Whole_genome_sequencing_of_Shigella_and_Salmonella_Typhi_from_Papua_New_Guinea-sc-4269
Whole_genome_sequencing_of_Shigella_and_Salmonella_Typhi_from_Papua_New_Guinea
Papua New Guinea (PNG) is the largest of the 'Pacific Island' nations, with a population of approximately 7 million people. PNG has a high burden of infectious diseases, including gastrointestinal diseases. We seek to conduct whole genome sequencing on isolates of Shigella and Salmonella Typhi from PNG, in order to investigate local population structure and patterns of local and regional transfer (by comparison with existing and developing global and regional genome collections). We also aim to identify the genetic determinants and evolution of antibiotic resistance in the PNG pathogen populations. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Gastrointestinal infections remain one of the leading causes of morbidity and mortality in Papua New Guinea (PNG). Shigellosis, along with rotavirus infection, is a leading cause of hospitalization in children with acute watery diarrhoea. The burden of shigellosis in adults in also appreciable, with culture confirmed shigellosis accounting for 28% of adult presentations to health clinics and hospital outpatients with diarrhoea/dystenery in our study site in the highlands of PNG. In addition to endemic disease, large outbreaks have been reported in PNG in recent years. The most commonly isolated species of Shigella is S. flexneri, with rare cases of illness due to S. dysenteriae, S. sonneii and S. boydi.   The burden of typhoid fever in PNG was once amongst the highest in the world. Up-to-date incidence data are lacking in PNG; however, as a clinical diagnosis the disease remains common in this setting. Salmonella Typhi is the leading cause of typhoid (enteric) fever in PNG. S. Paratyphi is rarely isolated, while historically a small number of cases were linked to S. Choleraesuis.  Beyond these basic species distributions, very little is known about the population structure of circulating strains of Shigella or S. Typhi, or how these relate to global pathogen populations. It is expected that the majority of disease comes from locally adapted clones, however the frequency of pathogen transfer into and out of PNG is unknown.  Antimicrobial resistance is increasingly common amongst Shigella isolates from PNG, however the spectrum of antibiotics appears to be different from the patterns commonly reported in the region. Resistance to amoxicillin, chloramphenicol, co-trimoxazole and tetracycline is common in PNG isolates, perhaps reflecting their widespread use in PNG. However, resistance to fluoroquinolones, macrolides and cephalosporins is rare in Shigella, despite the recent rise of resistance to these antibiotics in Shigella and other clinically important bacteria in other global settings. A similar trend appears to be emerging for S. Typhi, with a small number of recent isolates showing comparable antimicrobial resistance patterns as Shigella isolated from the same setting in PNG.   Here we propose to whole genome sequence both recent and historic isolate collections of Shigella and Salmonella Typhi from PNG, in order to investigate local population structure and patterns of local and regional transfer (by comparison with existing and developing global and regional genome collections). We also aim to identify the genetic determinants and evolution of antibiotic resistance in the PNG pathogen populations.