title: Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa.
abstract: BACKGROUND
  The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with Salmonella enterica serovar Typhi (S. Typhi) as an important cause of bacteremia in children.
  
  
  METHODS
  A total of 128 S. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance.
  
  
  RESULTS
  Several distinct S. Typhi genotypes were identified in Nigeria that were related to other clusters of S. Typhi isolates from north, west and central regions of Africa. The rapidly expanding S. Typhi clade 4.3.1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with S. Typhi.
  
  
  CONCLUSIONS
  These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid.
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authors.initials: VK
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authors.affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.|Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.|Addenbrooke's Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom.
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authors.affiliation: 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, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom.|Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
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authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
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authors.affiliation: Department of Medical Microbiology, Aminu Kano Teaching Hospital, Kano, Nigeria.
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authors.affiliation: Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.
authors.forename: Roxanne
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authors.affiliation: Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.
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authors.affiliation: Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom.
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authors.affiliation: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France.
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authors.affiliation: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France.
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authors.affiliation: Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.|Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.|Emory Global Health Institute, Atlanta, Georgia, United States of America.
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authors.affiliation: Institute of Infection and Global Health, University of Liverpool, United Kingdom.|Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi.
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authors.initials: MA
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authors.affiliation: Malawi-Liverpool-Wellcome-Trust Clinical Research Programme, College of Medicine, University of Malawi, Chichiri, Blantyre, Malawi.|Division of Infection and Immunity, University College London, London, United Kingdom.
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authors.affiliation: Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.|KU Leuven, University of Leuven, Department of Microbiology and Immunology, Belgium.
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authors.affiliation: National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo.|University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo.
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authors.affiliation: Division of Infection and Immunity, University College London, London, United Kingdom.|Microbiology Department, College of Medicine, University of Malawi, Malawi.
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authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.|Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.|The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
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authors.affiliation: Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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authors.affiliation: Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
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authors.affiliation: Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.|University of Abuja Teaching Hospital, Gwagwalada, Nigeria.|Bingham University, Karu, Nassarawa State, Nigeria.
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