BMJ Global Health (Aug 2021)
The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries
- Gordon Dougan,
- Stephen Baker,
- Gi Deok Pak,
- Robert F Breiman,
- Justin Im,
- Ellis Owusu-Dabo,
- Jin Kyung Park,
- Se Eun Park,
- Mekonnen Teferi,
- Raphaël Rakotozandrindrainy,
- Florian Marks,
- Ursula Panzner,
- Mohammad Ali,
- Leonard Cosmas,
- Anna Jaeger,
- Abraham Aseffa,
- Barry Fields,
- Morten Bjerregaard-Andersen,
- John A Crump,
- Julian T Hertz,
- Jürgen May,
- Adama Tall,
- Yaw Adu-Sarkodie,
- Duy Thanh Pham,
- Ligia Maria Cruz Espinoza,
- Vera von Kalckreuth,
- Ondari D. Mogeni,
- Heidi Schütt-Gerowitt,
- Abdramane Bassiahi Soura,
- Nagla Gasmelseed,
- Arvinda Sooka,
- Karen H Keddy,
- Holly M Biggs,
- Joel M Montgomery,
- Beatrice Olack,
- Nimako Sarpong,
- Tsiriniaina Jean Luco Razafindrabe,
- Tiana Mirana Raminosoa,
- Leon Parfait Kabore,
- Emmanuel Sampo,
- Biruk Yeshitela,
- Muna Ahmed El Tayeb,
- Ralf Krumkamp,
- Denise Myriam Dekker,
- Amy Gassama,
- Aissatou Niang,
- Sandra Valborg Løfberg,
- Jessica Fung Deerin,
- Frank Konings,
- Megan E Carey,
- Sandra Van Puyvelde,
- John Clemens
Affiliations
- Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
- Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
- Gi Deok Pak
- International Vaccine Institute, Seoul, Republic of Korea
- Robert F Breiman
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
- Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
- Ellis Owusu-Dabo
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Jin Kyung Park
- International Vaccine Institute, Seoul, Republic of Korea
- Se Eun Park
- International Vaccine Institute, Seoul, Republic of Korea
- Mekonnen Teferi
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Raphaël Rakotozandrindrainy
- University of Antananarivo, Antananarivo, Madagascar
- Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Ursula Panzner
- International Vaccine Institute, Seoul, Republic of Korea
- Mohammad Ali
- International Vaccine Institute, Seoul, Republic of Korea
- Leonard Cosmas
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
- Anna Jaeger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Barry Fields
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
- Morten Bjerregaard-Andersen
- Bandim Health Project, Bissau, Guinea-Bissau
- John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Julian T Hertz
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA
- Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Adama Tall
- Institute Pasteur de Dakar, Dakar, Senegal
- Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Duy Thanh Pham
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Ligia Maria Cruz Espinoza
- International Vaccine Institute, Seoul, Republic of Korea
- Vera von Kalckreuth
- International Vaccine Institute, Seoul, Republic of Korea
- Ondari D. Mogeni
- International Vaccine Institute, Seoul, Republic of Korea
- Heidi Schütt-Gerowitt
- International Vaccine Institute, Seoul, Republic of Korea
- Abdramane Bassiahi Soura
- Institut Supérieur des Sciences de la Population, University of Ouagadougou, Ouagadougou, Burkina Faso
- Nagla Gasmelseed
- Faculty of Medicine, University of Gezira, Wad Medani, Sudan
- Arvinda Sooka
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Karen H Keddy
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Holly M Biggs
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina, USA
- Joel M Montgomery
- Centers for Disease Control and Prevention, KEMRI Complex, Nairobi, Kenya
- Beatrice Olack
- Kenya Medical Research Institute, Nairobi, Kenya
- Nimako Sarpong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Tsiriniaina Jean Luco Razafindrabe
- University of Antananarivo, Antananarivo, Madagascar
- Tiana Mirana Raminosoa
- University of Antananarivo, Antananarivo, Madagascar
- Leon Parfait Kabore
- Schiphra Hospital, Ouagadougou, Burkina Faso
- Emmanuel Sampo
- Schiphra Hospital, Ouagadougou, Burkina Faso
- Biruk Yeshitela
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Muna Ahmed El Tayeb
- Faculty of Medicine, University of Gezira, Wad Medani, Sudan
- Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Denise Myriam Dekker
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Amy Gassama
- Institute Pasteur de Dakar, Dakar, Senegal
- Aissatou Niang
- Institute Pasteur de Dakar, Dakar, Senegal
- Sandra Valborg Løfberg
- Bandim Health Project, Bissau, Guinea-Bissau
- Jessica Fung Deerin
- International Vaccine Institute, Seoul, Republic of Korea
- Frank Konings
- International Vaccine Institute, Seoul, Republic of Korea
- Megan E Carey
- Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
- Sandra Van Puyvelde
- Medicine, Cambridge University, Cambridge, UK
- John Clemens
- International Vaccine Institute, Seoul, Republic of Korea
- DOI
- https://doi.org/10.1136/bmjgh-2021-005659
- Journal volume & issue
-
Vol. 6,
no. 8
Abstract
Background Invasive non-typhoidal Salmonella (iNTS) is one of the leading causes of bacteraemia in sub-Saharan Africa. We aimed to provide a better understanding of the genetic characteristics and transmission patterns associated with multi-drug resistant (MDR) iNTS serovars across the continent.Methods A total of 166 iNTS isolates collected from a multi-centre surveillance in 10 African countries (2010–2014) and a fever study in Ghana (2007–2009) were genome sequenced to investigate the geographical distribution, antimicrobial genetic determinants and population structure of iNTS serotypes–genotypes. Phylogenetic analyses were conducted in the context of the existing genomic frameworks for various iNTS serovars. Population-based incidence of MDR-iNTS disease was estimated in each study site.Results Salmonella Typhimurium sequence-type (ST) 313 and Salmonella Enteritidis ST11 were predominant, and both exhibited high frequencies of MDR; Salmonella Dublin ST10 was identified in West Africa only. Mutations in the gyrA gene (fluoroquinolone resistance) were identified in S. Enteritidis and S. Typhimurium in Ghana; an ST313 isolate carrying blaCTX-M-15 was found in Kenya. International transmission of MDR ST313 (lineage II) and MDR ST11 (West African clade) was observed between Ghana and neighbouring West African countries. The incidence of MDR-iNTS disease exceeded 100/100 000 person-years-of-observation in children aged <5 years in several West African countries.Conclusions We identified the circulation of multiple MDR iNTS serovar STs in the sampled sub-Saharan African countries. Investment in the development and deployment of iNTS vaccines coupled with intensified antimicrobial resistance surveillance are essential to limit the impact of these pathogens in Africa.
