Ashorn, Per; Hallamaa, Lotta; Allen, Lindsay H; Ashorn, Ulla; Chandrasiri, Upeksha; Deitchler, Megan; Doyle, Ronan; Harjunmaa, Ulla; Jorgensen, Josh M; Kamiza, Steve; +9 more... Klein, Nigel; Maleta, Kenneth; Nkhoma, Minyanga; Oaks, Brietta M; Poelman, Basho; Rogerson, Stephen J; Stewart, Christine P; Zeilani, Mamane; Dewey, Kathryn G; (2018) Co-causation of reduced newborn size by maternal undernutrition, infections, and inflammation. MATERNAL AND CHILD NUTRITION, 14 (3). e12585-. ISSN 1740-8695 DOI: https://doi.org/10.1111/mcn.12585

Busby, Eloise J; Doyle, Ronan M; Leboreiro Babe, Clara; Harris, Kathryn A; Mack, Damien; Méndez-Cervantes, Gema; O'Sullivan, Denise M; Pang, Vicky; Sadouki, Zahra; Solanki, Priya; +3 more... Huggett, Jim F; McHugh, Timothy D; Wey, Emmanuel Q; (2023) Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Molecular Typing of Acinetobacter baumannii in Comparison with Orthogonal Methods. Microbiology Spectrum, 11 (3). e0499522-. ISSN 2165-0497 DOI: https://doi.org/10.1128/spectrum.04995-22

Clark, Stephen A; Doyle, Ronan; Lucidarme, Jay; Borrow, Ray; Breuer, Judith; (2018) Targeted DNA enrichment and whole genome sequencing of Neisseria meningitidis directly from clinical specimens. INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, 308 (2). pp. 256-262. ISSN 1438-4221 DOI: https://doi.org/10.1016/j.ijmm.2017.11.004

Doyle, RM; Alber, DG; Jones, HE; Harris, K; Fitzgerald, F; Peebles, D; Klein, N; (2014) Term and preterm labour are associated with distinct microbial community structures in placental membranes which are independent of mode of delivery. PLACENTA, 35 (12). pp. 1099-1101. ISSN 0143-4004 DOI: https://doi.org/10.1016/j.placenta.2014.10.007

Doyle, Ronan M; Burgess, Carrie; Williams, Rachel; Gorton, Rebecca; Booth, Helen; Brown, James; Bryant, Josephine M; Chan, Jackie; Creer, Dean; Holdstock, Jolyon; +10 more... Kunst, Heinke; Lozewicz, Stefan; Platt, Gareth; Romero, Erika Yara; Speight, Graham; Tiberi, Simon; Abubakar, Ibrahim; Lipman, Marc; McHugh, Timothy D; Breuer, Judith; (2018) Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing. JOURNAL OF CLINICAL MICROBIOLOGY, 56 (8). ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.00666-18

Doyle, Ronan M; Harris, Kathryn; Kamiza, Steve; Harjunmaa, Ulla; Ashorn, Ulla; Nkhoma, Minyanga; Dewey, Kathryn G; Maleta, Kenneth; Ashorn, Per; Klein, Nigel; (2017) Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes. PLOS ONE, 12 (7). ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0180167

Doyle, Ronan M; Harris, Kathryn; Kamiza, Steve; Harjunmaa, Ulla; Ashorn, Ulla; Nkhoma, Minyanga; Dewey, Kathryn G; Maleta, Kenneth; Ashorn, Per; Klein, Nigel; (2017) Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes. PLOS ONE, 12 (7). e0180167-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0180167

Doyle, Ronan M; O'Sullivan, Denise M; Aller, Sean D; Bruchmann, Sebastian; Clark, Taane; Coello Pelegrin, Andreu; Cormican, Martin; Diez Benavente, Ernest; Ellington, Matthew J; McGrath, Elaine; +11 more... Motro, Yair; Phuong Thuy Nguyen, Thi; Phelan, Jody; Shaw, Liam P; Stabler, Richard A; van Belkum, Alex; van Dorp, Lucy; Woodford, Neil; Moran-Gilad, Jacob; Huggett, Jim F; Harris, Kathryn A; (2020) Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microbial Genomics, 6 (2). DOI: https://doi.org/10.1099/mgen.0.000335

Doyle, Ronan M; O’Sullivan, Denise M; Aller, Sean D; Bruchmann, Sebastian; Clark, Taane; Pelegrin, Andreu Coello; Cormican, Martin; Benavente, Ernest Diez; Ellington, Matthew J; McGrath, Elaine; +11 more... Motro, Yair; Thuy Nguyen, Thi Phuong; Phelan, Jody; Shaw, Liam P; Stabler, Richard A; van Belkum, Alex; van Dorp, Lucy; Woodford, Neil; Moran-Gilad, Jacob; Huggett, Jim F; Harris, Kathryn A; (2019) Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study. BioRxiv. DOI: https://doi.org/10.1101/793885

Doyle, Ronan M; Rubio, Marc; Dixon, Garth; Hartley, John; Klein, Nigel; Coll, Pere; Harris, Kathryn A; (2019) Cross-transmission Is Not the Source of New Mycobacterium abscessus Infections in a Multicenter Cohort of Cystic Fibrosis Patients. Clinical Infectious Diseases, 70 (9). pp. 1855-1864. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciz526

Doyle, Ronan M; Rubio, Marc; Dixon, Garth; Hartley, John; Klein, Nigel; Coll, Pere; Harris, Kathryn A; (2019) Cross-transmission is not the source of new<i>Mycobacterium abscessus</i>infections in a multi-centre cohort of cystic fibrosis patients. DOI: https://doi.org/10.1101/582684

Doyle, Ronan; Gondwe, Austridia; Fan, Yue-Mei; Maleta, Kenneth; Ashorn, Per; Klein, Nigel; Harris, Kathryn; (2018) A Lactobacillus-Deficient Vaginal Microbiota Dominates Postpartum Women in Rural Malawi. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 84 (6). ISSN 0099-2240 DOI: https://doi.org/10.1128/AEM.02150-17

Fitzgerald, Felicity C; Lhomme, Edouard; Harris, Kathryn; Kenny, Julia; Doyle, Ronan; Kityo, Cissy; Shaw, Liam P; Abongomera, George; Musiime, Victor; Cook, Adrian; +9 more... Brown, Julianne R; Brooks, Anthony; Owen-Powell, Ellen; Gibb, Diana M; Prendergast, Andrew J; Sarah Walker, A; Thiebaut, Rodolphe; Klein, Nigel; CHAPAS-3 Trial Team; (2019) Microbial Translocation Does Not Drive Immune Activation in Ugandan Children Infected With HIV. JOURNAL OF INFECTIOUS DISEASES, 219 (1). pp. 89-100. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiy495

Handley, Becca L; Sokana, Oliver; Addo, Kennedy Kwasi; Wagner, Josef; Fookes, María; Harding-Esch, Emma; Marks, Michael; Thomson, Nicholas R; Doyle, Ronan M; (2024) Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment. Microbial genomics, 10 (5). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.001234

Harjunmaa, U; Doyle, R; Järnstedt, J; Kamiza, S; Jorgensen, JM; Stewart, CP; Shaw, L; Hallamaa, L; Ashorn, U; Klein, N; +3 more... Dewey, KG; Maleta, K; Ashorn, P; (2018) Periapical infection may affect birth outcomes via systemic inflammation. ORAL DISEASES, 24 (5). pp. 847-855. ISSN 1354-523X DOI: https://doi.org/10.1111/odi.12817

Kannambath, Shichina; Jarvis, Joseph N; Wake, Rachel M; Longley, Nicky; Loyse, Angela; Matzaraki, Vicky; Aguirre-Gamboa, Raúl; Wijmenga, Cisca; Doyle, Ronan; Paximadis, Maria; +7 more... Tiemessen, Caroline T; Kumar, Vinod; Pittman, Alan; Meintjes, Graeme; Harrison, Thomas S; Netea, Mihai G; Bicanic, Tihana; (2020) Genome-Wide Association Study Identifies Novel Colony Stimulating Factor 1 Locus Conferring Susceptibility to Cryptococcosis in Human Immunodeficiency Virus-Infected South Africans. Open Forum Infectious Diseases, 7 (11). ofaa489-. DOI: https://doi.org/10.1093/ofid/ofaa489

Leon, Lydia J; Doyle, Ronan; Diez-Benavente, Ernest; Clark, Taane G; Klein, Nigel; Stanier, Philip; Moore, Gudrun E; (2018) Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom. Applied and environmental microbiology, 84 (14). ISSN 0099-2240 DOI: https://doi.org/10.1128/AEM.00483-18

Milburn, J E; (2024) Strategies to improve diagnosis of central nervous system infections in high HIV-prevalence African settings. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04674550

Milburn, James; Lechiile, Kwana; Siamisang, Keatlaretse; Williams, Christopher G; Owen, Leah; Gwakuba, Ezekiel; Machiya, Tichaona; Leeme, Tshepo; Barton, Hannah E; Doyle, Ronan; +5 more... Tenforde, Mark W; Mine, Madisa; Goldfarb, David M; Mokomane, Margaret; Jarvis, Joseph N; (2022) Human Herpesvirus-6 Detection in Cerebrospinal Fluid on the BioFire FilmArray Meningitis/Encephalitis Panel in a High Human Immunodeficiency Virus-Prevalence African Setting. Open forum infectious diseases, 9 (7). ofac229-. ISSN 2328-8957 DOI: https://doi.org/10.1093/ofid/ofac229

Milburn, James; Ntwayagae, Ookeditse; Ngoni, Kebatshabile; Suresh, Rachita; Lemme, Neo; Northcott, Cassie; Penney, James; Kinsella, Matthew; Mechie, Imogen; Ensor, Samuel; +10 more... Chebani, Tony; Grint, Daniel; Tenforde, Mark W; Avalos, Ava; Ramaabya, Dinah; Doyle, Ronan; Mokomane, Margaret; Mine, Madisa; Kranzer, Katharina; Jarvis, Joseph N; (2024) The Impact of GeneXpert Cerebrospinal Fluid Testing on Tuberculous Meningitis Diagnosis in Routine Care in Botswana. Open forum infectious diseases, 11 (9). ofae489-. ISSN 2328-8957 DOI: https://doi.org/10.1093/ofid/ofae489

Nimmo, Camus; Doyle, Ronan; Burgess, Carrie; Williams, Rachel; Gorton, Rebecca; McHugh, Timothy D; Brown, Mike; Morris-Jones, Stephen; Booth, Helen; Breuer, Judith; (2017) Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum. INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 62. pp. 44-46. ISSN 1201-9712 DOI: https://doi.org/10.1016/j.ijid.2017.07.007

Nimmo, Camus; Shaw, Liam P; Doyle, Ronan; Williams, Rachel; Brien, Kayleen; Burgess, Carrie; Breuer, Judith; Balloux, Francois; Pym, Alexander S; (2018) Whole genome sequencing <i>Mycobacterium tuberculosis</i> directly from sputum identifies more genetic diversity than sequencing from culture. DOI: https://doi.org/10.1101/446849

Nimmo, Camus; Shaw, Liam P; Doyle, Ronan; Williams, Rachel; Brien, Kayleen; Burgess, Carrie; Breuer, Judith; Balloux, Francois; Pym, Alexander S; (2019) Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture. BMC Genomics, 20 (1). 389-. DOI: https://doi.org/10.1186/s12864-019-5782-2

Nimmo, Camus; Shaw, Liam P; Doyle, Ronan; Williams, Rachel; Brien, Kayleen; Burgess, Carrie; Breuer, Judith; Balloux, Francois; Pym, Alexander S; (2019) Correction to: Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture. BMC genomics, 20 (1). 433-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-019-5841-8

O'Sullivan, Denise M; Doyle, Ronan M; Temisak, Sasithon; Redshaw, Nicholas; Whale, Alexandra S; Logan, Grace; Huang, Jiabin; Fischer, Nicole; Amos, Gregory CA; Preston, Mark D; +18 more... Marchesi, Julian R; Wagner, Josef; Parkhill, Julian; Motro, Yair; Denise, Hubert; Finn, Robert D; Harris, Kathryn A; Kay, Gemma L; O'Grady, Justin; Ransom-Jones, Emma; Wu, Huihai; Laing, Emma; Studholme, David J; Benavente, Ernest Diez; Phelan, Jody; Clark, Taane G; Moran-Gilad, Jacob; Huggett, Jim F; (2021) An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. Scientific Reports, 11 (1). 10590-. DOI: https://doi.org/10.1038/s41598-021-89881-2

Peters, Remco PH; Doyle, Ronan; Redelinghuys, Mathys J; McIntyre, James A; Verjans, Georges M; Breuer, Judith; Kock, Marleen M; (2017) Chlamydia trachomatis Biovar L2 Infection in Women in South Africa. EMERGING INFECTIOUS DISEASES, 23 (11). pp. 1913-1915. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2311.170758

Peters, Remco; Redelinghuys, Mathys; Mcintyre, James; Doyle, Ronan; Verjans, Georges; Breuer, Judith; Kock, Marleen; (2017) Presence of genital Chlamydia trachomatis serotype l2 infection in South African women. In: STI and HIV World Congress Abstracts, July 9–12 2017, Rio de Janeiro, Brazil. DOI: https://doi.org/10.1136/sextrans-2017-053264.213

Pitt, Rachel; Doyle, Ronan; Theilgaard Christiansen, Mette; Horner, Paddy; Hathorn, Emma; Alexander, Sarah; Woodford, Neil; Cole, Michelle; Breuer, Judith; (2022) Whole-genome sequencing of Chlamydia trachomatis isolates from persistently infected patients. International Journal of STD & AIDS, 33 (5). pp. 442-446. ISSN 0956-4624 DOI: https://doi.org/10.1177/09564624211048662

Shaw, Liam P; Doyle, Ronan M; Kavaliunaite, Ema; Spencer, Helen; Balloux, Francois; Dixon, Garth; Harris, Kathryn A; (2019) Children With Cystic Fibrosis Are Infected With Multiple Subpopulations of Mycobacterium abscessus With Different Antimicrobial Resistance Profiles. Clinical infectious diseases, 69 (10). pp. 1678-1686. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciz069

Shaw, Liam P; Doyle, Ronan M; Kavaliunaite, Ema; Spencer, Helen; Balloux, Francois; Dixon, Garth; Harris, Kathryn A; (2018) Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles. biorXiv. DOI: https://doi.org/10.1101/436261

Shaw, Liam; Harjunmaa, Ulla; Doyle, Ronan; Mulewa, Simeon; Charlie, Davie; Maleta, Ken; Callard, Robin; Walker, A Sarah; Balloux, Francois; Ashorn, Per; +1 more... Klein, Nigel; (2016) Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: a Cross-Sectional Cohort Study in Malawi. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 82 (19). pp. 6057-6067. ISSN 0099-2240 DOI: https://doi.org/10.1128/AEM.01756-16

Stabler, Richard A; Rosado, Helena; Doyle, Ronan; Negus, David; Carvil, Philip A; Kristjánsson, Juan G; Green, David A; Franco-Cendejas, Rafael; Davies, Cadi; Mogensen, Andreas; +2 more... Scott, Jonathan; Taylor, Peter W; (2017) Impact of the Mk VI SkinSuit on skin microbiota of terrestrial volunteers and an International Space Station-bound astronaut. NPJ Microgravity, 3 (1). 23-. ISSN 2373-8065 DOI: https://doi.org/10.1038/s41526-017-0029-5

Doyle, Ronan M; Kannambath, Shichina; Pittman, Alan; Goliath, Rene; Kumar, Vinod; Meintjes, Graeme; Milburn, James; Netea, Mihai G; Harrison, Thomas S; Jarvis, Joseph N; +1 more... Bicanic, Tihana; (2024) Ex vivo host transcriptomics during Cryptococcus neoformans, Cryptococcus gattii, and Candida albicans infection of PBMCs from South African volunteers. J Infect Dis. jiae410-. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiae410 Item availability may be restricted.

Fitzgerald, Felicity; Harris, Kathryn; Doyle, Ronan; Alber, Dagmar; Klein, Nigel; (2013) Short communication: Evidence that microbial translocation occurs in HIV-infected children in the United Kingdom. AIDS RESEARCH AND HUMAN RETROVIRUSES, 29 (12). pp. 1589-1593. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2013.0097 Item availability may be restricted.

Rosser, EC; Oleinika, K; Doyle, R; Bosma, A; Carter, NA; Harris, KA; Jones, SA; Klein, N; Mauri, C; (2014) Regulatory B-cell differentiation is under the control of gut-microbiota induced IL-1 beta and IL-6. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4652980 Item availability may be restricted.

Rosser, Elizabeth C; Oleinika, Kristine; Tonon, Silvia; Doyle, Ronan; Bosma, Anneleen; Carter, Natalie A; Harris, Kathryn A; Jones, Simon A; Klein, Nigel; Mauri, Claudia; (2014) Regulatory B cells are induced by gut microbiota-driven interleukin-1β and interleukin-6 production. NATURE MEDICINE, 20 (11). pp. 1334-1339. ISSN 1078-8956 DOI: https://doi.org/10.1038/nm.3680 Item availability may be restricted.