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Marais G, Moodley C, Claassen-Weitz S, Patel F, Prentice E, Tootla H, Nyakutira N, Lennard K, Reddy K, Bamford C, Niehaus A, Whitelaw A, Brink A. Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization. JAC Antimicrob Resist 2024; 6:dlae050. [PMID: 38529003 PMCID: PMC10963078 DOI: 10.1093/jacamr/dlae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/03/2024] [Indexed: 03/27/2024] Open
Abstract
Background The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown. Objectives This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices. Methods Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa. Results MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was blaOXA-48-like, detected in 71% of isolates, with blaNDM detected in 5%. Notably, co-detection of two carbapenemase genes (blaOXA-48-like and blaNDM) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICEKp5 mobile element. All carbapenemases were located on plasmids. The genes blaOXA-181 and blaOXA-232 colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively. Conclusions CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was blaOXA-48-like, in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both blaOXA-48-like and blaNDM, such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.
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Affiliation(s)
- Gert Marais
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Clinton Moodley
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Shantelle Claassen-Weitz
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Fadheela Patel
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Elizabeth Prentice
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Hafsah Tootla
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Nyasha Nyakutira
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Katie Lennard
- Division of Computational Biology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Kessendri Reddy
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Colleen Bamford
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Pathcare, Cape Town, South Africa
| | - Abraham Niehaus
- Division of Medical Microbiology, Ampath, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
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Ehtewish H, Mesleh A, Ponirakis G, Lennard K, Al Hamad H, Chandran M, Parray A, Abdesselem H, Wijten P, Decock J, Alajez NM, Ramadan M, Khan S, Ayadathil R, Own A, Elsotouhy A, Albagha O, Arredouani A, Blackburn JM, Malik RA, El-Agnaf OMA. Profiling the autoantibody repertoire reveals autoantibodies associated with mild cognitive impairment and dementia. Front Neurol 2023; 14:1256745. [PMID: 38107644 PMCID: PMC10722091 DOI: 10.3389/fneur.2023.1256745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/31/2023] [Indexed: 12/19/2023] Open
Abstract
Background Dementia is a debilitating neurological disease affecting millions of people worldwide. The exact mechanisms underlying the initiation and progression of the disease remain to be fully defined. There is an increasing body of evidence for the role of immune dysregulation in the pathogenesis of dementia, where blood-borne autoimmune antibodies have been studied as potential markers associated with pathological mechanisms of dementia. Methods This study included plasma from 50 cognitively normal individuals, 55 subjects with MCI (mild cognitive impairment), and 22 subjects with dementia. Autoantibody profiling for more than 1,600 antigens was performed using a high throughput microarray platform to identify differentially expressed autoantibodies in MCI and dementia. Results The differential expression analysis identified 33 significantly altered autoantibodies in the plasma of patients with dementia compared to cognitively normal subjects, and 38 significantly altered autoantibodies in the plasma of patients with dementia compared to subjects with MCI. And 20 proteins had significantly altered autoantibody responses in MCI compared to cognitively normal individuals. Five autoantibodies were commonly dysregulated in both dementia and MCI, including anti-CAMK2A, CKS1B, ETS2, MAP4, and NUDT2. Plasma levels of anti-ODF3, E6, S100P, and ARHGDIG correlated negatively with the cognitive performance scores (MoCA) (r2 -0.56 to -0.42, value of p < 0.001). Additionally, several proteins targeted by autoantibodies dysregulated in dementia were significantly enriched in the neurotrophin signaling pathway, axon guidance, cholinergic synapse, long-term potentiation, apoptosis, glycolysis and gluconeogenesis. Conclusion We have shown multiple dysregulated autoantibodies in the plasma of subjects with MCI and dementia. The corresponding proteins for these autoantibodies are involved in neurodegenerative pathways, suggesting a potential impact of autoimmunity on the etiology of dementia and the possible benefit for future therapeutic approaches. Further investigations are warranted to validate our findings.
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Affiliation(s)
- Hanan Ehtewish
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Areej Mesleh
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Georgios Ponirakis
- Department of Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation (QF), Doha, Qatar
| | - Katie Lennard
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur, Malaysia
| | - Hanadi Al Hamad
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha, Qatar
| | - Mani Chandran
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha, Qatar
| | - Aijaz Parray
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha, Qatar
| | - Houari Abdesselem
- Proteomics Core Facility, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Patrick Wijten
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Julie Decock
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Nehad M. Alajez
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Marwan Ramadan
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha, Qatar
| | - Shafi Khan
- Geriatric and Memory Clinic, Rumailah Hospital, Hamad Medical Corporation (HMC), Doha, Qatar
| | - Raheem Ayadathil
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha, Qatar
| | - Ahmed Own
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha, Qatar
- Department of Neuroradiology, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | - Ahmed Elsotouhy
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation (HMC), Doha, Qatar
- Department of Clinical Radiology, Weill Cornell Medicine-Qatar, Qatar Foundation, Doha, Qatar
| | - Omar Albagha
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Abdelilah Arredouani
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Jonathan M. Blackburn
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur, Malaysia
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rayaz A. Malik
- Department of Medicine, Weill Cornell Medicine-Qatar, Qatar Foundation (QF), Doha, Qatar
| | - Omar M. A. El-Agnaf
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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Mesleh A, Ehtewish H, Lennard K, Abdesselem HB, Al-Shaban F, Decock J, Alajez NM, Arredouani A, Emara MM, Albagha O, Stanton LW, Abdulla SA, Blackburnand JM, El-Agnaf OMA. High-throughput autoantibody screening identifies differentially abundant autoantibodies in autism spectrum disorder. Front Mol Neurosci 2023; 16:1222506. [PMID: 37908488 PMCID: PMC10613655 DOI: 10.3389/fnmol.2023.1222506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/22/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by defects in two core domains, social/communication skills and restricted/repetitive behaviors or interests. There is no approved biomarker for ASD diagnosis, and the current diagnostic method is based on clinical manifestation, which tends to vary vastly between the affected individuals due to the heterogeneous nature of ASD. There is emerging evidence that supports the implication of the immune system in ASD, specifically autoimmunity; however, the role of autoantibodies in ASD children is not yet fully understood. Materials and methods In this study, we screened serum samples from 93 cases with ASD and 28 healthy controls utilizing high-throughput KoRectly Expressed (KREX) i-Ome protein-array technology. Our goal was to identify autoantibodies with differential expressions in ASD and to gain insights into the biological significance of these autoantibodies in the context of ASD pathogenesis. Result Our autoantibody expression analysis identified 29 differential autoantibodies in ASD, 4 of which were upregulated and 25 downregulated. Subsequently, gene ontology (GO) and network analysis showed that the proteins of these autoantibodies are expressed in the brain and involved in axonal guidance, chromatin binding, and multiple metabolic pathways. Correlation analysis revealed that these autoantibodies negatively correlate with the age of ASD subjects. Conclusion This study explored autoantibody reactivity against self-antigens in ASD individuals' serum using a high-throughput assay. The identified autoantibodies were reactive against proteins involved in axonal guidance, synaptic function, amino acid metabolism, fatty acid metabolism, and chromatin binding.
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Affiliation(s)
- Areej Mesleh
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Hanan Ehtewish
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Katie Lennard
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur, Malaysia
| | - Houari B. Abdesselem
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Proteomics Core Facility, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Fouad Al-Shaban
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Julie Decock
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Nehad M. Alajez
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Abdelilah Arredouani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Mohamed M. Emara
- Basic Medical Sciences Department, College of Medicine, Qatar University Health, Qatar University, Doha, Qatar
| | - Omar Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Lawrence W. Stanton
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Sara A. Abdulla
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Jonathan M. Blackburnand
- Sengenics Corporation, Level M, Plaza Zurich, Damansara Heights, Kuala Lumpur, Malaysia
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Omar M. A. El-Agnaf
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
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Overmeyer AJ, Prentice E, Brink A, Lennard K, Moodley C. The genomic characterization of carbapenem-resistant Serratia marcescens at a tertiary hospital in South Africa. JAC Antimicrob Resist 2023; 5:dlad089. [PMID: 37497336 PMCID: PMC10368080 DOI: 10.1093/jacamr/dlad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Background Serratia marcescens is an opportunistic nosocomial pathogen, and recent reports have highlighted the rapid increase in multidrug resistance in this organism. There is a paucity in genomic data for carbapenem-resistant S. marcescens (CRSM). Methods A retrospective cohort study describing laboratory-confirmed CRSM from a tertiary academic hospital in Cape Town, South Africa, for the period 2015-20, was performed. Stored CRSM and contemporary isolates were submitted for WGS using Illumina MiSeq, with the Nextera DNA Flex Library Preparation Kit. Sequence data were analysed in-house using srst2 and Tychus, and CRSM and contemporary isolates were compared. Results Twenty-one CRSM and four contemporary isolates were sequenced and analysed. Twenty-four different resistance genes were identified, with all isolates having at least two resistance genes, and seventeen isolates harbouring three or more genes. This correlated well with phenotypic results. The blaOXA-48-like carbapenemase was the most common carbapenemase identified, in 86% (18/21) of CRSM. A core SNP difference tree indicated that the CRSM could be grouped into three clusters. Eleven isolates had shared plasmids. Several genes and SNPs were identified in the CRSM, which may putatively augment virulence, but this requires further functional characterization. Conclusions A diverse resistome was observed in CRSM, which was also reflected phenotypically, with blaOXA-48-like the most commonly carbapenemase. Though distinct clusters were observed, no clonality was noted, and a limited number of isolates shared plasmids. This study provides genomic data for emerging CRSM and highlights the importance of ongoing genomic surveillance to inform infection prevention control and antimicrobial stewardship initiatives.
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Affiliation(s)
| | - Elizabeth Prentice
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Katie Lennard
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Clinton Moodley
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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5
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Harrison V, Khan SF, Damerell V, Bleloch J, ArulJothi KN, Sinkala M, Lennard K, Mulder N, Calder B, Blackburn J, Prince S. Strongylopus grayii tadpole blastema extract exerts cytotoxic effects on embryonal rhabdomyosarcoma cells. In Vitro Cell Dev Biol Anim 2022; 58:679-692. [PMID: 35947290 DOI: 10.1007/s11626-022-00714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022]
Abstract
Amphibians have regenerative capacity and are resistant to developing cancer. This suggests that the developing blastema, located at the tissue regeneration site, may secrete anti-cancer factors. Here, we investigate the anti-cancer potential of tadpole tail blastema extracts (TAD) from the stream frog, Strongylopus grayii, in embryonal rhabdomyosarcoma (ERMS) cells. ERMS originates in skeletal muscle tissue and is a common pediatric soft tissue sarcoma. We show using MTT assays that TAD inhibited ERMS cell viability in a concentration-dependent manner, and phase contrast/fluorescent microscopy revealed that it induced morphological markers of senescence and apoptosis. Western blotting showed that this was associated with DNA damage (γH2AX) and activation of the p38/MAPK stress signaling pathway as well as molecular markers of senescence (p16INK4a), apoptosis (cleaved PARP), and inhibition of cell cycle promoters (cyclin A, CDK2, and cyclin B1). Furthermore, proteomics followed by gene ontology analyses showed that TAD treatment inhibited known tumor promoters and proteins required for cancer cell survival. Lastly, using the LINCS drug perturbation library, we show that there is an overlap between the proteomics signature induced by TAD and common anti-cancer drugs. Taken together, this study provides novel evidence that TAD exhibits cytotoxicity in ERMS cells.
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Affiliation(s)
| | - Saif F Khan
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Victoria Damerell
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Jenna Bleloch
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - K N ArulJothi
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, India
| | - Musalula Sinkala
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Bridget Calder
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Jonathan Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Sharon Prince
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
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Balle C, Gupta PM, Tharp GK, Nelson SA, Konstantinus IN, Lennard K, Jaumdally SZ, Happel AU, Barnabas SL, Gill K, Bekker LG, Passmore JAS, Jaspan HB, Bosinger SE. Systems Analysis Reveals Contraceptive-Induced Alteration of Cervicovaginal Gene Expression in a Randomized Trial. Front Reprod Health 2022; 4:781687. [PMID: 36303659 PMCID: PMC9580795 DOI: 10.3389/frph.2022.781687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
Hormonal contraceptives (HCs) are vital in managing the reproductive health of women. However, HC usage has been linked to perturbations in cervicovaginal immunity and increased risk of sexually transmitted infections. Here, we evaluated the impact of three HCs on the cervicovaginal environment using high-throughput transcriptomics. From 2015 to 2017, 130 adolescent females aged 15-19 years were enrolled into a substudy of UChoose, a single-site, open-label randomized, crossover trial (NCT02404038) and randomized to injectable norethisterone-enanthate (Net-En), combined oral contraceptives (COC), or etonorgesterol/ethinyl-estradiol-combined contraceptive vaginal ring (CCVR). Cervicovaginal samples were collected after 16 weeks of randomized HC use and analyzed by RNA-Seq, 16S rRNA gene sequencing, and Luminex analysis. Participants in the CCVR arm had a significant elevation of transcriptional networks driven by IL-6, IL-1, and NFKB, and lower expression of genes supporting epithelial barrier integrity. An integrated multivariate analysis demonstrated that networks of microbial dysbiosis and inflammation best discriminated the CCVR arm from the other contraceptive groups, while genes involved in epithelial cell differentiation were predictive of the Net-En and COC arms. Collectively, these data from a randomized trial represent the most comprehensive "omics" analyses of the cervicovaginal response to HCs and provide important mechanistic guidelines for the provision of HCs in sub-Saharan Africa.
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Affiliation(s)
- Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Prachi M. Gupta
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Gregory K. Tharp
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Sydney A. Nelson
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Iyaloo N. Konstantinus
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Namibia Institute of Pathology, Windhoek, Namibia
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Shameem Z. Jaumdally
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shaun L. Barnabas
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Desmond Tutu Health Centre, University of Cape Town, Cape Town, South Africa,Family Clinical Research Center, Stellenbosch University, Tygerberg, South Africa
| | - Katherine Gill
- Desmond Tutu Health Centre, University of Cape Town, Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu Health Centre, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S. Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Cape Town, South Africa
| | - Heather B. Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States,Department of Pediatrics and Global Health, University of Washington, Seattle, WA, United States
| | - Steven E. Bosinger
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States,Emory Vaccine Center, Emory University, Atlanta, GA, United States,*Correspondence: Steven E. Bosinger
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7
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Dzanibe S, Lennard K, Kiravu A, Seabrook MSS, Alinde B, Holmes SP, Blish CA, Jaspan HB, Gray CM. Stereotypic Expansion of T Regulatory and Th17 Cells during Infancy Is Disrupted by HIV Exposure and Gut Epithelial Damage. J Immunol 2022; 208:27-37. [PMID: 34819390 PMCID: PMC8702481 DOI: 10.4049/jimmunol.2100503] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/01/2021] [Indexed: 01/03/2023]
Abstract
Few studies have investigated immune cell ontogeny throughout the neonatal and early pediatric period, when there is often increased vulnerability to infections. In this study, we evaluated the dynamics of two critical T cell populations, T regulatory (Treg) cells and Th17 cells, over the first 36 wk of human life. First, we observed distinct CD4+ T cells phenotypes between cord blood and peripheral blood, collected within 12 h of birth, showing that cord blood is not a surrogate for newborn blood. Second, both Treg and Th17 cells expanded in a synchronous fashion over 36 wk of life. However, comparing infants exposed to HIV in utero, but remaining uninfected, with HIV-unexposed uninfected control infants, there was a lower frequency of peripheral blood Treg cells at birth, resulting in a delayed expansion, and then declining again at 36 wk. Focusing on birth events, we found that Treg cells coexpressing CCR4 and α4β7 inversely correlated with plasma concentrations of CCL17 (the ligand for CCR4) and intestinal fatty acid binding protein, IL-7, and CCL20. This was in contrast with Th17 cells, which showed a positive association with these plasma analytes. Thus, despite the stereotypic expansion of both cell subsets over the first few months of life, there was a disruption in the balance of Th17 to Treg cells at birth likely being a result of gut damage and homing of newborn Treg cells from the blood circulation to the gut.
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Affiliation(s)
- Sonwabile Dzanibe
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa;
| | - Katie Lennard
- Division of Computational Biology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Agano Kiravu
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Melanie S S Seabrook
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Berenice Alinde
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Susan P Holmes
- Department of Statistic, Stanford University, Stanford, CA
| | - Catherine A Blish
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Heather B Jaspan
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children's Research Institute and Departments of Paediatrics and Global Health, University of Washington, Seattle, WA; and
| | - Clive M Gray
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa;
- Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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8
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Opperman CJ, Moodley C, Lennard K, Smith M, Ncayiyana J, Vulindlu M, Gafoor M, Govender N, Ismail H, Bamford C, McCarthy KM, Nicol MP, Centner CM. A citywide, clonal outbreak of Pseudomonas aeruginosa. Int J Infect Dis 2022; 117:74-86. [DOI: 10.1016/j.ijid.2022.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022] Open
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9
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de Waal P, Murray S, Lennard K, Korsman J, Levin M. Bacterial microbiota composition of fresh unpasteurized cow's milk and home-made and commercially available fermented milk products. Pediatr Allergy Immunol 2021; 32:1879-1882. [PMID: 34314532 DOI: 10.1111/pai.13607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Pieter de Waal
- Division of Allergology, Department of Paediatrics, University of Cape Town, Rondebosch, South Africa
| | - Shane Murray
- Centre of Proteomic and Genomic Research, Cape Town, South Africa
| | - Katie Lennard
- Department of Biostatistics, University of Cape Town, Observatory, South Africa
| | - Jeanne Korsman
- Centre of Proteomic and Genomic Research, Cape Town, South Africa
| | - Michael Levin
- Division of Allergology, Department of Paediatrics, University of Cape Town, Rondebosch, South Africa.,InVIVO planetary health research group of the Worldwide Universities Network, South Africa
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10
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Vermeire ML, Thoresen J, Lennard K, Vikram S, Kirkman K, Swemmer AM, Te Beest M, Siebert F, Gordijn P, Venter Z, Brunel C, Wolfaard G, Krumins JA, Cramer MD, Hawkins HJ. Fire and herbivory drive fungal and bacterial communities through distinct above- and belowground mechanisms. Sci Total Environ 2021; 785:147189. [PMID: 33933764 DOI: 10.1016/j.scitotenv.2021.147189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Fire and herbivory are important natural disturbances in grassy biomes. Both drivers are likely to influence belowground microbial communities but no studies have unravelled the long-term impact of both fire and herbivory on bacterial and fungal communities. We hypothesized that soil bacterial communities change through disturbance-induced shifts in soil properties (e.g. pH, nutrients) while soil fungal communities change through vegetation modification (biomass and species composition). To test these ideas, we characterised soil physico-chemical properties (pH, acidity, C, N, P and exchangeable cations content, texture, bulk density, moisture), plant species richness and biomass, microbial biomass and bacterial and fungal community composition and diversity (using 16S and ITS rRNA amplicon sequencing, respectively) in six long-term (18 to 70 years) ecological research sites in South African savanna and grassland ecosystems. We found that fire and herbivory regimes profoundly modified soil physico-chemical properties, plant species richness and standing biomass. In all sites, an increase in woody biomass (ranging from 12 to 50%) was observed when natural disturbances were excluded. The intensity and direction of changes in soil properties were highly dependent on the topo-pedo-climatic context. Overall, fire and herbivory shaped bacterial and fungal communities through distinct driving forces: edaphic properties (including Mg, pH, Ca) for bacteria, and vegetation (herbaceous biomass and woody cover) for fungi. Fire and herbivory explained on average 7.5 and 9.8% of the fungal community variability, respectively, compared to 6.0 and 5.6% for bacteria. The relatively small changes in microbial communities due to natural disturbance is in stark contrast to dramatic vegetation and edaphic changes and suggests that soil microbial communities, having evolved with disturbance, are resistant to change. This represents both a buffer to short-term anthropogenic-induced changes and a restoration challenge in the face of long-term changes.
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Affiliation(s)
- M-L Vermeire
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa; IRD, CIRAD, University of Montpellier, PHIM, Montpellier, France.
| | - J Thoresen
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
| | - K Lennard
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - S Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, South Africa
| | - K Kirkman
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - A M Swemmer
- South African Environmental Observation Network (SAEON), Phalaborwa, South Africa
| | - M Te Beest
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, the Netherlands; Centre for African Conservation Ecology, Nelson Mandela University, Port Elizabeth 6031, South Africa; South African Environmental Observation Network, Grasslands-Forests-Wetlands Node, Montrose 3201, South Africa
| | - F Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - P Gordijn
- South African Environmental Observation Network, Grasslands-Forests-Wetlands Node, Montrose 3201, South Africa
| | - Z Venter
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa; Department of Terrestrial Ecology, Norwegian Institute for Nature Research, Trondheim, Norway (present affiliation)
| | - C Brunel
- IRD, CIRAD, University of Montpellier, PHIM, Montpellier, France
| | - G Wolfaard
- Sustineri Ecological Consulting (Pty) Ltd., Mbombela 1200, South Africa
| | - J A Krumins
- Department of Biology, Montclair State University, Montclair, NJ, USA
| | - M D Cramer
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
| | - H-J Hawkins
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa; Conservation South Africa, 301 Heritage House, Claremont 7375, South Africa
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11
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Gudza-Mugabe M, Havyarimana E, Jaumdally S, Garson KL, Lennard K, Tarupiwa A, Mugabe F, Marere T, Mavenyengwa RT, Masson L, Jaspan HB. Human Immunodeficiency Virus Infection Is Associated With Preterm Delivery Independent of Vaginal Microbiota in Pregnant African Women. J Infect Dis 2021; 221:1194-1203. [PMID: 31722395 DOI: 10.1093/infdis/jiz584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/11/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND During pregnancy, the vaginal microbiota is relatively stable. However, African women have more diverse vaginal microbiota than their European counterparts, in addition to high human immunodeficiency virus (HIV) prevalence and risk of adverse birth outcomes. Although HIV is associated with alterations in vaginal microbiota and inflammation in nonpregnant women, these relationships are underexplored in pregnant women. METHODS In this study, we characterize the vaginal microbiota and immune factors in pregnant African women who were HIV-uninfected (n = 314) versus HIV-infected (n = 42). Mucosal samples were collected once at the enrollment visit (between 15 and 35 weeks of gestation) and women were followed until delivery. RESULTS Vaginal microbial communities of pregnant women with HIV were significantly more diverse than women without HIV (P = .004), with community structure also differing by HIV status (P = .002, R2 = 0.02). Human immunodeficiency virus infection was also associated with increased risk of preterm birth (PTB) (31% versus 15.3%; P = .066). In a multivariate analysis, HIV infection was independently associated with diverse vaginal community state type (CST)-IVA (P = .005) and CST-IVB (P = .018) as well as PTB (P = .049). No association between HIV status and cytokine concentrations was found. CONCLUSIONS Longitudinal studies with accurate gestational age assessment would be important to confirm these relationships.
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Affiliation(s)
- Muchaneta Gudza-Mugabe
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.,National Microbiology Reference Laboratory, Harare, Zimbabwe.,Department of Medical Microbiology, University of Zimbabwe, Harare, Zimbabwe
| | - Enock Havyarimana
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Shameem Jaumdally
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Kirsty Lee Garson
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | | | - Tarisai Marere
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | - Lindi Masson
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Heather B Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Departments of Pediatrics and Global Health, University of Washington, Seattle, Washington, USA
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12
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Balle C, Konstantinus IN, Jaumdally SZ, Havyarimana E, Lennard K, Esra R, Barnabas SL, Happel AU, Moodie Z, Gill K, Pidwell T, Karaoz U, Brodie E, Maseko V, Gamieldien H, Bosinger SE, Myer L, Bekker LG, Passmore JAS, Jaspan HB. Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial. Nat Commun 2020; 11:5578. [PMID: 33149114 PMCID: PMC7643181 DOI: 10.1038/s41467-020-19382-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Young women in sub-Saharan Africa are disproportionally affected by HIV infection and unintended pregnancies. However, hormonal contraceptive (HC) use may influence HIV risk through changes in genital tract microbiota and inflammatory cytokines. To investigate this, 130 HIV negative adolescent females aged 15-19 years were enrolled into a substudy of UChoose, an open-label randomized crossover study (NCT02404038), comparing acceptability and contraceptive product preference as a proxy for HIV prevention delivery methods. Participants were randomized to injectable norethisterone enanthate (Net-En), combined oral contraceptives (COC) or etonorgesterol/ethinyl estradiol combined contraceptive vaginal ring (CCVR) for 16 weeks, then crossed over to another HC for 16 weeks. Cervicovaginal samples were collected at baseline, crossover and exit for characterization of the microbiota and measurement of cytokine levels; primary endpoints were cervical T cell activation, vaginal microbial diversity and cytokine concentrations. Adolescents randomized to COCs had lower vaginal microbial diversity and relative abundance of HIV risk-associated taxa compared to Net-En or CCVR. Cervicovaginal inflammatory cytokine concentrations were significantly higher in adolescents randomized to CCVR compared to COC and Net-En. This suggests that COC use may induce an optimal vaginal ecosystem by decreasing bacterial diversity and inflammatory taxa, while CCVR use is associated with genital inflammation.
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Affiliation(s)
- Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Iyaloo N Konstantinus
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shameem Z Jaumdally
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Enock Havyarimana
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Rachel Esra
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shaun L Barnabas
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Tanya Pidwell
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley, CA, 94720, USA
| | - Eoin Brodie
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley, CA, 94720, USA.,University of California, Berkeley, CA, USA
| | - Venessa Maseko
- National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Hoyam Gamieldien
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Steven E Bosinger
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine; Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Landon Myer
- Division of Epidemiology, Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Cape Town, South Africa
| | - Heather B Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. .,Seattle Children's Research Institute, Seattle, WA, USA. .,University of Washington Department of Pediatrics and Global Health, Seattle, WA, USA.
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13
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Manenzhe RI, Dube FS, Wright M, Lennard K, Mounaud S, Lo SW, Zar HJ, Nierman WC, Nicol MP, Moodley C. Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants. Front Public Health 2020; 8:543898. [PMID: 33072693 PMCID: PMC7536305 DOI: 10.3389/fpubh.2020.543898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal (NP) samples at 2-weekly intervals from birth through the first year of life from 137 infants. As a proof of concept, 196 NP samples were retrieved from a subset of 23 infants to explore strain-level pneumococcal colonization patterns and associated antimicrobial-resistance determinants. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of pneumococcal and non-pneumococcal bacterial reads. Pneumococcal contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. In silico pneumococcal capsular and multilocus sequence typing were performed. Results: Of the 196 samples sequenced, 174 had corresponding positive cultures for pneumococci, of which, 152 were assigned an in silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of the samples. Twenty-two different pneumococcal serotypes were identified, with 15B/15C and 16F being the most common non-PCV13 serotypes, while 23F and 19A were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including four novel STs were identified in silico. Mutations in the folA and folP genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci, as well as in the pbp1a and pbp2x genes, in penicillin non-susceptible ST705215B/15C isolates. Conclusions: Metagenomic sequencing of NP samples is a valuable culture-independent technique for a detailed evaluation of the pneumococcal component and resistome of the NP microbiome. This method allowed for the detection of novel STs, as well as co-colonization, with a predominance of non-PCV13 serotypes in this cohort. Forty-eight resistance genes, as well as mutations associated with resistance were detected, but the correlation with phenotypic non-susceptibility was lower than expected.
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Affiliation(s)
- Rendani I Manenzhe
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Felix S Dube
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | | | - Katie Lennard
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Stephanie W Lo
- Parasites and Microbes Program, The Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African - Medical Research Council Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | - Mark P Nicol
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Division of Infection and Immunity, University of Western Australia, Perth, WA, Australia
| | - Clinton Moodley
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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14
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Balle C, Gill K, Konstantinus IN, Jaumdally SZ, Lennard K, Esra R, Happel AU, Barnabas SL, Gamieldien H, Pidwell T, Maseko V, Lesosky M, Myer L, Passmore JAS, Bekker LG, Jaspan HB. Hormonal contraception and risk of STIs and bacterial vaginosis in South African adolescents: secondary analysis of a randomised trial. Sex Transm Infect 2020; 97:112-117. [PMID: 32989170 DOI: 10.1136/sextrans-2020-054483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/30/2020] [Accepted: 08/29/2020] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Young women in sub-Saharan Africa are at high risk of STIs and unintended pregnancies, yet hormonal contraceptive (HC) use may affect STI risk. We compared the influence of three HCs on the incidence and prevalence of STIs and bacterial vaginosis (BV) in South African adolescents. METHODS One hundred and thirty adolescents between 15 and 19 years were randomised to the injectable norethisterone enanthate (Net-En), combined oral contraceptives (COC) (Triphasil or Nordette) or a combined contraceptive vaginal ring (CCVR; NuvaRing) for 16 weeks (clinicaltrials.gov/NCT02404038). Vaginal samples were collected at baseline and 16 weeks post contraceptive initiation for STI and BV testing. RESULTS In an intention-to-treat analysis, no significant differences in BV prevalence were found between study arms. The overall incidence of any STI at follow-up was high: 16.2% in the COC arm; 25.7% in the Net-En arm; and 37.1% in the CCVR arm. The incidence rate (IR) of any STI was similar between Net-En (IR 0.74 (95% CI 0.34 to 1.41)) and the oestrogen-containing contraceptives (IR 0.78 (95% CI 0.47 to 1.22)). A lower IR of Chlamydia trachomatis (incidence rate ratio (IRR) 0.68 (95% CI 0.19 to 1.99)) and Neisseria gonorrhoeae (IRR 0.25 (95% CI 0.01 to 1.35)) but a higher IR of Mycoplasma genitalium (IRR 16.0 (95% CI 2.96 to 400)), was observed in the Net-En arm compared with the oestrogen-containing contraceptives, although the overall incidence of M. genitalium was low (4.7%). In an exploratory analysis, the risk of any STI and N. gonorrhoeae was lower in the COC arm compared with CCVR. A per-protocol analysis yielded similar results. CONCLUSION Our results suggest that use of Net-En may be associated with increased risk of M. genitalium compared with oestrogen-containing contraceptives but not with overall STI risk. COC use may decrease STI risk relative to CCVR.
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Affiliation(s)
- Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Iyaloo N Konstantinus
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Shameem Z Jaumdally
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Rachel Esra
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Shaun L Barnabas
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa.,Family Clinical Research Centre, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Hoyam Gamieldien
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Tanya Pidwell
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Venessa Maseko
- National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Maia Lesosky
- Division of Epidemiology, Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Landon Myer
- Division of Epidemiology, Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Jo-Ann S Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa.,National Health Laboratory Service, Johannesburg, Gauteng, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Heather B Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa .,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, DC, USA.,Pediatrics and Global Health, University of Washington, Seattle, WA, USA
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15
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Manenzhe RI, Dube FS, Wright M, Lennard K, Zar HJ, Mounaud S, Nierman WC, Nicol MP, Moodley C. Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing. PLoS One 2020; 15:e0231887. [PMID: 32320455 PMCID: PMC7176138 DOI: 10.1371/journal.pone.0231887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/02/2020] [Indexed: 11/18/2022] Open
Abstract
Introduction Nasopharyngeal (NP) colonization with antimicrobial-resistant bacteria is a global public health concern. Antimicrobial-resistance (AMR) genes carried by the resident NP microbiota may serve as a reservoir for transfer of resistance elements to opportunistic pathogens. Little is known about the NP antibiotic resistome. This study longitudinally investigated the composition of the NP antibiotic resistome in Streptococcus-enriched samples in a South African birth cohort. Methods As a proof of concept study, 196 longitudinal NP samples were retrieved from a subset of 23 infants enrolled as part of broader birth cohort study. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of streptococcal and non-streptococcal bacterial reads. Contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. Results AMR genes were detected in 64% (125/196) of the samples. A total of 329 AMR genes were detected, including 36 non-redundant genes, ranging from 1 to 14 genes per sample. The predominant AMR genes detected encoded resistance mechanisms to beta-lactam (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline antibiotics (12%, 38/329). MsrD, ermB, and mefA genes were only detected from streptococcal reads. The predominant genes detected from non- streptococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Different patterns of carriage of AMR genes were observed, with only one infant having a stable carriage of mefA, msrD and tetM over a long period. Conclusion This study demonstrates that WMGS can provide a broad snapshot of the NP resistome and has the potential to provide a comprehensive assessment of resistance elements present in this niche.
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Affiliation(s)
- Rendani I. Manenzhe
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Felix S. Dube
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Meredith Wright
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Katie Lennard
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and MRC unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | | | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- Division of Infection and Immunity, University of Western Australia, Perth, Australia
| | - Clinton Moodley
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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16
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Wood LF, Brown BP, Lennard K, Karaoz U, Havyarimana E, Passmore JAS, Hesseling AC, Edlefsen PT, Kuhn L, Mulder N, Brodie EL, Sodora DL, Jaspan HB. Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants. Clin Infect Dis 2019; 67:1237-1246. [PMID: 29659737 DOI: 10.1093/cid/ciy265] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background Exclusive breastfeeding reduces the rate of postnatal human immunodeficiency virus (HIV) transmission compared to nonexclusive breastfeeding; however, the mechanisms of this protection are unknown. Our study aimed to interrogate the mechanisms underlying the protective effect of exclusive breastfeeding. Methods We performed a prospective, longitudinal study of infants from a high-HIV-prevalence, low-income setting in South Africa. We evaluated the role of any non-breast milk feeds, excluding prescribed medicines on stool microbial communities via 16S rRNA gene sequencing, peripheral T-cell activation via flow cytometry, and buccal mucosal gene expression via quantitative polymerase chain reaction assay. Results A total of 155 infants were recruited at birth with mean gestational age of 38.9 weeks and mean birth weight of 3.2 kg. All infants were exclusively breastfed (EBF) at birth, but only 43.5% and 20% remained EBF at 6 or 14 weeks of age, respectively. We observed lower stool microbial diversity and distinct microbial composition in exclusively breastfed infants. These microbial communities, and the relative abundance of key taxa, were correlated with peripheral CD4+ T-cell activation, which was lower in EBF infants. In the oral mucosa, gene expression of chemokine and chemokine receptors involved in recruitment of HIV target cells to tissues, as well as epithelial cytoskeletal proteins, was lower in EBF infants. Conclusions These data suggest that nonexclusive breastfeeding alters the gut microbiota, increasing T-cell activation and, potentially, mucosal recruitment of HIV target cells. Study findings highlight a biologically plausible mechanistic explanation for the reduced postnatal HIV transmission observed in EBF infants.
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Affiliation(s)
- Lianna F Wood
- University of Washington Schools of Medicine and Public Health, Seattle
| | - Bryan P Brown
- Duke University, Durham, North Carolina.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Katie Lennard
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley.,University of California, Berkeley
| | - Enock Havyarimana
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Jo-Ann S Passmore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa.,National Health Laboratory Services, Cape Town, South Africa
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Stellenbosch University, Cape Town, South Africa
| | | | | | - Nicola Mulder
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Eoin L Brodie
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley.,University of California, Berkeley
| | | | - Heather B Jaspan
- University of Washington Schools of Medicine and Public Health, Seattle.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa.,Seattle Children's Research Institute, Washington
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17
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Masson L, Barnabas S, Deese J, Lennard K, Dabee S, Gamieldien H, Jaumdally SZ, Williamson AL, Little F, Van Damme L, Ahmed K, Crucitti T, Abdellati S, Bekker LG, Gray G, Dietrich J, Jaspan H, Passmore JAS. Inflammatory cytokine biomarkers of asymptomatic sexually transmitted infections and vaginal dysbiosis: a multicentre validation study. Sex Transm Infect 2018; 95:5-12. [PMID: 30018088 DOI: 10.1136/sextrans-2017-053506] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/11/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Vaginal dysbiosis and STIs are important drivers of the HIV epidemic and reproductive complications. These conditions remain prevalent, partly because most cases are asymptomatic. We have shown that inflammatory cytokines interleukin (IL)-1α, IL-1β and interferon-γ-induced protein (IP)-10 are biomarkers for detecting asymptomatic STIs and vaginal dysbiosis (bacterial vaginosis (BV) or intermediate microbiota). This study aimed to validate the performance of these biomarkers in African women recruited regardless of symptoms. METHODS IL-1α, IL-1β and IP-10 were measured in menstrual cup secretions, endocervical, lateral vaginal wall and vulvovaginal swabs from 550 women from Pretoria, Soweto and Cape Town, South Africa and Bondo, Kenya using Luminex and ELISA. STIs were assessed by PCR, BV by Nugent scoring and vaginal microbiota by 16S rRNA sequencing. RESULTS Across four study populations and four types of genital specimens, the performance of IL-1α, IL-1β and IP-10 for identification of women with STIs, BV or intermediate microbiota was consistent. Of the genital samples assessed, biomarkers measured in lateral vaginal wall swabs performed best, correctly classifying 76%(95% CI 70% to 81%) of women according to STI, BV or intermediate microbiota status (sensitivity 77%, specificity 71%) and were more accurate than clinical symptoms (sensitivity 41%, specificity 57%) (p=0.0003). Women incorrectly classified as STI/BV positive using the biomarkers had more abundant dysbiosis-associated bacteria, including Prevotella bivia and Gardnerella sp, detected by 16S rRNA sequencing, but not Nugent scoring. Including vaginal pH with the cytokine biomarkers improved the accuracy of the test (82% (95% CI 75% to 88%) correctly classified), although pH alone had poor specificity (61%). CONCLUSIONS An inexpensive, point-of-care screening test including IL-1α, IL-1β and IP-10 (and potentially pH) could be used in resource-limited settings to identify women with asymptomatic STIs and dysbiosis. These women could then be referred for aetiological testing, followed by specific treatment.
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Affiliation(s)
- Lindi Masson
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Shaun Barnabas
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Desmond Tutu HIV Foundation, University of Cape Town, Cape Town, South Africa
| | - Jennifer Deese
- Contraceptive Technology and Innovation Department, Family Health International 360, Durham, North Carolina, USA.,Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katie Lennard
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Smritee Dabee
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Hoyam Gamieldien
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Shameem Z Jaumdally
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
| | - Francesca Little
- Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Lut Van Damme
- The Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Tania Crucitti
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Saïd Abdellati
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Linda-Gail Bekker
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Desmond Tutu HIV Foundation, University of Cape Town, Cape Town, South Africa
| | - Glenda Gray
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,South African Medical Research Council, Cape Town, South Africa
| | - Janan Dietrich
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather Jaspan
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Seattle Children's Research Institute, University of Washington, Seattle, Washington, USA
| | - Jo-Ann S Passmore
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
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18
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Lennard K, Dabee S, Barnabas SL, Havyarimana E, Blakney A, Jaumdally SZ, Botha G, Mkhize NN, Bekker LG, Lewis DA, Gray G, Mulder N, Passmore JAS, Jaspan HB. Microbial Composition Predicts Genital Tract Inflammation and Persistent Bacterial Vaginosis in South African Adolescent Females. Infect Immun 2018; 86:e00410-17. [PMID: 29038128 PMCID: PMC5736802 DOI: 10.1128/iai.00410-17] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/10/2017] [Indexed: 11/20/2022] Open
Abstract
Young African females are at an increased risk of HIV acquisition, and genital inflammation or the vaginal microbiome may contribute to this risk. We studied these factors in 168 HIV-negative South African adolescent females aged 16 to 22 years. Unsupervised clustering of 16S rRNA gene sequences revealed three clusters (subtypes), one of which was strongly associated with genital inflammation. In a multivariate model, the microbiome compositional subtype and hormonal contraception were significantly associated with genital inflammation. We identified 40 taxa significantly associated with inflammation, including those reported previously (Prevotella, Sneathia, Aerococcus, Fusobacterium, and Gemella) as well as several novel taxa (including increased frequencies of bacterial vaginosis-associated bacterium 1 [BVAB1], BVAB2, BVAB3, Prevotella amnii, Prevotella pallens, Parvimonas micra, Megasphaera, Gardnerella vaginalis, and Atopobium vaginae and decreased frequencies of Lactobacillus reuteri, Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners). Women with inflammation-associated microbiomes had significantly higher body mass indices and lower levels of endogenous estradiol and luteinizing hormone. Community functional profiling revealed three distinct vaginal microbiome subtypes, one of which was characterized by extreme genital inflammation and persistent bacterial vaginosis (BV); this subtype could be predicted with high specificity and sensitivity based on the Nugent score (≥9) or BVAB1 abundance. We propose that women with this BVAB1-dominated subtype may have chronic genital inflammation due to persistent BV, which may place them at a particularly high risk for HIV infection.
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Affiliation(s)
- Katie Lennard
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Smritee Dabee
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Shaun L Barnabas
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Enock Havyarimana
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, University of Cape Town, Cape Town, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Anna Blakney
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Shameem Z Jaumdally
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Gerrit Botha
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Nonhlanhla N Mkhize
- National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Linda-Gail Bekker
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - David A Lewis
- Western Sydney Sexual Health Centre, Parramatta, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
- Sydney Medical School-Westmead, University of Sydney, Sydney, Australia
- National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Glenda Gray
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Cape Town, South Africa
| | - Nicola Mulder
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S Passmore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
| | - Heather B Jaspan
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pathology, University of Cape Town, Cape Town, South Africa
- Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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