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Xu L, He Q, Tang Y, Wen W, Chen L, Li Y, Yi C, Fu B. Multi‑locus sequence and drug resistance analysis of Salmonella infection in children with diarrhea in Guangdong to identify the dominant ST and cause of antibiotic‑resistance. Exp Ther Med 2022; 24:678. [PMID: 36337293 PMCID: PMC9623445 DOI: 10.3892/etm.2022.11614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/08/2022] [Indexed: 02/05/2023] Open
Abstract
Multi-locus sequence typing (MLST) can be used to analyze the homology among the drug resistance gene cassettes in Salmonella and determine the prevalence. Information extracted using this technique can provide a theoretical basis for hospitals to devise protocols to control Salmonella infections. The aim of the present study was to investigate the possible association between drug resistance and integrons in clinical isolates of Salmonella from human fecal samples. Therefore, in the present study, 52 clinical fecal isolates of non-duplicate (i.e., not genome contamination) Salmonella were harvested from children with diarrhea and used for bacterial identification using biochemical tests, drug susceptibility analysis by antibiotic susceptibility testing and serotype identification using an agglutination assay. In total, seven Salmonella housekeeping genes (chorismate synthase, β sliding clamp of DNA polymerase III, uroporphyrinogen-III synthase, histidinol dehydrogenase, phosphoribosylaminoimidazole carboxylase catalytic subunit, 2-oxoglutarate dehydrogenase E1 component and homoserine dehydrogenase) were amplified and sequenced using MLST, before sequence alignment was performed against the Pub MLST database to determine the sequence-typed (ST) strains and construct genotypic evolutionary diagrams. Subsequently, the 52 Salmonella strains were subdivided into 11 serotypes and 11 sequence types. The dominant subtypes were found to be Salmonella typhimurium ST34 and ST19, which were diversely distributed. However, no new subtypes were found. Although the serotypes, including ST19, ST29, ST34, ST40, ST11, ST27, ST469, ST365, ST1499, ST413 and ST588, were closely associated with the MLST subtype, they did not correspond entirely. The detection rate of class I integrons was 38.46% (20/52), but no class II and III integrons were detected. The variable regions of three of 20 class I integrons were found to be amplified, whereas nine gene cassettes, including dihydrofolate reductase A12, open reading frame F, aminoglycoside-adenylyltransferase (aad)A2, aadA22, aadA23, aadA1, cadmium-translocating P-type ATPase 2, lincosamide and linF, were associated with drug resistance. These data suggest that Class I integrons are important factors underlying drug resistance in Salmonella, which may serve a role in the spread of drug resistance and warrant specific focus. In addition, MLST typing and serotyping should be applied cooperatively in epidemiological research.
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Affiliation(s)
- Lingqing Xu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
| | - Qianjun He
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
| | - Yinxian Tang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
| | - Weihong Wen
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
| | - Linjuan Chen
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
| | - Yuzhen Li
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
| | - Changhong Yi
- Department of Interventional Radiology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong 515000, P.R. China
| | - Bishi Fu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, P.R. China
- Department of Microbiology, School of Basic Medical Sciences, Guangzhou Medical University, Panyu, Guangzhou, Guangdong 511436, P.R. China
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Zhang SX, Zhou YM, Tian LG, Chen JX, Tinoco-Torres R, Serrano E, Li SZ, Chen SH, Ai L, Chen JH, Xia S, Lu Y, Lv S, Teng XJ, Xu W, Gu WP, Gong ST, Zhou XN, Geng LL, Hu W. Antibiotic resistance and molecular characterization of diarrheagenic Escherichia coli and non-typhoidal Salmonella strains isolated from infections in Southwest China. Infect Dis Poverty 2018; 7:53. [PMID: 29792233 PMCID: PMC5964730 DOI: 10.1186/s40249-018-0427-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 04/18/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Bacterial diarrhea is one of the most common causes for medical consultations, mortality and morbidity in the world. Diarrheagenic Escherichia coli (DEC) and non-typhoidal Salmonella (NTS) are major intestinal pathogens in developing countries, and the indiscriminate use of antibiotics has greatly contributed to resistant strains. Hence, the aim of the present study is to identify the antimicrobial resistance patterns and the molecular characteristics of DEC and NTS in southwest, China. METHODS 1121 diarrheal patients and 319 non-diarrheal subjects across all age groups were recruited from four sentinel hospitals from June 2014 to July 2015 in Kunming City, Yunnan Province. Each stool specimen was collected to detect DEC and NTS with standard microbiological and molecular methods. Antimicrobial resistance testing was performed with the Kirby-Bauer disk diffusion method, and the standards for antimicrobial susceptibility testing complied with the Clinical and Laboratory Standards Institute (CLSI). Molecular characterization of strains was carried out using pulsed-field gel electrophoresis (PFGE). A structured questionnaire was used to record basic epidemiological data (e.g. sex, age, residence, season, etc.). Data were analyzed using Chi-square or Fisher's exact test. RESULTS DEC was detected in 127 (11.33%) diarrhea cases and 9 (2.82%) non-diarrheal cases (χ2 = 20.69, P < 0.001, OR = 4.36, 95% CI: 2.19-8.65), and the prevalence of NTS isolated from diarrhea cases was higher than that of non-diarrheal cases across all age groups (n = 42, 3.75%, n = 1, 0.31%, χ2 = 10.10, P = 0.002, OR = 12.38, 95% CI: 1.70-90.29). The rates of resistance to ten antibiotics of DEC and NTS showed significant differences (χ 2 = 386.77, P < 0.001; χ2 = 191.16, P < 0.001). The rates of resistance to Amoxicillin and Clavulafiate (AMC), Cephalothin (CEP), Gentamicin (GEN) and Sulfamethoxazole-Trimethoprim (SXT) of DEC isolated from diarrhea cases were higher than those of NTS isolated from diarrhea patients (37.01% vs 14.29%, χ2 = 7.57, P = 0.006; 29.92% vs 11.90%, χ2 = 5.40, P = 0.02; 37.01% vs 11.90%, χ2 = 5.80, P = 0.016; 62.20% vs 26.19%, χ2 = 16.44, P < 0.001; respectively). Ciprofloxacin (CIP) was the most sensitive antibiotic for DEC and NTS strains isolated from diarrhea cases. Resistance rates of DEC isolates from cases and controls to more than three kinds antimicrobials (multidrug resistance, MDR) showed no significant differences (81.10% vs 88.89%, P = 0.33). Pulsotype patterns of DEC strains were highly diverse; however, the pulsotype pattern of NTS strains was closely related to the serotype. The pattern of S. enteritidis was highly similar, but the S. enterica Typhimurium strain was discrete. CONCLUSIONS Antibiotic resistance of Enterobacteriaceae is of great concern. The societal effects of antibiotic use justify strict monitoring to combat increases in antimicrobial resistance. Molecular epidemiology and systematic epidemiological investigation can provide accurate evidence for tracking the infection source.
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Affiliation(s)
- Shun-Xian Zhang
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China.,Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China
| | - Yong-Ming Zhou
- Yunnan Provincial Center for Disease Control and Prevention, Kunming, 650022, People's Republic of China
| | - Li-Guang Tian
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Jia-Xu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Rita Tinoco-Torres
- Department of Biology & CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Emmanuel Serrano
- Wildlife Ecology and Health group and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Shi-Zhu Li
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Shao-Hong Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Lin Ai
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Shang Xia
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Yan Lu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Shan Lv
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Xue-Jiao Teng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China
| | - Wen Xu
- Yunnan Provincial Center for Disease Control and Prevention, Kunming, 650022, People's Republic of China
| | - Wen-Peng Gu
- Yunnan Provincial Center for Disease Control and Prevention, Kunming, 650022, People's Republic of China
| | - Si-Tang Gong
- Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China. .,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China.
| | - Lan-Lan Geng
- Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China.
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China. .,Chinese Center for Tropical Diseases Research; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, 200025, People's Republic of China. .,Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China.
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Kuijpers LMF, Le Hello S, Fawal N, Fabre L, Tourdjman M, Dufour M, Sar D, Kham C, Phe T, Vlieghe E, Bouchier C, Jacobs J, Weill FX. Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013-2015. Microb Genom 2016; 2:e000092. [PMID: 28348832 PMCID: PMC5320704 DOI: 10.1099/mgen.0.000092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/05/2016] [Indexed: 01/01/2023] Open
Abstract
In 2013, an unusual increase in the number of Salmonella enterica serotype Paratyphi A (Salmonella Paratyphi A) infections was reported in patients in Phnom Penh, Cambodia, and in European, American and Japanese travellers returning from Cambodia. Epidemiological investigations did not identify a common source of exposure. To analyse the population structure and genetic diversity of these Salmonella Paratyphi A isolates, we used whole-genome sequencing on 65 isolates collected from 1999 to 2014: 55 from infections acquired in Cambodia and 10 from infections acquired in other countries in Asia, Africa and Europe. Short-read sequences from 80 published genomes from around the world and from 13 published genomes associated with an outbreak in China were also included. Pulsed-field gel electrophoresis (PFGE) was performed on a subset of isolates. Genomic analyses were found to provide much more accurate information for tracking the individual strains than PFGE. All but 2 of the 36 isolates acquired in Cambodia during 2013–2014 belonged to the same clade, C5, of lineage C. This clade has been isolated in Cambodia since at least 1999. The Chinese outbreak isolates belonged to a different clade (C4) and were resistant to nalidixic acid, whereas the Cambodian outbreak isolates displayed pan-susceptibility to antibiotics. Since 2014, the total number of cases has decreased, but there has been an increase in the frequency with which nalidixic acid-resistant C5 isolates are isolated. The frequency of these isolates should be monitored over time, because they display decreased susceptibility to ciprofloxacin, the first-choice antibiotic for treating paratyphoid fever.
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Affiliation(s)
- Laura Maria Francisca Kuijpers
- 1Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,2Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Simon Le Hello
- 3Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Nizar Fawal
- 3Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Laetitia Fabre
- 3Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
| | - Mathieu Tourdjman
- 4Santé Publique France, Direction des Maladies Infectieuses, Saint-Maurice, France
| | - Muriel Dufour
- 5Institute of Environmental Science and Research Limited, NCBID, Wallaceville, New Zealand
| | - Dara Sar
- 6Sihanouk Hospital Centre of HOPE, Phnom Penh, Cambodia
| | - Chun Kham
- 6Sihanouk Hospital Centre of HOPE, Phnom Penh, Cambodia
| | - Thong Phe
- 6Sihanouk Hospital Centre of HOPE, Phnom Penh, Cambodia
| | - Erika Vlieghe
- 1Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,7Department of Tropical Diseases, University Hospital Antwerp, Antwerp, Belgium
| | | | - Jan Jacobs
- 1Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,2Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - François-Xavier Weill
- 3Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France
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Smith AM, Tau N, Sooka A, Keddy KH, Germs-Sa Surveillance Network. Microbiological characterization of Salmonella enterica serotype Paratyphi, South Africa, 2003-2014. J Med Microbiol 2015; 64:1450-1453. [PMID: 26306409 DOI: 10.1099/jmm.0.000161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nomsa Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arvinda Sooka
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, Johannesburg, South Africa
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Kariuki S, Gordon MA, Feasey N, Parry CM. Antimicrobial resistance and management of invasive Salmonella disease. Vaccine 2015; 33 Suppl 3:C21-9. [PMID: 25912288 PMCID: PMC4469558 DOI: 10.1016/j.vaccine.2015.03.102] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 01/08/2023]
Abstract
Invasive Salmonella infections (typhoidal and non-typhoidal) cause a huge burden of illness estimated at nearly 3.4 million cases and over 600,000 deaths annually especially in resource-limited settings. Invasive non-typhoidal Salmonella (iNTS) infections are particularly important in immunosuppressed populations especially in sub-Saharan Africa, causing a mortality of 20-30% in vulnerable children below 5 years of age. In these settings, where routine surveillance for antimicrobial resistance is rare or non-existent, reports of 50-75% multidrug resistance (MDR) in NTS are common, including strains of NTS also resistant to flouroquinolones and 3rd generation cephalosporins. Typhoid (enteric) fever caused by Salmonella Typhi and Salmonella Paratyphi A remains a major public health problem in many parts of Asia and Africa. Currently over a third of isolates in many endemic areas are MDR, and diminished susceptibility or resistance to fluoroquinolones, the drugs of choice for MDR cases over the last decade is an increasing problem. The situation is particularly worrying in resource-limited settings where the few remaining effective antimicrobials are either unavailable or altogether too expensive to be afforded by either the general public or by public health services. Although the prudent use of effective antimicrobials, improved hygiene and sanitation and the discovery of new antimicrobial agents may offer hope for the management of invasive salmonella infections, it is essential to consider other interventions including the wider use of WHO recommended typhoid vaccines and the acceleration of trials for novel iNTS vaccines. The main objective of this review is to describe existing data on the prevalence and epidemiology of antimicrobial resistant invasive Salmonella infections and how this affects the management of these infections, especially in endemic developing countries.
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Affiliation(s)
- Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, PO Box 43640-00100, Nairobi, Kenya; The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
| | - Melita A Gordon
- Institute for Infection and Global Health, University of Liverpool, United Kingdom; Malawi Liverpool Wellcome Trust Clinical Research Programme, United Kingdom
| | - Nicholas Feasey
- Malawi Liverpool Wellcome Trust Clinical Research Programme, United Kingdom; Liverpool School of Tropical Medicine, United Kingdom
| | - Christopher M Parry
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 5HT, United Kingdom; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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