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Paton NI, Gurumurthy M, Lu Q, Leek F, Kwan P, Koh HWL, Molton J, Mortera L, Naval S, Abu Bakar Z, Pang YK, Lum L, Lim TK, Cross GB, Lekurwale G, Choi H, Au V, Connolly J, Hibberd M, Green JA. Adjunctive pascolizumab in rifampicin-susceptible pulmonary tuberculosis: proof-of-concept, partially-randomised, double-blind, placebo-controlled, dose-escalation trial. J Infect Dis 2024:jiae104. [PMID: 38527849 DOI: 10.1093/infdis/jiae104] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/12/2024] [Accepted: 02/25/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Interleukin-4 (IL-4), increased in tuberculosis infection, may impair bacterial killing. Blocking IL-4 confers benefit in animal models. We evaluated safety and efficacy of pascolizumab (humanised anti-IL-4 monoclonal antibody) as adjunctive tuberculosis treatment. METHODS Participants with rifampicin-susceptible pulmonary tuberculosis received a single intravenous infusion of pascolizumab or placebo; and standard 6-month tuberculosis treatment. Pascolizumab dose increased in successive cohorts: [1] non-randomised 0.05 mg/kg (n = 4); [2] non-randomised 0.5 mg/kg (n = 4); [3] randomised 2.5 mg/kg (n = 9) or placebo (n = 3); [4] randomised 10 mg/kg (n = 9) or placebo (n = 3). Co-primary safety outcome was study-drug-related grade 4 or serious adverse event (G4/SAE); in all cohorts (1-4). Co-primary efficacy outcome was week-8 sputum culture time-to-positivity (TTP); in randomised cohorts (3-4) combined. RESULTS Pascolizumab levels exceeded IL-4 50% neutralising dose for 8 weeks in 78-100% of participants in cohorts 3-4. There were no study-drug-related G4/SAEs. Median week-8 TTP was 42 days in pascolizumab and placebo groups (p = 0.185). Rate of TTP increase was greater with pascolizumab (difference from placebo 0.011 [95% Bayesian credible interval 0.006 to 0.015] log10TTP/day. CONCLUSIONS There was no evidence to suggest blocking IL-4 was unsafe. Preliminary efficacy findings are consistent with animal models. This supports further investigation of adjunctive anti-IL-4 interventions for tuberculosis in larger phase 2 trials.
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Affiliation(s)
- Nicholas I Paton
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
- Infectious Diseases Translational Research Programme, National University of Singapore
- London School of Hygiene and Tropical Medicine, UK
| | - Meera Gurumurthy
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | - Qingshu Lu
- Singapore Clinical Research Institute, Singapore
| | - Francesca Leek
- Clinical Imaging Research Centre, National University of Singapore
| | - Philip Kwan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | - Hiromi W L Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | - James Molton
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | | | - Sullian Naval
- Lung Centre of the Philippines, Quezon City, Philippines
| | | | - Yong-Kek Pang
- University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Lionel Lum
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | - Tow Keang Lim
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | - Gail B Cross
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | | | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | - Veonice Au
- Institute of Cellular and Molecular Biology, Singapore
| | - John Connolly
- Institute of Cellular and Molecular Biology, Singapore
| | - Martin Hibberd
- London School of Hygiene and Tropical Medicine, UK
- Department of Microbiology, National University of Singapore
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2
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Arashiro T, Miwa M, Nakagawa H, Takamatsu J, Oba K, Fujimi S, Kikuchi H, Iwasawa T, Kanbe F, Oyama K, Kanai M, Ogata Y, Asakura T, Asami T, Mizuno K, Sugita M, Jinta T, Nishida Y, Kato H, Atagi K, Higaki T, Nakano Y, Tsutsumi T, Doi K, Okugawa S, Ueda A, Nakamura A, Yoshida T, Shimada-Sammori K, Shimizu K, Fujita Y, Okochi Y, Tochitani K, Nakanishi A, Rinka H, Taniyama D, Yamaguchi A, Uchikura T, Matsunaga M, Aono H, Hamaguchi M, Motoda K, Nakayama S, Yamamoto K, Oka H, Tanaka K, Inoue T, Kobayashi M, Fujitani S, Tsukahara M, Takeda S, Stucky A, Suzuki T, Smith C, Hibberd M, Ariyoshi K, Fujino Y, Arima Y, Takeda S, Hashimoto S, Suzuki M. COVID-19 vaccine effectiveness against severe COVID-19 requiring oxygen therapy, invasive mechanical ventilation, and death in Japan: A multicenter case-control study (MOTIVATE study). Vaccine 2024; 42:677-688. [PMID: 38114409 DOI: 10.1016/j.vaccine.2023.12.033] [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: 10/16/2023] [Revised: 12/03/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Since the SARS-CoV-2 Omicron variant became dominant, assessing COVID-19 vaccine effectiveness (VE) against severe disease using hospitalization as an outcome became more challenging due to incidental infections via admission screening and variable admission criteria, resulting in a wide range of estimates. To address this, the World Health Organization (WHO) guidance recommends the use of outcomes that are more specific to severe pneumonia such as oxygen use and mechanical ventilation. METHODS A case-control study was conducted in 24 hospitals in Japan for the Delta-dominant period (August-November 2021; "Delta") and early Omicron (BA.1/BA.2)-dominant period (January-June 2022; "Omicron"). Detailed chart review/interviews were conducted in January-May 2023. VE was measured using various outcomes including disease requiring oxygen therapy, disease requiring invasive mechanical ventilation (IMV), death, outcome restricting to "true" severe COVID-19 (where oxygen requirement is due to COVID-19 rather than another condition(s)), and progression from oxygen use to IMV or death among COVID-19 patients. RESULTS The analysis included 2125 individuals with respiratory failure (1608 cases [75.7%]; 99.2% of vaccinees received mRNA vaccines). During Delta, 2 doses provided high protection for up to 6 months (oxygen requirement: 95.2% [95% CI:88.7-98.0%] [restricted to "true" severe COVID-19: 95.5% {89.3-98.1%}]; IMV: 99.6% [97.3-99.9%]; fatal: 98.6% [92.3-99.7%]). During Omicron, 3 doses provided high protection for up to 6 months (oxygen requirement: 85.5% [68.8-93.3%] ["true" severe COVID-19: 88.1% {73.6-94.7%}]; IMV: 97.9% [85.9-99.7%]; fatal: 99.6% [95.2-99.97]). There was a trend towards higher VE for more severe and specific outcomes. CONCLUSION Multiple outcomes pointed towards high protection of 2 doses during Delta and 3 doses during Omicron. These results demonstrate the importance of using severe and specific outcomes to accurately measure VE against severe COVID-19, as recommended in WHO guidance in settings of intense transmission as seen during Omicron.
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Affiliation(s)
- Takeshi Arashiro
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan; Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
| | - Maki Miwa
- Emergency and Critical Care Center, Tokyo Metropolitan Hiroo Hospital, Tokyo, Japan
| | - Hidenori Nakagawa
- Department of Infectious Diseases, Osaka City General Hospital, Osaka, Japan
| | - Junpei Takamatsu
- Department of Emergency Medicine, Kansai Rosai Hospital, Hyogo, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Tokyo, Japan
| | - Satoshi Fujimi
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, Japan
| | - Hitoshi Kikuchi
- Department of Emergency Medicine, Sagamihara Kyodo Hospital, Kanagawa, Japan
| | - Takamasa Iwasawa
- Department of Cardiology, Yokosuka General Hospital Uwamachi, Kanagawa, Japan
| | - Fumiko Kanbe
- Intensive Care Unit, Ageo Central General Hospital, Saitama, Japan
| | - Keisuke Oyama
- Kawaguchi Cardiovascular and Respiratory Hospital, Saitama, Japan
| | - Masayuki Kanai
- Department of Emergency and Critical Care Medicine, Tokyo Metropolitan Police Hospital, Tokyo, Japan
| | - Yoshitaka Ogata
- Department of Critical Care Medicine, Yao Tokushukai General Hospital, Osaka, Japan
| | - Takanori Asakura
- Department of Respiratory Medicine, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Takahiro Asami
- Department of Internal Medicine, Sano Kosei General Hospital, Tochigi, Japan
| | - Keiko Mizuno
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Tokyo, Japan
| | - Manabu Sugita
- Department of Emergency and Critical Care Medicine, Juntendo University Nerima Hospital, Tokyo, Japan
| | - Torahiko Jinta
- Department of Pulmonary Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Yusuke Nishida
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Kazuaki Atagi
- Division of Critical Care Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Taiki Higaki
- Division of Critical Care Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Yoshio Nakano
- Department of Internal Medicine, Kinan Hospital, Wakayama, Japan
| | - Takeya Tsutsumi
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Kent Doi
- Department of Emergency and Critical Care Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Shu Okugawa
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Akihiro Ueda
- Department of Infectious Diseases, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Akira Nakamura
- Department of Internal Medicine, Asahi General Hospital, Chiba, Japan
| | - Toru Yoshida
- Department of Emergency and Critical Care Medicine, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Kaoru Shimada-Sammori
- Department of Emergency and Critical Care Medicine, Tokyo Metropolitan TAMA Medical Center, Tokyo, Japan
| | - Keiki Shimizu
- Department of Emergency and Critical Care Medicine, Tokyo Metropolitan TAMA Medical Center, Tokyo, Japan
| | - Yasuo Fujita
- Department of Emergency, Akita Red Cross Hospital, Akita, Japan
| | - Yasumi Okochi
- Department of Respiratory Medicine, Japan Community Health Care Organization Tokyo Yamate Medical Center, Tokyo, Japan
| | - Kentaro Tochitani
- Department of Infectious Diseases, Kyoto City Hospital, Kyoto, Japan
| | - Asuka Nakanishi
- Department of Pulmonary Medicine, Tokyo Metropolitan Hiroo Hospital, Tokyo, Japan
| | - Hiroshi Rinka
- Department of Emergency and Critical Care Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Daisuke Taniyama
- Department of Infectious Diseases, Showa General Hospital, Tokyo, Japan
| | - Asase Yamaguchi
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, Japan
| | - Toshio Uchikura
- Department of Emergency and General Internal Medicine, Yokosuka General Hospital Uwamachi, Kanagawa, Japan
| | - Maiko Matsunaga
- Department of Pharmacy, Tokyo Metropolitan Police Hospital, Tokyo, Japan
| | - Hiromi Aono
- Department of Respiratory Medicine, Tokyo Metropolitan Police Hospital, Tokyo, Japan
| | - Masanari Hamaguchi
- Department of Critical Care Medicine, Yao Tokushukai General Hospital, Osaka, Japan
| | - Kentaro Motoda
- Department of Clinical Research, Yao Tokushukai General Hospital, Osaka, Japan
| | - Sohei Nakayama
- Department of Respiratory Medicine, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Kei Yamamoto
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Hideaki Oka
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Katsushi Tanaka
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Inoue
- Clinical Research Support Center, Asahi General Hospital, Chiba, Japan
| | - Mieko Kobayashi
- Clinical Research Support Center, Asahi General Hospital, Chiba, Japan
| | - Shigeki Fujitani
- Department of Emergency and Critical Care Medicine, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Maki Tsukahara
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Saki Takeda
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ashley Stucky
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chris Smith
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Yuji Fujino
- Non-Profit Organization Japan ECMO Network, Tokyo, Japan; Department of Anesthesiology and Intensive Care, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuzo Arima
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinhiro Takeda
- Kawaguchi Cardiovascular and Respiratory Hospital, Saitama, Japan; Non-Profit Organization Japan ECMO Network, Tokyo, Japan; Non-Profit Organization ICU Collaboration Network (ICON), Tokyo, Japan
| | - Satoru Hashimoto
- Non-Profit Organization Japan ECMO Network, Tokyo, Japan; Non-Profit Organization ICU Collaboration Network (ICON), Tokyo, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
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Arashiro T, Arima Y, Kuramochi J, Muraoka H, Sato A, Chubachi K, Oba K, Yanai A, Arioka H, Uehara Y, Ihara G, Kato Y, Yanagisawa N, Nagura Y, Yanai H, Ueda A, Numata A, Kato H, Oka H, Nishida Y, Ishii K, Ooki T, Nidaira Y, Asami T, Jinta T, Nakamura A, Taniyama D, Yamamoto K, Tanaka K, Ueshima K, Fuwa T, Stucky A, Suzuki T, Smith C, Hibberd M, Ariyoshi K, Suzuki M. Immune escape and waning immunity of COVID-19 monovalent mRNA vaccines against symptomatic infection with BA.1/BA.2 and BA.5 in Japan. Vaccine 2023; 41:6969-6979. [PMID: 37839947 DOI: 10.1016/j.vaccine.2023.10.021] [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: 02/16/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND Repeated emergence of variants with immune escape capacity and waning immunity from vaccination are major concerns for COVID-19. We examined whether the surge in Omicron subvariant BA.5 cases was due to immune escape or waning immunity through vaccine effectiveness (VE) evaluation. METHODS A test-negative case-control study was conducted in 16 clinics/hospitals during the BA.1/BA.2-dominant and BA.5-dominant periods. VE against symptomatic infection was estimated after adjusting for age, sex, comorbidity, occupation, testing frequency, prior infection, close contact history, clinic/hospital, week, and preventive measures. Absolute VE (aVE) was calculated for 2/3/4 doses, compared to the unvaccinated. Relative VE (rVE) was calculated, comparing 3 vs 2 and 4 vs 3 doses. RESULTS 13,025 individuals were tested during the BA.1/BA.2-dominant and BA.5-dominant periods with similar baseline characteristics. For BA.1/BA.2, aVE was 52 % (95 %CI:34-66) 14 days-3 months post-dose 2, 42 % (29-52) > 6 months post-dose 2, 71 % (64-77) 14 days-3 months post-dose 3, and 68 % (52-79) 3-6 months post-dose 3. rVE was 49 % (38-57) 14 days-3 months post-dose 3 and 45 % (18-63) 3-6 months post-dose 3. For BA.5, aVE was 56 % (27-73) 3-6 months post-dose 2, 32 % (12-47) > 6 months post-dose 2, 70 % (61-78) 14 days-3 months post-dose 3, 59 % (48-68) 3-6 months post-dose 3, 50 % (29-64) > 6 months post-dose 3, and 74 % (61-83) ≥ 14 days post-dose 4. rVE was 56 % (45-65) 14 days-3 months post-dose 3, 39 % (27-48) 3-6 months post-dose 3, 25 % (-2-45) > 6 months post-dose 3, and 30 % (-6-54) ≥ 14 days post-dose 4. CONCLUSIONS Booster doses initially provided high protection against BA.5 at a level similar to that against BA.1/BA.2. However, the protection seemed shorter-lasting against BA.5, which likely contributed to the surge. Furthermore, rVE post-dose 4 was low even among recent vaccinees. These results support the introduction of variant-containing vaccines and emphasize the need for vaccines with longer duration of protection.
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Affiliation(s)
- Takeshi Arashiro
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan; Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
| | - Yuzo Arima
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jin Kuramochi
- Kuramochi Clinic Interpark, Tochigi, Japan; Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | | | | | - Kumi Chubachi
- Chubachi Internal Respiratory Medicine Clinic, Tokyo, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Tokyo, Japan
| | - Atsushi Yanai
- Department of General Internal Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Hiroko Arioka
- Department of General Internal Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Yuki Uehara
- Department of Clinical Laboratory, St. Luke's International Hospital, Tokyo, Japan; Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | | | - Yasuyuki Kato
- Department of Infectious Diseases, International University of Health and Welfare Narita Hospital, Chiba, Japan
| | | | | | - Hideki Yanai
- Fukujuji Hospital, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Akihiro Ueda
- Department of Infectious Diseases, Japanese Red Cross Medical Center, Tokyo, Japan
| | | | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Hideaki Oka
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Yusuke Nishida
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Koji Ishii
- Saitama Sekishinkai Hospital, Saitama, Japan
| | - Takao Ooki
- Saitama Sekishinkai Hospital, Saitama, Japan
| | | | - Takahiro Asami
- Department of Internal Medicine, Sano Kosei General Hospital, Tochigi, Japan
| | - Torahiko Jinta
- Department of Pulmonary Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Akira Nakamura
- Department of Internal Medicine, Asahi General Hospital, Chiba, Japan
| | - Daisuke Taniyama
- Department of Infectious Diseases, Showa General Hospital, Tokyo, Japan
| | - Kei Yamamoto
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Katsushi Tanaka
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | | | | | - Ashley Stucky
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chris Smith
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
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4
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Hackman J, Sheppard C, Phelan J, Jones-Warner W, Sobkowiak B, Shah S, Litt D, Fry NK, Toizumi M, Yoshida LM, Hibberd M, Miller E, Flasche S, Hué S. Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. Wellcome Open Res 2023; 8:427. [PMID: 38638914 PMCID: PMC11024593 DOI: 10.12688/wellcomeopenres.19219.1] [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] [Accepted: 08/03/2023] [Indexed: 04/20/2024] Open
Abstract
Background: Inference on pneumococcal transmission has mostly relied on longitudinal studies which are costly and resource intensive. Therefore, we conducted a pilot study to test the ability to infer who infected whom from cross-sectional pneumococcal sequences using phylogenetic inference. Methods: Five suspected transmission pairs, for which there was epidemiological evidence of who infected whom, were selected from a household study. For each pair, Streptococcus pneumoniae full genomes were sequenced from nasopharyngeal swabs collected on the same day. The within-host genetic diversity of the pneumococcal population was used to infer the transmission direction and then cross-validated with the direction suggested by the epidemiological records. Results: The pneumococcal genomes clustered into the five households from which the samples were taken. The proportion of concordantly inferred transmission direction generally increased with increasing minimum genome fragment size and single nucleotide polymorphisms. We observed a larger proportion of unique polymorphic sites in the source bacterial population compared to that of the recipient in four of the five pairs, as expected in the case of a transmission bottleneck. The only pair that did not exhibit this effect was also the pair that had consistent discordant transmission direction compared to the epidemiological records suggesting potential misdirection as a result of false-negative sampling. Conclusions: This pilot provided support for further studies to test if the direction of pneumococcal transmission can be reliably inferred from cross-sectional samples if sequenced with sufficient depth and fragment length.
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Affiliation(s)
- Jada Hackman
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Carmen Sheppard
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - William Jones-Warner
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ben Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sonal Shah
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - David Litt
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
| | - Norman K. Fry
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
- Immunisation & Countermeasures Division, UK Health Security Agency, London, UK
| | - Michiko Toizumi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Paediatric Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Lay-Myint Yoshida
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Paediatric Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Elizabeth Miller
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Stefan Flasche
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Stéphane Hué
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
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5
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Sabo MC, Thuong NTT, Chang X, Ardiansyah E, Tram TTB, Hai HT, Nghia HDT, Bang ND, Dian S, Ganiem AR, Shaporifar S, Kumar V, Li Z, Hibberd M, Khor CC, Thwaites GE, Heemskerk D, van Laarhoven A, van Crevel R, Dunstan SJ, Shah JA. MUC5AC Genetic Variation Is Associated With Tuberculous Meningitis Cerebral Spinal Fluid Cytokine Responses and Mortality. J Infect Dis 2023; 228:343-352. [PMID: 36823694 PMCID: PMC10420404 DOI: 10.1093/infdis/jiad050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/11/2022] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND The purpose of this study was to assess if single nucleotide polymorphisms (SNPs) in lung mucins MUC5B and MUC5AC are associated with Mycobacterium tuberculosis outcomes. METHODS Independent SNPs in MUC5B and MUC5AC (genotyped by Illumina HumanOmniExpress array) were assessed for associations with tumor necrosis factor (TNF) concentrations (measured by immunoassay) in cerebral spinal fluid (CSF) from tuberculous meningitis (TBM) patients. SNPs associated with CSF TNF concentrations were carried forward for analyses of pulmonary and meningeal tuberculosis susceptibility and TBM mortality. RESULTS MUC5AC SNP rs28737416 T allele was associated with lower CSF concentrations of TNF (P = 1.8 × 10-8) and IFN-γ (P = 2.3 × 10-6). In an additive genetic model, rs28737416 T/T genotype was associated with higher susceptibility to TBM (odds ratio [OR], 1.24; 95% confidence interval [CI], 1.03-1.49; P = .02), but not pulmonary tuberculosis (OR, 1.11, 95% CI, .98-1.25; P = .10). TBM mortality was higher among participants with the rs28737416 T/T and T/C genotypes (35/119, 30.4%) versus the C/C genotype (11/89, 12.4%; log-rank P = .005) in a Vietnam discovery cohort (n = 210), an independent Vietnam validation cohort (n = 87; 9/87, 19.1% vs 1/20, 2.5%; log-rank P = .02), and an Indonesia validation cohort (n = 468, 127/287, 44.3% vs 65/181, 35.9%; log-rank P = .06). CONCLUSIONS MUC5AC variants may contribute to immune changes that influence TBM outcomes.
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Affiliation(s)
- Michelle C Sabo
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Nguyen T T Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Xuling Chang
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | | | - Trinh T B Tram
- Oxford University Clinical Research Unit, Ho Chi Minh, Vietnam
| | - Hoang T Hai
- Oxford University Clinical Research Unit, Ho Chi Minh, Vietnam
| | - Ho D T Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen D Bang
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Pham Ngoc Thach Hospital, Ho Chi Minh, Vietnam
| | - Sofiati Dian
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Rizal Ganiem
- Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neurology, Universitas Padjadjaran/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Shima Shaporifar
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Vinod Kumar
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zheng Li
- Genome Institute of Singapore, Singapore, Singapore
| | - Martin Hibberd
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | | | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Dorothee Heemskerk
- Oxford University Clinical Research Unit, Ho Chi Minh, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | | | | | - Sarah J Dunstan
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Javeed A Shah
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Veterans Affairs Puget Sound Healthcare System, Seattle, Washington, USA
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Arashiro T, Arima Y, Kuramochi J, Muraoka H, Sato A, Chubachi K, Yanai A, Arioka H, Uehara Y, Ihara G, Kato Y, Yanagisawa N, Ueda A, Kato H, Oka H, Nishida Y, Nidaira Y, Asami T, Jinta T, Nakamura A, Oba K, Taniyama D, Yamamoto K, Tanaka K, Ueshima K, Fuwa T, Stucky A, Suzuki T, Smith C, Hibberd M, Ariyoshi K, Suzuki M. Effectiveness of BA.1- and BA.4/BA. 5-Containing Bivalent COVID-19 mRNA Vaccines Against Symptomatic SARS-CoV-2 Infection During the BA.5-Dominant Period in Japan. Open Forum Infect Dis 2023; 10:ofad240. [PMID: 37351451 PMCID: PMC10284337 DOI: 10.1093/ofid/ofad240] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/27/2023] [Indexed: 06/24/2023] Open
Abstract
In this multicenter, prospective, test-negative, case-control study in Japan, the effectiveness of both BA.1-containing and BA.4/BA.5-containing bivalent coronavirus disease 2019 mRNA vaccines against symptomatic infection during the BA.5-dominant period was high compared with no vaccination (65% and 76%) and moderate compared with monovalent vaccines administered over half a year earlier (46% combined).
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Affiliation(s)
- Takeshi Arashiro
- Correspondence: Takeshi Arashiro, MD, Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo 162-8640, Japan ()
| | - Yuzo Arima
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jin Kuramochi
- Kuramochi Clinic Interpark, Tochigi, Japan
- Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | | | | | - Kumi Chubachi
- Chubachi Internal Respiratory Medicine Clinic, Tokyo, Japan
| | - Atsushi Yanai
- Department of General Internal Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Hiroko Arioka
- Department of General Internal Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Yuki Uehara
- Department of Clinical Laboratory, St. Luke's International Hospital, Tokyo, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | | | - Yasuyuki Kato
- Department of Infectious Diseases, International University of Health and Welfare Narita Hospital, Chiba, Japan
| | | | - Akihiro Ueda
- Department of Infectious Diseases, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Hideaki Oka
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Yusuke Nishida
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | | | - Takahiro Asami
- Department of Internal Medicine, Sano Kosei General Hospital, Tochigi, Japan
| | - Torahiko Jinta
- Department of Pulmonary Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Akira Nakamura
- Department of Internal Medicine, Asahi General Hospital, Chiba, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Tokyo, Japan
| | - Daisuke Taniyama
- Department of Infectious Diseases, Showa General Hospital, Tokyo, Japan
| | - Kei Yamamoto
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Katsushi Tanaka
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | | | | | - Ashley Stucky
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chris Smith
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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7
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Arashiro T, Arima Y, Kuramochi J, Muraoka H, Sato A, Chubachi K, Oba K, Yanai A, Arioka H, Uehara Y, Ihara G, Kato Y, Yanagisawa N, Nagura Y, Yanai H, Ueda A, Numata A, Kato H, Oka H, Nishida Y, Ooki T, Nidaira Y, Stucky A, Suzuki T, Smith C, Hibberd M, Ariyoshi K, Suzuki M. Letter to the editor: Importance of considering high-risk behaviours in COVID-19 vaccine effectiveness estimates with observational studies. Euro Surveill 2023; 28:2300034. [PMID: 36700869 PMCID: PMC9881180 DOI: 10.2807/1560-7917.es.2023.28.4.2300034] [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] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Takeshi Arashiro
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan,Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Yuzo Arima
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Jin Kuramochi
- Kuramochi Clinic Interpark, Tochigi, Japan,Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | | | | | - Kumi Chubachi
- Chubachi Internal Respiratory Medicine Clinic, Tokyo, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Tokyo, Japan
| | - Atsushi Yanai
- Department of General Internal Medicine, St. Luke’s International Hospital, Tokyo, Japan
| | - Hiroko Arioka
- Department of General Internal Medicine, St. Luke’s International Hospital, Tokyo, Japan
| | - Yuki Uehara
- Department of Clinical Laboratory, St. Luke’s International Hospital, Tokyo, Japan,Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | | | - Yasuyuki Kato
- Department of Infectious Diseases, International University of Health and Welfare Narita Hospital, Chiba, Japan
| | | | | | - Hideki Yanai
- Fukujuji Hospital, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Akihiro Ueda
- Department of Infectious Diseases, Japanese Red Cross Medical Center, Tokyo, Japan
| | | | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Hideaki Oka
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Yusuke Nishida
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Takao Ooki
- Saitama Sekishinkai Hospital, Saitama, Japan
| | | | - Ashley Stucky
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chris Smith
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
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8
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van der Velden FJS, de Vries G, Martin A, Lim E, von Both U, Kolberg L, Carrol ED, Khanijau A, Herberg JA, De T, Galassini R, Kuijpers TW, Martinón-Torres F, Rivero-Calle I, Vermont CL, Hagedoorn NN, Pokorn M, Pollard AJ, Schlapbach LJ, Tsolia M, Elefhteriou I, Yeung S, Zavadska D, Fink C, Voice M, Zenz W, Kohlmaier B, Agyeman PKA, Usuf E, Secka F, de Groot R, Levin M, van der Flier M, Emonts M, Cunnington A, De T, Herberg J, Kaforou M, Wright V, Baumard L, Bellos E, D’Souza G, Galassini R, Habgood-Coote D, Hamilton S, Hoggart C, Hourmat S, Jackson H, Maconochie I, Menikou S, Lin N, Nichols S, Nijman R, Powell O, Pena Paz I, Shah P, Shen CF, Vito O, Wilson C, Abdulla A, Ali L, Darnell S, Jorgensen R, Mustafa S, Persand S, Stevens MM, Kim N, Kim E, Fidler K, Dudley J, Richmond V, Tavliavini E, Shen CF, Liu CC, Wang SM, Martinón-Torres F, Salas A, González FÁ, Farto CB, Barral-Arca R, Castro MB, Bello X, García MB, Carnota S, Cebey-López M, Curras-Tuala MJ, Suárez CD, Vicente LG, Gómez-Carballa A, Rial JG, Iglesias PL, Martinón-Torres F, Martinón-Torres N, Sánchez JMM, Pérez BM, Pardo-Seco J, Rodríguez LP, Pischedda S, Vázquez SR, Calle IR, Rodríguez-Tenreiro C, Redondo-Collazo L, Ora MS, Salas A, Fernández SS, Trasorras CS, Iglesias MV, Zavadska D, Balode A, Bārzdiņa A, Deksne D, Gardovska D, Grāvele D, Grope I, Meiere A, Nokalna I, Pavāre J, Pučuka Z, Selecka K, Rudzāte A, Svile D, Urbāne UN, Usuf E, Bojang K, Zaman SMA, Secka F, Anderson S, Sarr AR, Saidykhan M, Darboe S, Ceesay S, D’alessandro U, Moll HA, Vermont CL, Borensztajn DM, Hagedoorn NN, Tan C, Zachariasse J, Dik W, Agyeman PKA, Berger C, Giannoni E, Stocker M, Posfay-Barbe KM, Heininger U, Bernhard-Stirnemann S, Niederer-Loher A, Kahlert CR, Natalucci G, Relly C, Riedel T, Aebi C, Schlapbach LJ, Carrol ED, Cocklin E, Jennings R, Johnston J, Khanijau A, Leigh S, Lewis-Burke N, Newall K, Romaine S, Tsolia M, Eleftheriou I, Tambouratzi M, Marmarinos A, Xagorari M, Syggelou K, Fink C, Voice M, Calvo-Bado L, Zenz W, Kohlmaier B, Schweintzger NA, Sagmeister MG, Kohlfürst DS, Zurl C, Binder A, Hösele S, Leitner M, Pölz L, Rajic G, Bauchinger S, Baumgart H, Benesch M, Ceolotto A, Eber E, Gallistl S, Gores G, Haidl H, Hauer A, Hude C, Keldorfer M, Krenn L, Pilch H, Pfleger A, Pfurtscheller K, Nordberg G, Niedrist T, Rödl S, Skrabl-Baumgartner A, Sperl M, Stampfer L, Strenger V, Till H, Trobisch A, Löffler S, Yeung S, Dewez JE, Hibberd M, Bath D, Miners A, Nijman R, Fitchett E, de Groot R, van der Flier M, de Jonge MI, van Aerde K, Alkema W, van den Broek B, Gloerich J, van Gool AJ, Henriet S, Huijnen M, Philipsen R, Willems E, Gerrits G, van Leur M, Heidema J, de Haan L, Miedema C, Neeleman C, Obihara C, Tramper-Stranders G, Pollard AJ, Kandasamy R, Paulus S, Carter MJ, O’Connor D, Bibi S, Kelly DF, Gurung M, Thorson S, Ansari I, Murdoch DR, Shrestha S, Oliver Z, Emonts M, Lim E, Valentine L, Allen K, Bell K, Chan A, Crulley S, Devine K, Fabian D, King S, McAlinden P, McDonald S, McDonnell A, Pickering A, Thomson E, Wood A, Wallia D, Woodsford P, Baxter F, Bell A, Rhodes M, Agbeko R, Mackerness C, Baas B, Kloosterhuis L, Oosthoek W, Arif T, Bennet J, Collings K, van der Giessen I, Martin A, Rashid A, Rowlands E, de Vries G, van der Velden F, Soon J, Valentine L, Martin M, Mistry R, von Both U, Kolberg L, Zwerenz M, Buschbeck J, Bidlingmaier C, Binder V, Danhauser K, Haas N, Griese M, Feuchtinger T, Keil J, Kappler M, Lurz E, Muench G, Reiter K, Schoen C, Mallet F, Brengel-Pesce K, Pachot A, Mommert M, Pokorn M, Kolnik M, Vincek K, Srovin TP, Bahovec N, Prunk P, Osterman V, Avramoska T, Kuijpers T, Jongerius I, van den Berg JM, Schonenberg D, Barendregt AM, Pajkrt D, van der Kuip M, van Furth AM, Sprenkeler E, Zandstra J, van Mierlo G, Geissler J. Correction to: Febrile illness in high-risk children: a prospective, international observational study. Eur J Pediatr 2023; 182:555-556. [PMID: 36689005 PMCID: PMC9899168 DOI: 10.1007/s00431-022-04788-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Fabian J. S. van der Velden
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.1006.70000 0001 0462 7212Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gabriella de Vries
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.416135.40000 0004 0649 0805Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Alexander Martin
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.1006.70000 0001 0462 7212Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lim
- grid.459561.a0000 0004 4904 7256Paediatric Immunology, Infectious Diseases & Allergy, Great North Children’s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK ,grid.1006.70000 0001 0462 7212Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ulrich von Both
- grid.5252.00000 0004 1936 973XDivision Paediatric Infectious Diseases, Dr. Von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - Laura Kolberg
- grid.5252.00000 0004 1936 973XDivision Paediatric Infectious Diseases, Dr. Von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - Enitan D. Carrol
- grid.10025.360000 0004 1936 8470Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK ,grid.417858.70000 0004 0421 1374Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Aakash Khanijau
- grid.10025.360000 0004 1936 8470Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK ,grid.417858.70000 0004 0421 1374Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Jethro A. Herberg
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Tisham De
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Rachel Galassini
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Taco W. Kuijpers
- grid.7177.60000000084992262Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Amsterdam University Medical Center, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Federico Martinón-Torres
- grid.411048.80000 0000 8816 6945Pediatrics Department, Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain ,grid.11794.3a0000000109410645Grupo de Genetica, Vacunas, Infecciones y Pediatria, Instituto de Investigacion Sanitaria de Santiago, Universidad de Santiago, Santiago de Compostela, Spain ,grid.512891.6Consorcio Centro de Investigacion Biomedicaen Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Irene Rivero-Calle
- grid.411048.80000 0000 8816 6945Pediatrics Department, Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Clementien L. Vermont
- grid.416135.40000 0004 0649 0805Department of Pediatrics, Division of Pediatric Infectious Diseases & Immunology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Nienke N. Hagedoorn
- grid.416135.40000 0004 0649 0805Department of General Paediatrics, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Marko Pokorn
- grid.29524.380000 0004 0571 7705University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Andrew J. Pollard
- grid.4991.50000 0004 1936 8948Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Luregn J. Schlapbach
- grid.412341.10000 0001 0726 4330Neonatal and Pediatric Intensive Care Unit, Children’s Research Center, University Children’s Hospital Zürich, University of Zürich, Zurich, Switzerland
| | - Maria Tsolia
- grid.5216.00000 0001 2155 08002nd Department of Pediatrics, National and Kapodistrian University of Athens, Children’s Hospital ‘P, and A. Kyriakou’, Athens, Greece
| | - Irini Elefhteriou
- grid.5216.00000 0001 2155 08002nd Department of Pediatrics, National and Kapodistrian University of Athens, Children’s Hospital ‘P, and A. Kyriakou’, Athens, Greece
| | - Shunmay Yeung
- grid.8991.90000 0004 0425 469XClinical Research Department, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - Dace Zavadska
- grid.17330.360000 0001 2173 9398Department of Pediatrics, Rīgas Stradina Universitāte, Children’s Clinical University Hospital, Riga, Latvia
| | - Colin Fink
- grid.7372.10000 0000 8809 1613Micropathology Ltd, University of Warwick, Warwick, UK
| | - Marie Voice
- grid.7372.10000 0000 8809 1613Micropathology Ltd, University of Warwick, Warwick, UK
| | - Werner Zenz
- grid.11598.340000 0000 8988 2476Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Benno Kohlmaier
- grid.11598.340000 0000 8988 2476Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Philipp K. A. Agyeman
- grid.5734.50000 0001 0726 5157Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Effua Usuf
- grid.415063.50000 0004 0606 294XMedical Research Council Unit, Serrekunda, The Gambia
| | - Fatou Secka
- grid.415063.50000 0004 0606 294XMedical Research Council Unit, Serrekunda, The Gambia
| | - Ronald de Groot
- grid.461578.9Pediatric Infectious Diseases and Immunology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Levin
- grid.7445.20000 0001 2113 8111Section of Paediatric Infectious Disease, Wright-Fleming Institute, Imperial College London, London, UK
| | - Michiel van der Flier
- grid.461578.9Pediatric Infectious Diseases and Immunology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.7692.a0000000090126352Pediatric Infectious Diseases and Immunology, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marieke Emonts
- Paediatric Immunology, Infectious Diseases & Allergy, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK. .,Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK. .,NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, UK.
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Arashiro T, Arima Y, Muraoka H, Sato A, Oba K, Uehara Y, Arioka H, Yanai H, Kuramochi J, Ihara G, Chubachi K, Yanagisawa N, Nagura Y, Kato Y, Ueda A, Numata A, Kato H, Ishii K, Ooki T, Oka H, Nishida Y, Stucky A, Smith C, Hibberd M, Ariyoshi K, Suzuki M. Coronavirus Disease 19 (COVID-19) Vaccine Effectiveness Against Symptomatic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Delta-Dominant and Omicron-Dominant Periods in Japan: A Multicenter Prospective Case-control Study (Factors Associated with SARS-CoV-2 Infection and the Effectiveness of COVID-19 Vaccines Study). Clin Infect Dis 2022; 76:e108-e115. [PMID: 35918782 PMCID: PMC9384625 DOI: 10.1093/cid/ciac635] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Although several coronavirus disease 2019 (COVID-19) vaccines initially showed high efficacy, there have been concerns because of waning immunity and the emergence of variants with immune escape capacity. METHODS A test-negative design case-control study was conducted in 16 healthcare facilities in Japan during the Delta-dominant period (August-September 2021) and the Omicron-dominant period (January-March 2022). Vaccine effectiveness (VE) against symptomatic severe acute respiratory syndrome coronavirus 2 infection was calculated for 2 doses for the Delta-dominant period and 2 or 3 doses for the Omicron-dominant period compared with unvaccinated individuals. RESULTS The analysis included 5795 individuals with 2595 (44.8%) cases. Among vaccinees, 2242 (55.8%) received BNT162b2 and 1624 (40.4%) received messenger RNA (mRNA)-1273 at manufacturer-recommended intervals. During the Delta-dominant period, VE was 88% (95% confidence interval [CI], 82-93) 14 days to 3 months after dose 2 and 87% (95% CI, 38-97) 3 to 6 months after dose 2. During the Omicron-dominant period, VE was 56% (95% CI, 37-70) 14 days to 3 months since dose 2, 52% (95% CI, 40-62) 3 to 6 months after dose 2, 49% (95% CI, 34-61) 6+ months after dose 2, and 74% (95% CI, 62-83) 14+ days after dose 3. Restricting to individuals at high risk of severe COVID-19 and additional adjustment for preventive measures (ie, mask wearing/high-risk behaviors) yielded similar estimates, respectively. CONCLUSIONS In Japan, where most are infection-naïve, and strict prevention measures are maintained regardless of vaccination status, 2-dose mRNA vaccines provided high protection against symptomatic infection during the Delta-dominant period and moderate protection during the Omicron-dominant period. Among individuals who received an mRNA booster dose, VE recovered to a high level.
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Affiliation(s)
- Takeshi Arashiro
- Correspondence: T. Arashiro, Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo 162-8640, Japan ()
| | - Yuzo Arima
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Tokyo, Japan
| | - Yuki Uehara
- Department of Clinical Laboratory, St. Luke’s International Hospital, Tokyo, Japan
| | - Hiroko Arioka
- Department of General Internal Medicine, St. Luke’s International Hospital, Tokyo, Japan
| | - Hideki Yanai
- Fukujuji Hospital, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | | | | | - Kumi Chubachi
- Chubachi Internal Respiratory Medicine Clinic, Tokyo, Japan
| | | | | | - Yasuyuki Kato
- Department of Infectious Diseases, International University of Health and Welfare Narita Hospital, Chiba, Japan
| | - Akihiro Ueda
- Department of Infectious Diseases, Japanese Red Cross Medical Center, Tokyo, Japan
| | | | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Koji Ishii
- Saitama Sekishinkai Hospital, Saitama, Japan
| | - Takao Ooki
- Saitama Sekishinkai Hospital, Saitama, Japan
| | - Hideaki Oka
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Yusuke Nishida
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Ashley Stucky
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chris Smith
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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10
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Arashiro T, Arima Y, Stucky A, Smith C, Hibberd M, Ariyoshi K, Suzuki M. Social and Behavioral Factors Associated with Lack of Intent to Receive COVID-19 Vaccine, Japan. Emerg Infect Dis 2022; 28:1909-1910. [PMID: 35793812 PMCID: PMC9423921 DOI: 10.3201/eid2809.220300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Persons in Japan who did not intend to receive COVID-19 vaccines after widespread rollout were less likely than others to engage in preventive measures or to be afraid of getting infected or infecting others. They were also not less likely to engage in potentially high-risk behaviors, suggesting similar or higher exposure risks.
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11
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van Beek AE, Pouw RB, Wright VJ, Sallah N, Inwald D, Hoggart C, Brouwer MC, Galassini R, Thomas J, Calvo-Bado L, Fink CG, Jongerius I, Hibberd M, Wouters D, Levin M, Kuijpers TW. Low Levels of Factor H Family Proteins During Meningococcal Disease Indicate Systemic Processes Rather Than Specific Depletion by Neisseria meningitidis. Front Immunol 2022; 13:876776. [PMID: 35720329 PMCID: PMC9204383 DOI: 10.3389/fimmu.2022.876776] [Citation(s) in RCA: 1] [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: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Neisseria meningitidis, the causative agent of meningococcal disease (MD), evades complement-mediated clearance upon infection by ‘hijacking’ the human complement regulator factor H (FH). The FH protein family also comprises the homologous FH-related (FHR) proteins, hypothesized to act as antagonists of FH, and FHR-3 has recently been implicated to play a major role in MD susceptibility. Here, we show that the circulating levels of all FH family proteins, not only FH and FHR-3, are equally decreased during the acute illness. We did neither observe specific consumption of FH or FHR-3 by N. meningitidis, nor of any of the other FH family proteins, suggesting that the globally reduced levels are due to systemic processes including dilution by fluid administration upon admission and vascular leakage. MD severity associated predominantly with a loss of FH rather than FHRs. Additionally, low FH levels associated with renal failure, suggesting insufficient protection of host tissue by the active protection by the FH protein family, which is reminiscent of reduced FH activity in hemolytic uremic syndrome. Retaining higher levels of FH may thus limit tissue injury during MD.
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Affiliation(s)
- Anna E van Beek
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Richard B Pouw
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Victoria J Wright
- Section for Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Neneh Sallah
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David Inwald
- Section for Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Clive Hoggart
- Section for Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mieke C Brouwer
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Rachel Galassini
- Section for Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - John Thomas
- Micropathology Ltd., University of Warwick, Warwick, United Kingdom
| | - Leo Calvo-Bado
- Micropathology Ltd., University of Warwick, Warwick, United Kingdom
| | - Colin G Fink
- Micropathology Ltd., University of Warwick, Warwick, United Kingdom
| | - Ilse Jongerius
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands.,Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Martin Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Diana Wouters
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Michael Levin
- Section for Paediatric Infectious Disease, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands.,Sanquin Research, Department of Blood Cell Research, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam, Netherlands
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12
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Arashiro T, Arima Y, Muraoka H, Sato A, Oba K, Uehara Y, Arioka H, Yanai H, Yanagisawa N, Nagura Y, Kato Y, Kato H, Ueda A, Ishii K, Ooki T, Oka H, Nishida Y, Stucky A, Miyahara R, Smith C, Hibberd M, Ariyoshi K, Suzuki M. Behavioral factors associated with SARS-CoV-2 infection in Japan. Influenza Other Respir Viruses 2022; 16:952-961. [PMID: 35470969 PMCID: PMC9111610 DOI: 10.1111/irv.12992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 12/15/2022] Open
Abstract
Background The relative burden of COVID‐19 has been less severe in Japan. One reason for this may be the uniquely strict restrictions imposed upon bars/restaurants. To assess if this approach was appropriately targeting high‐risk individuals, we examined behavioral factors associated with SARS‐CoV‐2 infection in the community. Methods This multicenter case–control study involved individuals receiving SARS‐CoV‐2 testing in June–August 2021. Behavioral exposures in the past 2 weeks were collected via questionnaire. SARS‐CoV‐2 PCR‐positive individuals were cases, while PCR‐negative individuals were controls. Results The analysis included 778 individuals (266 [34.2%] positives; median age [interquartile range] 33 [27–43] years). Attending three or more social gatherings was associated with SARS‐CoV‐2 infection (adjusted odds ratio [aOR] 2.00 [95% CI 1.31–3.05]). Attending gatherings with alcohol (aOR 2.29 [1.53–3.42]), at bars/restaurants (aOR 1.55 [1.04–2.30]), outdoors/at parks (aOR 2.87 [1.01–8.13]), at night (aOR 2.07 [1.40–3.04]), five or more people (aOR 1.81 [1.00–3.30]), 2 hours or longer (aOR 1.76 [1.14–2.71]), not wearing a mask during gatherings (aOR 4.18 [2.29–7.64]), and cloth mask use (aOR 1.77 [1.11–2.83]) were associated with infection. Going to karaoke (aOR 2.53 [1.25–5.09]) and to a gym (aOR 1.87 [1.11–3.16]) were also associated with infection. Factors not associated with infection included visiting a cafe with others, ordering takeout, using food delivery services, eating out by oneself, and work/school/travel‐related exposures including teleworking. Conclusions We identified multiple behavioral factors associated with SARS‐CoV‐2 infection, many of which were in line with the policy/risk communication implemented in Japan. Rapid assessment of risk factors can inform decision making.
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Affiliation(s)
- Takeshi Arashiro
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Yuzo Arima
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Tokyo, Japan
| | - Yuki Uehara
- Department of Clinical Laboratory, St. Luke's International Hospital, Tokyo, Japan
| | - Hiroko Arioka
- Department of General Internal Medicine, St. Luke's International Hospital, Tokyo, Japan
| | - Hideki Yanai
- Department of Clinical Laboratory, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | | | | | - Yasuyuki Kato
- Department of Infectious Diseases, Graduate School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Japan
| | - Akihiro Ueda
- Department of Infectious Diseases, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Koji Ishii
- Saitama Sekishinkai Hospital, Saitama, Japan
| | - Takao Ooki
- Saitama Sekishinkai Hospital, Saitama, Japan
| | - Hideaki Oka
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Yusuke Nishida
- Department of General Internal Medicine and Infectious Diseases, Saitama Medical Center, Saitama, Japan
| | - Ashley Stucky
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Miyahara
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Chris Smith
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Koya Ariyoshi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
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13
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Shah JA, Warr AJ, Graustein AD, Saha A, Dunstan SJ, Thuong NTT, Thwaites GE, Caws M, Thai PVK, Bang ND, Chau TTH, Khor CC, Li Z, Hibberd M, Chang X, Nguyen FK, Hernandez CA, Jones MA, Sassetti CM, Fitzgerald KA, Musvosvi M, Gela A, Hanekom WA, Hatherill M, Scriba TJ, Hawn TR. REL and BHLHE40 Variants Are Associated with IL-12 and IL-10 Responses and Tuberculosis Risk. J Immunol 2022; 208:1352-1361. [PMID: 35217585 PMCID: PMC8917052 DOI: 10.4049/jimmunol.2100671] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/03/2022] [Indexed: 11/19/2022]
Abstract
The major human genes regulating Mycobacterium tuberculosis-induced immune responses and tuberculosis (TB) susceptibility are poorly understood. Although IL-12 and IL-10 are critical for TB pathogenesis, the genetic factors that regulate their expression in humans are unknown. CNBP, REL, and BHLHE40 are master regulators of IL-12 and IL-10 signaling. We hypothesized that common variants in CNBP, REL, and BHLHE40 were associated with IL-12 and IL-10 production from dendritic cells, and that these variants also influence adaptive immune responses to bacillus Calmette-Guérin (BCG) vaccination and TB susceptibility. We characterized the association between common variants in CNBP, REL, and BHLHE40, innate immune responses in dendritic cells and monocyte-derived macrophages, BCG-specific T cell responses, and susceptibility to pediatric and adult TB in human populations. BHLHE40 single-nucleotide polymorphism (SNP) rs4496464 was associated with increased BHLHE40 expression in monocyte-derived macrophages and increased IL-10 from peripheral blood dendritic cells and monocyte-derived macrophages after LPS and TB whole-cell lysate stimulation. SNP BHLHE40 rs11130215, in linkage disequilibrium with rs4496464, was associated with increased BCG-specific IL-2+CD4+ T cell responses and decreased risk for pediatric TB in South Africa. SNPs REL rs842634 and rs842618 were associated with increased IL-12 production from dendritic cells, and SNP REL rs842618 was associated with increased risk for TB meningitis. In summary, we found that genetic variations in REL and BHLHE40 are associated with IL-12 and IL-10 cytokine responses and TB clinical outcomes. Common human genetic regulation of well-defined intermediate cellular traits provides insights into mechanisms of TB pathogenesis.
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Affiliation(s)
- Javeed A Shah
- University of Washington, Seattle, WA;
- VA Puget Sound Health Care System, Seattle, WA
| | | | - Andrew D Graustein
- University of Washington, Seattle, WA
- VA Puget Sound Health Care System, Seattle, WA
| | | | | | - Nguyen T T Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | | | | | | | - Zheng Li
- Genome Institute of Singapore, A-STAR, Singapore
| | - Martin Hibberd
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - Xuling Chang
- University of Melbourne, Melbourne, Victoria, Australia
| | | | | | | | | | | | | | - Anele Gela
- South African Tuberculosis Vaccine Initiative, Cape Town, South Africa
| | - Willem A Hanekom
- South African Tuberculosis Vaccine Initiative, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Cape Town, South Africa
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14
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Sallah N, Miley W, Labo N, Carstensen T, Gurdasani D, Sandhu M, Kellam P, Hibberd M, Newton R, Whitby D, Barroso I. The contribution of host genetics and environmental variation to immune response in gamma-herpesvirus infections. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.1071] [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] [Indexed: 11/25/2022] Open
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15
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Farrukee R, Tai CMK, Oh DY, Anderson DE, Gunalan V, Hibberd M, Lau GYF, Barr IG, von Messling V, Maurer-Stroh S, Hurt AC. Utilising animal models to evaluate oseltamivir efficacy against influenza A and B viruses with reduced in vitro susceptibility. PLoS Pathog 2020; 16:e1008592. [PMID: 32555740 PMCID: PMC7326275 DOI: 10.1371/journal.ppat.1008592] [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: 03/03/2020] [Revised: 06/30/2020] [Accepted: 05/02/2020] [Indexed: 11/19/2022] Open
Abstract
The neuraminidase (NA) inhibitor (NAI) oseltamivir (OST) is the most widely used influenza antiviral drug. Several NA amino acid substitutions are reported to reduce viral susceptibility to OST in in vitro assays. However, whether there is a correlation between the level of reduction in susceptibility in vitro and the efficacy of OST against these viruses in vivo is not well understood. In this study, a ferret model was utilised to evaluate OST efficacy against circulating influenza A and B viruses with a range of in vitro generated 50% inhibitory concentrations (IC50) values for OST. OST efficacy against an A(H1N1)pdm09 and an A(H1N1)pdm09 virus with the H275Y substitution in neuraminidase was also tested in the macaque model. The results from this study showed that OST had a significant impact on virological parameters compared to placebo treatment of ferrets infected with wild-type influenza A viruses with normal IC50 values (~1 nM). However, this efficacy was lower against wild-type influenza B and other viruses with higher IC50 values. Differing pathogenicity of the viruses made evaluation of clinical parameters difficult, although some effect of OST in reducing clinical signs was observed with influenza A(H1N1) and A(H1N1)pdm09 (H275Y) viruses. Viral titres in macaques were too low to draw conclusive results. Analysis of the ferret data revealed a correlation between IC50 and OST efficacy in reducing viral shedding but highlighted that the current WHO guidelines/criteria for defining normal, reduced or highly reduced inhibition in influenza B viruses based on in vitro data are not well aligned with the low in vivo OST efficacy observed for both wild-type influenza B viruses and those with reduced OST susceptibility.
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Affiliation(s)
- Rubaiyea Farrukee
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Celeste Ming-Kay Tai
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ding Yuan Oh
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Health and Life Sciences, Federation University, Churchill, Victoria, Australia
| | | | - Vithiagaran Gunalan
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Martin Hibberd
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Gary Yuk-Fai Lau
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Ian G. Barr
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Health and Life Sciences, Federation University, Churchill, Victoria, Australia
| | - Veronika von Messling
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Veterinary Medicine Division, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore
- National Public Health Laboratories, National Centre for Infectious Diseases, Ministry of Health, Singapore
- Department of Biological Sciences, National University Singapore, Singapore
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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16
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Stamou M, Ng SY, Brand H, Wang H, Plummer L, Best L, Havlicek S, Hibberd M, Khor CC, Gusella J, Balasubramanian R, Talkowski M, Stanton LW, Crowley WF. A Balanced Translocation in Kallmann Syndrome Implicates a Long Noncoding RNA, RMST, as a GnRH Neuronal Regulator. J Clin Endocrinol Metab 2020; 105:5601163. [PMID: 31628846 PMCID: PMC7112981 DOI: 10.1210/clinem/dgz011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/20/2019] [Indexed: 12/16/2022]
Abstract
CONTEXT Kallmann syndrome (KS) is a rare, genetically heterogeneous Mendelian disorder. Structural defects in KS patients have helped define the genetic architecture of gonadotropin-releasing hormone (GnRH) neuronal development in this condition. OBJECTIVE Examine the functional role a novel structural defect affecting a long noncoding RNA (lncRNA), RMST, found in a KS patient. DESIGN Whole genome sequencing, induced pluripotent stem cells and derived neural crest cells (NCC) from the KS patient were contrasted with controls. SETTING The Harvard Reproductive Sciences Center, Massachusetts General Hospital Center for Genomic Medicine, and Singapore Genome Institute. PATIENT A KS patient with a unique translocation, t(7;12)(q22;q24). INTERVENTIONS/MAIN OUTCOME MEASURE/RESULTS A novel translocation was detected affecting the lncRNA, RMST, on chromosome 12 in the absence of any other KS mutations. Compared with controls, the patient's induced pluripotent stem cells and NCC provided functional information regarding RMST. Whereas RMST expression increased during NCC differentiation in controls, it was substantially reduced in the KS patient's NCC coincident with abrogated NCC morphological development and abnormal expression of several "downstream" genes essential for GnRH ontogeny (SOX2, PAX3, CHD7, TUBB3, and MKRN3). Additionally, an intronic single nucleotide polymorphism in RMST was significantly implicated in a genome-wide association study associated with age of menarche. CONCLUSIONS A novel deletion in RMST implicates the loss of function of a lncRNA as a unique cause of KS and suggests it plays a critical role in the ontogeny of GnRH neurons and puberty.
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Affiliation(s)
- Maria Stamou
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital, Boston
| | - Shi-Yan Ng
- Institute of Molecular & Cell Biology, Singapore
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
- Neurology, Psychiatry, & Pathology Departments, Massachusetts General Hospital, Boston
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA
| | - Harold Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
| | - Lacey Plummer
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital, Boston
| | - Lyle Best
- Turtle Mountain Community College, Belcourt, ND
- Family Medicine Department, University of North Dakota, Grand Forks, ND
| | | | - Martin Hibberd
- London School of Hygiene & Tropical Medicine, Keppel Street, London
- Genome Institute of Singapore, Singapore
| | | | - James Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
| | | | - Michael Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
- Neurology, Psychiatry, & Pathology Departments, Massachusetts General Hospital, Boston
- Program in Medical & Population Genetics, Broad Institute, Cambridge, MA
| | - Lawrence W Stanton
- Genome Institute of Singapore, Singapore
- Qatar Biomedical Research Institute (QBRI), Hamad BIn Khalifa University (HBRI), Doha, Qatar
| | - William F Crowley
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital, Boston
- Center for Genomic Medicine, Massachusetts General Hospital, Boston
- Correspondence and Reprint Requests: William F. Crowley, Jr., M.D., Center for Genomic Medicine CPZN-6.6312 - 185 Cambridge Street, Boston, MA 02114. E-mail:
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17
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Perdigão J, Modesto A, Pereira AL, Neto O, Matos V, Godinho A, Phelan J, Charleston J, Spadar A, de Sessions PF, Hibberd M, Campino S, Costa A, Fernandes F, Ferreira F, Correia AB, Gonçalves L, Clark TG, Duarte A. Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital. Microb Genom 2019; 7:000349. [PMID: 32234124 PMCID: PMC8627661 DOI: 10.1099/mgen.0.000349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/14/2020] [Indexed: 01/08/2023] Open
Abstract
Klebsiella pneumoniae has emerged as an important nosocomial pathogen, with whole-genome sequencing (WGS) significantly improving our ability to characterize associated outbreaks. Our study sought to perform a genome-wide analysis of multiclonal K. pneumoniae isolates (n=39; 23 patients) producing extended spectrum beta-lactamases and/or carbapenemases sourced between 2011 and 2016 in a Portuguese tertiary-care hospital. All isolates showed resistance to third-generation cephalosporins and six isolates (five patients) were also carbapenem resistant. Genome-wide-based phylogenetic analysis revealed a topology representing ongoing dissemination of three main sequence-type (ST) clades (ST15, ST147 and ST307) and transmission across different wards, compatible with missing links that can take the form of undetected colonized patients. Two carbapenemase-coding genes were detected: blaKPC-3, located on a Tn4401d transposon, and blaGES-5 on a novel class 3 integron. Additionally, four genes coding for ESBLs (blaBEL-1, blaCTX-M-8, blaCTX-M-15 and blaCTX-M-32) were also detected. ESBL horizontal dissemination across five clades is highlighted by the similar genetic environments of blaCTX-M-15 gene upstream of ISEcp1 on a Tn3-like transposon. Overall, this study provides a high-resolution genome-wide perspective on the epidemiology of ESBL and carbapenemase-producing K. pneumoniae in a healthcare setting while contributing for the adoption of appropriate intervention and prevention strategies.
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Affiliation(s)
- João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - A. L. Pereira
- Clinical Pathology Unit. Hospital SAMS, Lisboa, Portugal
| | - O. Neto
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - V. Matos
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - A. Godinho
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - A. Costa
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - F. Fernandes
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - F. Ferreira
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - A. B. Correia
- Clinical Pathology Unit. Hospital SAMS, Lisboa, Portugal
| | | | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Portugal
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18
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Zhu YO, Aw P, Aung MM, Lee HK, Hibberd M, Lee GH. Patterns of mutation within an emerging endemic lineage of HEV-3a. J Viral Hepat 2019; 26:191-198. [PMID: 30315669 DOI: 10.1111/jvh.13015] [Citation(s) in RCA: 4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/13/2018] [Indexed: 12/12/2022]
Abstract
The hepatitis E virus can cause chronic infections in immuno-suppressed patients, and cases have been on the rise globally. Viral mutations during such infections are difficult to characterize. We deep-sequenced viral populations from 15 immunocompromised patients with chronic HEV to identify the viral lineage and describe viral mutational hotspots within and across patients. A total of 21 viral RNA samples were collected between 2012 and 2017 from a single hospital in Singapore. Sequences covering a total of 3894 bp of the HEV genome were obtained. Phylogenetic analyses identified all sequences as belonging to the HEV-3a sub-clade and clearly indicate a unique local lineage. Deep sequencing reveals variable viral population complexity during infections. Comparisons of viral samples from the same patients spaced 2-19 months apart revealed rapid nucleotide replacements in the dominant viral sequence in both ribavirin treated and treatment-naive patients. Mutational hotspots were identified within ORF3 and the PCP/HVR domain of ORF1.
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Affiliation(s)
- Yuan O Zhu
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore City, Singapore
| | - Pauline Aw
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore City, Singapore
| | - Myo Myint Aung
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Hong Kai Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Hospital, National University Health System, Singapore City, Singapore
| | - Martin Hibberd
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore City, Singapore.,London School of Hygiene and Tropical Medicine, London, UK
| | - Guan Huei Lee
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
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19
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Borghini L, Hibberd M, Davila S. Changes in H3K27ac following lipopolysaccharide stimulation of nasopharyngeal epithelial cells. BMC Genomics 2018; 19:969. [PMID: 30587130 PMCID: PMC6307289 DOI: 10.1186/s12864-018-5295-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 03/08/2018] [Accepted: 11/21/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The epithelium is the first line of defense against pathogens. Notably the epithelial cells lining the respiratory track are crucial in sensing airborne microbes and mounting an effective immune response via the expression of target genes such as cytokines and chemokines. Gene expression regulation following microbial recognition is partly regulated by chromatin re-organization and has been described in immune cells but data from epithelial cells is not as detailed. Here, we report genome-wide changes of the H3K27ac mark, characteristic of activated enhancers and promoters, after stimulation of nasopharyngeal epithelial cells with the bacterial endotoxin Lipopolysaccharide (LPS). RESULTS In this study, we have identified 626 regions where the H3K27ac mark showed reproducible increase following LPS induction in epithelial cells. This indicated that sensing of LPS led to opening of the chromatin in our system. Moreover, this phenomenon seemed to happen extensively at enhancers regions and we could observe instances of Super-enhancer formation. As expected, LPS-increased H3K27ac regions were found in the vicinity of genes relevant for LPS response and these changes correlated with up-regulation of their expression. In addition, we found the induction of H3K27ac mark to overlap with the binding of one of the NF-kB members and key regulator of the innate immune response, RELA, following LPS sensing. Indeed, inhibiting the NF-kB pathway abolished the deposition of H3K27ac at the TNF locus, a target of RELA, suggesting that these two phenomena are associated. CONCLUSIONS Enhancers' selection and activation following microbial or inflammatory stimuli has been described previously and shown to be mediated via the NF-kB pathway. Here, we demonstrate that this is also likely to occur in the case of LPS-sensing by nasopharyngeal epithelial cells as well. In addition to validating previous findings, we generated a valuable data set relevant to the host immune response to epithelial cell colonizing or infecting pathogens.
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Affiliation(s)
- Lisa Borghini
- Human Genetics, Genome Institute of Singapore, Singapore, 138672, Singapore. .,Infectious Disease, Genome Institute of Singapore, Singapore, 138672, Singapore.
| | - Martin Hibberd
- Infectious Disease, Genome Institute of Singapore, Singapore, 138672, Singapore.,Present Address: Pathogen Molecular Biology, Infectious & Tropical Disease, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore, 138672, Singapore.,Present Address: SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, 169609, Singapore
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20
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Wright VJ, Herberg JA, Kaforou M, Shimizu C, Eleftherohorinou H, Shailes H, Barendregt AM, Menikou S, Gormley S, Berk M, Hoang LT, Tremoulet AH, Kanegaye JT, Coin LJM, Glodé MP, Hibberd M, Kuijpers TW, Hoggart CJ, Burns JC, Levin M. Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature. JAMA Pediatr 2018; 172:e182293. [PMID: 30083721 PMCID: PMC6233768 DOI: 10.1001/jamapediatrics.2018.2293] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
IMPORTANCE To date, there is no diagnostic test for Kawasaki disease (KD). Diagnosis is based on clinical features shared with other febrile conditions, frequently resulting in delayed or missed treatment and an increased risk of coronary artery aneurysms. OBJECTIVE To identify a whole-blood gene expression signature that distinguishes children with KD in the first week of illness from other febrile conditions. DESIGN, SETTING, AND PARTICIPANTS The case-control study comprised a discovery group that included a training and test set and a validation group of children with KD or comparator febrile illness. The setting was pediatric centers in the United Kingdom, Spain, the Netherlands, and the United States. The training and test discovery group comprised 404 children with infectious and inflammatory conditions (78 KD, 84 other inflammatory diseases, and 242 bacterial or viral infections) and 55 healthy controls. The independent validation group comprised 102 patients with KD, including 72 in the first 7 days of illness, and 130 febrile controls. The study dates were March 1, 2009, to November 14, 2013, and data analysis took place from January 1, 2015, to December 31, 2017. MAIN OUTCOMES AND MEASURES Whole-blood gene expression was evaluated using microarrays, and minimal transcript sets distinguishing KD were identified using a novel variable selection method (parallel regularized regression model search). The ability of transcript signatures (implemented as disease risk scores) to discriminate KD cases from controls was assessed by area under the curve (AUC), sensitivity, and specificity at the optimal cut point according to the Youden index. RESULTS Among 404 patients in the discovery set, there were 78 with KD (median age, 27 months; 55.1% male) and 326 febrile controls (median age, 37 months; 56.4% male). Among 202 patients in the validation set, there were 72 with KD (median age, 34 months; 62.5% male) and 130 febrile controls (median age, 17 months; 56.9% male). A 13-transcript signature identified in the discovery training set distinguished KD from other infectious and inflammatory conditions in the discovery test set, with AUC of 96.2% (95% CI, 92.5%-99.9%), sensitivity of 81.7% (95% CI, 60.0%-94.8%), and specificity of 92.1% (95% CI, 84.0%-97.0%). In the validation set, the signature distinguished KD from febrile controls, with AUC of 94.6% (95% CI, 91.3%-98.0%), sensitivity of 85.9% (95% CI, 76.8%-92.6%), and specificity of 89.1% (95% CI, 83.0%-93.7%). The signature was applied to clinically defined categories of definite, highly probable, and possible KD, resulting in AUCs of 98.1% (95% CI, 94.5%-100%), 96.3% (95% CI, 93.3%-99.4%), and 70.0% (95% CI, 53.4%-86.6%), respectively, mirroring certainty of clinical diagnosis. CONCLUSIONS AND RELEVANCE In this study, a 13-transcript blood gene expression signature distinguished KD from other febrile conditions. Diagnostic accuracy increased with certainty of clinical diagnosis. A test incorporating the 13-transcript disease risk score may enable earlier diagnosis and treatment of KD and reduce inappropriate treatment in those with other diagnoses.
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Affiliation(s)
| | - Jethro A. Herberg
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Chisato Shimizu
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | | | - Hannah Shailes
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Anouk M. Barendregt
- Department of Pediatric Hematology, Immunology & Infectious Diseases, Emma Children’s Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephanie Menikou
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Stuart Gormley
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Maurice Berk
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | | | - Adriana H. Tremoulet
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | - John T. Kanegaye
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | - Lachlan J. M. Coin
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, United Kingdom,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Mary P. Glodé
- Section of Infectious Diseases, Department of Pediatrics, University of Colorado Denver School of Medicine Anschutz Medical Campus, Aurora,Children’s Hospital Colorado, Aurora
| | - Martin Hibberd
- Infectious Diseases, Genome Institute of Singapore, Singapore
| | - Taco W. Kuijpers
- Department of Pediatric Hematology, Immunology & Infectious Diseases, Emma Children’s Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands,Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Clive J. Hoggart
- Section of Paediatrics, Imperial College London, London, United Kingdom
| | - Jane C. Burns
- Department of Pediatrics, University of California San Diego, La Jolla,Rady Children’s Hospital–San Diego, San Diego, California
| | - Michael Levin
- Section of Paediatrics, Imperial College London, London, United Kingdom
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21
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Campos MC, Dombrowski JG, Phelan J, Marinho CRF, Hibberd M, Clark TG, Campino S. Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil. PLoS One 2018; 13:e0201452. [PMID: 30110370 PMCID: PMC6093667 DOI: 10.1371/journal.pone.0201452] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 10/24/2017] [Accepted: 07/16/2018] [Indexed: 01/14/2023] Open
Abstract
Zika virus infections can cause a range of neurologic disorders including congenital microcephaly. However, while Zika infections have been notified across all regions in Brazil, there has been an unusual number of congenital microcephaly case notifications concentrated in the Northeast of the country. To address this observation, we investigated epidemiological data (2014–2016) on arbovirus co-distribution, environmental and socio-economic factors for each region in Brazil. Data on arbovirus reported cases and microcephaly were collected from several Brazilian Ministry of Health databases for each Federal unit. These were complemented by environmental management, social economic and Aedes aegypti infestation index data, extracted from multiple databases. Spatial time “ecological” analysis on the number of arboviruses transmitted by Aedes mosquitoes in Brazil show that the distribution of dengue and Zika was widespread in the whole country, with higher incidence in the West-Central region. However, reported chikungunya cases were higher in the Northeast, the region also with the highest number of microcephaly cases registered. Social economic factors (human development index and poverty index) and environmental management (water supply/storage and solid waste management) pointed the Northeast as the less wealthy region. The Northeast is also the region with the highest risk of Aedes aegypti house infestation due to the man-made larval habitats. In summary, the results of our ecological analysis support the hypothesis that the unusual distribution of microcephaly might not be due to Zika infection alone and could be accentuated by poverty and previous or co-infection with other pathogens. Our study reinforces the link between poverty and the risk of disease and the need to understand the effect on pathogenesis of sequential exposure to arboviruses and co-viral infections. Comprehensive large-scale cohort studies are required to corroborate our findings. We recommend that the list of infectious diseases screened, particularly during pregnancy, be regularly updated to include and effectively differentiate all viruses from ongoing outbreaks.
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Affiliation(s)
- Monica C. Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Jamille G. Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Claudio R. F. Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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22
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Ho EXP, Cheung CMG, Sim S, Chu CW, Wilm A, Lin CB, Mathur R, Wong D, Chan CM, Bhagarva M, Laude A, Lim TH, Wong TY, Cheng CY, Davila S, Hibberd M. Human pharyngeal microbiota in age-related macular degeneration. PLoS One 2018; 13:e0201768. [PMID: 30089174 PMCID: PMC6082546 DOI: 10.1371/journal.pone.0201768] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/20/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND While the aetiology of age-related macular degeneration (AMD)-a major blinding disease-remains unknown, the disease is strongly associated with variants in the complement factor H (CFH) gene. CFH variants also confer susceptibility to invasive infection with several bacterial colonizers of the nasopharyngeal mucosa. This shared susceptibility locus implicates complement deregulation as a common disease mechanism, and suggests the possibility that microbial interactions with host complement may trigger AMD. In this study, we address this possibility by testing the hypothesis that AMD is associated with specific microbial colonization of the human nasopharynx. RESULTS High-throughput Illumina sequencing of the V3-V6 region of the microbial 16S ribosomal RNA gene was used to comprehensively and accurately describe the human pharyngeal microbiome, at genus level, in 245 AMD patients and 386 controls. Based on mean and differential microbial abundance analyses, we determined an overview of the pharyngeal microbiota, as well as candidate genera (Prevotella and Gemella) suggesting an association towards AMD health and disease conditions. CONCLUSIONS Utilizing an extensive study population from Singapore, our results provided an accurate description of the pharyngeal microbiota profiles in AMD health and disease conditions. Through identification of candidate genera that are different between conditions, we provide preliminary evidence for the existence of microbial triggers for AMD. Ethical approval for this study was obtained through the Singapore Health Clinical Institutional Review Board, reference numbers R799/63/2010 and 2010/585/A.
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Affiliation(s)
| | - Chui Ming Gemmy Cheung
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Shuzhen Sim
- Genome Institute of Singapore,Singapore, Singapore
| | | | - Andreas Wilm
- Genome Institute of Singapore,Singapore, Singapore
| | | | - Ranjana Mathur
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Doric Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Choi Mun Chan
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Mayuri Bhagarva
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
| | - Augustinus Laude
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tock Han Lim
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Ching Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Sonia Davila
- Genome Institute of Singapore,Singapore, Singapore
| | - Martin Hibberd
- Genome Institute of Singapore,Singapore, Singapore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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23
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Borghini L, Lu J, Hibberd M, Davila S. Variation in Genome-Wide NF-κB RELA Binding Sites upon Microbial Stimuli and Identification of a Virus Response Profile. J Immunol 2018; 201:1295-1305. [PMID: 29959281 DOI: 10.4049/jimmunol.1800246] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/04/2018] [Indexed: 12/22/2022]
Abstract
NF-κB transcription factors are master regulators of the innate immune response. Activated downstream of pathogen recognition receptors, they regulate the expression of genes to help fight infections as well as recruit the adaptive immune system. NF-κB responds to a wide variety of signals, but the processes by which stimulus specificity is attained remain unclear. In this article, we characterized the response of one NF-κB member, RELA, to four stimuli mimicking infection in human nasopharyngeal epithelial cells. Comparing genome-wide RELA binding, we observed stimulus-specific sites, although most sites overlapped across stimuli. Specifically, the response to poly I:C (mimicking viral dsRNA and signaling through TLR3) induced a distinct RELA profile, binding in the vicinity of antiviral genes and correlating with corresponding gene expression. This group of binding sites was also enriched in IFN regulatory factor motifs and showed overlapping with IFN regulatory factor binding sites. A novel NF-κB target, OASL, was further validated and showed TLR3-specific activation. This work showed that some RELA DNA binding sites varied in activation response following different stimulations and that interaction with more specialized factors could help achieve this stimulus-specific activity. Our data provide a genomic view of regulated host response to different pathogen stimuli.
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Affiliation(s)
- Lisa Borghini
- Department of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore; .,Department of Infectious Diseases, Genome Institute of Singapore, Singapore 138672, Singapore; and
| | - Jinhua Lu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Program, National University of Singapore, Singapore 119077
| | - Martin Hibberd
- Department of Infectious Diseases, Genome Institute of Singapore, Singapore 138672, Singapore; and
| | - Sonia Davila
- Department of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore;
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24
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The HC, Florez de Sessions P, Jie S, Pham Thanh D, Thompson CN, Nguyen Ngoc Minh C, Chu CW, Tran TA, Thomson NR, Thwaites GE, Rabaa MA, Hibberd M, Baker S. Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. Gut Microbes 2018; 9:38-54. [PMID: 28767339 PMCID: PMC5914913 DOI: 10.1080/19490976.2017.1361093] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023] Open
Abstract
Diarrheal diseases remain the second most common cause of mortality in young children in developing countries. Efforts have been made to explore the impact of diarrhea on bacterial communities in the human gut, but a thorough understanding has been impeded by inadequate resolution in bacterial identification and the examination of only few etiological agents. Here, by profiling an extended region of the 16S rRNA gene in the fecal microbiome, we aimed to elucidate the nature of gut microbiome perturbations during the early phase of infectious diarrhea caused by various etiological agents in Vietnamese children. Fecal samples from 145 diarrheal cases with a confirmed infectious etiology before antimicrobial therapy and 54 control subjects were analyzed. We found that the diarrheal fecal microbiota could be robustly categorized into 4 microbial configurations that either generally resembled or were highly divergent from a healthy state. Factors such as age, nutritional status, breastfeeding, and the etiology of the infection were significantly associated with these microbial community structures. We observed a consistent elevation of Fusobacterium mortiferum, Escherichia, and oral microorganisms in all diarrheal fecal microbiome configurations, proposing similar mechanistic interactions, even in the absence of global dysbiosis. We additionally found that Bifidobacterium pseudocatenulatum was significantly depleted during dysenteric diarrhea regardless of the etiological agent, suggesting that further investigations into the use of this species as a dysentery-orientated probiotic therapy are warranted. Our findings contribute to the understanding of the complex influence of infectious diarrhea on gut microbiome and identify new opportunities for therapeutic interventions.
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Affiliation(s)
- Hao Chung The
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Song Jie
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
| | - Duy Pham Thanh
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Corinne N. Thompson
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chau Nguyen Ngoc Minh
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Collins Wenhan Chu
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
| | - Tuan-Anh Tran
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nicholas R. Thomson
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
- Infection Genomics, The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Guy E. Thwaites
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Maia A. Rabaa
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Martin Hibberd
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Stephen Baker
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The Department of Medicine, The University of Cambridge, Cambridge, United Kingdom
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25
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Zhu YO, Aw PPK, de Sessions PF, Hong S, See LX, Hong LZ, Wilm A, Li CH, Hue S, Lim SG, Nagarajan N, Burkholder WF, Hibberd M. Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history. BMC Genomics 2017; 18:829. [PMID: 29078745 PMCID: PMC5660452 DOI: 10.1186/s12864-017-4217-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/16/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. RESULTS With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. CONCLUSIONS Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history.
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Affiliation(s)
- Yuan O Zhu
- Genome Institute of Singapore, Singapore, 138672, Singapore.
| | - Pauline P K Aw
- Genome Institute of Singapore, Singapore, 138672, Singapore
| | | | - Shuzhen Hong
- Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Lee Xian See
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | - Lewis Z Hong
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | - Andreas Wilm
- Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Chen Hao Li
- Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Stephane Hue
- London School of Hygiene and Tropical Medicine, London, UK
| | - Seng Gee Lim
- National University Hospital, Singapore, 119074, Singapore
| | | | | | - Martin Hibberd
- Genome Institute of Singapore, Singapore, 138672, Singapore.,London School of Hygiene and Tropical Medicine, London, UK
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26
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Whitehorn J, Kien DTH, Quyen NTH, Wills B, Van Vinh Chau N, Tam DTH, Tuan NM, Jaenisch T, Hibberd M, Khor CC, Simmons CP. Genetic variants of MICB and PLCE1 and associations with the laboratory features of dengue. BMC Infect Dis 2017; 17:412. [PMID: 28599625 PMCID: PMC5466782 DOI: 10.1186/s12879-017-2514-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/01/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND A previous genome-wide association study identified 2 susceptibility loci for severe dengue at MICB rs3132468 and PLCE1 rs3740360 and further work showed these mutations to be also associated with less severe clinical presentations. The aim of this study was to determine if these specific loci were associated with laboratory features of dengue that correlate with clinical severity with the aim of elucidating the functional basis of these genetic variants. METHODS This was a case-only analysis of laboratory-confirmed dengue patients obtained from 2 prospective cohort studies and 1 randomised clinical trial in Vietnam (Trial registration: ISRCTN ISRCTN03147572. Registered 24th July 2012). 2742 dengue cases were successfully genotyped at MICB rs3132468 and PLCE1 rs3740360. Laboratory variables were compared between genotypes and stratified by DENV serotype. RESULTS The analysis showed no association between MICB and PLCE1 genotype and early viraemia level, platelet nadir, white cell count nadir, or maximum haematocrit in both overall analysis and in analysis stratified by serotype. DISCUSSION The lack of an association between genotype and viremia level may reflect the sampling procedures within the included studies. The study findings mean that the functional basis of these mutations remains unclear. TRIAL REGISTRATION ISRCTN ISRCTN03147572 . Registered 24th July 2012.
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Affiliation(s)
- James Whitehorn
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK. .,Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam.
| | - Duong Thi Hue Kien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Nguyen Than Ha Quyen
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Bridget Wills
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nguyen Van Vinh Chau
- Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | - Dong Thi Hoai Tam
- Hospital for Tropical Diseases, 764 Vo Van Kiet, District 5, Ho Chi Minh City, Viet Nam
| | | | - Thomas Jaenisch
- Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Hibberd
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK.,Genome Institute of Singapore, Biopolis Way, Singapore, Singapore
| | - Chiea Chuen Khor
- School of Public Health, National University of Singapore, Singapore, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore.,Department of Ophthalmology, National University of Singapore, Singapore, Singapore
| | - Cameron P Simmons
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute, Melbourne, VIC, 3010, Australia
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27
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Jiang L, Lee VJM, Cui L, Lin R, Tan CL, Tan LWL, Lim WY, Leo YS, Low L, Hibberd M, Chen MIC. Detection of viral respiratory pathogens in mild and severe acute respiratory infections in Singapore. Sci Rep 2017; 7:42963. [PMID: 28218288 PMCID: PMC5317157 DOI: 10.1038/srep42963] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 10/13/2016] [Accepted: 01/17/2017] [Indexed: 11/09/2022] Open
Abstract
To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Community-ARI and inpatient-ARI was also combined with mild and severe cases of influenza from a historical prospective study as mild-ARI and severe-ARI respectively to evaluate the performance of clinical case definitions. We analysed 130 community-ARI and 140 inpatient-ARI episodes (5 inpatient-ARI excluded because multiple pathogens were detected), involving 138 and 207 samples respectively. Detection by PCR declined with days post-onset for influenza virus; decrease was faster for community-ARI than for inpatient-ARI. No such patterns were observed for non-influenza respiratory virus infections. PathChip added substantially to viruses detected for community-ARI only. Clinical case definitions discriminated influenza from other mild-ARI but performed poorly for severe-ARI and for older participants. Rational strategies for diagnosis and surveillance of influenza and other respiratory virus must acknowledge the differences between ARIs presenting in community and hospital settings.
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Affiliation(s)
- Lili Jiang
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore
| | - Vernon Jian Ming Lee
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.,Biodefence Centre, Singapore Armed Forces, Singapore
| | - Lin Cui
- National Public Health Laboratory, Ministry of Health, Singapore
| | - Raymond Lin
- National Public Health Laboratory, Ministry of Health, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Chyi Lin Tan
- Department of Infectious Diseases, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore
| | - Yee-Sin Leo
- Department of Infectious Diseases, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
| | - Louie Low
- Genome Institute Singapore, Singapore
| | | | - Mark I-Cheng Chen
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore.,Department of Clinical Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, Singapore
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28
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Jones LA, Skibinski DA, Xie LW, Au B, Lee B, Zhu Y, Fairhurst AM, Lee A, Kaliaperumal N, Poidinger M, Hibberd M, Ooi EE, Hanson BJ, Diermayr V, Matter A, Bachmann M, Saudan P, Connolly JE. Type-1 T cell responses and gene signatures driven by a novel virus-like particle (VLP) influenza A (H1N1) vaccine. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.215.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Effective influenza vaccination is currently assessed by the induction of antibodies directed against the influenza virus envelope glycoprotein hemagglutinin (HA; HAI test) otherwise known as seroconversion. However, protective antibody responses are sub-optimal in some vaccinated populations, particularly in the elderly. Furthermore, many clinical studies highlight the importance of T cells in driving protection. Therefore, a need exists for vaccine strategies which can engage both the humoral and cell mediated arms of the immune response. Herein, we describe the induction of anti-influenza T cell responses following vaccination with a novel VLP vaccine. Peripheral blood mononuclear cells (PBMCs) stimulated ex vivo with either influenza or vaccine specific antigens led to increased CD4+ and CD8+ T cell proliferation and increased production of cytokines such as IL-17A, IL-17F, IL-5, IL-13, IL-9, IL-10, IL-21 and, most significantly, IFN-γ. A subset of individuals demonstrated a shift from a pre-vaccination IL-5- and IL-13- driven type-2 response to a more protective IFN-γ driven type-1 response following vaccination with VLP. Microarray of whole blood samples collected pre- and post-vaccination with VLP revealed significantly different transcriptional profiles. The top most significantly downregulated gene following VLP vaccination, DEAD Box Helicase 17 (DDX17), was also found to have reduced protein expression in PBMCs by flow cytometry. Finally, weighted gene correlation network analysis (WGCNA) revealed that the post vaccination reduction in protein expression of DDX17, increase in HAI titres and increase in T cell proliferation correlates with particular gene modules.
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Affiliation(s)
- Leigh A Jones
- 1Agency for Sci., Technol. and Res. (A*STAR), Singapore
| | | | - Lin Wu Xie
- 1Agency for Sci., Technol. and Res. (A*STAR), Singapore
| | - Bijin Au
- 1Agency for Sci., Technol. and Res. (A*STAR), Singapore
| | - Bernett Lee
- 1Agency for Sci., Technol. and Res. (A*STAR), Singapore
| | - Yuan Zhu
- 1Agency for Sci., Technol. and Res. (A*STAR), Singapore
| | | | - Audrey Lee
- 1Agency for Sci., Technol. and Res. (A*STAR), Singapore
| | | | | | | | | | | | | | - Alex Matter
- 1Agency for Sci., Technol. and Res. (A*STAR), Singapore
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29
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Dewey EC, Tan MJA, Hibberd M, Gale MJ. Programming of RIG-I signaling through co-factor interactions. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.203.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Retinoic acid-inducible gene I (RIG-I) functions as a cytosolic pathogen recognition receptor by binding the pathogen associated molecular patterns (PAMPs) in viral RNA. The molecular signature for RIG-I recognition has been identified as 5′-triphosphate-containing short double stranded or poly-uridine RNA (5′pppRNA) structures found in RNA species that amass in the cytoplasm during virus infection. PAMP-mediated activation of RIG-I triggers many signaling cascades that mediates its effector functions in innate immunity and apoptosis. In the innate immune response to virus infection, RIG-I sets off both IRF3/7 and NF-κB signaling to induce type I interferon (IFN) and pro-inflammatory cytokine production respectively. PAMP-induced RIG-I activation can also induce apoptosis in cancer cells. Since PAMP RNA can act as the activator of RIG-I’s pro-apoptotic and innate immune functions, we hypothesized that the induction of these separate pathways is programmed through differential RIG-I-cofactor interactions. We have identified and characterized novel co-factors of RIG-I by using a systems proteomic approach. These co-factors serve to program apoptotic versus innate immune signaling actions through their interaction with RIG-I. These co-factors and their biologic functions will be presented.
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Jenkins H, Sakurai Y, Nishimura A, Okamoto H, Hibberd M, Jenkins R, Yoneyama T, Ashida K, Ogama Y, Warrington S. Randomised clinical trial: safety, tolerability, pharmacokinetics and pharmacodynamics of repeated doses of TAK-438 (vonoprazan), a novel potassium-competitive acid blocker, in healthy male subjects. Aliment Pharmacol Ther 2015; 41:636-48. [PMID: 25707624 PMCID: PMC4654261 DOI: 10.1111/apt.13121] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 09/25/2014] [Accepted: 01/26/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND TAK-438 (vonoprazan) is a potassium-competitive acid blocker that reversibly inhibits gastric H(+) , K(+) -ATPase. AIM To evaluate the safety, tolerability, pharmacokinetics and pharmacodynamics of TAK-438 in healthy Japanese and non-Japanese men. METHODS In two Phase I, randomised, double-blind, placebo-controlled studies, healthy men (Japan N = 60; UK N = 48) received TAK-438 10-40 mg once daily at a fixed dose level for 7 consecutive days. Assessments included safety, tolerability, pharmacokinetics and pharmacodynamics (intragastric pH). RESULTS Plasma concentration-time profiles of TAK-438 at all dose levels showed rapid absorption (median Tmax ≤2 h). Mean elimination half-life was up to 9 h. Exposure was slightly greater than dose proportional, with no apparent time-dependent inhibition of metabolism. There was no important difference between the two studies in AUC0-tau on Day 7. TAK-438 caused dose-dependent acid suppression. On Day 7, mean 24-h intragastric pH>4 holding time ratio (HTR) with 40 mg TAK-438 was 100% (Japan) and 93.2% (UK), and mean night-time pH>4 HTR was 100% (Japan) and 90.4% (UK). TAK-438 was well tolerated. The frequency of adverse events was similar at all dose levels and there were no serious adverse events. There were no important increases in serum alanine transaminase activity. Serum gastrin and pepsinogen I and II concentrations increased with TAK-438 dose. CONCLUSIONS TAK-438 in multiple rising oral dose levels of 10-40 mg once daily for 7 days was safe and well tolerated in healthy men and caused rapid, profound and sustained suppression of gastric acid secretion throughout each 24-h dosing interval. Clinicaltrials.gov identifiers: NCT02123953 and NCT02141711.
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Affiliation(s)
- H Jenkins
- Takeda Development Centre Europe LtdLondon, UK
| | - Y Sakurai
- Takeda Pharmaceutical Company LtdOsaka, Japan
| | - A Nishimura
- Takeda Pharmaceutical Company LtdOsaka, Japan
| | - H Okamoto
- Takeda Pharmaceutical Company LtdOsaka, Japan
| | - M Hibberd
- Takeda Development Centre Europe LtdLondon, UK
| | - R Jenkins
- Takeda Development Centre Europe LtdLondon, UK
| | - T Yoneyama
- Takeda Pharmaceutical Company Ltd, FujisawaJapan
| | - K Ashida
- Department of Gastroenterology and Hepatology, Saiseikai Nakatsu HospitalOsaka, Japan
| | - Y Ogama
- Medical Co. LTA Honjo Clinic (current Sumida Hospital)Tokyo, Japan
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31
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Jauneikaite E, Churton N, Lin R, Jefferies J, Hibberd M, Clarke S. Prevalence of serotypes and molecular types among Streptococcus pneumoniae isolates causing invasive disease in Singapore between June 2009 and August 2010. Int J Infect Dis 2012. [DOI: 10.1016/j.ijid.2012.05.825] [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] [Indexed: 10/28/2022] Open
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32
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Wong M, Öhrmalm L, Broliden K, Aust C, Hibberd M, Tolfvenstam T. Mannose-binding lectin 2 polymorphisms do not influence frequency or type of infection in adults with chemotherapy induced neutropaenia. PLoS One 2012; 7:e30819. [PMID: 22363494 PMCID: PMC3281882 DOI: 10.1371/journal.pone.0030819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/21/2011] [Indexed: 11/20/2022] Open
Abstract
Background Mannose-binding Lectin protein (MBL) has been suggested to be relevant in the defence against infections in immunosuppressed individuals. In a Swedish adult cohort immunosuppressed from both the underlying disease and from iatrogenic treatments for their underlying disease we investigated the role of MBL in susceptibility to infection. Methods In this cross sectional, prospective study, blood samples obtained from 96 neutropaenic febrile episodes, representing 82 individuals were analysed for single nucleotide polymorphism (SNP) in the MBL2 gene. Concurrent measurement of plasma MBL protein concentrations was also performed for observation of acute response during febrile episodes. Findings No association was observed between MBL2 genotype or plasma MBL concentrations, and the type or frequency of infection. Adding to the literature, we found no evidence that viral infections or co-infections with virus and bacteria would be predisposed by MBL deficiency. We further saw no correlation between MBL2 genotype and the risk of fever. However, fever duration in febrile neutropaenic episodes was negatively associated with MBL2 SNP mutations (p<0.05). Patients with MBL2 SNP mutations presented a median febrile duration of 1.8 days compared with 3 days amongst patients with wildtype MBL2 genotype. Interpretation We found no clear association between infection, or infection type to MBL2 genotypes or plasma MBL concentration, and add to the reports casting doubts on the benefit of recombinant MBL replacement therapy use during iatrogenic neutropaenia.
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Affiliation(s)
- Michelle Wong
- Infectious Disease Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.
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33
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Thuong NTT, Hawn TR, Chau TTH, Bang ND, Yen NTB, Thwaites GE, Teo YY, Seielstad M, Hibberd M, Lan NTN, Caws M, Farrar JJ, Dunstan SJ. Epiregulin (EREG) variation is associated with susceptibility to tuberculosis. Genes Immun 2011; 13:275-81. [PMID: 22170233 DOI: 10.1038/gene.2011.83] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Although host genetics influences susceptibility to Mycobacterium tuberculosis, the human genes regulating pathogenesis remain largely unknown. We used M. tuberculosis-stimulated macrophage gene expression profiling in conjunction with a case-control genetic association study to discover epiregulin (EREG), as a novel candidate tuberculosis (TB) susceptibility gene. Using a genome-wide association study dataset, we found that among the 21 genes with greater than 50-fold induction, EREG had the most polymorphisms associated with TB. We genotyped haplotype-tagging polymorphisms in discovery (N = 337 cases, N = 380 controls) and validation (N = 332 cases) datasets and an EREG polymorphism (rs7675690) was associated with susceptibility to TB (genotypic comparison; corrected P = 0.00007). rs7675690 was also associated more strongly with infections caused by the Beijing lineage of M. tuberculosis when compared with non-Beijing strains (controls vs Beijing, OR 7.81, P = 8.7 × 10(-5); non-Beijing, OR 3.13, P = 0.074). Furthermore, EREG expression was induced in monocytes and peripheral blood mononuclear cells stimulated with M. tuberculosis as well as TLR4 and TLR2/1/6 ligands. In murine macrophages, EREG expression induced by M. tuberculosis was MYD88- and TLR2-dependent. Together, these data provide the first evidence for an important role for EREG as a susceptibility gene for human TB.
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Affiliation(s)
- N T T Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
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Khor CC, Ramdas WD, Vithana EN, Cornes BK, Sim X, Tay WT, Saw SM, Zheng Y, Lavanya R, Wu R, Wang JJ, Mitchell P, Uitterlinden AG, Rivadeneira F, Teo YY, Chia KS, Seielstad M, Hibberd M, Vingerling JR, Klaver CCW, Jansonius NM, Tai ES, Wong TY, van Duijn CM, Aung T. Genome-wide association studies in Asians confirm the involvement of ATOH7 and TGFBR3, and further identify CARD10 as a novel locus influencing optic disc area. Hum Mol Genet 2011; 20:1864-72. [PMID: 21307088 DOI: 10.1093/hmg/ddr060] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Damage to the optic nerve (e.g. from glaucoma) has an adverse and often irreversible impact on vision. Earlier studies have suggested that the size of the optic nerve head could be governed by hereditary factors. We conducted a genome-wide association study (GWAS) on 4445 Singaporean individuals (n = 2132 of Indian and n = 2313 of Malay ancestry, respectively), with replication in Rotterdam, the Netherlands (n = 9326 individuals of Caucasian ancestry) using the most widely reported parameter for optic disc traits, the optic disc area. We identified a novel locus on chromosome 22q13.1, CARD10, which strongly associates with optic disc area in both Singaporean cohorts as well as in the Rotterdam Study (RS; rs9607469, per-allele change in optic disc area = 0.051 mm(2); P(meta) = 2.73×10(-12)) and confirmed the association between CDC7/TGFBR3 (lead single nucleotide polymorphism (SNP) rs1192415, P(meta) = 7.57×10(-17)) and ATOH7 (lead SNP rs7916697, P(meta) = 2.00 × 10(-15)) and optic disc area in Asians. This is the first Asian-based GWAS on optic disc area, identifying a novel locus for the optic disc area, but also confirming the results found in Caucasian persons suggesting that there are general genetic determinants applicable to the size of the optic disc across different ethnicities.
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Affiliation(s)
- Chiea Chuen Khor
- Infectious Diseases, Genome Institute of Singapore, A*STAR, Singapore
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Lee KS, Lai YL, Lo S, Barkham T, Aw P, Ooi PL, Tai JC, Hibberd M, Johansson P, Khoo SP, Ng LC. Dengue virus surveillance for early warning, Singapore. Emerg Infect Dis 2010; 16:847-9. [PMID: 20409381 PMCID: PMC2953985 DOI: 10.3201/eid1605.091006] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In Singapore, after a major outbreak of dengue in 2005, another outbreak occurred in 2007. Laboratory-based surveillance detected a switch from dengue virus serotype 1 (DENV-1) to DENV-2. Phylogenetic analysis showed a clade replacement within DENV-2 cosmopolitan genotype, which accompanied the predominant serotype switch, and cocirculation of multiple genotypes of DENV-3.
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Ooi PL, Lai FYL, Low CL, Lin R, Wong C, Hibberd M, Tambyah PA. Clinical and molecular evidence for transmission of novel influenza A(H1N1/2009) on a commercial airplane. ACTA ACUST UNITED AC 2010; 170:913-5. [PMID: 20498421 DOI: 10.1001/archinternmed.2010.127] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Thuong NTT, Dunstan SJ, Chau TTH, Thorsson V, Simmons CP, Quyen NTH, Thwaites GE, Thi Ngoc Lan N, Hibberd M, Teo YY, Seielstad M, Aderem A, Farrar JJ, Hawn TR. Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles. PLoS Pathog 2008; 4:e1000229. [PMID: 19057661 PMCID: PMC2585058 DOI: 10.1371/journal.ppat.1000229] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [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: 04/03/2008] [Accepted: 11/05/2008] [Indexed: 11/18/2022] Open
Abstract
Although host genetics influences susceptibility to tuberculosis (TB), few genes determining disease outcome have been identified. We hypothesized that macrophages from individuals with different clinical manifestations of Mycobacterium tuberculosis (Mtb) infection would have distinct gene expression profiles and that polymorphisms in these genes may also be associated with susceptibility to TB. We measured gene expression levels of >38,500 genes from ex vivo Mtb-stimulated macrophages in 12 subjects with 3 clinical phenotypes: latent, pulmonary, and meningeal TB (n = 4 per group). After identifying differentially expressed genes, we confirmed these results in 34 additional subjects by real-time PCR. We also used a case-control study design to examine whether polymorphisms in differentially regulated genes were associated with susceptibility to these different clinical forms of TB. We compared gene expression profiles in Mtb-stimulated and unstimulated macrophages and identified 1,608 and 199 genes that were differentially expressed by >2- and >5-fold, respectively. In an independent sample set of 34 individuals and a subset of highly regulated genes, 90% of the microarray results were confirmed by RT-PCR, including expression levels of CCL1, which distinguished the 3 clinical groups. Furthermore, 6 single nucleotide polymorphisms (SNPs) in CCL1 were found to be associated with TB in a case-control genetic association study with 273 TB cases and 188 controls. To our knowledge, this is the first identification of CCL1 as a gene involved in host susceptibility to TB and the first study to combine microarray and DNA polymorphism studies to identify genes associated with TB susceptibility. These results suggest that genome-wide studies can provide an unbiased method to identify critical macrophage response genes that are associated with different clinical outcomes and that variation in innate immune response genes regulate susceptibility to TB.
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Affiliation(s)
- Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Sarah J. Dunstan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- * E-mail:
| | | | - Vesteinn Thorsson
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Cameron P. Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Nguyen Than Ha Quyen
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- Centre for Molecular Microbiology and Infection, Imperial College, London, United Kingdom
| | - Nguyen Thi Ngoc Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Martin Hibberd
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore
| | - Yik Y. Teo
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Mark Seielstad
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore
| | - Alan Aderem
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Jeremy J. Farrar
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Thomas R. Hawn
- University of Washington School of Medicine, Seattle, Washington, United States of America
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Cheung WK, Sia LL, Hibberd M, Pearse S, Woodward DL, Desjardins RE, Bernstein J, Yacobi A, Silber BM. Pharmacokinetics of Nilvadipine After Multiple Oral Dosing to Steady-State. Drug Dev Ind Pharm 2008. [DOI: 10.3109/03639048909040196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Nejentsev S, Thye T, Szeszko JS, Stevens H, Balabanova Y, Chinbuah AM, Hibberd M, van de Vosse E, Alisjahbana B, van Crevel R, Ottenhoff THM, Png E, Drobniewski F, Todd JA, Seielstad M, Horstmann RD. Analysis of association of the TIRAP (MAL) S180L variant and tuberculosis in three populations. Nat Genet 2008; 40:261-2; author reply 262-3. [DOI: 10.1038/ng0308-261] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Lundin A, Bok CM, Aronsson L, Björkholm B, Gustafsson JA, Pott S, Arulampalam V, Hibberd M, Rafter J, Pettersson S. Gut flora, Toll-like receptors and nuclear receptors: a tripartite communication that tunes innate immunity in large intestine. Cell Microbiol 2007; 10:1093-103. [PMID: 18088401 DOI: 10.1111/j.1462-5822.2007.01108.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Separating the large intestine from gut flora is a robust layer of epithelial cells. This barrier is armed with an array of recognizing receptors that collectively set the host innate response. Here, we use nuclear receptors (NRs) and Toll-like receptors (TLRs), suggested to act as second messengers in the communication between microorganisms and epithelial cells, as probes to assess the impact of gut flora on innate immunity in germ-free (GF) mice. Using quantitative real-time polymerase chain reaction analyses, we show that 37/49 NRs are expressed in colonic cells of GF mice. Of these, 5 can be modulated by resident flora: LXRalpha, RORgamma and CAR show reduced expression and Nur77 and GCNF display elevated expression in conventionally raised mice compared with GF. Moreover, increased expression levels of TLR-2 and TLR-5 are observed in specific pathogen-free (SPF) mice compared with GF mice, and CAR expression is connected to the TLR-2 signalling pathway. Infections of GF or SPF mice with Yersinia pseudotuberculosis, show that GF intestinal epithelial cells fail to respond, except for CAR, which is downregulated. In contrast, SPF epithelial cells show a downregulation of all the NRs except CAR, which appears to be unaffected. Our findings indicate that gut flora contributes to the development of an intact barrier function.
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Affiliation(s)
- Annelie Lundin
- Department of Microbiology, Cell and Tumor Biology, Karolinska Institutet, Stockholm 171 77, Sweden
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Lim CA, Yao F, Wong JJY, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J, Shahab A, Zhao XD, Hibberd M, Wei CL, Lim B, Ng HH, Ruan Y, Chin KC. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell 2007; 27:622-35. [PMID: 17707233 DOI: 10.1016/j.molcel.2007.06.038] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 05/04/2007] [Accepted: 06/25/2007] [Indexed: 12/18/2022]
Abstract
NF-kappaB is a key mediator of inflammation. Here, we mapped the genome-wide loci bound by the RELA subunit of NF-kappaB in lipopolysaccharide (LPS)-stimulated human monocytic cells, and together with global gene expression profiling, found an overrepresentation of the E2F1-binding motif among RELA-bound loci associated with NF-kappaB target genes. Knockdown of endogenous E2F1 impaired the LPS inducibility of the proinflammatory cytokines CCL3(MIP-1alpha), IL23A(p19), TNF-alpha, and IL1-beta. Upon LPS stimulation, E2F1 is rapidly recruited to the promoters of these genes along with p50/RELA heterodimer via a mechanism that is dependent on NF-kappaB activation. Together with the observation that E2F1 physically interacts with p50/RELA in LPS-stimulated cells, our findings suggest that NF-kappaB recruits E2F1 to fully activate the transcription of NF-kappaB target genes. Global gene expression profiling subsequently revealed a spectrum of NF-kappaB target genes that are positively regulated by E2F1, further demonstrating the critical role of E2F1 in the Toll-like receptor 4 pathway.
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Affiliation(s)
- Ching-Aeng Lim
- Laboratory of Immunology and Virology, Genome Institute of Singapore, 138672 Singapore
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Kampmann B, Hemingway C, Stephens A, Davidson R, Goodsall A, Anderson S, Nicol M, Schölvinck E, Relman D, Waddell S, Langford P, Sheehan B, Semple L, Wilkinson KA, Wilkinson RJ, Ress S, Hibberd M, Levin M. Acquired predisposition to mycobacterial disease due to autoantibodies to IFN-gamma. J Clin Invest 2005; 115:2480-8. [PMID: 16127458 PMCID: PMC1190367 DOI: 10.1172/jci19316] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Accepted: 06/21/2005] [Indexed: 11/17/2022] Open
Abstract
Genetic defects in the IFN-gamma response pathway cause unique susceptibility to intracellular pathogens, particularly mycobacteria, but are rare and do not explain mycobacterial disease in the majority of affected patients. We postulated that acquired defects in macrophage activation by IFN-gamma may cause a similar immunological phenotype and thus explain the occurrence of disseminated intracellular infections in some patients without identifiable immune deficiency. Macrophage activation in response to IFN-gamma and IFN-gamma production were studied in whole blood and PBMCs of 3 patients with severe, unexplained nontuberculous mycobacterial infection. In all 3 patients, IFN-gamma was undetectable following mitogen stimulation of whole blood, but significant quantities were detectable in the supernatants of PBMCs when stimulated in the absence of the patients' own plasma. The patients' plasma inhibited the ability of IFN-gamma to increase production of TNF-alpha by both autologous and normal donor PBMCs, and recovery of exogenous IFN-gamma from the patients' plasma was greatly reduced. Using affinity chromatography, surface-enhanced laser desorption/ionization mass spectrometry, and sequencing, we isolated an IFN-gamma-neutralizing factor from the patients' plasma and showed it to be an autoantibody against IFN-gamma. The purified anti-IFN-gamma antibody was shown to be functional first in blocking the upregulation of TNF-alpha production in response to endotoxin; second in blocking induction of IFN-gamma-inducible genes (according to results of high-density cDNA microarrays); and third in inhibiting upregulation of HLA class II expression on PBMCs. Acquired defects in the IFN-gamma pathway may explain unusual susceptibility to intracellular pathogens in other patients without underlying, genetically determined immunological defects.
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Affiliation(s)
- Beate Kampmann
- Department of Paediatrics and Wellcome Centre for Clinical Tropical Medicine, Imperial College London, London, United Kingdom
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Dolly S, Haralambous E, Levin M, Hibberd M. Association and linkage of the factor H NFκB responsive element polymorphism with susceptibility to meningococcal disease. J Infect 2002. [DOI: 10.1016/s0163-4453(02)90280-x] [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] [Indexed: 10/27/2022]
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Von Keitz AT, Ströberg P, Bukofzer S, Mallard N, Hibberd M. A European multicentre study to evaluate the tolerability of apomorphine sublingual administered in a forced dose-escalation regimen in patients with erectile dysfunction. BJU Int 2002; 89:409-15. [PMID: 11872034 DOI: 10.1046/j.1464-4096.2001.01453.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine the risk-benefit ratio of a forced dose-escalation regimen (2 to 3 to 4 mg) in a European clinical study evaluating apomorphine sublingual (SL) in treating erectile dysfunction (ED), by evaluating the overall tolerability and efficacy of the regimen compared with placebo in patients with ED, and evaluating efficacy by assessing the proportion of successful attempts resulting in sexual intercourse. PATIENTS AND METHODS This randomized, double-blind, two-arm, parallel-group study was conducted in 507 patients enrolled at 34 European sites. After a 1-2 week screening period, patients were treated for 8 weeks with either placebo or apomorphine SL administered as a forced dose-escalation regimen. Heterosexual men (aged 18-70 years) were eligible for participation in the study if they were in stable health, a stable relationship of > or = 6 months duration, had a history of erectile inability, and were diagnosed with ED (successful in fewer than half of attempts to attain and maintain an erection firm enough for intercourse during the 30 days before screening). Patients provided information (recorded on diary cards and reviewed at each study visit) about the frequency and success in achieving erections and of sexual intercourse attempts during both the screening and treatment periods. The dosing regimen required patients to take one tablet of apomorphine SL (2 mg for 2 weeks, then 3 mg for 2 weeks and finally 4 mg for the remaining 4 weeks) or placebo 15-25 min before intercourse, and intercourse was to be attempted at least twice a week. Safety data were collected throughout the 8-week study period, and included recording adverse events, vital signs and changes in laboratory test values for standard haematology and biochemistry variables. The primary efficacy variable was the proportion of successful attempts, defined as an erection rigid enough for sexual intercourse, occurring after dosing (successful intercourse rate). The proportion of erections achieved was a secondary efficacy variable. RESULTS Of the 507 patients, 254 received apomorphine SL and 253 received placebo; 87% of patients in both groups completed the 8-week treatment period. Of the patients receiving apomorphine SL, 24% had hypertension, 11% had coronary artery disease, 10% had diabetes, and 5.5% had benign prostatic hypertrophy; 62.6% of treated patients received concomitant medications for these maladies. The treatment groups were balanced for demographic and baseline variables, including comorbidity factors. Treatment-emergent adverse events, reported by > 5% of patients in the treated group, were nausea (9.8%), dizziness (7.1%) and headache (6.7%), compared with 0.4%, 2.4% and 4.0%, respectively, in the placebo group. Sixty-six patients withdrew from the study, 16 because of study drug-related adverse events (12 from the apomorphine and four from the placebo group). Six patients (three in each group) reported a total of nine serious treatment-emergent adverse events, all of which resolved by the end of the study. In the intention-to-treat population, the proportion of successful attempts at sexual intercourse and of erections were statistically greater in the apomorphine than in the placebo group (P = 0.001 and 0.021, respectively); analysis of the per-protocol population results confirmed this significant difference. CONCLUSION This European study supports the safety and tolerability of apomorphine SL despite the forced escalation to a 4-mg dose (exceeding the approved 2-3 mg dose). Adverse effects were not treatment-limiting. These results further support the clinically significant efficacy of apomorphine SL for treating ED at all doses used. The risk/benefit ratio supports apomorphine SL as a safe and effective alternative in managing ED.
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Hosangady A, Haralambous E, Levin M, Hibberd M. The role of E-selectin polymorphism S128R in meningococcal disease. J Infect 2002. [DOI: 10.1016/s0163-4453(02)90360-9] [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] [Indexed: 10/27/2022]
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Pollard AJ, Galassini R, Rouppe van der Voort EM, Hibberd M, Booy R, Langford P, Nadel S, Ison C, Kroll JS, Poolman J, Levin M. Cellular immune responses to Neisseria meningitidis in children. Infect Immun 1999; 67:2452-63. [PMID: 10225908 PMCID: PMC115991 DOI: 10.1128/iai.67.5.2452-2463.1999] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/1998] [Accepted: 02/05/1999] [Indexed: 11/20/2022] Open
Abstract
There is an urgent need for effective vaccines against serogroup B Neisseria meningitidis. Current experimental vaccines based on the outer membrane proteins (OMPs) of this organism provide a measure of protection in older children but have been ineffective in infants. We postulated that the inability of OMP vaccines to protect infants might be due to age-dependent defects in cellular immunity. We measured proliferation and in vitro production of gamma interferon (IFN-gamma), tumor necrosis factor alpha, and interleukin-10 (IL-10) in response to meningococcal antigens by peripheral blood mononuclear cells (PBMCs) from children convalescing from meningococcal disease and from controls. After meningococcal infection, the balance of cytokine production by PBMCs from the youngest children was skewed towards a TH1 response (low IL-10/IFN-gamma ratio), while older children produced more TH2 cytokine (higher IL-10/IFN-gamma ratio). There was a trend to higher proliferative responses by PBMCs from older children. These responses were not influenced by the presence or subtype of class 1 (PorA) OMP or by the presence of class 2/3 (PorB) or class 4 OMP. Even young infants might be expected to develop adequate cellular immune responses to serogroup B N. meningitidis vaccines if a vaccine preparation can be formulated to mimic the immune stimulus of invasive disease, which may include stimulation of TH2 cytokine production.
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Affiliation(s)
- A J Pollard
- Departments of Paediatrics and Infectious Diseases & Microbiology, Imperial College School of Medicine, St. Mary's Hospital, London W2 1PG, United Kingdom.
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Wong S, Wen L, Hibberd M, Millward A, Demaine A. Analysis of the peripheral T-cell receptor V beta repertoire in newly diagnosed patients with type I diabetes. Autoimmunity 1994; 18:77-83. [PMID: 7999959 DOI: 10.3109/08916939409014682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Type I diabetes is an autoimmune disease characterised by a marked activation of peripheral T cells around the time of clinical diagnosis. Studies of T-cell antigen receptor V beta (TCRBV) gene usage in type I diabetes have been conflicting. Using a semi-quantitative polymerase chain reaction technique and flow cytometry we have investigated the TCRBV gene usage of 13 newly diagnosed patients with type I diabetes and 11 normal healthy controls. No preferential TCRBV gene usage was found between patients and controls even after matching for HLA-DR3 and/or -DR4. In addition, no significant differences in TCRBV gene usage were found between sequential samples taken over a period of up to 7 months following diagnosis. These results suggest that the TCR repertoire of these patients is heterogeneous and it is unlikely that a single 'pathogenic' T-cell clone is dominant at the clinical onset of the disease.
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Affiliation(s)
- S Wong
- Department of Medicine, University of Plymouth, England
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Coles NA, Hibberd M, Russell M, Love T, Ory D, Field TS, Dec GW, Eagle KA. Potential impact of pulmonary artery catheter placement on short-term management decisions in the medical intensive care unit. Am Heart J 1993; 126:815-9. [PMID: 8213436 DOI: 10.1016/0002-8703(93)90693-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The purpose of this study was to examine the potential impact of pulmonary artery (PA) catheter placement on short-term management decisions in the medical intensive care unit (ICU). One hundred three patients were examined over an 18-month period. The predominant indications for PA-catheter placement included refractory congestive heart failure, airspace disease, uncertain cardiac filling pressures, or hypotension. In 58 (56%) of the 103 patients, management recommendations changed as a direct result of knowledge gained by PA catheter placement. These changes involved fluid therapy recommendations in 41 patients, vasopressor use in 17 patients, intravenous vasodilator use in 24 patients, and recommendations for the use of inotropic agents in 15 patients. Although 18 patients experienced early or late complications, major events were limited to a single pneumothorax requiring chest tube insertion and four episodes of bacteremia. No deaths were directly attributable to the catheter insertion. In critically ill patients in the medical intensive care unit, PA-catheter placement leads to changes in recommendations for management in a substantial portion of patients with little risk of life-threatening complications in those who receive such invasive monitoring.
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Affiliation(s)
- N A Coles
- Cardiac Unit, Massachusetts General Hospital, Boston 02114
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