can be enhanced. Additionally, with the advance of significant sample volume minimization (∼pl) using droplet technology, gene quantification is possible. These improvements in cost, automation, usability, and portability have thereby allowed point-of-care applications to decentralize testing platforms from laboratory-based settings to field use against infections.
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Affiliation(s)
- Ahmad Ismat Kathrada
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Block 4, #04-08, Singapore 117583
| | | | - Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, Room Y6700, 6/F, Yeung Kin Man Academic Building, 83 Tat Chee Avenue, Hong Kong, China
| | | | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Room Y6700, 6/F, Yeung Kin Man Academic Building, 83 Tat Chee Avenue, Hong Kong, China
- Author to whom correspondence should be addressed:
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15
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Versteeg B, Vasileva H, Houghton J, Last A, Shafi Abdurahman O, Sarah V, Macleod D, Solomon AW, Holland MJ, Thomson N, Burton MJ. Viability PCR shows that non-ocular surfaces could contribute to transmission of Chlamydia trachomatis infection in trachoma. PLoS Negl Trop Dis 2020; 14:e0008449. [PMID: 32667914 PMCID: PMC7384675 DOI: 10.1371/journal.pntd.0008449] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/27/2020] [Accepted: 06/03/2020] [Indexed: 11/24/2022] Open
Abstract
Background The presence of Chlamydia trachomatis (Ct) DNA at non-ocular sites suggests that these sites may represent plausible routes of Ct transmission in trachoma. However, qPCR cannot discriminate between DNA from viable and non-viable bacteria. Here we use a propodium monoazide based viability PCR to investigate how long Ct remains viable at non-ocular sites under laboratory-controlled conditions. Methods Cultured Ct stocks (strain A2497) were diluted to final concentrations of 1000, 100, 10 and 1 omcB copies/μL and applied to plastic, woven mat, cotton cloth and pig skin. Swabs were then systemically collected from each surface and tested for the presence Ct DNA using qPCR. If Ct DNA was recovered, Ct viability was assessed over time by spiking multiple areas of the same surface type with the same final concentrations. Swabs were collected from each surface at 0, 2, 4, 6, 8 and 24 hours after spiking. Viability PCR was used to determine Ct viability at each timepoint. Results We were able to detect Ct DNA on all surfaces except the woven mat. Total Ct DNA remained detectable and stable over 24 hours for all concentrations applied to plastic, pig skin and cotton cloth. The amount of viable Ct decreased over time. For plastic and skin surfaces, only those where concentrations of 100 or 1000 omcB copies/μL were applied still had viable loads detectable after 24 hours. Cotton cloth showed a more rapid decrease and only those where concentrations of 1000 omcB copies/μL were applied still had viable DNA detectable after 24 hours. Conclusion Plastic, cotton cloth and skin may contribute to transmission of the Ct strains that cause trachoma, by acting as sites where reservoirs of bacteria are deposited and later collected and transferred mechanically into previously uninfected eyes. Trachoma elimination efforts are hampered by limited understanding of Ct transmission routes. We have recently demonstrated the presence of Ct DNA at non-ocular sites in individuals living in households in Ethiopia where at least one resident had an ocular Ct infection detectable by quantitative PCR (qPCR). Ct DNA was most frequently detected on faces, hands and clothing, being found in such locations in 10–16% of samples tested. However, qPCR cannot discriminate between DNA from viable and non-viable organisms, and potentially misinform our understanding of Ct transmission routes. In this study, we used a propidium monoazide based viability PCR to investigate how long Ct remains viable on non-ocular sites by spiking different surfaces including pig skin, plastic and cotton cloth. These surfaces mimic non-ocular sites previously found to be positive for Ct DNA using standard qPCR. The results of our study show that viable Ct DNA could be recovered from plastic, cotton cloth and skin surfaces for up to 24 hours suggesting that these surfaces a role in ocular Ct transmission.
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Affiliation(s)
- Bart Versteeg
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Hristina Vasileva
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joanna Houghton
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Anna Last
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Oumer Shafi Abdurahman
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- The Fred Hollows Foundation, Addis Ababa, Ethiopia
| | | | - David Macleod
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Anthony W. Solomon
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Martin J. Holland
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Nicholas Thomson
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Matthew J. Burton
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
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16
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Bowman EK, Alper HS. Microdroplet-Assisted Screening of Biomolecule Production for Metabolic Engineering Applications. Trends Biotechnol 2020; 38:701-714. [DOI: 10.1016/j.tibtech.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 12/19/2022]
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17
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Nash SD, Chernet A, Moncada J, Stewart AEP, Astale T, Sata E, Zerihun M, Gessese D, Melak B, Ayenew G, Ayele Z, Chanyalew M, Lietman TM, Callahan EK, Schachter J, Tadesse Z. Ocular Chlamydia trachomatis infection and infectious load among pre-school aged children within trachoma hyperendemic districts receiving the SAFE strategy, Amhara region, Ethiopia. PLoS Negl Trop Dis 2020; 14:e0008226. [PMID: 32421719 PMCID: PMC7259799 DOI: 10.1371/journal.pntd.0008226] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 05/29/2020] [Accepted: 03/17/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND After approximately 5 years of SAFE (surgery, antibiotics, facial cleanliness, environmental improvement) interventions for trachoma, hyperendemic (trachomatous inflammation-follicular (TF) ≥30%) districts remained in Amhara, Ethiopia. This study's aim was to characterize the epidemiology of Chlamydia trachomatis (Ct) infection and load among pre-school aged children living under the SAFE strategy. METHODS Conjunctival swabs from a population-based sample of children aged 1-5 years collected between 2011 and 2015 were assayed to provide Ct infection data from 4 endemic zones (comprised of 58 districts). Ct load was determined using a calibration curve. Children were graded for TF and trachomatous inflammation-intense (TI). RESULTS 7,441 children were swabbed in 4 zones. TF and TI prevalence were 39.9% (95% confidence Interval [CI]: 37.5%, 42.4%), and 9.2% (95% CI: 8.1%, 10.3%) respectively. Ct infection prevalence was 6.0% (95% CI: 5.0%, 7.2%). Infection was highest among children aged 2 to 4 years (6.6%-7.0%). Approximately 10% of infection occurred among children aged 1 year. Ct load decreased with age (P = 0.002), with the highest loads observed in children aged 1 year (P = 0.01) vs. aged 5 years. Participants with TF (P = 0.20) and TI (P<0.01) had loads greater than individuals without active trachoma. CONCLUSIONS In this hyperendemic setting, it appears that the youngest children may contribute in meaningful ways towards persistent active trachoma.
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Affiliation(s)
- Scott D. Nash
- Trachoma Control Program, The Carter Center, Atlanta, United States of America
| | - Ambahun Chernet
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Jeanne Moncada
- Department of Laboratory Medicine, University of California, San Francisco, United States of America
| | - Aisha E. P. Stewart
- Trachoma Control Program, The Carter Center, Atlanta, United States of America
| | - Tigist Astale
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Eshetu Sata
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Mulat Zerihun
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Demelash Gessese
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Berhanu Melak
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Gedefaw Ayenew
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Zebene Ayele
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
| | - Melsew Chanyalew
- Health Promotion and Disease Prevention Core Process, Amhara Regional Health Bureau, Bahir Dar, Ethiopia
| | - Thomas M. Lietman
- Francis I. Proctor Foundation, University of California, San Francisco, United States of America
| | - E. Kelly Callahan
- Trachoma Control Program, The Carter Center, Atlanta, United States of America
| | - Julius Schachter
- Department of Laboratory Medicine, University of California, San Francisco, United States of America
| | - Zerihun Tadesse
- Trachoma Control Program, The Carter Center, Addis Ababa, Ethiopia
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18
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Deepthi KG, Prabagaran SR. Ocular bacterial infections: Pathogenesis and diagnosis. Microb Pathog 2020; 145:104206. [PMID: 32330515 DOI: 10.1016/j.micpath.2020.104206] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
The human eye is a rigid asymmetric structure with unique defence system. Despite considerable resident microbiota, eye is exposed to external environment where a range of microorganisms also inhabits. Opportunistically, some of these microorganisms could associate with eye pathogen that could contact incidentally, leading to destructive visual consequences. Among such microbiota, bacteria form the major proportion concerning ocular complications worldwide. The succession of genome based approach through 16S rRNA gene based identification tremendously augmented the knowledge on diversity of ocular surface bacteria. Such evidence suggests that while few bacteria contribute towards normal ocular functions, considerable number of bacteria play active role in pathophysiology of ocular diseases. Thus, understanding the complexity of ocular microflora not only throw light on their critical role towards normal function of the eye, but also enlighten on certain visual exigencies. Under these circumstances, development of a rapid, reliable and cost effective method is essential that eventually evolve as a routine diagnostic protocol. Such precise prognostic modalities facilitate ophthalmologists to formulate pioneering therapeutics towards challenging ocular diseases.
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19
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Ocular Chlamydia trachomatis infection, anti-Pgp3 antibodies and conjunctival scarring in Vanuatu and Tarawa, Kiribati before antibiotic treatment for trachoma. J Infect 2020; 80:454-461. [PMID: 32017971 PMCID: PMC7113835 DOI: 10.1016/j.jinf.2020.01.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 11/21/2022]
Abstract
In Vanuatu, ocular Chlamydia infection prevalence is low; in Kiribati it is high. In Vanuatu, Pgp3 seroprevalence does not increase in childhood; in Kiribati it does. Conjunctival scarring is more common in adults in Kiribati than in Vanuatu. Trachomatous inflammation—follicular lacks specificity for ocular Chlamydia infection. Non-TF markers may help to determine need for interventions against active trachoma.
Introduction In the peri-elimination setting, the positive predictive value of trachomatous inflammation–follicular (TF), the primary marker used to determine need for antibiotics for trachoma, is suboptimal. Here, three non-TF measures are used to compare two regions where TF prevalence exceeds the threshold for intervention, but where the Chlamydia trachomatis (Ct) prevalence is different. Methods Population prevalence of trachoma was measured in Vanuatu (n = 3470) and Kiribati (n = 2922). Dried blood spots (DBS) and conjunctival photographs were collected from every survey participant, and conjunctival swabs were collected from those aged 1–9 years. Individuals were tested for blood anti-Pgp3 antibodies, Ct DNA at the conjunctiva and severity of conjunctival scarring. Results The prevalence of TF in 1–9-year-olds was 16.5% in Vanuatu and 38.2% in Tarawa. 7% of people aged ≥1 year in Vanuatu had conjunctival scarring compared to 27% in Tarawa. The prevalence of ocular Ct infection in 1–9-year-olds was 1.5% in Vanuatu and 27.4% in Tarawa. The seroconversion rate amongst 1–9-year-old children in Vanuatu and Tarawa was 0.018 and 0.197 events per child per year, respectively. Conclusions Comparing Vanuatu to Tarawa demonstrates several markers that could be used to differentiate the trachoma status of populations in these (and other) locations.
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Salipante SJ, Jerome KR. Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clin Chem 2019; 66:117-123. [DOI: 10.1373/clinchem.2019.304048] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Abstract
BACKGROUND
The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.
CONTENT
Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.
SUMMARY
dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.
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Affiliation(s)
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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Alkhidir AAI, Holland MJ, Elhag WI, Williams CA, Breuer J, Elemam AE, El Hussain KMK, Ournasseir MEH, Pickering H. Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan. Parasit Vectors 2019; 12:518. [PMID: 31685017 PMCID: PMC6829945 DOI: 10.1186/s13071-019-3770-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan. METHODS This study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates. RESULTS All isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were focused in two genomic loci (CTA0172-CTA0173 and CTA0482). CONCLUSIONS Limited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal transmission between and slow diversification within trachoma-endemic communities. However, diversity may have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes suggests they may have an impact on C. trachomatis growth and transmission in this population.
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Affiliation(s)
| | - Martin J Holland
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Wafa Ibrahim Elhag
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan
| | | | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK.,Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | | | | | | | - Harry Pickering
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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Pickering H, Palmer CD, Houghton J, Makalo P, Joof H, Derrick T, Goncalves A, Mabey DCW, Bailey RL, Burton MJ, Roberts CH, Burr SE, Holland MJ. Conjunctival Microbiome-Host Responses Are Associated With Impaired Epithelial Cell Health in Both Early and Late Stages of Trachoma. Front Cell Infect Microbiol 2019; 9:297. [PMID: 31552195 PMCID: PMC6736612 DOI: 10.3389/fcimb.2019.00297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/31/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Trachoma, a neglected tropical disease, is the leading infectious cause of blindness and visual impairment worldwide. Host responses to ocular chlamydial infection resulting in chronic inflammation and expansion of non-chlamydial bacteria are hypothesized risk factors for development of active trachoma and conjunctival scarring. Methods: Ocular swabs from trachoma endemic populations in The Gambia were selected from archived samples for 16S sequencing and host conjunctival gene expression. We recruited children with active trachoma and adults with conjunctival scarring, alongside corresponding matched controls. Findings: In children, active trachoma was not associated with significant changes in the ocular microbiome. Haemophilus enrichment was associated with antimicrobial responses but not linked to active trachoma. Adults with scarring trachoma had a reduced ocular bacterial diversity compared to controls, with increased relative abundance of Corynebacterium. Increased abundance of Corynebacterium in scarring disease was associated with innate immune responses to the microbiota, dominated by altered mucin expression and increased matrix adhesion. Interpretation: In the absence of current Chlamydia trachomatis infection, changes in the ocular microbiome associate with differential expression of antimicrobial and inflammatory genes that impair epithelial cell health. In scarring trachoma, expansion of non-pathogenic bacteria such as Corynebacterium and innate responses are coincident, warranting further investigation of this relationship. Comparisons between active and scarring trachoma supported the relative absence of type-2 interferon responses in scarring, whilst highlighting a common suppression of re-epithelialization with altered epithelial and bacterial adhesion, likely contributing to development of scarring pathology.
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Affiliation(s)
- Harry Pickering
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christine D Palmer
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Joanna Houghton
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pateh Makalo
- Disease Control and Elimination Theme, MRC Unit the Gambia at LSHTM, Banjul, Gambia
| | - Hassan Joof
- Disease Control and Elimination Theme, MRC Unit the Gambia at LSHTM, Banjul, Gambia
| | - Tamsyn Derrick
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Adriana Goncalves
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David C W Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Robin L Bailey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew J Burton
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chrissy H Roberts
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sarah E Burr
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Disease Control and Elimination Theme, MRC Unit the Gambia at LSHTM, Banjul, Gambia
| | - Martin J Holland
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.,Disease Control and Elimination Theme, MRC Unit the Gambia at LSHTM, Banjul, Gambia
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Ramadhani AM, Derrick T, Macleod D, Massae P, Mafuru E, Malisa A, Mbuya K, Roberts CH, Makupa W, Mtuy T, Bailey RL, Mabey DCW, Holland MJ, Burton MJ. Progression of scarring trachoma in Tanzanian children: A four-year cohort study. PLoS Negl Trop Dis 2019; 13:e0007638. [PMID: 31412025 PMCID: PMC6709924 DOI: 10.1371/journal.pntd.0007638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/26/2019] [Accepted: 07/17/2019] [Indexed: 11/18/2022] Open
Abstract
Background Trachoma is a progressive blinding disease initiated by infection of the conjunctiva with Chlamydia trachomatis. Repeated infections are thought to cause chronic inflammation, which drives scarring, leading to in-turning of the eyelids. The relationship between C. trachomatis, clinical inflammation and scarring development in children is not fully understood due to a paucity of longitudinal studies with infection data at frequent follow-up. Methods and findings This longitudinal cohort study took place in northern Tanzania. Children aged 6–10 years at baseline were eligible for inclusion. Participants were visited every three months for four years. Clinical signs and conjunctival swabs for C. trachomatis detection by qPCR were collected at each time-point. Conjunctival photographs from baseline and final time-points were graded and compared side-by-side to determine scarring incidence and progression. Of the 666 children enrolled in the study, outcome data were obtained for 448. Scarring progression was detected in 103/448 (23%) children; 48 (11%) of which had incident scarring and 55 (12%) had progression of existing scarring. Scarring was strongly associated with increasing episodes of trachomatous papillary inflammation (TP). Weaker associations were found between episodes of C. trachomatis infection and follicular trachoma (TF) with scarring progression in unadjusted models, which were absent in multivariable analysis after adjusting for inflammation (multivariable results: C. trachomatis p = 0.44, TF p = 0.25, TP p = <0.0001, age p = 0.13, female sex p = 0.05). Individuals having TP at 30% or more of the time-points they were seen had an odds ratio of 7.5 (95%CI = 2.7–20.8) for scarring progression relative to individuals without any TP detected during the study period. Conclusions These data suggest that the effect of infection on scarring progression is mediated through papillary inflammation, and that other factors contributing to the development of inflammation, in addition to C. trachomatis infection, may be important in driving conjunctival scarring progression in children. The addition of TP as a measure in trachoma control programs would provide an indication of the future risk of developing scarring sequelae. Trachoma is the leading cause of preventable blindness worldwide and is targeted for elimination as a public health problem by 2020. The natural history of trachoma is not completely understood however. We conducted a four-year longitudinal study in a trachoma-endemic area of northern Tanzania with detailed follow up every three months. In the four-year study period, nearly one quarter of children developed progression of conjunctival scarring, despite three rounds of annual mass drug administration (MDA) for trachoma control. Disease progression was strongly associated with increasing proportion of episodes with conjunctival papillary inflammation (TP), and only weakly associated with Chlamydia trachomatis infection and trachomatous inflammation–follicular (TF). Analysis revealed that associations between infection and TF with scarring progression were mediated through TP, and that other factors causing individual differences in TP were also contributing to scarring progression. These data have significant implications for trachoma control. We hypothesise that in individuals who have previously experienced ocular C. trachomatis infection, TP is the primary driver of scarring progression. The addition of TP to trachoma surveillance programs would provide an indicator for active disease progression in the community and a more accurate guide to the need for future trichiasis interventions.
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Affiliation(s)
- Athumani M. Ramadhani
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- * E-mail:
| | - Tamsyn Derrick
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - David Macleod
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Elias Mafuru
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Aiweda Malisa
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Kelvin Mbuya
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | | | - Tara Mtuy
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Robin L. Bailey
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David C. W. Mabey
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin J. Holland
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew J. Burton
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Ramadhani AM, Derrick T, Macleod D, Massae P, Malisa A, Mbuya K, Mtuy T, Makupa W, Roberts CH, Bailey RL, Mabey DCW, Holland MJ, Burton MJ. Ocular immune responses, Chlamydia trachomatis infection and clinical signs of trachoma before and after azithromycin mass drug administration in a treatment naïve trachoma-endemic Tanzanian community. PLoS Negl Trop Dis 2019; 13:e0007559. [PMID: 31306419 PMCID: PMC6658141 DOI: 10.1371/journal.pntd.0007559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 07/25/2019] [Accepted: 06/18/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Trachoma, caused by Chlamydia trachomatis, remains the leading infectious cause of blindness worldwide. Persistence and progression of the resulting clinical disease appears to be an immunologically mediated process. Azithromycin, which is distributed at the community level for trachoma control, has immunomodulatory properties. We investigated the impact of one round of oral azithromycin on conjunctival immune responses, C. trachomatis infection and clinical signs three- and six- months post treatment relative to three pre-treatment time-points. METHODOLOGY A cohort of children aged 6 to 10 years were recruited from a trachoma endemic region of northern Tanzania and were visited five times in a 12-month period. They were examined for clinical signs of trachoma and conjunctival swabs were collected for laboratory analysis. C. trachomatis infection was detected and the expression of 46 host genes was quantified using quantitative PCR. All community members were offered azithromycin treatment immediately after the six-month timepoint according to international guidelines. FINDINGS The prevalence of C. trachomatis infection and inflammatory disease signs were significantly reduced three- and six- months post-mass drug administration (MDA). C. trachomatis infection was strongly associated with clinical signs at all five time-points. A profound anti-inflammatory effect on conjunctival gene expression was observed 3 months post-MDA, however, gene expression had largely returned to pre-treatment levels of variation by 6 months. This effect was less marked, but still observed, after adjusting for C. trachomatis infection and when the analysis was restricted to individuals who were free from both infection and clinical disease at all five time-points. Interestingly, a modest effect was also observed in individuals who did not receive treatment. CONCLUSION Conjunctival inflammation is the major clinical risk factor for progressive scarring trachoma, therefore, the reduction in inflammation associated with azithromycin treatment may be beneficial in limiting the development of potentially blinding disease sequelae. Future work should seek to determine whether this effect is mediated directly through inhibition of pro-inflammatory intracellular signalling molecules, through reductions in concurrent, sub-clinical infections, and/or through reduction of infection exposure.
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Affiliation(s)
- Athumani M. Ramadhani
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Tamsyn Derrick
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - David Macleod
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Aiweda Malisa
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Kelvin Mbuya
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Tara Mtuy
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | - Chrissy H. Roberts
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Robin L. Bailey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David C. W. Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin J. Holland
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew J. Burton
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Cheng X, Sun L, Zhao Q, Mi Z, Yu G, Wang Z, Sun Y, Wang C, Man C, Fu F, Liu H, Zhang F. Development and evaluation of a droplet digital PCR assay for the diagnosis of paucibacillary leprosy in skin biopsy specimens. PLoS Negl Trop Dis 2019; 13:e0007284. [PMID: 30883558 PMCID: PMC6438576 DOI: 10.1371/journal.pntd.0007284] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/28/2019] [Accepted: 03/07/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The reduced amounts of Mycobacterium leprae (M. leprae) among paucibacillary (PB) patients reflect the need to further optimize methods for leprosy diagnosis. An increasing number of reports have shown that droplet digital polymerase chain reaction (ddPCR) is a promising tool for diagnosis of infectious disease among samples with low copy number. To date, no publications have investigated the utility of ddPCR in the detection of M. leprae. The aim of this study was to develop and evaluate a ddPCR assay for the diagnosis of PB leprosy. METHODOLOGY The two most sensitive DNA targets for detection of M. leprae were selected from electronic databases for assessment of sensitivity and specificity by quantitative polymerase chain reaction (qPCR) and ddPCR. Control patients (n = 59) suffering from other dermatological diseases were used to define the cut-off of the duplex ddPCR assay. For comparative evaluation, qPCR and ddPCR assays were performed in 44 PB patients and 68 multibacillary (MB) patients. PRINCIPAL FINDINGS M. leprae-specific repetitive element (RLEP) and groEL (encoding the 65 kDa molecular chaperone GroEL) were used to develop the ddPCR assay by systematically analyzing specificity and sensitivity. Based on the defined cut-off value, the ddPCR assay showed greater sensitivity in detecting M. leprae DNA in PB patients compared with qPCR (79.5% vs 36.4%), while both assays have a 100% sensitivity in MB patients. CONCLUSIONS/SIGNIFICANCE We developed and evaluated a duplex ddPCR assay for leprosy diagnosis in skin biopsy samples from leprosy patients. While still costly, ddPCR might be a promising diagnostic tool for detection of PB leprosy.
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Affiliation(s)
- Xiujun Cheng
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
| | - Lele Sun
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
| | - Qing Zhao
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong, China
| | - Zihao Mi
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
| | - Gongqi Yu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
| | - Zhenzhen Wang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
| | - Yonghu Sun
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
| | - Chuan Wang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
| | - Chunhua Man
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
- School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Fanghui Fu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong, China
| | - Hong Liu
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
- School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
- * E-mail: (HL); (FZ)
| | - Furen Zhang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
- National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong, China
- School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
- * E-mail: (HL); (FZ)
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Ramírez JD, Herrera G, Hernández C, Cruz-Saavedra L, Muñoz M, Flórez C, Butcher R. Evaluation of the analytical and diagnostic performance of a digital droplet polymerase chain reaction (ddPCR) assay to detect Trypanosoma cruzi DNA in blood samples. PLoS Negl Trop Dis 2018; 12:e0007063. [PMID: 30586355 PMCID: PMC6324824 DOI: 10.1371/journal.pntd.0007063] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/08/2019] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The recent development of novel Polymerase Chain Reaction (PCR) technologies that confer theoretical advantages over quantitative PCR has considerable potential in the diagnosis of low load infections, such as Trypanosoma cruzi in the chronic phase of Chagas disease. We evaluated the utility of the digital droplet (dd)PCR platform in the detection of T. cruzi infection. METHODOLOGY/PRINCIPAL FINDINGS We imported a validated qPCR assay targeting the T. cruzi satellite tandem repeat (TcSTR) region to the ddPCR platform. Following optimization, we tested and repeated a standard curve of TcI epimastigotes to characterise the analytical performance of the assay on the ddPCR platform. We compared this to published qPCR performance data, and the performance of the qPCR assay in our own testing. We subsequently tested a panel of 192 previously characterized DNA specimens, extracted from the blood of individuals with and without T. cruzi infection. The assay performed well on the ddPCR platform, showing a limit of detection of 5 copies/μL or 1 parasite/mL. This was higher than the published limit of detection for qPCR, which was 0.46 parasites/mL. The ddPCR platform was not significantly more accurate than qPCR at any concentration tested. However, the clinical sensitivity and specificity of the assay were both 100% with perfect agreement between qPCR and ddPCR positive and negative result calling in clinical specimens. An average of 9,286 copies of TcSTR were detected per parasite. CONCLUSIONS/SIGNIFICANCE The use of the ddPCR platform to run this assay was comparable, but not superior in terms of performance, to the qPCR platform.
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Affiliation(s)
- Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Hernández
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Flórez
- Grupo de Parasitología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Robert Butcher
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
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28
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Application of droplet digital PCR to detect the pathogens of infectious diseases. Biosci Rep 2018; 38:BSR20181170. [PMID: 30341241 PMCID: PMC6240714 DOI: 10.1042/bsr20181170] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022] Open
Abstract
Polymerase chain reaction (PCR) is a molecular biology technique used to multiply certain deoxyribonucleic acid (DNA) fragments. It is a common and indispensable technique that has been applied in many areas, especially in clinical laboratories. The third generation of polymerase chain reaction, droplet digital polymerase chain reaction (ddPCR), is a biotechnological refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify DNA. Droplet digital polymerase chain reaction is now widely used in low-abundance nucleic acid detection and is useful in diagnosis of infectious diseases. Here, we summarized the potential advantages of droplet digital polymerase chain reaction in clinical diagnosis of infectious diseases, including viral diseases, bacterial diseases and parasite infections, concluded that ddPCR provides a more sensitive, accurate, and reproducible detection of low-abundance pathogens and may be a better choice than quantitative polymerase chain reaction for clinical applications in the future.
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Anderson EM, Maldarelli F. Quantification of HIV DNA Using Droplet Digital PCR Techniques. ACTA ACUST UNITED AC 2018; 51:e62. [PMID: 30253074 DOI: 10.1002/cpmc.62] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
HIV persists, despite effective antiretroviral therapy, in long-lived cells, posing a major barrier toward a cure. A key step in the HIV replication cycle and a hallmark of the Retroviridae family is the integration of the viral DNA into the host genome. Once integrated, HIV expression is regulated by host machinery and the provirus persists until the cell dies. A reservoir of cells harboring replication-competent proviruses can survive for years, and mechanisms that maintain that reservoir are under investigation. The majority of integrated proviruses, however, are defective or have large deletions, and the composition of the proviral landscape during therapy remains unknown. Methods to quantify HIV proviruses are useful in investigating HIV persistence. Presented in this unit is a method for total HIV DNA quantification of various HIV genome targets that utilizes the next-generation PCR platform, digital PCR. The abundance of various HIV gene targets reflects the overall proviral composition. In this protocol, total genomic DNA is isolated from patient-derived cells and then used as a template for droplet digital PCR, in which the PCR reaction is partitioned into approximately 20,000 individual droplets, PCR amplified to an end point, and subjected to absolute quantification by counting the number of positive and negative droplets. Copy number is directly calculated using straightforward Poisson correction. Additionally, this methodological approach can be used to obtain absolute quantification of other DNA targets. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, Maryland
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30
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Xue J, Caton K, Sherchan S. Comparison of next-generation droplet digital PCR with quantitative PCR for enumeration ofNaegleria fowleriin environmental water and clinical samples. Lett Appl Microbiol 2018; 67:322-328. [DOI: 10.1111/lam.13051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/25/2018] [Accepted: 07/11/2018] [Indexed: 11/28/2022]
Affiliation(s)
- J. Xue
- Department of Global Environmental Health Sciences; School of Public Health and Tropical Medicine, Tulane University; New Orleans LA USA
| | - K. Caton
- Department of Global Environmental Health Sciences; School of Public Health and Tropical Medicine, Tulane University; New Orleans LA USA
| | - S.P. Sherchan
- Department of Global Environmental Health Sciences; School of Public Health and Tropical Medicine, Tulane University; New Orleans LA USA
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31
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Song N, Tan Y, Zhang L, Luo W, Guan Q, Yan MZ, Zuo R, Liu W, Luo FL, Zhang XL. Detection of circulating Mycobacterium tuberculosis-specific DNA by droplet digital PCR for vaccine evaluation in challenged monkeys and TB diagnosis. Emerg Microbes Infect 2018; 7:78. [PMID: 29691363 PMCID: PMC5915492 DOI: 10.1038/s41426-018-0076-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis (M. tb) is emerging as a more serious pathogen due to the increased multidrug-resistant TB and co-infection of human immunodeficiency virus (HIV). The development of an effective and sensitive detection method is urgently needed for bacterial load evaluation in vaccine development, early TB diagnosis, and TB treatment. Droplet digital polymerase chain reaction (ddPCR) is a newly developed sensitive PCR method for the absolute quantification of nucleic acid concentrations. Here, we used ddPCR to quantify the circulating virulent M. tb-specific CFP10 (10-kDa culture filtrate protein, Rv3874) and Rv1768 DNA copy numbers in the blood samples from Bacille Calmette-Guerin (BCG)-vaccinated and/or virulent M. tb H37Rv-challenged rhesus monkeys. We found that ddPCR was more sensitive compared to real-time fluorescence quantitative PCR (qPCR), as the detection limits of CFP10 were 1.2 copies/μl for ddPCR, but 15.8 copies/μl for qPCR. We demonstrated that ddPCR could detect CFP10 and Rv1768 DNA after 3 weeks of infection and at least two weeks earlier than qPCR in M.tb H37Rv-challenged rhesus monkey models. DdPCR could also successfully quantify CFP10 and Rv1768 DNA copy numbers in clinical TB patients’ blood samples (active pulmonary TB, extrapulmonary TB (EPTB), and infant TB). To our knowledge, this study is the first to demonstrate that ddPCR is an effective and sensitive method of measuring the circulating CFP10 and Rv1768 DNA for vaccine development, bacterial load evaluation in vivo, and early TB (including EPTB and infant TB) diagnosis as well.
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Affiliation(s)
- Neng Song
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Yang Tan
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Lingyun Zhang
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Wei Luo
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Qing Guan
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Ming-Zhe Yan
- Wuhan Medical Treatment Center, Wuhan, 430071, China
| | - Ruiqi Zuo
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Weixiang Liu
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Feng-Ling Luo
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
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Chen Y, Wang Z, Liu Y, Wang X, Li Y, Ma P, Gu B, Li H. Recent advances in rapid pathogen detection method based on biosensors. Eur J Clin Microbiol Infect Dis 2018; 37:1021-1037. [DOI: 10.1007/s10096-018-3230-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/12/2018] [Indexed: 12/28/2022]
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Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J, Cutcliffe LT, Clarke IN, Mabey DCW, Bailey RL, Clark TG, Thomson NR, Holland MJ. Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. Genome Med 2018; 10:15. [PMID: 29482619 PMCID: PMC5828069 DOI: 10.1186/s13073-018-0521-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. RESULTS All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* = 0.032), CTA0744 (OR = 0.12, p* = 0.041), glgA (OR = 0.10, p* = 0.026), alaS (OR = 0.10, p* = 0.032), pmpE (OR = 0.08, p* = 0.001) and the intergenic region CTA0744-CTA0745 (OR = 0.13, p* = 0.043). CONCLUSIONS This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct and is the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.
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Affiliation(s)
- A. R. Last
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - H. Pickering
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - C. h. Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - F. Coll
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - J. Phelan
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - S. E. Burr
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, Gambia
| | - E. Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - M. Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - H. M. B. Seth-Smith
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Clinical Microbiology, Universitätsspital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - J. Hadfield
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - L. T. Cutcliffe
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - I. N. Clarke
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - D. C. W. Mabey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - R. L. Bailey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - T. G. Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - N. R. Thomson
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M. J. Holland
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
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Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay. Sci Rep 2018; 8:3626. [PMID: 29483619 PMCID: PMC5827666 DOI: 10.1038/s41598-018-21882-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 02/13/2018] [Indexed: 12/31/2022] Open
Abstract
Quantification of antiretroviral (ARV) drug concentrations in peripheral blood mononuclear cells (PBMCs) and tissue isolated mononuclear cells (TIMCs) from lymph node (LNMC) and rectum (RMC) is an important measure of bio-distribution. Normalization of drug concentrations is critical to represent tissue drug concentrations and to analyze both intra-individual and inter-individual variability in drug distribution. However, a molecular method to normalize intracellular drug concentrations in PBMCs and TIMCs methanol extracts is currently unavailable. In this study, a novel droplet digital PCR (ddPCR) assay was designed to amplify RPP30 gene sequence conserved in human and non-human primates (NHP). Genomic DNA (gDNA) isolated from 70 percent methanol embedded PBMCs and TIMCs was used as ddPCR template to quantitate precise RPP30 copies to derive cell counts. The novel molecular method quantitated RPP30 copies in human and rhesus macaque gDNA templates with greater accuracy and precision than qPCR. RPP30 ddPCR derived cell counts are strongly correlated with automated cytometer based cell counts in PBMC (R = 0.90, p = 0.001 and n = 20); LNMC (R = 0.85 p = 0.0001 and n = 22) and RMC (R = 0.92, p = 0.0001 and n = 20) and achieved comparable normalized drug concentrations. Therefore, the RPP30 ddPCR assay is an important normalization method in drug bio-distribution and pharmacokinetic studies in humans and NHPs.
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35
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Last A, Burr S, Alexander N, Harding-Esch E, Roberts CH, Nabicassa M, Cassama ETDS, Mabey D, Holland M, Bailey R. Spatial clustering of high load ocular Chlamydia trachomatis infection in trachoma: a cross-sectional population-based study. Pathog Dis 2018; 75:3791466. [PMID: 28472466 PMCID: PMC5808645 DOI: 10.1093/femspd/ftx050] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/02/2017] [Indexed: 11/12/2022] Open
Abstract
Chlamydia trachomatis (Ct) is the most common cause of bacterial sexually transmitted infection and infectious cause of blindness (trachoma) worldwide. Understanding the spatial distribution of Ct infection may enable us to identify populations at risk and improve our understanding of Ct transmission. In this study, we sought to investigate the spatial distribution of Ct infection and the clinical features associated with high Ct load in trachoma-endemic communities on the Bijagós Archipelago (Guinea Bissau). We collected 1507 conjunctival samples and corresponding detailed clinical data during a cross-sectional population-based geospatially representative trachoma survey. We used droplet digital PCR to estimate Ct load on conjunctival swabs. Geostatistical tools were used to investigate clustering of ocular Ct infections. Spatial clusters (independent of age and gender) of individuals with high Ct loads were identified using local indicators of spatial association. We did not detect clustering of individuals with low load infections. These data suggest that infections with high bacterial load may be important in Ct transmission. These geospatial tools may be useful in the study of ocular Ct transmission dynamics and as part of trachoma surveillance post-treatment, to identify clusters of infection and thresholds of Ct load that may be important foci of re-emergent infection in communities.
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Affiliation(s)
- Anna Last
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Sarah Burr
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, PO Box 273 Banjul, Atlantic Boulevard, Fajara, The Gambia
| | - Neal Alexander
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Emma Harding-Esch
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Chrissy H Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Meno Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, PO Box 50, Avenida de Unidade Africana, Bisssau, Guiné Bissau
| | | | - David Mabey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Martin Holland
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Robin Bailey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Butcher R, Sokana O, Jack K, Sui L, Russell C, Last A, Martin DL, Burton MJ, Solomon AW, Mabey DCW, Roberts CH. Clinical signs of trachoma are prevalent among Solomon Islanders who have no persistent markers of prior infection with Chlamydia trachomatis. Wellcome Open Res 2018; 3:14. [PMID: 29588922 PMCID: PMC5854984 DOI: 10.12688/wellcomeopenres.13423.2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2018] [Indexed: 01/15/2023] Open
Abstract
Background: The low population prevalence of trachomatous trichiasis and high prevalence of trachomatous inflammation–follicular (TF) provide contradictory estimates of the magnitude of the public health threat from trachoma in the Solomon Islands. Improved characterisation of the biology of trachoma in the region may support policy makers as they decide what interventions are required. Here, age-specific profiles of anti-Pgp3 antibodies and conjunctival scarring were examined to determine whether there is evidence of ongoing transmission and pathology from ocular
Chlamydia trachomatis (
Ct)
infection. Methods: A total of 1511 individuals aged ≥1 year were enrolled from randomly selected households in 13 villages in which >10% of children aged 1–9 years had TF prior to a single round of azithromycin mass drug administration undertaken six months previously. Blood was collected to be screened for antibodies to the
Ct antigen Pgp3. Tarsal conjunctival photographs were collected for analysis of scarring severity. Results: Anti-Pgp3 seropositivity was 18% in 1–9 year olds, sharply increasing around the age of sexual debut to reach 69% in those over 25 years. Anti-Pgp3 seropositivity did not increase significantly between the ages of 1–9 years and was not associated with TF (p=0.581) or scarring in children (p=0.472). Conjunctival scars were visible in 13.1% of photographs. Mild (p<0.0001) but not severe (p=0.149) scars increased in prevalence with age. Conclusions: Neither conjunctival scars nor lymphoid follicles were associated with antibodies to
Ct, suggesting that they are unlikely to be a direct result of ocular
Ct infection
. Clinical signs of trachoma were prevalent in this population but were not indicative of the underlying rates of
Ct infection. The current World Health Organization guidelines for trachoma elimination indicated that this population should receive intervention with mass distribution of antibiotics, but the data presented here suggest that this may not have been appropriate.
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Affiliation(s)
- Robert Butcher
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Oliver Sokana
- Eye Department, Solomon Islands Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - Kelvin Jack
- Eye Department, Solomon Islands Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - Leslie Sui
- Primary Care Department, Lata Hospital, Lata, Solomon Islands
| | | | - Anna Last
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Diana L Martin
- Division of Parasitic Diseases and Malaria, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Matthew J Burton
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Anthony W Solomon
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - David C W Mabey
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Chrissy H Roberts
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
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37
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Butcher R, Sokana O, Jack K, Sui L, Russell C, Last A, Martin DL, Burton MJ, Solomon AW, Mabey DC, Roberts CH. Clinical signs of trachoma are prevalent among Solomon Islanders who have no persistent markers of prior infection with Chlamydia trachomatis. Wellcome Open Res 2018. [DOI: 10.12688/wellcomeopenres.13423.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The low population-prevalence of trachomatous trichiasis and high prevalence of trachomatous inflammation–follicular (TF) provide contradictory estimates of the magnitude of the public health threat from trachoma in the Solomon Islands. Improved characterisation of the biology of trachoma in the region may support policy makers as they decide what interventions are required. Here, age-specific profiles of anti-Pgp3 antibodies and conjunctival scarring were examined to determine whether there is evidence of ongoing transmission and pathology from ocular Chlamydia trachomatis (Ct) infection. Methods: A total of 1511 individuals aged ≥1 year were enrolled from randomly selected households in 13 villages in which >10% of children aged 1–9 years had TF prior to a single round of azithromycin mass drug administration undertaken six months previously. Blood was collected to be screened for antibodies to the Ct antigen Pgp3. Tarsal conjunctival photographs were collected for analysis of scarring severity. Results: Anti-Pgp3 seropositivity was 18% in 1–9 year olds, sharply increasing around the age of sexual debut to reach 69% in those over 25 years. Anti-Pgp3 seropositivity did not increase significantly between the ages of 1–9 years and was not associated with TF (p=0.581) or scarring in children (p=0.472). Conjunctival scars were visible in 13.1% of photographs. Mild (p<0.0001) but not severe (p=0.149) scars increased in prevalence with age. Conclusions: Neither conjunctival scars nor lymphoid follicles were associated with antibodies to Ct, suggesting that they are unlikely to be a direct result of ocular Ct infection. Clinical signs of trachoma were prevalent in this population but were not indicative of the underlying rates of Ct infection. The current World Health Organization guidelines for trachoma elimination indicated that this population should receive intervention with mass distribution of antibiotics, but the data presented here suggest that this may not have been appropriate.
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38
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Vasileva H, Butcher R, Pickering H, Sokana O, Jack K, Solomon AW, Holland MJ, Roberts CH. Conjunctival transcriptome profiling of Solomon Islanders with active trachoma in the absence of Chlamydia trachomatis infection. Parasit Vectors 2018; 11:104. [PMID: 29467021 PMCID: PMC5822555 DOI: 10.1186/s13071-018-2682-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/29/2018] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Clinical signs of active (inflammatory) trachoma are found in many children in the Solomon Islands, but the majority of these individuals have no serological evidence of previous infection with Chlamydia trachomatis. In Temotu and Rennell and Bellona provinces, ocular infections with C. trachomatis were seldom detected among children with active trachoma; a similar lack of association was seen between active trachoma and other common bacterial and viral causes of follicular conjunctivitis. Here, we set out to characterise patterns of gene expression at the conjunctivae of children in these provinces with and without clinical signs of trachomatous inflammation-follicular (TF) and C. trachomatis infection. METHODS Purified RNA from children with and without active trachoma was run on Affymetrix GeneChip Human Transcriptome Array 2.0 microarrays. Profiles were compared between individuals with ocular C. trachomatis infection and TF (group DI; n = 6), individuals with TF but no C. trachomatis infection (group D; n = 7), and individuals without TF or C. trachomatis infection (group N; n = 7). Differential gene expression and gene set enrichment for pathway membership were assessed. RESULTS Conjunctival gene expression profiles were more similar within-group than between-group. Principal components analysis indicated that the first and second principal components combined explained almost 50% of the variance in the dataset. When comparing the DI group to the N group, genes involved in T-cell proliferation, B-cell signalling and CD8+ T cell signalling pathways were differentially regulated. When comparing the DI group to the D group, CD8+ T-cell regulation, interferon-gamma and IL17 production pathways were enriched. Genes involved in RNA transcription and translation pathways were upregulated when comparing the D group to the N group. CONCLUSIONS Gene expression profiles in children in the Solomon Islands indicate immune responses consistent with bacterial infection when TF and C. trachomatis infection are concurrent. The transcriptomes of children with TF but without identified infection were not consistent with allergic or viral conjunctivitis.
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Affiliation(s)
- Hristina Vasileva
- Clinical Research Department, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Robert Butcher
- Clinical Research Department, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Harry Pickering
- Clinical Research Department, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Oliver Sokana
- Eye Department, Solomon Islands Ministry of Health and Medical Services, PO Box 349, Honiara, Solomon Islands
| | - Kelvin Jack
- Eye Department, Solomon Islands Ministry of Health and Medical Services, PO Box 349, Honiara, Solomon Islands
| | - Anthony W. Solomon
- Clinical Research Department, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Martin J. Holland
- Clinical Research Department, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Chrissy h. Roberts
- Clinical Research Department, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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Li X, Liang QF, Su GY, Wu LY, Lu XX, Wang NL. Current Research of Chlamydial Infection Diseases in China. Chin Med J (Engl) 2018; 131:486-489. [PMID: 29451157 PMCID: PMC5830837 DOI: 10.4103/0366-6999.225063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Xue Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Qing-Feng Liang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
| | - Guan-Yu Su
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
| | - Li-Yuan Wu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Xin-Xin Lu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Ning-Li Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing 100005, China
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Pickering H, Holland MJ, Last AR, Burton MJ, Burr SE. Evaluation of a Chlamydia trachomatis-specific, commercial, real-time PCR for use with ocular swabs. Parasit Vectors 2018; 11:102. [PMID: 29463279 PMCID: PMC5819642 DOI: 10.1186/s13071-018-2686-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/30/2018] [Indexed: 12/02/2022] Open
Abstract
Background Trachoma, the leading infectious cause of blindness worldwide, is caused by conjunctival Chlamydia trachomatis infection. Trachoma is diagnosed clinically by observation of conjunctival inflammation and/or scarring; however, there is evidence that monitoring C. trachomatis infection may be required for elimination programmes. There are many commercial and ‘in-house’ nucleic acid amplification tests for the detection of C. trachomatis DNA, but the majority have not been validated for use with ocular swabs. This study evaluated a commercial assay, the Fast-Track Vaginal swab kit, using conjunctival samples from trachoma-endemic areas. An objective, biostatistical-based method for binary classification of continuous PCR data was developed, to limit potential user-bias in diagnostic settings. Methods The Fast-Track Vaginal swab assay was run on 210 ocular swab samples from Guinea-Bissau and Tanzania. Fit of individual amplification curves to exponential or sigmoid models, derivative and second derivative of the curves and final fluorescence value were examined for utility in thresholding for determining positivity. The results from the Fast-Track Vaginal swab assay were evaluated against a commercial test (Amplicor CT/NG) and a non-commercial test (in-house droplet digital PCR), both of whose performance has previously been evaluated. Results Significant evidence of exponential amplification (R2 > 0.99) and final fluorescence > 0.15 were combined for thresholding. This objective approach identified a population of positive samples, however there were a subset of samples that amplified towards the end of the cycling protocol (at or later than 35 cycles), which were less clearly defined. The Fast-Track Vaginal swab assay showed good sensitivity against the commercial (95.71) and non-commercial (97.18) tests. Specificity was lower against both (90.00 and 96.55, respectively). Conclusions This study defined a simple, automated protocol for binary classification of continuous, real-time qPCR data, for use in an end-point diagnostic test. This method identified a population of positive samples, however, as with manual thresholding, a subset of samples that amplified towards the end of the cycling program were less easily classified. When used with ocular swabs, the Fast-Track Vaginal swab assay had good sensitivity for C. trachomatis detection, but lower specificity than the commercial and non-commercial assays it was evaluated against, possibly leading to false positives.
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Affiliation(s)
| | | | - Anna R Last
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Sarah E Burr
- London School of Hygiene and Tropical Medicine, London, UK
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Butcher RMR, Sokana O, Jack K, Kalae E, Sui L, Russell C, Houghton J, Palmer C, Holland MJ, Le Mesurier RT, Solomon AW, Mabey DCW, Roberts CH. Active Trachoma Cases in the Solomon Islands Have Varied Polymicrobial Community Structures but Do Not Associate with Individual Non-Chlamydial Pathogens of the Eye. Front Med (Lausanne) 2018; 4:251. [PMID: 29410954 PMCID: PMC5787070 DOI: 10.3389/fmed.2017.00251] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/19/2017] [Indexed: 11/17/2022] Open
Abstract
Background Several non-chlamydial microbial pathogens are associated with clinical signs of active trachoma in trachoma-endemic communities with a low prevalence of ocular Chlamydia trachomatis (Ct) infection. In the Solomon Islands, the prevalence of Ct among children is low despite the prevalence of active trachoma being moderate. Therefore, we set out to investigate whether active trachoma was associated with a common non-chlamydial infection or with a dominant polymicrobial community dysbiosis in the Solomon Islands. Methods We studied DNA from conjunctival swabs collected from 257 Solomon Islanders with active trachoma and matched controls. Droplet digital PCR was used to test for pathogens suspected to be able to induce follicular conjunctivitis. Polymicrobial community diversity and composition were studied by sequencing of hypervariable regions of the 16S ribosomal ribonucleic acid gene in a subset of 54 cases and 53 controls. Results Although Ct was associated with active trachoma, the number of infections was low (cases, 3.9%; controls, 0.4%). Estimated prevalence (cases and controls, respectively) of each non-chlamydial infection was as follows: Staphylococcus aureus: 1.9 and 1.9%, Adenoviridae: 1.2 and 1.2%, coagulase-negative Staphylococcus: 5.8 and 4.3%, Haemophilus influenzae: 7.4 and 11.7%, Moraxella catarrhalis: 2.3 and 4.7%, and Streptococcus pneumoniae: 7.0 and 6.2%. There was no statistically significant association between the clinical signs of trachoma and the presence or load of any of the non-Ct infections that were assayed. Interindividual variations in the conjunctival microbiome were characterized by differences in the levels of Corynebacterium, Propionibacterium, Helicobacter, and Paracoccus, but diversity and relative abundance of these specific genera did not differ significantly between cases and controls. Discussion It is unlikely that the prevalent trachoma-like follicular conjunctivitis in this region of the Solomon Islands has a dominant bacterial etiology. Before implementing community-wide azithromycin distribution for trachoma, policy makers should consider that clinical signs of trachoma can be observed in the absence of any detectable azithromycin-susceptible organism.
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Affiliation(s)
- Robert M R Butcher
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Oliver Sokana
- Eye Department, Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - Kelvin Jack
- Eye Department, Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - Eric Kalae
- Primary Care Department, Lata Hospital, Santa Cruz Island, Solomon Islands
| | - Leslie Sui
- Primary Care Department, Lata Hospital, Santa Cruz Island, Solomon Islands
| | | | - Joanna Houghton
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Christine Palmer
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Martin J Holland
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Anthony W Solomon
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David C W Mabey
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Chrissy H Roberts
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Burr SE, Camara B, Oluwalana C, Bojang E, Bottomley C, Bojang A, Bailey RL, D'Alessandro U, Roca A. Does azithromycin given to women in labour decrease ocular bacterial infection in neonates? A double-blind, randomized trial. BMC Infect Dis 2017; 17:799. [PMID: 29282015 PMCID: PMC5746019 DOI: 10.1186/s12879-017-2909-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 12/12/2017] [Indexed: 11/22/2022] Open
Abstract
Background Vertical transmission can result in neonatal infection and disease. Reducing the transmission of bacterial pathogens from mother to infant may be an effective means of preventing neonatal infection, including bacterial conjunctivitis. Methods In a double-blind, randomized trial, we assessed the effect of administering a single dose of oral azithromycin to women in labour on bacterial colonization of the neonate. A reduction in purulent neonatal conjunctivitis was a secondary objective of the trial. Ocular samples were collected from the lower fornix of infants presenting with clinical signs of purulent conjunctivitis during the first eight weeks of life. Incidence of purulent conjunctivitis was compared between trial arms. Bacterial infection was assessed using PCR and incidence of purulent conjunctivitis due to bacteria was also compared between arms. Results Forty of 843 infants (4.7%) presented clinical signs of purulent conjunctivitis. No significant difference in incidence of purulent conjunctivitis was seen between azithromycin and placebo arms [4.3% (18/419) versus 5.2% (22/424), OR = 0.82, 95% CI (0.44,1.54), p = 0.628]. S. aureus was the most commonly identified pathogen, detected in 38% of cases. Incidence of purulent-conjunctivitis due to bacterial infection was lower in the azithromycin arm [1.2% (5/419) versus 3.8% (16/424), OR = 0.31, 95% CI (0.12–0.82), p = 0.025)]. The incidence of gram-positive bacteria was also lower in the azithromycin arm [1.0% (4/419) versus 3.3% (14/424), OR = 0.28, 95%CI (0.10–0.82), p = 0.029]. Conclusions Oral azithromycin given to women during labour may have the potential to reduce the incidence of bacterial neonatal conjunctivitis. Trial registration ClinicalTrials.gov, identifier NCT01800942, registration date 26 Feb 2013.
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Affiliation(s)
- Sarah E Burr
- London School of Hygiene and Tropical Medicine, London, UK
| | - Bully Camara
- Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia
| | - Claire Oluwalana
- Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia
| | - Ebrima Bojang
- Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia
| | | | - Abdoulie Bojang
- Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia
| | - Robin L Bailey
- London School of Hygiene and Tropical Medicine, London, UK
| | - Umberto D'Alessandro
- London School of Hygiene and Tropical Medicine, London, UK.,Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia
| | - Anna Roca
- London School of Hygiene and Tropical Medicine, London, UK. .,Medical Research Council Unit, The Gambia, Fajara, Banjul, The Gambia.
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Last AR, Burr SE, Harding-Esch E, Cassama E, Nabicassa M, Roberts CH, Mabey DCW, Holland MJ, Bailey RL. The impact of a single round of community mass treatment with azithromycin on disease severity and ocular Chlamydia trachomatis load in treatment-naïve trachoma-endemic island communities in West Africa. Parasit Vectors 2017; 10:624. [PMID: 29282126 PMCID: PMC5745817 DOI: 10.1186/s13071-017-2566-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 12/03/2017] [Indexed: 10/29/2022] Open
Abstract
BACKGROUND Trachoma, a neglected tropical disease, is caused by ocular infection with Chlamydia trachomatis (Ct). The World Health Organization (WHO) recommends three annual rounds of community mass drug treatment with azithromycin (MDA) if the prevalence of follicular trachoma in 1-9 year olds (TF1-9) exceeds 10% at district level to achieve an elimination target of district-level TF1-9 below 5% after. To evaluate this strategy in treatment-naïve trachoma-endemic island communities in Guinea Bissau, we conducted a cross-sectional population-based trachoma survey on four islands. The upper tarsal conjunctivae of each participant were clinically assessed for trachoma and conjunctival swabs were obtained (n = 1507). We used a droplet digital PCR assay to detect Ct infection and estimate bacterial load. We visited the same households during a second cross-sectional survey and repeated the ocular examination and obtained conjunctival swabs from these households one year after MDA (n = 1029). RESULTS Pre-MDA TF1-9 was 22.0% (136/618). Overall Ct infection prevalence (CtI) was 18.6% (25.4% in 1-9 year olds). Post-MDA (estimated coverage 70%), TF1-9 and CtI were significantly reduced (7.4% (29/394, P < 0.001) and 3.3% (34/1029, P < 0.001) (6.6% in 1-9 year olds, P < 0.001), respectively. Median ocular Ct load was reduced from 2038 to 384 copies/swab (P < 0.001). Following MDA cases of Ct infection were highly clustered (Moran's I 0.27, P < 0.001), with fewer clusters of Ct infection overall, fewer clusters of cases with high load infections and less severe disease. CONCLUSIONS Despite a significant reduction in the number of clusters of Ct infection, mean Ct load, disease severity and presence of clusters of cases of high load Ct infection suggesting the beginning of trachoma control in isolated island communities, following a single round of MDA we demonstrate that transmission is still ongoing. These detailed data are useful in understanding the epidemiology of ocular Ct infection in the context of MDA and the tools employed may have utility in determining trachoma elimination and surveillance activities in similar settings.
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Affiliation(s)
- Anna R Last
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Sarah E Burr
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, P.OBox 273, Banjul, Atlantic Boulevard, Fajara, The, Gambia
| | - Emma Harding-Esch
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Eunice Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, P.O. Box 50, Avenida de Unidade Africana, Bisssau, Guinea-Bissau
| | - Meno Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, P.O. Box 50, Avenida de Unidade Africana, Bisssau, Guinea-Bissau
| | - Chrissy H Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - David C W Mabey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin J Holland
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Robin L Bailey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Ramadhani AM, Derrick T, Macleod D, Massae P, Mtuy T, Jeffries D, Roberts CH, Bailey RL, Mabey DCW, Holland MJ, Burton MJ. Immunofibrogenic Gene Expression Patterns in Tanzanian Children with Ocular Chlamydia trachomatis Infection, Active Trachoma and Scarring: Baseline Results of a 4-Year Longitudinal Study. Front Cell Infect Microbiol 2017; 7:406. [PMID: 28966918 PMCID: PMC5605569 DOI: 10.3389/fcimb.2017.00406] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/31/2017] [Indexed: 12/11/2022] Open
Abstract
Trachoma, caused by Chlamydia trachomatis, is the world's leading infectious cause of blindness and remains a significant public health problem. Much of trachomatous disease pathology is thought to be caused indirectly by host cellular and immune responses, however the immune response during active trachoma and how this initiates progressive scarring is not clearly understood. Defining protective vs. pathogenic immune response to C. trachomatis is important for vaccine design and evaluation. This study reports the baseline results of a longitudinal cohort of Tanzanian children, who were monitored for 4 years in order to determine the immunofibrogenic and infectious correlates of progressive scarring trachoma. In this cohort baseline, 506 children aged 6-10 years were assessed for clinical signs, infection status and the expression of 91 genes of interest prior to mass azithromycin administration for trachoma control. C. trachomatis was detected using droplet digital PCR and gene expression was measured using quantitative real-time PCR. The prevalence of follicles, papillary inflammation and scarring were 33.6, 31.6, and 28.5%, respectively. C. trachomatis was detected in 78/506 (15.4%) individuals, 62/78 of whom also had follicles. C. trachomatis infection was associated with a strong upregulation of IFNG and IL22, the enrichment of Th1 and NK cell pathways and Th17 cell-associated cytokines. In individuals with inflammation in the absence of infection the IFNG/IL22 and NK cell response was reduced, however, pro-inflammatory, growth and matrix factors remained upregulated and mucins were downregulated. Our data suggest that, strong IFNG/IL22 responses, probably related to Th1 and NK cell involvement, is important for clearance of C. trachomatis and that the residual pro-inflammatory and pro-fibrotic phenotype that persists after infection might contribute to pathological scarring. Interestingly, females appear more susceptible to developing papillary inflammation and scarring than males, even at this young age, despite comparable levels of C. trachomatis infection. Females also had increased expression of a number of IFNγ pathway related genes relative to males, suggesting that overexpression of this pathway in response to infection might contribute to more severe scarring. Longitudinal investigation of these factors will reveal their relative contributions to protection from C. trachomatis infection and development of scarring complications.
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Affiliation(s)
- Athumani M Ramadhani
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
- Kilimanjaro Christian Medical CentreMoshi, Tanzania
| | - Tamsyn Derrick
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
- Kilimanjaro Christian Medical CentreMoshi, Tanzania
| | - David Macleod
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical MedicineLondon, United Kingdom
| | | | - Tara Mtuy
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
- Kilimanjaro Christian Medical CentreMoshi, Tanzania
| | - David Jeffries
- Support Services (Statistics), Medical Research Council Unit The GambiaFajara, Gambia
| | - Chrissy H Roberts
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
| | - Robin L Bailey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
| | - David C W Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
| | - Martin J Holland
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
| | - Matthew J Burton
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical MedicineLondon, United Kingdom
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Cama A, Müller A, Taoaba R, Butcher RMR, Itibita I, Migchelsen SJ, Kiauea T, Pickering H, Willis R, Roberts CH, Bakhtiari A, Le Mesurier RT, Alexander NDE, Martin DL, Tekeraoi R, Solomon AW. Prevalence of signs of trachoma, ocular Chlamydia trachomatis infection and antibodies to Pgp3 in residents of Kiritimati Island, Kiribati. PLoS Negl Trop Dis 2017; 11:e0005863. [PMID: 28898240 PMCID: PMC5609772 DOI: 10.1371/journal.pntd.0005863] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 09/22/2017] [Accepted: 08/08/2017] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE In some Pacific Island countries, such as Solomon Islands and Fiji, active trachoma is common, but ocular Chlamydia trachomatis (Ct) infection and trachomatous trichiasis (TT) are rare. On Tarawa, the most populous Kiribati island, both the active trachoma sign "trachomatous inflammation-follicular" (TF) and TT are present at prevalences warranting intervention. We sought to estimate prevalences of TF, TT, ocular Ct infection, and anti-Ct antibodies on Kiritimati Island, Kiribati, to assess local relationships between these parameters, and to help determine the need for interventions against trachoma on Kiribati islands other than Tarawa. METHODS As part of the Global Trachoma Mapping Project (GTMP), on Kiritimati, we examined 406 children aged 1-9 years for active trachoma. We collected conjunctival swabs (for droplet digital PCR against Ct plasmid targets) from 1-9-year-olds with active trachoma, and a systematic selection of 1-9-year-olds without active trachoma. We collected dried blood spots (for anti-Pgp3 ELISA) from all 1-9-year-old children. We also examined 416 adults aged ≥15 years for TT. Prevalence of TF and TT was adjusted for age (TF) or age and gender (TT) in five-year age bands. RESULTS The age-adjusted prevalence of TF in 1-9-year-olds was 28% (95% confidence interval [CI]: 24-35). The age- and gender-adjusted prevalence of TT in those aged ≥15 years was 0.2% (95% CI: 0.1-0.3%). Twenty-six (13.5%) of 193 swabs from children without active trachoma, and 58 (49.2%) of 118 swabs from children with active trachoma were positive for Ct DNA. Two hundred and ten (53%) of 397 children had anti-Pgp3 antibodies. Both infection (p<0.0001) and seropositivity (p<0.0001) were strongly associated with active trachoma. In 1-9-year-olds, the prevalence of anti-Pgp3 antibodies rose steeply with age. CONCLUSION Trachoma presents a public health problem on Kiritimati, where the high prevalence of ocular Ct infection and rapid increase in seropositivity with age suggest intense Ct transmission amongst young children. Interventions are required here to prevent future blindness.
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Affiliation(s)
- Anaseini Cama
- International Agency for the Prevention of Blindness, Western Pacific Region, Suva, Fiji
- The Fred Hollows Foundation, Sydney, Australia
| | - Andreas Müller
- Centre for Eye Research, University of Melbourne, Melbourne, Australia
| | - Raebwebwe Taoaba
- Eye Department, Ministry of Health and Medical Services, South Tarawa, Kiribati
| | - Robert M. R. Butcher
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Iakoba Itibita
- Kiritimati Hospital, London, Kiritimati Island, Kiribati
| | - Stephanie J. Migchelsen
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Harry Pickering
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Rebecca Willis
- International Trachoma Initiative, Task Force for Global Health, Decatur, Georgia, United States of America
| | - Chrissy h. Roberts
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Ana Bakhtiari
- International Trachoma Initiative, Task Force for Global Health, Decatur, Georgia, United States of America
| | - Richard T. Le Mesurier
- International Agency for the Prevention of Blindness, Western Pacific Region, Suva, Fiji
- The Fred Hollows Foundation, Sydney, Australia
| | - Neal D. E. Alexander
- MRC Tropical Epidemiology Group, Infectious Disease Epidemiology Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Diana L. Martin
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rabebe Tekeraoi
- Eye Department, Ministry of Health and Medical Services, South Tarawa, Kiribati
| | - Anthony W. Solomon
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Control of Neglected Tropical Diseases, World Health Organization, Geneva, Switzerland
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Digital PCR for Detection and Quantification of Fluoroquinolone Resistance in Legionella pneumophila. Antimicrob Agents Chemother 2017; 61:AAC.00628-17. [PMID: 28674045 DOI: 10.1128/aac.00628-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022] Open
Abstract
The emergence of fluoroquinolone (FQ)-resistant mutants of Legionella pneumophila in infected humans was previously reported using a next-generation DNA sequencing (NGS) approach. This finding could explain part of the therapeutic failures observed in legionellosis patients treated with these antibiotics. The aim of this study was to develop digital PCR (dPCR) assays allowing rapid and accurate detection and quantification of these resistant mutants in respiratory samples, especially when the proportion of mutants in a wild-type background is low. We designed three dPCRgyrA assays to detect and differentiate the wild-type and one of the three gyrA mutations previously described as associated with FQ resistance in L. pneumophila: at positions 248C→T (T83I), 259G→A (D87N), and 259G→C (D87H). To assess the performance of these assays, mixtures of FQ-resistant and -susceptible strains of L. pneumophila were analyzed, and the results were compared with those obtained with Sanger DNA sequencing and real-time quantitative PCR (qPCR) technologies. The dPCRgyrA assays were able to detect mutated gyrA sequences in the presence of wild-type sequences at up to 1:1,000 resistant/susceptible allele ratios. By comparison, Sanger DNA sequencing and qPCR were less sensitive, allowing the detection of gyrA mutants at up to 1:1 and 1:10 ratios, respectively. When testing 38 respiratory samples from 23 legionellosis patients (69.6% treated with an FQ), dPCRgyrA detected small amounts of gyrA mutants in four (10.5%) samples from three (13.0%) patients. These results demonstrate that dPCR is a highly sensitive alternative to quantify FQ resistance in L. pneumophila, and it could be used in clinical practice to detect patients that could be at higher risk of therapeutic failure.
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Butcher R, Houghton J, Derrick T, Ramadhani A, Herrera B, Last AR, Massae PA, Burton MJ, Holland MJ, Roberts CH. Reduced-cost Chlamydia trachomatis-specific multiplex real-time PCR diagnostic assay evaluated for ocular swabs and use by trachoma research programmes. J Microbiol Methods 2017; 139:95-102. [PMID: 28487054 PMCID: PMC5496587 DOI: 10.1016/j.mimet.2017.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/21/2017] [Accepted: 04/22/2017] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Trachoma, caused by the intracellular bacterium Chlamydia trachomatis (Ct), is the leading infectious cause of preventable blindness. Many commercial platforms are available that provide highly sensitive and specific detection of Ct DNA. However, the majority of these commercial platforms are inaccessible for population-level surveys in resource-limited settings typical to trachoma control programmes. We developed two low-cost quantitative PCR (qPCR) tests for Ct using readily available reagents on standard real-time thermocyclers. METHODS Each multiplex qPCR test targets one genomic and one plasmid Ct target in addition to an endogenous positive control for Homo sapiens DNA. The quantitative performance of the qPCR assays in clinical samples was determined by comparison to a previously evaluated droplet digital PCR (ddPCR) test. The diagnostic performance of the qPCR assays were evaluated against a commercial assay (artus C. trachomatis Plus RG PCR, Qiagen) using molecular diagnostics quality control standards and clinical samples. We examined the yield of Ct DNA prepared from five different DNA extraction kits and a cold chain-free dry-sample preservation method using swabs spiked with fixed concentrations of human and Ct DNA. RESULTS The qPCR assay was highly reproducible (Ct plasmid and genomic targets mean total coefficients of variance 41.5% and 48.3%, respectively). The assay detected 8/8 core specimens upon testing of a quality control panel and performed well in comparison to commercially marketed comparator test (sensitivity and specificity>90%). Optimal extraction and sample preservation methods for research applications were identified. CONCLUSION We describe a pipeline from collection to diagnosis providing the most efficient sample preservation and extraction with significant per test cost savings over a commercial qPCR diagnostic assay. The assay and its evaluation should allow control programs wishing to conduct independent research within the context of trachoma control, access to an affordable test with defined performance characteristics.
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Affiliation(s)
- Robert Butcher
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
| | - Jo Houghton
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Tamsyn Derrick
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom; Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Athumani Ramadhani
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom; Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Beatriz Herrera
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Anna R Last
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | | | - Matthew J Burton
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Martin J Holland
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Chrissy H Roberts
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
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Derrick T, Ramadhani AM, Mtengai K, Massae P, Burton MJ, Holland MJ. miRNAs that associate with conjunctival inflammation and ocular Chlamydia trachomatis infection do not predict progressive disease. Pathog Dis 2017; 75:2975572. [PMID: 28175294 PMCID: PMC5399916 DOI: 10.1093/femspd/ftx016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/06/2017] [Indexed: 11/14/2022] Open
Abstract
We previously showed that conjunctival miR-147b and miR-1285 were upregulated in Gambian adults with inflammatory scarring trachoma, and miR-155 and miR-184 expression was strongly associated with conjunctival inflammation and ocular Chlamydia trachomatis infection in children from Guinea-Bissau. We investigated whether the single or combined expression of miR-147b, miR-1285, miR-155 and miR-184 was able to identify individuals with increased risk of incident or progressive scarring trachoma. Conjunctival swab samples were collected from 506 children between the ages of 4 and 12 living in northern Tanzania. These 506 samples formed the baseline sample set of a 4-year longitudinal study. Chlamydia trachomatis infection was diagnosed by droplet digital PCR and expression of miR-155, miR-184, miR-1285 and miR-147b was tested by qPCR. Individuals were assessed for incidence and progression of conjunctival scarring by comparison of conjunctival photographs taken at baseline and 4 years later. miR-184 and miR-155 were strongly associated with inflammation and infection at baseline; however, no miR was associated with 4-year scarring incidence or progression. miR-184 expression was more strongly downregulated during inflammation in non-progressors relative to progressors, suggesting that a disequilibrium in the efficiency of wound healing is a significant determinant of progressive conjunctival fibrosis.
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Affiliation(s)
- Tamsyn Derrick
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Kilimanjaro Christian Medical Centre, PO Box 3010, Moshi, Kilimanjaro, Tanzania
| | - Athumani M Ramadhani
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Kilimanjaro Christian Medical Centre, PO Box 3010, Moshi, Kilimanjaro, Tanzania
| | - Karim Mtengai
- Kilimanjaro Christian Medical Centre, PO Box 3010, Moshi, Kilimanjaro, Tanzania
| | - Patrick Massae
- Kilimanjaro Christian Medical Centre, PO Box 3010, Moshi, Kilimanjaro, Tanzania
| | - Matthew J Burton
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Martin J Holland
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Four human Plasmodium species quantification using droplet digital PCR. PLoS One 2017; 12:e0175771. [PMID: 28423028 PMCID: PMC5396971 DOI: 10.1371/journal.pone.0175771] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/30/2017] [Indexed: 02/06/2023] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a partial PCR based on water-oil emulsion droplet technology. It is a highly sensitive method for detecting and delineating minor alleles from complex backgrounds and provides absolute quantification of DNA targets. The ddPCR technology has been applied for detection of many pathogens. Here the sensitive assay utilizing ddPCR for detection and quantification of Plasmodium species was investigated. The assay was developed for two levels of detection, genus specific for all Plasmodium species and for specific Plasmodium species detection. The ddPCR assay was developed based on primers and probes specific to the Plasmodium genus 18S rRNA gene. Using ddPCR for ultra-sensitive P. falciparum assessment, the lower level of detection from concentrated DNA obtained from a high volume (1 mL) blood sample was 11 parasites/mL. For species identification, in particular for samples with mixed infections, a duplex reaction was developed for detection and quantification P. falciparum/ P. vivax and P. malariae/ P. ovale. Amplification of each Plasmodium species in the duplex reaction showed equal sensitivity to singleplex single species detection. The duplex ddPCR assay had higher sensitivity to identify minor species in 32 subpatent parasitaemia samples from Cambodia, and performed better than real-time PCR. The ddPCR assay shows high sensitivity to assess very low parasitaemia of all human Plasmodium species. This provides a useful research tool for studying the role of the asymptomatic parasite reservoir for transmission in regions aiming for malaria elimination.
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Fischer A, Harrison KS, Ramirez Y, Auer D, Chowdhury SR, Prusty BK, Sauer F, Dimond Z, Kisker C, Hefty PS, Rudel T. Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense. eLife 2017; 6. [PMID: 28347402 PMCID: PMC5370187 DOI: 10.7554/elife.21465] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/09/2017] [Indexed: 12/25/2022] Open
Abstract
Obligate intracellular Chlamydia trachomatis replicate in a membrane-bound vacuole called inclusion, which serves as a signaling interface with the host cell. Here, we show that the chlamydial deubiquitinating enzyme (Cdu) 1 localizes in the inclusion membrane and faces the cytosol with the active deubiquitinating enzyme domain. The structure of this domain revealed high similarity to mammalian deubiquitinases with a unique α-helix close to the substrate-binding pocket. We identified the apoptosis regulator Mcl-1 as a target that interacts with Cdu1 and is stabilized by deubiquitination at the chlamydial inclusion. A chlamydial transposon insertion mutant in the Cdu1-encoding gene exhibited increased Mcl-1 and inclusion ubiquitination and reduced Mcl-1 stabilization. Additionally, inactivation of Cdu1 led to increased sensitivity of C. trachomatis for IFNγ and impaired infection in mice. Thus, the chlamydial inclusion serves as an enriched site for a deubiquitinating activity exerting a function in selective stabilization of host proteins and protection from host defense.
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Affiliation(s)
- Annette Fischer
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Kelly S Harrison
- Department of Molecular Biosciences, University of Kansas, lawrence, United States
| | - Yesid Ramirez
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Daniela Auer
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Bhupesh K Prusty
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Florian Sauer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Zoe Dimond
- Department of Molecular Biosciences, University of Kansas, lawrence, United States
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, lawrence, United States
| | - Thomas Rudel
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
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