Oxford University Clinical Research Unit

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. Results for the final phase of the 1000 Genomes Project are presented including whole-genome sequencing, targeted exome sequencing, and genotyping on high-density SNP arrays for 2,504 individuals across 26 populations, providing a global reference data set to support biomedical genetics. The 1000 Genomes Project has sought to comprehensively catalogue human genetic variation across populations, providing a valuable public genomic resource. The data obtained so far have found applications ranging from association studies and fine mapping studies to the filtering of likely neutral variants in rare-disease cohorts. The authors now report on the final phase of the project, phase 3, which covers previously uncharacterized areas of human genetic diversity in terms of the populations sampled and categories of characterized variation. The sample now includes more than 2,500 individuals from 26 global populations, with low coverage whole-genome and deep exome sequencing, as well as dense microarray genotyping. They find that while most common variants are shared across populations, rarer variants are often restricted to closely related populations. The authors also demonstrate the use of the phase 3 dataset as a reference panel for imputation to improve the resolution in genetic association studies.

IMPORTANCE: Cancer is among the leading causes of death worldwide. Current estimates of cancer burden in individual countries and regions are necessary to inform local cancer control strategies. OBJECTIVE: To estimate mortality, incidence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 28 cancers in 188 countries by sex from 1990 to 2013. EVIDENCE REVIEW: The general methodology of the Global Burden of Disease (GBD) 2013 study was used. Cancer registries were the source for cancer incidence data as well as mortality incidence (MI) ratios. Sources for cause of death data include vital registration system data, verbal autopsy studies, and other sources. The MI ratios were used to transform incidence data to mortality estimates and cause of death estimates to incidence estimates. Cancer prevalence was estimated using MI ratios as surrogates for survival data; YLDs were calculated by multiplying prevalence estimates with disability weights, which were derived from population-based surveys; YLLs were computed by multiplying the number of estimated cancer deaths at each age with a reference life expectancy; and DALYs were calculated as the sum of YLDs and YLLs. FINDINGS: In 2013 there were 14.9 million incident cancer cases, 8.2 million deaths, and 196.3 million DALYs. Prostate cancer was the leading cause for cancer incidence (1.4 million) for men and breast cancer for women (1.8 million). Tracheal, bronchus, and lung (TBL) cancer was the leading cause for cancer death in men and women, with 1.6 million deaths. For men, TBL cancer was the leading cause of DALYs (24.9 million). For women, breast cancer was the leading cause of DALYs (13.1 million). Age-standardized incidence rates (ASIRs) per 100 000 and age-standardized death rates (ASDRs) per 100 000 for both sexes in 2013 were higher in developing vs developed countries for stomach cancer (ASIR, 17 vs 14; ASDR, 15 vs 11), liver cancer (ASIR, 15 vs 7; ASDR, 16 vs 7), esophageal cancer (ASIR, 9 vs 4; ASDR, 9 vs 4), cervical cancer (ASIR, 8 vs 5; ASDR, 4 vs 2), lip and oral cavity cancer (ASIR, 7 vs 6; ASDR, 2 vs 2), and nasopharyngeal cancer (ASIR, 1.5 vs 0.4; ASDR, 1.2 vs 0.3). Between 1990 and 2013, ASIRs for all cancers combined (except nonmelanoma skin cancer and Kaposi sarcoma) increased by more than 10% in 113 countries and decreased by more than 10% in 12 of 188 countries. CONCLUSIONS AND RELEVANCE: Cancer poses a major threat to public health worldwide, and incidence rates have increased in most countries since 1990. The trend is a particular threat to developing nations with health systems that are ill-equipped to deal with complex and expensive cancer treatments. The annual update on the Global Burden of Cancer will provide all stakeholders with timely estimates to guide policy efforts in cancer prevention, screening, treatment, and palliation.

BACKGROUND: Artemisinin resistance in Plasmodium falciparum has emerged in Southeast Asia and now poses a threat to the control and elimination of malaria. Mapping the geographic extent of resistance is essential for planning containment and elimination strategies. METHODS: Between May 2011 and April 2013, we enrolled 1241 adults and children with acute, uncomplicated falciparum malaria in an open-label trial at 15 sites in 10 countries (7 in Asia and 3 in Africa). Patients received artesunate, administered orally at a daily dose of either 2 mg per kilogram of body weight per day or 4 mg per kilogram, for 3 days, followed by a standard 3-day course of artemisinin-based combination therapy. Parasite counts in peripheral-blood samples were measured every 6 hours, and the parasite clearance half-lives were determined. RESULTS: The median parasite clearance half-lives ranged from 1.9 hours in the Democratic Republic of Congo to 7.0 hours at the Thailand-Cambodia border. Slowly clearing infections (parasite clearance half-life >5 hours), strongly associated with single point mutations in the "propeller" region of the P. falciparum kelch protein gene on chromosome 13 (kelch13), were detected throughout mainland Southeast Asia from southern Vietnam to central Myanmar. The incidence of pretreatment and post-treatment gametocytemia was higher among patients with slow parasite clearance, suggesting greater potential for transmission. In western Cambodia, where artemisinin-based combination therapies are failing, the 6-day course of antimalarial therapy was associated with a cure rate of 97.7% (95% confidence interval, 90.9 to 99.4) at 42 days. CONCLUSIONS: Artemisinin resistance to P. falciparum, which is now prevalent across mainland Southeast Asia, is associated with mutations in kelch13. Prolonged courses of artemisinin-based combination therapies are currently efficacious in areas where standard 3-day treatments are failing. (Funded by the U.K. Department of International Development and others; ClinicalTrials.gov number, NCT01350856.).

The cytokine storm has captured the attention of the public and the scientific community alike, and while the general notion of an excessive or uncontrolled release of proinflammatory cytokines is well known, the concept of a cytokine storm and the biological consequences of cytokine overproduction are not clearly defined. Cytokine storms are associated with a wide variety of infectious and noninfectious diseases. The term was popularized largely in the context of avian H5N1 influenza virus infection, bringing the term into popular media. In this review, we focus on the cytokine storm in the context of virus infection, and we highlight how high-throughput genomic methods are revealing the importance of the kinetics of cytokine gene expression and the remarkable degree of redundancy and overlap in cytokine signaling. We also address evidence for and against the role of the cytokine storm in the pathology of clinical and infectious disease and discuss why it has been so difficult to use knowledge of the cytokine storm and immunomodulatory therapies to improve the clinical outcomes for patients with severe acute infections.

Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.

BACKGROUND: Nasal carriers of Staphylococcus aureus are at increased risk for health care-associated infections with this organism. Decolonization of nasal and extranasal sites on hospital admission may reduce this risk. METHODS: In a randomized, double-blind, placebo-controlled, multicenter trial, we assessed whether rapid identification of S. aureus nasal carriers by means of a real-time polymerase-chain-reaction (PCR) assay, followed by treatment with mupirocin nasal ointment and chlorhexidine soap, reduces the risk of hospital-associated S. aureus infection. RESULTS: From October 2005 through June 2007, a total of 6771 patients were screened on admission. A total of 1270 nasal swabs from 1251 patients were positive for S. aureus. We enrolled 917 of these patients in the intention-to-treat analysis, of whom 808 (88.1%) underwent a surgical procedure. All the S. aureus strains identified on PCR assay were susceptible to methicillin and mupirocin. The rate of S. aureus infection was 3.4% (17 of 504 patients) in the mupirocin-chlorhexidine group, as compared with 7.7% (32 of 413 patients) in the placebo group (relative risk of infection, 0.42; 95% confidence interval [CI], 0.23 to 0.75). The effect of mupirocin-chlorhexidine treatment was most pronounced for deep surgical-site infections (relative risk, 0.21; 95% CI, 0.07 to 0.62). There was no significant difference in all-cause in-hospital mortality between the two groups. The time to the onset of nosocomial infection was shorter in the placebo group than in the mupirocin-chlorhexidine group (P=0.005). CONCLUSIONS: The number of surgical-site S. aureus infections acquired in the hospital can be reduced by rapid screening and decolonizing of nasal carriers of S. aureus on admission. (Current Controlled Trials number, ISRCTN56186788.)

BACKGROUND: Tuberculous meningitis kills or disables more than half of those affected with the disease. Previous studies have been too small to determine whether adjunctive treatment with corticosteroids can reduce the risk of disability or death among adults with tuberculous meningitis, and the effect of coinfection with the human immunodeficiency virus (HIV) is unclear. METHODS: We performed a randomized, double-blind, placebo-controlled trial in Vietnam in patients over 14 years of age who had tuberculous meningitis, with or without HIV infection, to determine whether adjunctive treatment with dexamethasone reduced the risk of death or severe disability after nine months of follow-up. We conducted prespecified subgroup analyses and intention-to-treat analyses. RESULTS: A total of 545 patients were randomly assigned to groups that received either dexamethasone (274 patients) or placebo (271 patients). Only 10 patients (1.8 percent) had been lost to follow-up at nine months of treatment. Treatment with dexamethasone was associated with a reduced risk of death (relative risk, 0.69; 95 percent confidence interval, 0.52 to 0.92; P=0.01). It was not associated with a significant reduction in the proportion of severely disabled patients (34 of 187 patients [18.2 percent] among survivors in the dexamethasone group vs. 22 of 159 patients [13.8 percent] in the placebo group, P=0.27) or in the proportion of patients who had either died or were severely disabled after nine months (odds ratio, 0.81; 95 percent confidence interval, 0.58 to 1.13; P=0.22). The treatment effect was consistent across subgroups that were defined by disease-severity grade (stratified relative risk of death, 0.68; 95 percent confidence interval, 0.52 to 0.91; P=0.007) and by HIV status (stratified relative risk of death, 0.78; 95 percent confidence interval, 0.59 to 1.04; P=0.08). Significantly fewer serious adverse events occurred in the dexamethasone group than in the placebo group (26 of 274 patients vs. 45 of 271 patients, P=0.02). CONCLUSIONS: Adjunctive treatment with dexamethasone improves survival in patients over 14 years of age with tuberculous meningitis but probably does not prevent severe disability.

Pandemic influenza virus has its origins in avian influenza viruses. The highly pathogenic avian influenza virus subtype H5N1 is already panzootic in poultry, with attendant economic consequences. It continues to cross species barriers to infect humans and other mammals, often with fatal outcomes. Therefore, H5N1 virus has rightly received attention as a potential pandemic threat. However, it is noted that the pandemics of 1957 and 1968 did not arise from highly pathogenic influenza viruses, and the next pandemic may well arise from a low-pathogenicity virus. The rationale for particular concern about an H5N1 pandemic is not its inevitability but its potential severity. An H5N1 pandemic is an event of low probability but one of high human health impact and poses a predicament for public health. Here, we review the ecology and evolution of highly pathogenic avian influenza H5N1 viruses, assess the pandemic risk, and address aspects of human H5N1 disease in relation to its epidemiology, clinical presentation, pathogenesis, diagnosis, and management.

Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of recombination. Sequencing 240 isolates of the PMEN1 (Spain(23F)-1) multidrug-resistant lineage enabled base substitutions to be distinguished from polymorphisms arising through horizontal sequence transfer. More than 700 recombinations were detected, with genes encoding major antigens frequently affected. Among these were 10 capsule-switching events, one of which accompanied a population shift as vaccine-escape serotype 19A isolates emerged in the USA after the introduction of the conjugate polysaccharide vaccine. The evolution of resistance to fluoroquinolones, rifampicin, and macrolides was observed to occur on multiple occasions. This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales.

Influenza A (H5N1) virus with an amino acid substitution in neuraminidase conferring high-level resistance to oseltamivir was isolated from two of eight Vietnamese patients during oseltamivir treatment. Both patients died of influenza A (H5N1) virus infection, despite early initiation of treatment in one patient. Surviving patients had rapid declines in the viral load to undetectable levels during treatment. These observations suggest that resistance can emerge during the currently recommended regimen of oseltamivir therapy and may be associated with clinical deterioration and that the strategy for the treatment of influenza A (H5N1) virus infection should include additional antiviral agents.

BACKGROUND: The management of complex orthopedic infections usually includes a prolonged course of intravenous antibiotic agents. We investigated whether oral antibiotic therapy is noninferior to intravenous antibiotic therapy for this indication. METHODS: We enrolled adults who were being treated for bone or joint infection at 26 U.K. centers. Within 7 days after surgery (or, if the infection was being managed without surgery, within 7 days after the start of antibiotic treatment), participants were randomly assigned to receive either intravenous or oral antibiotics to complete the first 6 weeks of therapy. Follow-on oral antibiotics were permitted in both groups. The primary end point was definitive treatment failure within 1 year after randomization. In the analysis of the risk of the primary end point, the noninferiority margin was 7.5 percentage points. RESULTS: Among the 1054 participants (527 in each group), end-point data were available for 1015 (96.3%). Treatment failure occurred in 74 of 506 participants (14.6%) in the intravenous group and 67 of 509 participants (13.2%) in the oral group. Missing end-point data (39 participants, 3.7%) were imputed. The intention-to-treat analysis showed a difference in the risk of definitive treatment failure (oral group vs. intravenous group) of -1.4 percentage points (90% confidence interval [CI], -4.9 to 2.2; 95% CI, -5.6 to 2.9), indicating noninferiority. Complete-case, per-protocol, and sensitivity analyses supported this result. The between-group difference in the incidence of serious adverse events was not significant (146 of 527 participants [27.7%] in the intravenous group and 138 of 527 [26.2%] in the oral group; P=0.58). Catheter complications, analyzed as a secondary end point, were more common in the intravenous group (9.4% vs. 1.0%). CONCLUSIONS: Oral antibiotic therapy was noninferior to intravenous antibiotic therapy when used during the first 6 weeks for complex orthopedic infection, as assessed by treatment failure at 1 year. (Funded by the National Institute for Health Research; OVIVA Current Controlled Trials number, ISRCTN91566927 .).

BACKGROUND: Recent outbreaks of avian influenza A (H5N1) in poultry throughout Asia have had major economic and health repercussions. Human infections with this virus were identified in Vietnam in January 2004. METHODS: We report the clinical features and preliminary epidemiologic findings among 10 patients with confirmed cases of avian influenza A (H5N1) who presented to hospitals in Ho Chi Minh City and Hanoi, Vietnam, in December 2003 and January 2004. RESULTS: In all 10 cases, the diagnosis of influenza A (H5N1) was confirmed by means of viral culture or reverse transcriptase-polymerase chain reaction with primers specific for H5 and N1. None of the 10 patients (mean age, 13.7 years) had preexisting medical conditions. Nine of them had a clear history of direct contact with poultry (median time before onset of illness, three days). All patients presented with fever (temperature, 38.5 to 40.0 degrees C), respiratory symptoms, and clinically significant lymphopenia (median lymphocyte count, 700 per cubic millimeter). The median platelet count was 75,500 per cubic millimeter. Seven patients had diarrhea. In all patients, there were marked abnormalities on chest radiography. There was no definitive evidence of human-to-human transmission. Eight patients died, one patient has recovered, and one is recovering. CONCLUSIONS: Influenza A (H5N1) infection, characterized by fever, respiratory symptoms, and lymphopenia, carries a high risk of death. Although in all 10 cases the infection appears to have been acquired directly from infected poultry, the potential exists for genetic reassortment with human influenzaviruses and the evolution of human-to-human transmission. Containment of influenza A (H5N1) in poultry throughout Asia is therefore urgently required.

ISSN:0035-9203

Zika virus (ZIKV), a mosquito-borne flavivirus with homology to Dengue virus (DENV), has become a public health emergency. By characterizing memory lymphocytes from ZIKV-infected patients, we dissected ZIKV-specific and DENV-cross-reactive immune responses. Antibodies to nonstructural protein 1 (NS1) were largely ZIKV-specific and were used to develop a serological diagnostic tool. In contrast, antibodies against E protein domain I/II (EDI/II) were cross-reactive and, although poorly neutralizing, potently enhanced ZIKV and DENV infection in vitro and lethally enhanced DENV disease in mice. Memory T cells against NS1 or E proteins were poorly cross-reactive, even in donors preexposed to DENV. The most potent neutralizing antibodies were ZIKV-specific and targeted EDIII or quaternary epitopes on infectious virus. An EDIII-specific antibody protected mice from lethal ZIKV infection, illustrating the potential for antibody-based therapy.

•The geography of type-specific global DENV circulation has not been well described.•We map the global distribution and co-circulation of each DENV type from 1943 to 2013.•Detection of all types has expanded worldwide together with growing hyperendemicity.•There remains a dearth of type-specific information in many parts of the world. Since the first isolation of dengue virus (DENV) in 1943, four types have been identified. Global phenomena such as urbanization and international travel are key factors in facilitating the spread of dengue. Documenting the type-specific record of DENV spread has important implications for understanding patterns in dengue hyperendemicity and disease severity as well as vaccine design and deployment strategies. Existing studies have examined the spread of DENV types at regional or local scales, or described phylogeographic relationships within a single type. Here we summarize the global distribution of confirmed instances of each DENV type from 1943 to 2013 in a series of global maps. These show the worldwide expansion of the types, the expansion of disease hyperendemicity, and the establishment of an increasingly important infectious disease of global public health significance. Since the first isolation of dengue virus (DENV) in 1943, four types have been identified. Global phenomena such as urbanization and international travel are key factors in facilitating the spread of dengue. Documenting the type-specific record of DENV spread has important implications for understanding patterns in dengue hyperendemicity and disease severity as well as vaccine design and deployment strategies. Existing studies have examined the spread of DENV types at regional or local scales, or described phylogeographic relationships within a single type. Here we summarize the global distribution of confirmed instances of each DENV type from 1943 to 2013 in a series of global maps. These show the worldwide expansion of the types, the expansion of disease hyperendemicity, and the establishment of an increasingly important infectious disease of global public health significance. DENV are members of the Flavivirus genus (see Glossary), related to other medically important arboviruses such as yellow fever and Japanese encephalitis viruses. There are four phylogenetically and antigenically distinct dengue viruses (DENV1–4), and although infection with one type confers long-term immunity, it is to that type only and not to the other three [1Gubler D.J. Epidemic dengue/dengue hemorrhagic fever as a public health, social and economic problem in the 21st century.Trends Microbiol. 2002; 10: 100-103Abstract Full Text Full Text PDF PubMed Scopus (1166) Google Scholar]. The ancestor of these viruses has been postulated to have emerged about 1 000 years ago in an infectious cycle involving non-human primates and mosquitoes, with transmission to humans having occurred independently for all four virus types only a few hundred years ago [2Holmes E.C. Twiddy S.S. The origin, emergence and evolutionary genetics of dengue virus.Infection, genetics and evolution. 2003; 3: 19-28Crossref PubMed Scopus (456) Google Scholar, 3Wang E. et al.Evolutionary relationships of endemic/epidemic and sylvatic dengue viruses.J. Virol. 2000; 74: 3227-3234Crossref PubMed Scopus (302) Google Scholar]. Although outbreaks of disease clinically consistent with dengue have been reported for centuries, it was not until 1943 in Japan and 1945 in Hawaii that the first two dengue viruses were isolated (named DENV1 and DENV2, respectively) [4Hotta S. Experimental studies on dengue. I. Isolation, identification and modification of the virus.J. Infect. Dis. 1952; 90: 1-9Crossref PubMed Scopus (115) Google Scholar]. At this point, epidemics of dengue illness were being reported across the region spanning from India to the Pacific Islands. In the latter half of the 20th century, DENV transmission followed the spread of its principal mosquito vector, Aedes aegypti [5Mousson L. et al.Phylogeography of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) based on mitochondrial DNA variations.Genet. Res. 2005; 86: 1-11Crossref PubMed Scopus (156) Google Scholar], and was likely accelerated by urbanization and globalization [6Gubler D.J. Dengue, urbanization and globalization: the unholy trinity of the 21st century.Trop. Med. Health. 2011; 39: 3-11Crossref PubMed Scopus (629) Google Scholar, 7Weaver S.C. Urbanization and geographic expansion of zoonotic arboviral diseases: mechanisms and potential strategies for prevention.Trends Microbiol. 2013; 21: 360-363Abstract Full Text Full Text PDF PubMed Scopus (141) Google Scholar]. The collapse of the Ae. aegypti eradication campaign in the Americas in the 1970s was also important in marking the beginning of transport of Asian dengue viruses to the Americas, followed by the rapid re-introduction of the principal mosquito vector throughout both continents [8Gubler D.J. Clark G.G. Dengue/dengue hemorrhagic fever: the emergence of a global health problem.Emerg. Infect. Dis. 1995; 1: 55-57Crossref PubMed Scopus (534) Google Scholar]. Spatial patterns in concurrent and/or sequential circulation of DENV1–4 should be considered along with virus and host genetics as potentially important population-level risk factors for severe dengue illness [9Guilarde A.O. et al.Dengue and dengue hemorrhagic fever among adults: clinical outcomes related to viremia, serotypes, and antibody response.J. Infect. Dis. 2008; 197: 817-824Crossref PubMed Scopus (123) Google Scholar, 10Chaturvedi U. et al.Dengue and dengue haemorrhagic fever: implications of host genetics.FEMS Immunol. Med. Microbiol. 2006; 47: 155-166Crossref PubMed Scopus (79) Google Scholar] because secondary infection with a heterologous DENV type may increase the probability of severe disease [11Green S. Rothman A. Immunopathological mechanisms in dengue and dengue hemorrhagic fever.Curr. Opin. Infect. Dis. 2006; 19: 429-436Crossref PubMed Scopus (311) Google Scholar, 12Vaughn D.W. et al.Dengue viremia titer, antibody response pattern, and virus serotype correlate with disease severity.J. Infect. Dis. 2000; 181: 2-9Crossref PubMed Scopus (1271) Google Scholar, 13Gibbons R.V. Vaughn D.W. Dengue: an escalating problem.BMJ. 2002; 324: 1563-1566Crossref PubMed Scopus (571) Google Scholar, 14Rico-Hesse R. Microevolution and virulence of dengue viruses.Adv. Virus Res. 2003; 59: 315-341Crossref PubMed Scopus (303) Google Scholar]. Despite this, no study has systematically reviewed all documented spatially explicit evidence of the global spread of the four DENV types since the first isolation in 1943. Rather, the majority of existing studies have focused on the evolution of individual DENV types at regional or local scales [15Raghwani J. et al.Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.PLoS Pathog. 2011; 7: e1002064Crossref PubMed Scopus (81) Google Scholar, 16Allicock O.M. et al.Phylogeography and population dynamics of dengue viruses in the Americas.Mol. Biol. Evol. 2012; 29: 1533-1543Crossref PubMed Scopus (89) Google Scholar, 17Liebman K.A. et al.Spatial dimensions of dengue virus transmission across interepidemic and epidemic periods in Iquitos, Peru (1999–2003).PLoS Negl. Trop. Dis. 2012; 6: e1472Crossref PubMed Scopus (69) Google Scholar, 18Endy T.P. et al.Prospective cohort studies of dengue viral transmission and severity of disease.Curr. Top. Microbiol. Immunol. 2010; 338: 1-13Crossref PubMed Google Scholar, 19Jarman R.G. et al.Microevolution of dengue viruses circulating among primary school children in Kamphaeng Phet, Thailand.J. Virol. 2008; 82: 5494-5500Crossref PubMed Scopus (47) Google Scholar, 20Carrington C.V. et al.Invasion and maintenance of dengue virus type 2 and type 4 in the Americas.J. Virol. 2005; 79: 14680-14687Crossref PubMed Scopus (110) Google Scholar]. Global descriptions of type-specific DENV distribution are few in number, lacking spatial and temporal precision, and are presented in a non-systematic manner [8Gubler D.J. Clark G.G. Dengue/dengue hemorrhagic fever: the emergence of a global health problem.Emerg. Infect. Dis. 1995; 1: 55-57Crossref PubMed Scopus (534) Google Scholar]. Reported cases do not comprise the entire range of each DENV type at any given time, meaning that a lack of reporting for a specific type at any time or place does not indicate its certain absence. This is due to spatial variability in several factors, namely in the degree of sampling, proportion of infections having been typed, reliability of typing methods, and finally reporting of these types. That said, the use of more advanced typing methods has expanded significantly across the globe since their development, and a thorough description of confirmed presences of each DENV type is needed if we are to gain a better understanding of the global dispersal of the four viruses and track changes moving forward. Here we provide this baseline depiction, also highlighting those geographic areas lacking in information about the specific DENV type(s) responsible for dengue occurrence. Brady et al. [21Brady O.J. et al.Refining the global spatial limits of dengue virus transmission by evidence-based consensus.PLoS Negl. Trop. Dis. 2012; 6: e1760Crossref PubMed Scopus (1075) Google Scholar] recently outlined the definitive extents of dengue presence globally, and their work was followed by that of Bhatt et al. [22Bhatt S. et al.The global distribution and burden of dengue.Nature. 2013; 496: 504-507Crossref PubMed Scopus (5919) Google Scholar] which generated high spatial-resolution (5 km × 5 km) estimates of contemporary global dengue risk and burden in 2010. Our efforts here provide further insight into the global distribution of dengue by reviewing the individual DENV types responsible for reported occurrence throughout the past seven decades. Our aim is to complement phylogenetic and disease occurrence analyses by presenting the sub-national distribution of reported confirmed instances of human infection with each DENV type globally from 1943 to 2013. We provide a more spatially and of the spread of each individual DENV type was also presenting contemporary of the of DENV types reported in an to global patterns in their co-circulation and establishment of We an by DENV type and information from and spanning the In were in PubMed the and or and all were the were on these only those with a and were of all and We were to information from a of and were also the and or and all DENV type that be to a were in a of 1 or DENV type from of were in of DENV were from 1 for a of from which type and information was for these are was to the of or In the of a we the as the of the occurrence. The was on 4 2013. The we to described the occurrence of more one DENV type at a time and/or multiple it was the that multiple were to the for these we a of an occurrence as the one or more of confirmed from a specific DENV type in a given within a single if multiple confirmed the presence of a DENV type in the within the were considered as a single occurrence is important to that of a type-specific occurrence does not to the of cases reported information was not to the presence of that DENV type in a given and and or as information was only at the in a it was in the for those in in at this occurrence a series of global were for each DENV type across 1943 and 2013. We also the of DENV types reported in a given across these by region and were also in the Although of cases were from the no were the specific typing to the DENV type(s) responsible for an occurrence because not all this This was for that reported cases as confirmed the of for in the identification were virus not The of confirmed by each of these methods is described in in the In or were to infection with these methods are not for type-specific DENV to DENV type et of Microbiol. 2010; PubMed Scopus Google Scholar]. these were in the not of 1 DENV1 1 1 and 1 000 were at the and across the entire study 1 confirmed DENV were not to a specific type due to lack of and/or Our the reporting of each DENV type for the periods and as presented in distribution of reported confirmed cases of since 1943. areas cases that were confirmed in the given areas cases that been reported not in the distribution of reported confirmed cases of since 1943. areas cases that were confirmed in the given areas cases that been reported not in the distribution of reported confirmed cases of since 1943. areas cases that were confirmed in the given areas cases that been reported not in the These are by in the that further the distribution of for each DENV type by region the Americas, and and by within those the of presented in the the Americas were considered to and the as well as and The region and the Pacific Islands. The also the of information on type-specific methods in the this is for only because any occurrence described as confirmed was in of to the of DENV type 1 the global spatial distribution of confirmed DENV1 by time DENV1 was first reported in 1943 in and followed by in Hawaii in and was not until the that reporting of DENV1 in the Asian region was first reported in in in and has been reported in the region with more periods of reporting in the and as well as several years of reporting in in the DENV1 was not reported in the Americas until it was in and these first reporting across the region the few with reporting in and in other in the region having more in the and and of DENV1 in to in the Since the in with the for in for in several in the and this may reporting of all DENV types since this was first reported in in and followed by the in and and have reported many years of occurrence since the as well as since the 1970s and the and since the reporting not in and until the In was reported in multiple and has not since been reported several have since been reported in the with the being from in and in 2013. was reported in the Americas as as in and reporting in the region not until the and in Since this time, more and more have reporting of DENV2, with reporting in in since for the majority of reporting of this type In the was an increase in the of the more severe hemorrhagic fever cases in the Americas, due to the of the with an and more Asian one R. et of dengue type 2 viruses associated with in the PubMed Scopus Google Scholar, R. et for dengue viruses in humans and Virol. 2005; 79: PubMed Scopus Google Scholar, et evolution of dengue 2 virus in in the viral Virol. 2006; PubMed Scopus Google Scholar, et of the Asian 1 of dengue virus serotype 2 in in and in Negl. Trop. Dis. 2010; PubMed Scopus Google Scholar]. This increase in cases may be responsible for the in reporting in this region since that time, as in The of reported to was in with and areas worldwide reporting in the was first reported in in the and and has been reported in since Although many in have reported throughout the study reported and with the reporting and and have also reported since the as well as since the of in and have been consistent since the The first in the Americas were in in which to until and from to to the of a from et and global spread of a dengue serotype Infect. Dis. 2003; PubMed Scopus Google Scholar]. The majority of other in the Americas not reporting the type until the and reporting occurred in in the In has been reported since the first in in and occurrence has been with the of more reporting and in was reported first in in the and Since this time the region has reported in reporting occurred and has also reported since Although reporting by has not been as consistent as for other DENV types, periods of more reporting have occurred in the region as well as and was not reported in the Americas until it was reported in and the Islands. Since this reporting has occurred in the with reporting in since the and since the and and Peru since the 5 the of DENV types having been reported in any given and by and the until the the majority of areas only reported one or two types of This the of potential in co-circulation of the four which may as a key of transmission et the emergence of dengue in Negl. Trop. Dis. 2011; PubMed Scopus Google Scholar]. In the the of types having been reported within a single to increase as more and type-specific were for dengue et of dengue by rapid of dengue virus in Virol. PubMed Scopus Google Scholar]. This may also in global reporting of specific DENV types at this time, although the of reported DENV types has since to increase in many areas across and the as well as in the and This is in the map by which time the majority of as well as of and reported DENV type. Although few areas in have reported all four DENV types, by the several areas reported it is these all the epidemic of the or are only from the sylvatic transmission of DENV type is and by many types of in in with and an of occurrence. it is important to that an of reporting for one DENV type is not with an of its occurrence. is also important to that of a type occurrence does not to the of cases to the presence of the DENV type in a given and because of a type occurrence does not to the of cases the presence of the DENV type in a given and it is to about the of each type in any given That said, the that this comprise the type-specific DENV to and its a more of spread was Although is that several factors have to an expansion of the geographic range of dengue study and in the latter half of the 20th [6Gubler D.J. Dengue, urbanization and globalization: the unholy trinity of the 21st century.Trop. Med. Health. 2011; 39: 3-11Crossref PubMed Scopus (629) Google Scholar, Global dengue Med. Trop. 2012; PubMed Scopus Google Scholar, D.J. The global of arboviral as public health Med. Res. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar, D.J. The of yellow fever and to Immunol. Microbiol. Infect. Dis. PubMed Scopus Google Scholar, D.J. epidemic dengue Med. 10: PubMed Scopus Google Scholar, an dengue Full Text Full Text PDF PubMed Scopus Google Scholar, Global of dengue hemorrhagic Asian J. Trop. Med. Health. 21: Google Scholar], the variability in reporting time as well as by region and be considered patterns of expansion fever: for a 2005; PubMed Scopus Google Scholar]. in reporting time have a on the of cases being by the that co-circulation of DENV types may be associated with more severe disease outcomes which are more likely to be this study it that dengue has across the globe since 1943, with DENV types being reported in areas more DENV1 was reported to the this study followed by DENV2, and The of confirmed type-specific DENV in the in DENV1 and in the Americas to the of rapid In although reporting has reporting has that of The increase in reporting of occurred in the in the reporting spread the the although it has been reported in since the in and the Although in DENV reporting across and the Americas, also the that remains a dearth of type-specific DENV information in many parts of understanding of the evolutionary and of DENV transmission and spread is also efforts and of have here to and the Americas, although several arboviral studies have been in the region since the et virus isolation from humans an in in Virol. PubMed Scopus Google Scholar, et infections and viral haemorrhagic in a in R. Trop. Med. Full Text PDF PubMed Scopus Google Scholar, et fever dengue 2 and other arboviruses isolated from in from to and 86: Google Scholar, distribution and of Med. Google Scholar, et evidence of arboviral infections among humans of Trop. Med. Google Scholar, E. et of the circulation of of in the region of 86: Google Scholar, transmission in Google Scholar, et al.The of dengue fever virus in studies and of a of dengue R. Trop. Med. Full Text PDF PubMed Scopus Google Scholar, et viral infections associated with a fever in the of Trop. Med. Google Scholar, The growing of transmission and outbreaks in a Med. J. PubMed Scopus Google Scholar, et of viruses and other infectious disease as the of in the of Med. Virol. PubMed Scopus Google Scholar, circulation in the of Google Scholar, S.C. and arboviral Res. 2010; PubMed Scopus Google Scholar, et evidence of arboviral infections among humans in J. Trop. Med. 2011; PubMed Scopus Google Scholar, et and antibody to Aedes in Trop. PubMed Scopus Google Scholar, et and distribution of arboviral infections among adults: a J. 2011; PubMed Scopus (79) Google Scholar, et and distribution of and arboviral infections in J. Trop. Med. 2006; 74: Google Scholar, et arboviral infections in J. Trop. Med. 2010; PubMed Scopus (47) Google Scholar, et circulation of arboviruses in Med. J. 2010; Google Scholar]. This problem is by the lack of DENV type-specific information in the few occurrence are This is in the of evidence for dengue presence is high [21Brady O.J. et al.Refining the global spatial limits of dengue virus transmission by evidence-based consensus.PLoS Negl. Trop. Dis. 2012; 6: e1760Crossref PubMed Scopus (1075) Google Scholar], information about the specific within these DENV has occurred or about the DENV type(s) responsible for occurrence. be with use of the presented such as those the of and in the spread of the of DENV types into DENV is or is not et transport and infectious disease 2006; PubMed Scopus Google Scholar], and DENV population and as well as on human DENV transmission at the and scales et the spatial of dengue transmission and in an 2012; PubMed Scopus Google Scholar]. The to these complement phylogenetic and may be with phylogeographic studies of DENV evolution and dispersal on a regional and global J. et a global dengue Med. Health. PubMed Scopus Google Scholar, et serotype and their on the of R. Biol. PubMed Scopus Google Scholar, et with The of dengue virus in Biol. Evol. 2013; Scopus Google Scholar]. The that has been be et al.Dengue type-specific global 2013; Google such that it be to in to DENV type identification in information about specific viruses were circulating in an at a the spread of DENV types also has important implications for [15Raghwani J. et al.Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.PLoS Pathog. 2011; 7: e1002064Crossref PubMed Scopus (81) Google Scholar] changes in dengue in a given we the of and in the global spread and evolution of DENV co-circulation of DENV types increase the of more severe disease outcomes in a given of studies involving are to this is the distribution of DENV types in Although are for the presence of certain types in these are and efforts are needed in we the of and in the global spread and evolution of DENV co-circulation of DENV types increase the of more severe disease outcomes in a given of studies involving are to this is the distribution of DENV types in Although are for the presence of certain types in these are and efforts are needed in Although international transmission of disease is not it is that have by since human to the viruses more et of the Asian 1 of dengue virus serotype 2 in in and in Negl. Trop. Dis. 2010; PubMed Scopus Google Scholar, et travel and disease 2012; PubMed Scopus (79) Google Scholar]. urbanization along with and provide an for Ae. aegypti in to human In the Americas, this may have been by the collapse of the Ae. aegypti eradication in the 1970s [8Gubler D.J. Clark G.G. Dengue/dengue hemorrhagic fever: the emergence of a global health problem.Emerg. Infect. Dis. 1995; 1: 55-57Crossref PubMed Scopus (534) Google Scholar]. in the of in and the in the and may have the establishment and spread of all four DENV types in the Americas vaccine of the 2011; PubMed Google Scholar]. to the and and together are to for of all in the (see it is that we the and spread of DENV types in these to and better to the global burden of dengue because have the of all four DENV types to into the for a DENV vaccine which all four types is more vaccine of the 2011; PubMed Google Scholar]. is also important to the of a DENV type dengue virus a in disease 2013; PubMed Scopus Google Scholar] if to be as as the other four DENV types, a of spread as with these types the past two decades. transmission of a type in human this be an for vaccine efforts vaccine of the 2011; PubMed Google Scholar, A. et of the dengue vaccine in a 2012; Full Text Full Text PDF PubMed Scopus Google Scholar], and an map of the spread of DENV types be In this the contemporary understanding of DENV type-specific geographic from 1943 to a and for the global spread of each DENV type. the co-circulation of types in of the in and has important implications for patterns in disease severity and hyperendemicity, as well as for vaccine also a of DENV type-specific geographic information in many across the globe that to be with a of viruses by and a and for the of and for and in the by the of certain by and and the

ABSTRACT Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi, the causative agent of typhoid. Multidrug-resistant (MDR) isolates are prevalent in parts of Asia and Africa and are often associated with the dominant H58 haplotype. Reduced susceptibility to fluoroquinolones is also widespread, and sporadic cases of resistance to third-generation cephalosporins or azithromycin have also been reported. Here, we report the first large-scale emergence and spread of a novel S . Typhi clone harboring resistance to three first-line drugs (chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole) as well as fluoroquinolones and third-generation cephalosporins in Sindh, Pakistan, which we classify as extensively drug resistant (XDR). Over 300 XDR typhoid cases have emerged in Sindh, Pakistan, since November 2016. Additionally, a single case of travel-associated XDR typhoid has recently been identified in the United Kingdom. Whole-genome sequencing of over 80 of the XDR isolates revealed remarkable genetic clonality and sequence conservation, identified a large number of resistance determinants, and showed that these isolates were of haplotype H58. The XDR S . Typhi clone encodes a chromosomally located resistance region and harbors a plasmid encoding additional resistance elements, including the bla CTX-M-15 extended-spectrum β-lactamase, and carrying the qnrS fluoroquinolone resistance gene. This antibiotic resistance-associated IncY plasmid exhibited high sequence identity to plasmids found in other enteric bacteria isolated from widely distributed geographic locations. This study highlights three concerning problems: the receding antibiotic arsenal for typhoid treatment, the ability of S . Typhi to transform from MDR to XDR in a single step by acquisition of a plasmid, and the ability of XDR clones to spread globally. IMPORTANCE Typhoid fever is a severe disease caused by the Gram-negative bacterium Salmonella enterica serovar Typhi. Antibiotic-resistant S . Typhi strains have become increasingly common. Here, we report the first large-scale emergence and spread of a novel extensively drug-resistant (XDR) S . Typhi clone in Sindh, Pakistan. The XDR S . Typhi is resistant to the majority of drugs available for the treatment of typhoid fever. This study highlights the evolving threat of antibiotic resistance in S . Typhi and the value of antibiotic susceptibility testing and whole-genome sequencing in understanding emerging infectious diseases. We genetically characterized the XDR S . Typhi to investigate the phylogenetic relationship between these isolates and a global collection of S . Typhi isolates and to identify multiple genes linked to antibiotic resistance. This S . Typhi clone harbored a promiscuous antibiotic resistance plasmid previously identified in other enteric bacteria. The increasing antibiotic resistance in S . Typhi observed here adds urgency to the need for typhoid prevention measures.

BACKGROUND: to dengue virus infection. METHODS: (intervention clusters) and 12 clusters to receive no deployments (control clusters). All clusters practiced local mosquito-control measures as usual. A test-negative design was used to assess the efficacy of the intervention. Patients with acute undifferentiated fever who presented to local primary care clinics and were 3 to 45 years of age were recruited. Laboratory testing was used to identify participants who had virologically confirmed dengue (VCD) and those who were test-negative controls. The primary end point was symptomatic VCD of any severity caused by any dengue virus serotype. RESULTS: Mel into the intervention clusters, 8144 participants were enrolled; 3721 lived in intervention clusters, and 4423 lived in control clusters. In the intention-to-treat analysis, VCD occurred in 67 of 2905 participants (2.3%) in the intervention clusters and in 318 of 3401 (9.4%) in the control clusters (aggregate odds ratio for VCD, 0.23; 95% confidence interval [CI], 0.15 to 0.35; P = 0.004). The protective efficacy of the intervention was 77.1% (95% CI, 65.3 to 84.9) and was similar against the four dengue virus serotypes. The incidence of hospitalization for VCD was lower among participants who lived in intervention clusters (13 of 2905 participants [0.4%]) than among those who lived in control clusters (102 of 3401 [3.0%]) (protective efficacy, 86.2%; 95% CI, 66.2 to 94.3). CONCLUSIONS: populations was effective in reducing the incidence of symptomatic dengue and resulted in fewer hospitalizations for dengue among the participants. (Funded by the Tahija Foundation and others; AWED ClinicalTrials.gov number, NCT03055585; Indonesia Registry number, INA-A7OB6TW.).

BACKGROUND: Current understanding of the spatial epidemiology and geographical distribution of Plasmodium vivax is far less developed than that for P. falciparum, representing a barrier to rational strategies for control and elimination. Here we present the first systematic effort to map the global endemicity of this hitherto neglected parasite. METHODOLOGY AND FINDINGS: We first updated to the year 2010 our earlier estimate of the geographical limits of P. vivax transmission. Within areas of stable transmission, an assembly of 9,970 geopositioned P. vivax parasite rate (PvPR) surveys collected from 1985 to 2010 were used with a spatiotemporal Bayesian model-based geostatistical approach to estimate endemicity age-standardised to the 1-99 year age range (PvPR(1-99)) within every 5×5 km resolution grid square. The model incorporated data on Duffy negative phenotype frequency to suppress endemicity predictions, particularly in Africa. Endemicity was predicted within a relatively narrow range throughout the endemic world, with the point estimate rarely exceeding 7% PvPR(1-99). The Americas contributed 22% of the global area at risk of P. vivax transmission, but high endemic areas were generally sparsely populated and the region contributed only 6% of the 2.5 billion people at risk (PAR) globally. In Africa, Duffy negativity meant stable transmission was constrained to Madagascar and parts of the Horn, contributing 3.5% of global PAR. Central Asia was home to 82% of global PAR with important high endemic areas coinciding with dense populations particularly in India and Myanmar. South East Asia contained areas of the highest endemicity in Indonesia and Papua New Guinea and contributed 9% of global PAR. CONCLUSIONS AND SIGNIFICANCE: This detailed depiction of spatially varying endemicity is intended to contribute to a much-needed paradigm shift towards geographically stratified and evidence-based planning for P. vivax control and elimination.

BACKGROUND: Combination antifungal therapy (amphotericin B deoxycholate and flucytosine) is the recommended treatment for cryptococcal meningitis but has not been shown to reduce mortality, as compared with amphotericin B alone. We performed a randomized, controlled trial to determine whether combining flucytosine or high-dose fluconazole with high-dose amphotericin B improved survival at 14 and 70 days. METHODS: We conducted a randomized, three-group, open-label trial of induction therapy for cryptococcal meningitis in patients with human immunodeficiency virus infection. All patients received amphotericin B at a dose of 1 mg per kilogram of body weight per day; patients in group 1 were treated for 4 weeks, and those in groups 2 and 3 for 2 weeks. Patients in group 2 concurrently received flucytosine at a dose of 100 mg per kilogram per day for 2 weeks, and those in group 3 concurrently received fluconazole at a dose of 400 mg twice daily for 2 weeks. RESULTS: A total of 299 patients were enrolled. Fewer deaths occurred by days 14 and 70 among patients receiving amphotericin B and flucytosine than among those receiving amphotericin B alone (15 vs. 25 deaths by day 14; hazard ratio, 0.57; 95% confidence interval [CI], 0.30 to 1.08; unadjusted P=0.08; and 30 vs. 44 deaths by day 70; hazard ratio, 0.61; 95% CI, 0.39 to 0.97; unadjusted P=0.04). Combination therapy with fluconazole had no significant effect on survival, as compared with monotherapy (hazard ratio for death by 14 days, 0.78; 95% CI, 0.44 to 1.41; P=0.42; hazard ratio for death by 70 days, 0.71; 95% CI, 0.45 to 1.11; P=0.13). Amphotericin B plus flucytosine was associated with significantly increased rates of yeast clearance from cerebrospinal fluid (-0.42 log10 colony-forming units [CFU] per milliliter per day vs. -0.31 and -0.32 log10 CFU per milliliter per day in groups 1 and 3, respectively; P<0.001 for both comparisons). Rates of adverse events were similar in all groups, although neutropenia was more frequent in patients receiving a combination therapy. CONCLUSIONS: Amphotericin B plus flucytosine, as compared with amphotericin B alone, is associated with improved survival among patients with cryptococcal meningitis. A survival benefit of amphotericin B plus fluconazole was not found. (Funded by the Wellcome Trust and the British Infection Society; Controlled-Trials.com number, ISRCTN95123928.).

The recent emergence of dengue viruses into new susceptible human populations throughout Asia and the Middle East, driven in part by human travel on both local and global scales, represents a significant global health risk, particularly in areas with changing climatic suitability for the mosquito vector. In Pakistan, dengue has been endemic for decades in the southern port city of Karachi, but large epidemics in the northeast have emerged only since 2011. Pakistan is therefore representative of many countries on the verge of countrywide endemic dengue transmission, where prevention, surveillance, and preparedness are key priorities in previously dengue-free regions. We analyze spatially explicit dengue case data from a large outbreak in Pakistan in 2013 and compare the dynamics of the epidemic to an epidemiological model of dengue virus transmission based on climate and mobility data from ∼40 million mobile phone subscribers. We find that mobile phone-based mobility estimates predict the geographic spread and timing of epidemics in both recently epidemic and emerging locations. We combine transmission suitability maps with estimates of seasonal dengue virus importation to generate fine-scale dynamic risk maps with direct application to dengue containment and epidemic preparedness.