Dataset Information

Genomic analysis of the emergence of 20th century epidemic dysentery.

ABSTRACT: BACKGROUND:Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is complicated by the rapid emergence of antibiotic resistant Sd1 strains. Sd1 is only detected in the context of human infections, and the circumstances under which epidemics emerge and regress remain unknown. RESULTS:Phylogenomic analyses of 56 isolates collected worldwide over the past 60 years indicate that the Sd1 clone responsible for the recent pandemics emerged at the turn of the 20th century, and that the two world wars likely played a pivotal role for its dissemination. Several lineages remain ubiquitous and their phylogeny indicates several recent intercontinental transfers. Our comparative genomics analysis reveals that isolates responsible for separate outbreaks, though closely related to one another, have independently accumulated antibiotic resistance genes, suggesting that there is little or no selection to retain these genes in-between outbreaks. The genomes appear to be subjected to genetic drift that affects a number of functions currently used by diagnostic tools to identify Sd1, which could lead to the potential failure of such tools. CONCLUSIONS:Taken together, the Sd1 population structure and pattern of evolution suggest a recent emergence and a possible human carrier state that could play an important role in the epidemic pattern of infections of this human-specific pathogen. This analysis highlights the important role of whole-genome sequencing in studying pathogens for which epidemiological or laboratory investigations are particularly challenging.

SUBMITTER: Rohmer L

PROVIDER: S-EPMC4038718 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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Genomic analysis of the emergence of 20th century epidemic dysentery.

Rohmer Laurence L Jacobs Michael A MA Brittnacher Mitchell J MJ Fong Christine C Hayden Hillary S HS Hocquet Didier D Weiss Eli J EJ Radey Matthew M Germani Yves Y Talukder Kaisar Ali KA Hager Anthony J AJ Kemner John M JM Sims-Day Elizabeth H EH Matamouros Susana S Hager Kyle R KR Miller Samuel I SI

BMC genomics 20140510

<h4>Background</h4>Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is complicated by the rapid emergence of antibiotic resistant Sd1 strains. Sd1 is only detected in the context of human infections, and the circumstances under which epidemics emerge and regress remain unknown.<h4>Results</h4>Phylogenomic analyses of 56 isolates collected w ...[more]

PMID: 24886041

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Project description:The four mosquito-borne dengue virus serotypes (DENV1-DENV4) cause a high burden of disease throughout the tropical and sub-tropical regions of the world. Nevertheless, their precise epidemiological history in Africa, including when and where they originated and were distributed during the 20th century, remains unclear stressing the need for One Health focused research. Accordingly, we conducted a time-scaled molecular epidemiological reconstruction using publicly available and newly sequenced dengue virus genomes of African origin representing all four serotypes to deduce the most likely temporal and spatial transmission routes of each DENV serotype from their ancestral regions to, within and from Africa. Our analyses suggest that during the 20th century, serotypes DENV1-DENV3 were introduced to Africa from South East Asia on multiple occasions. The earliest evidence recorded indicates introduction of DENV2 during the early-1940s and of DENV1 during the mid-1940s to Western Africa from South East Asia. The analysis also implies an early introduction of DENV4 during the mid-1940s to Western Africa, alongside DENV1, probably originating in South East Asia. Establishment of DENV3 in Africa appears to have occurred later in the 1960s, apparently originating from South East Asia. However, with the re-establishment of DENV in the Americas, following the cessation of the PAHO mosquito control programme during the mid-20th century, evidence of introductions of DENV1 and DENV2 from the Americas to Western Africa was also observed. The data also identify intra-regional circulation of DENV, but also inter-regional dispersal of all four serotypes within Africa, which has led to a high degree of geographical overlap among serotypes. It is also noteworthy that DENV from both Eastern and Western Africa, have been introduced into Central Africa but there is no support for the converse relationship. For serotypes DENV1-DENV3, we observed probable exports from within established African DENV clusters (≥2 sequences) primarily to Eastern and Southern Asia. Collectively, our findings support the view that all DENV serotypes, apart from DENV4, have been introduced on multiple occasions to Africa, primarily originating from South East Asia, and subsequently to neighbouring regions within Africa.

Project description:Objectives: Between the 1980s and 2000s, an epidemic of silicosis was identified in migrant black gold miners, many from neighbouring countries, who had worked in the South African gold mines. This study uses the newly available employment database of a large gold mining company to demonstrate how a sustained rise in employment duration in a new cohort of black migrant workers resulted from changes in recruitment policy, and it examines the implications for current surveillance and redress. Methods: Contract data of 300,774 workers from the employment database of a multi-mine gold mining company were analysed for 1973–2018. Piecewise linear regression was applied to determine trends in cumulative employment, including South African versus cross-border miners. The proportions with cumulative employment of at least 10, 15, or 20 years, typical thresholds for chronic silicosis, were also calculated. Results: Five calendar phases were identified between 1973 and 2018. During the second phase, 1985–2013, mean cumulative duration of employment rose fivefold, from 4 to 20 years. Cumulative employment continued to rise, although more slowly, before peaking in 2014 at 23.5 years and falling thereafter to 20.1 years in 2018. Over most of the 1973–2018 period, miners from neighbouring countries had greater cumulative employment than South African miners. Overall, the proportion of miners exiting with at least 15 years of cumulative employment rose from 5% in 1988 to 75% in 2018. This report identifies a number of fundamental changes in labour recruitment policy in the gold mining industry in the 1970s which provide an explanation for the subsequent rise in cumulative exposure and associated silicosis risk. Conclusions: These new data support the hypothesis of a silicosis epidemic driven by increasing cumulative silica dust exposure in a new cohort of circular migrant workers from the 1970s. They inform current programmes to improve surveillance of this neglected population for silicosis and related disease and to provide medical examinations and compensation to a large number of former gold mines. The analysis highlights the lack of information on cumulative employment and silicosis risk among migrant miners in previous decades. The findings have global relevance to the plight of such migrant workers in hazardous occupations.

Dataset Information

Genomic analysis of the emergence of 20th century epidemic dysentery.

Publications

Genomic analysis of the emergence of 20th century epidemic dysentery.

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