Infectious Diseases: A Collection of Translational and Clinical Research Articles

Collection

1. 1. Epidemiology and Global Health
   2. Medicine

   Investigating phenotypes of pulmonary COVID-19 recovery: A longitudinal observational prospective multicenter trial

   Thomas Sonnweber, Piotr Tymoszuk ... Judith Löffler-Ragg

   Protracted systemic and microvascular inflammation, as well as high anti-SARS-CoV-2 antibody levels, is associated with a high risk of persistent structural and functional lung deficits 6 months after COVID-19.
2. 1. Epidemiology and Global Health

   Anopheles salivary antigens as serological biomarkers of vector exposure and malaria transmission: A systematic review with multilevel modelling

   Ellen A Kearney, Paul A Agius ... Freya JI Fowkes

   A systematic review with multilevel modelling quantified the positive association between human antibodies to Anopheles salivary proteins with Anopheles-human biting rate and epidemiological measures of malaria transmission, highlighting their potential as a tool to measure vector exposure and malaria transmission.
3. 1. Immunology and Inflammation
   2. Microbiology and Infectious Disease

   Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case–control study

   Gemma Moncunill, Jason Carnes ... Raphael Gottardo

   Prevaccination levels of transcriptional modules related to monocytes, dendritic cells, and other immune categories correlate with clinical malaria risk in RTS,S/AS01E-vaccinated African children, suggesting that certain monocyte subsets may inhibit RTS,S/AS01E-induced protective responses.
4. 1. Epidemiology and Global Health
   2. Medicine

   Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: An observational cohort

   ISARIC Clinical Characterisation Group, Matthew D Hall ... Piero L Olliaro

   Patient outcomes, and the time spent by patients during hospital admission, showed considerable variation over the first year of the COVID-19 pandemic.
5. 1. Immunology and Inflammation
   2. Microbiology and Infectious Disease

   Cross-reactive antibodies after SARS-CoV-2 infection and vaccination

   Marloes Grobben, Karlijn van der Straten ... Marit J van Gils

   SARS-CoV-2 infection and vaccination elicit antibodies that cross-react with other human coronavirus spike proteins, indicating the spike S2 subdomain as a potential target strategy to develop a pan-coronavirus vaccine.
6. 1. Epidemiology and Global Health
   2. Microbiology and Infectious Disease

   Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers

   Mark Ferris, Rebecca Ferris ... Michael P Weekes

   Healthcare workers working on COVID-19 wards experience a 31-fold increased risk of infection with SARS-CoV-2 compared to colleagues on non-COVID-19 wards whilst wearing fluid-resistant surgical masks, and FFP3 respirators provide up to 100% protection against infection.
7. 1. Microbiology and Infectious Disease

   Total parasite biomass but not peripheral parasitaemia is associated with endothelial and haematological perturbations in Plasmodium vivax patients

   João L Silva-Filho, João CK Dos-Santos ... Fabio TM Costa

   Data exploring host and parasite signatures in the peripheral blood indicate that total parasite biomass is a better predictor of P. vivax-induced host responses and pathogenesis than peripheral parasitemia.
8. 1. Medicine
   2. Microbiology and Infectious Disease

   An open label randomized controlled trial of tamoxifen combined with amphotericin B and fluconazole for cryptococcal meningitis

   Nguyen Thi Thuy Ngan, Nhat Thanh Hoang Le ... Jeremy N Day

   Despite evidence of significant anti-cryptococcal activity in vitro and animal models, including synergy with other antifungal agents, high-dose tamoxifen has no impact on cerebrospinal fluid sterilization in cryptococcal meningitis.
9. 1. Microbiology and Infectious Disease

   Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1

   Shida Shangguan, Philip K Ehrenberg ... Rasmi Thomas

   Using single-cell CITE-seq to implicate monocytes as the cellular origin of a protective HIV vaccine gene signature.
10. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya

    Samuel Kariuki, Zoe A Dyson ... Gordon Dougan

    Carriage of MDR S. Typhi H58 sublineages that also cause acute disease provides understanding of the transmission dynamics of typhoid fever and maintenance of local pathogen populations in Kenya children.
11. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    SARS-CoV-2 shedding dynamics across the respiratory tract, sex, and disease severity for adult and pediatric COVID-19

    Paul Z Chen, Niklas Bobrovitz ... Frank X Gu

    COVID-19 severity, rather than sex or age, predicts SARS-CoV-2 kinetics, and SARS-CoV-2 viral load from lower respiratory tract specimens may predict severe disease days before clinical deterioration for COVID-19 patients.
12. 1. Medicine
    2. Microbiology and Infectious Disease

    Non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy is associated with lower cell-associated HIV RNA and DNA levels compared to protease inhibitor-based therapy

    Alexander O Pasternak, Jelmer Vroom ... The Co-morBidity in Relation to Aids (COBRA) Collaboration

    In two independent cohorts, NNRTI-based cART regimens are associated with significantly lower cell-associated HIV RNA levels than PI-based regimens, suggesting more potent suppression of residual virus replication by NNRTI-based regimens.
13. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination

    Christopher G Jacob, Nguyen Thuy-Nhien ... Olivo Miotto

    Large-scale genetic surveillance of malaria implemented by National Malaria Control Programmes informs public health decision makers about the spread of strains resistant to antimalarials.
14. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Malaria: A genetic intervention

    Colin Sutherland, Didier Menard

    A tool that analyzes the genome of parasites found in the blood of malaria patients can help inform policy decisions on how best to tackle the rise in drug-resistant infections.
15. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Identification of drugs associated with reduced severity of COVID-19 – a case-control study in a large population

    Ariel Israel, Alejandro A Schäffer ... Eytan Ruppin

    Large-scale retrospective analysis suggests medications and dietary supplements, such as rosuvastatin, ezetimibe, ubiquinone, risedronate, vitamin D, and magnesium, are associated with a lower rate of severe COVID-19 disease.
16. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Impact of asymptomatic Plasmodium falciparum infection on the risk of subsequent symptomatic malaria in a longitudinal cohort in Kenya

    Kelsey M Sumner, Judith N Mangeni ... Steve M Taylor

    The increased risk for symptomatic malaria following an asymptomatic Plasmodium falciparum infection supports targeting asymptomatic infections as a tool to reduce clinical malaria in high-transmission settings.
17. 1. Medicine
    2. Microbiology and Infectious Disease

    Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

    A Sarah Walker, Emma Pritchard ... COVID-19 Infection Survey team

    Wide variation in cycle threshold (Ct) values from SARS-CoV-2 RT-PCR tests over calendar time offers the potential for their broader use in public testing programmes as an ‘early-warning’ system for shifts in infectious load and hence transmission.
18. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

    Oliver Stirrup, Joseph Hughes ... Judith Breuer

    Epidemiological and viral sequence data can be combined to provide standardised feedback on cases of hospital onset COVID-19 infection that would be useful for infection prevention and control.
19. 1. Medicine
    2. Microbiology and Infectious Disease

    Combination of inflammatory and vascular markers in the febrile phase of dengue is associated with more severe outcomes

    Nguyen Lam Vuong, Phung Khanh Lam ... Sophie Yacoub

    Relationships of biomarkers with clinical outcome differed between children and adults and the best combinations associated with moderate/severe dengue comprised of six/seven vascular and immune biomarkers.
20. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link

    Huyen Nguyen, Christian Wandell Thorball ... The Swiss HIV Cohort Study

    The presence of certain HLA alleles drives the emergence or maintenance of otherwise deleterious drug-resistant mutations in patients living with HIV, even when the patient is antiretroviral treatment naïve.
21. 1. Medicine

    Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2

    Salwa Naushin, Viren Sardana ... Shantanu Sengupta

    Widespread asymptomatic SARS-CoV2 infection affected nearly 100 million Indians by September 2020 with a subsequent decline in new cases, which may be attributable to increased population immunity, albeit seeing reduced neutralization activity at 6 months this respite may be temporary.
22. 1. Medicine

    Sensitivity of ID NOW and RT–PCR for detection of SARS-CoV-2 in an ambulatory population

    Yuan-Po Tu, Jameel Iqbal, Timothy O'Leary

    Although the ID NOW platform is less sensitive than RT–PCR for identification of SARS-CoV-2 infection, it provides high positive and negative predictive values in low-prevalence populations.
23. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols

    Paul Z Chen, Niklas Bobrovitz ... Frank X Gu

    Broader case variation in respiratory viral load, and in shedding virus via droplets and aerosols, for SARS-CoV-2 than influenza A(H1N1)pdm09 facilitates greater transmission heterogeneity in the COVID-19 pandemic than the 2009 flu pandemic.
24. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

    Nick K Jones, Lucy Rivett ... Michael P Weekes

    A fourfold reduction in the rate of asymptomatic SARS-CoV-2 infection in healthcare workers ≥12 days after a single dose of BNT162b2 mRNA COVID-19 vaccine (Pfizer-BioNTech) has been found.
25. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage

    Stefanie Deinhardt-Emmer, Daniel Wittschieber ... Gita Mall

    Early postmortem autopsy of COVID-19 patients shows high viral loads and damage of the lung, although extrapulmonary cells demonstrate no injury, they contribute to inflammation, hyper-coagulation, and multiple organ dysfunction.
26. 1. Microbiology and Infectious Disease

    Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers

    Qing Yang, Nicholas R Meyerson ... Sara L Sawyer

    A quick and portable test makes saliva samples turn yellow when people are carrying SARS-CoV-2, the virus that causes COVID-19.
27. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

    Jamie M Ellingford, Ryan George ... Graeme CM Black

    Characterisation of SARS-CoV-2 genomic divergence in healthcare-associated outbreaks demonstrates that the inclusion of healthcare workers in contact networks identifies additional links in SARS-CoV-2 transmission pathways.
28. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys

    Daniel B Larremore, Bailey K Fosdick ... Yonatan H Grad

    Integrating over multiple forms of statistical uncertainty associated with serological surveys can improve serosurvey design while also enabling that uncertainty to be appropriately propagated through epidemiological models.
29. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events

    Ashish Goyal, Daniel B Reeves ... Bryan T Mayer

    A mathematical model was used to establish a simple conceptual basis for why super-spreader events fundamentally drive the spread of SARS-CoV-2 but not influenza.
30. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    In-host population dynamics of Mycobacterium tuberculosis complex during active disease

    Roger Vargas, Luca Freschi ... Maha Reda Farhat

    Bulk whole genome sequencing data can be used to study the genetic variation present in pathogenic bacterial populations over the time-course of a single infection within a host.
31. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A Bayesian analysis of the association between Leukotriene A4 Hydrolase genotype and survival in tuberculous meningitis

    Laura Whitworth, Jacob Coxon ... Lalita Ramakrishnan

    In this ideal example of pharmacogenomics, individuals with a common variant in a gene encoding for an inflammatory lipid mediator benefit selectively from standard-of-care anti-inflammatory treatment used for tuberculous meningitis.
32. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Mixed cytomegalovirus genotypes in HIV-positive mothers show compartmentalization and distinct patterns of transmission to infants

    Juanita Pang, Jennifer A Slyker ... Judith Breuer

    Genomic analyses provide new insights into natural history and pathogenesis of cytomegalovirus infection and suggest new testable hypotheses that could be important for the design and implementation of new vaccines.
33. 1. Medicine

    A novel haemocytometric COVID-19 prognostic score developed and validated in an observational multicentre European hospital-based study

    Joachim Linssen, Anthony Ermens ... Andre J van der Ven

    Distinct haemocytometric parameters, including cell activation markers, combined in a prognostic score may support early identification of COVID-19 patients likely to deteriorate and thus may benefit from ICU admission.
34. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Sex-based differences in clearance of chronic Plasmodium falciparum infection

    Jessica Briggs, Noam Teyssier ... Bryan Greenhouse

    Lower malaria prevalence in females does not appear to be due to lower rates of infection but rather due to faster clearance of asymptomatic infections.
35. 1. Medicine
    2. Microbiology and Infectious Disease

    Early prediction of level-of-care requirements in patients with COVID-19

    Boran Hao, Shahabeddin Sotudian ... Ioannis Ch Paschalidis

    Using data for 2566 COVID-19 patients from five hospitals, models are developed to predict for each patient hospitalization and critical care needs, based on demographics, comorbidities, medications, and laboratory findings.
36. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Poultry farmer response to disease outbreaks in smallholder farming systems in southern Vietnam

    Alexis Delabouglise, Nguyen Thi Le Thanh ... Maciej F Boni

    Longitudinal monitoring of poultry farms in southern Vietnam reveals that when outbreaks occur with symptoms similar to highly pathogenic avian influenza, farmers respond by sending their chickens to market early.
37. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The contribution of asymptomatic SARS-CoV-2 infections to transmission on the Diamond Princess cruise ship

    Jon C Emery, Timothy W Russell ... Rein MGJ Houben

    Nearly 75% of SARS-CoV-2 infections on the Diamond Princess were asymptomatic, half were never detected, and asymptomatic infections may have contributed substantially to transmission.
38. 1. Medicine

    Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC)

    Colin Pawlowski, Tyler Wagner ... Venky Soundararajan

    Longitudinal laboratory testing results tied to SARS-CoV-2 diagnostic PCR results of more than 2500 patients reveal the temporal evolution of COVID-associated coagulopathy.
39. 1. Medicine
    2. Microbiology and Infectious Disease

    Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis

    Tyler Wagner, FNU Shweta ... Venky Soundararajan

    Applying deep learning technology for the large-scale curation of symptoms from unstructured EHR clinical notes accurately predicts the differential signals of COVID-19 diagnosis over the week preceding typical PCR testing.
40. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Earliest infections predict the age distribution of seasonal influenza A cases

    Philip Arevalo, Huong Q McLean ... Sarah Cobey

    First influenza infections determine susceptibility to future seasonal influenza infection throughout life, and may impact vaccine effectiveness.
41. 1. Computational and Systems Biology
    2. Medicine

    A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm

    Michael R Garvin, Christiane Alvarez ... Daniel Jacobson

    Gene expression analysis reveals a novel, integrated molecular mechanism for much of the pathogenesis of COVID-19 that provides therapeutic intervention points that can be addressed with existing approved pharmaceuticals.
42. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants

    Allison L Hicks, Stephen M Kissler ... Yonatan H Grad

    Sampling informed by pathogen genomic data may facilitate more efficient detection of novel antibiotic resistance than random sampling.
43. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Antibiotic Resistance: Genomics against gonorrhoea

    Nicholas Medland

    Surveillance strategies based on whole genome sequencing could help with the early identification and detection of new forms of drug-resistant gonorrhoea.
44. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance

    Luana C Mathieu, Horace Cox ... Lise Musset

    The de novo selection of a mutation responsible for Plasmodium falciparum in vitro artemisinin resistance is confirmed in Guyana, making artemisinin combination therapies vulnerable to complete resistance in this region.
45. 1. Medicine
    2. Immunology and Inflammation

    Kallikrein-kinin blockade in patients with COVID-19 to prevent acute respiratory distress syndrome

    Frank L van de Veerdonk, Mihai G Netea ... Hans van der Hoeven

    The kinin-kallikrein system is a crucial target for the treatment of COVID-19.
46. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital

    Daniel R Evans, Marissa P Griffith ... Daria Van Tyne

    Mobile genetic elements were identified and tracked as they exchanged between multidrug-resistant bacteria causing infections at a single hospital.
47. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Impact of community piped water coverage on re-infection with urogenital schistosomiasis in rural South Africa

    Polycarp Mogeni, Alain Vandormael ... Frank Tanser

    Scale-up of piped water coverage in the local community strongly protects against S. haematobium re-infection intensity among primary school-going children following treatment with praziquantel.
48. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens

    Christine Tedijanto, Yonatan H Grad, Marc Lipsitch

    Antibiotic stewardship in the outpatient setting can substantially reduce exposures of potential pathogens to common antibiotics, and complementary efforts are needed to reduce remaining exposures that occur in 'necessary' contexts.
49. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Zika seroprevalence declines and neutralizing antibodies wane in adults following outbreaks in French Polynesia and Fiji

    Alasdair D Henderson, Maite Aubry ... Adam J Kucharski

    A combination of eight serological surveys shows a decline in seroprevalence over a two-year period following the first reports of Zika transmission in Fiji and French Polynesia.
50. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country

    Thomas Crellen, Paul Turner ... Ben S Cooper

    Colonisation with resistant Klebsiella pneumoniae in a Cambodian neonatal unit is driven by person-to-person transmission, transmissibility varies by sequence type, and antibiotic consumption generally increases the risk of acquisition.
51. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes

    Nimisha Chaturvedi, Evguenia S Svarovskaia ... Jacques Fellay

    Integrated analysis of IFN-λ and HCV amino acid variation indicates the key role of host innate immunity in viral control.
52. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria

    Sha Joe Zhu, Jason A Hendry ... Gil McVean

    Variation in the rate of mixed infections by malaria parasites and the relatedness structure among infecting strains reveals diversity in local epidemiological processes.
53. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Persistent inflammation during anti-tuberculosis treatment with diabetes comorbidity

    Nathella Pavan Kumar, Kiyoshi F Fukutani ... Hardy Kornfeld

    Systemic inflammation is greater in individuals with concurrent TB and diabetes than in euglycemic individuals with TB, and this disparity persists through the full 6-month course of anti-tubercular treatment.
54. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Potential herd protection against Plasmodium falciparum infections conferred by mass antimalarial drug administrations

    Daniel M Parker, Sai Thein Than Tun ... François Nosten

    Given sufficient population adherence, mass drug administration for falciparum malaria can provide group level benefits, also known as ‘herd effects’.
55. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Panton–Valentine leucocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial GWAS

    Bernadette C Young, Sarah G Earle ... Catrin E Moore

    Genome-wide association studies have established staphylococcal pyomyositis as a disease whose pathogenesis depends critically on expression of a single toxin, Panton–Valentine leukocidin.
56. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination

    Joseph J Campo, Timothy Q Le ... Nicholas J Croucher

    Panproteome array analysis of antibody responses to a pneumococcal whole cell vaccine reveals consistent induction of immune responses to multiple surface proteins, despite individuals' unique pre-existing antibody profiles.
57. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji

    Adam J Kucharski, Mike Kama ... Martin L Hibberd

    A combination of surveillance data, paired sera and mathematical modelling reveals which factors may influence dengue transmission and control in island settings.
58. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Synergy in anti-malarial pre-erythrocytic and transmission-blocking antibodies is achieved by reducing parasite density

    Ellie Sherrard-Smith, Katarzyna A Sala ... Andrew M Blagborough

    Combining pre-erythrocytic and transmission blocking antibodies enhances the overall control and potential elimination of malaria within both mosquito and vertebrate populations.
59. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Two complement receptor one alleles have opposing associations with cerebral malaria and interact with α⁺thalassaemia

    D Herbert Opi, Olivia Swann ... J Alexandra Rowe

    Analysis of a large Kenyan dataset may resolve previously conflicting studies by identifying polymorphisms which interact to modify the risk of cerebral malaria.
60. 1. Microbiology and Infectious Disease
    2. Medicine

    A randomised double blind placebo controlled phase 2 trial of adjunctive aspirin for tuberculous meningitis in HIV-uninfected adults

    Nguyen TH Mai, Nicholas Dobbs ... Guy E Thwaites

    Adjunctive aspirin may reduce new brain infarcts and deaths in the first 60 days of treatment for HIV-uninfected adults with tuberculous meningitis.
61. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Impact of the scale-up of piped water on urogenital schistosomiasis infection in rural South Africa

    Frank Tanser, Daniel K Azongo ... Christopher Appleton

    Scale-up of safe water supplies decreases a child's risk of urogenital schistosomiasis infection by eight-fold in a typical rural African population.
62. 1. Microbiology and Infectious Disease
    2. Medicine

    A randomized feasibility trial comparing four antimalarial drug regimens to induce Plasmodium falciparum gametocytemia in the controlled human malaria infection model

    Isaie J Reuling, Lisanne A van de Schans ... Teun Bousema

    Controlled human malaria infection model allows the study of gametocyte biology and dynamics providing novel insights and tools in malaria transmission and elimination efforts.
63. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    MERS-CoV spillover at the camel-human interface

    Gytis Dudas, Luiz Max Carvalho ... Trevor Bedford

    MERS-CoV infections in the Arabian Peninsula are the result of several hundred spillover events from viruses circulating in camels into the human population.
64. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

    Teja Turk, Nadine Bachmann ... Swiss HIV Cohort Study

    A method to assess the risk of self-sustained HIV transmission in heterosexuals from phylogenetic and epidemiological data is developed and, when applied to the Swiss HIV epidemic, shows that this risk is negligibly small for Switzerland.
65. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Epidemiological and ecological determinants of Zika virus transmission in an urban setting

    José Lourenço, Maricelia Maia de Lima ... Mario Recker

    An ento-epidemiological model reveals that what made the Zika virus a public health problem in Feira de Santana, Brazil, was a surprisingly high attack rate coupled with a low risk of Microcephaly per challenged pregnancy.
66. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

    John A Lees, Nicholas J Croucher ... Stephen D Bentley

    Sequence changes in the pneumococcal genome explain most of the variability in duration of asymptomatic carriage with serotype, antibiotic resistance and prophage accounting for the largest effects.
67. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Epidemiology: Promiscuous bacteria have staying power

    Ruth C Massey, Daniel J Wilson

    Being able to take up DNA from their environment might allow pneumococcal bacteria to colonize the human nose and throat for longer periods of time.
68. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis

    Anneli Cooper, Hamidou Ilboudo ... Annette MacLeod

    Common kidney disease risk variants in African populations are associated with reduced susceptibility to deadly African trypanosomes.
69. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Gene Variation: The double-edged sword of evolution

    Etty Kruzel-Davila, Karl Skorecki

    Two gene variants provide different levels of protection against sleeping sickness, but this comes with an increased risk of developing chronic kidney disease.
70. 1. Medicine
    2. Microbiology and Infectious Disease

    Reproducible diagnostic metabolites in plasma from typhoid fever patients in Asia and Africa

    Elin Näsström, Christopher M Parry ... Stephen Baker

    Mass spectrometry on plasma from patients with typhoid fever and other febrile disease identified and validated 24 metabolites that can distinguish typhoid from other febrile diseases, providing a new approach for typhoid diagnostics.
71. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The skin is a significant but overlooked anatomical reservoir for vector-borne African trypanosomes

    Paul Capewell, Christelle Cren-Travaillé ... Annette MacLeod

    African trypanosomes residing within the skin of infected humans represent an important yet overlooked transmissible parasite population that may thwart efforts to eliminate African sleeping sickness.
72. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Trypanosomiasis: Skin deep

    Aitor Casas-Sánchez, Álvaro Acosta-Serrano
73. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Updates to the zoonotic niche map of Ebola virus disease in Africa

    David M Pigott, Anoushka I Millear ... Simon I Hay

    Building on previous work (Pigott et al. 2014), estimates of areas of potential transmission of Ebola virus are revised and updated to provide a contemporary map for use by researchers and policymakers.
74. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure

    Duy Pham Thanh, Abhilasha Karkey ... Stephen Baker

    A fluoroquinolone resistant variant of Salmonella Typhi has emerged that is likely to be widespread in the Indian subcontinent; therefore fluoroquinolones should not be recommended for empirical typhoid fever therapy in this setting.
75. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping global environmental suitability for Zika virus

    Jane P Messina, Moritz UG Kraemer ... Simon I Hay

    A global map of environmental suitability for Zika virus and the estimated population living at potential risk can help refine public health guidelines, travel advisories and intervention strategies at a crucial time in the global emergence of this arbovirus.
76. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent

    Hideo Imamura, Tim Downing ... James A Cotton

    Genome sequencing reveals the evolution and epidemiology of Leishmania donovani in the Indian subcontinent, where epidemics have caused up to 30,000 deaths per year.
77. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

    Kirsten I Bos, Alexander Herbig ... Hendrik N Poinar

    The analysis of 18^th century Y. pestis genomes reveals a bacterial lineage that might be responsible for the 400-year period of European plague epidemics from the Renaissance through early modern times.
78. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Genomic epidemiology of artemisinin resistant malaria

    MalariaGEN Plasmodium falciparum Community Project

    Plasmodium falciparum kelch13 mutations that cause artemisinin resistant malaria in Southeast Asia show markedly different patterns of evolutionary selection in Africa.
79. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Evaluating probabilistic dengue risk forecasts from a prototype early warning system for Brazil

    Rachel Lowe, Caio AS Coelho ... Xavier Rodó

    The evaluation of a dengue early warning system demonstrates its potential to assist dengue prevention and control up to three months ahead of future epidemics.
80. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping influenza transmission in the ferret model to transmission in humans

    Michael G Buhnerkempe, Katelyn Gostic ... James O Lloyd-Smith

    Influenza transmission among ferrets correlates strongly with transmission among humans, so the ferret model for influenza transmission is a valid tool for pandemic potential in humans.
81. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance

    Caroline Colijn, Ted Cohen

    Both within and between hosts, the key factor guiding whether increasing treatment strength will increase or decrease antibiotic resistance is whether inter-strain competition is effective, not whether it is present.
82. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Integrating between-host transmission and within-host immunity to analyze the impact of varicella vaccination on zoster

    Benson Ogunjimi, Lander Willem ... Niel Hens

    An individual-based model estimates exogenous boosting of immunity following re-exposure to chickenpox is limited to 2 years after re-exposure, but an increase in herpes zoster incidence is still expected to occur following universal varicella vaccination.
83. 1. Medicine
    2. Microbiology and Infectious Disease

    Mucosal effects of tenofovir 1% gel

    Florian Hladik, Adam Burgener ... Ian McGowan

    Mucosal application of the anti-retroviral drug tenofovir, which is intended to prevent HIV transmission, has many off-target effects on the mucosa itself.
84. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Epidemiological dynamics of Ebola outbreaks

    Thomas House

    The pattern of past Ebola outbreaks is indicative of an effective reproductive ratio of less than 1, which can lead to the generation of a range of outbreak sizes consistent with the scale of the ongoing epidemic.
85. 1. Medicine
    2. Microbiology and Infectious Disease

    HIV-1 DNA predicts disease progression and post-treatment virological control

    James P Williams, Jacob Hurst ... John Frater

    Measuring HIV-1 DNA levels at the time of stopping antiretroviral therapy (when initiated during primary infection) predicts clinical progression and the time taken for plasma viraemia to become detectable.
86. 1. Medicine
    2. Microbiology and Infectious Disease

    HIV Cure Research: Biomarker reveals HIV's hidden reservoir

    Leslie R Cockerham, Steven G Deeks
87. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping the zoonotic niche of Ebola virus disease in Africa

    David M Pigott, Nick Golding ... Simon I Hay

    Understanding where future Ebola virus outbreaks may start and the changing nature of the populations living in these places is of critical importance in helping to prepare for future outbreaks.
88. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Epidemiology: Mapping Ebola in wild animals for better disease control

    Sebastian Funk, Peter Piot
89. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Global distribution maps of the leishmaniases

    David M Pigott, Samir Bhatt ... Simon I Hay

    Maps defining environmental risk of the leishmaniases provide insights into the ecology of these diseases and identify regions to target public health measures and inform future burden estimates.
90. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Salmonella Typhi and Salmonella Paratyphi A elaborate distinct systemic metabolite signatures during enteric fever

    Elin Näsström, Nga Tran Vu Thieu ... Henrik Antti

    Metabolite analysis of plasma from enteric fever patients define signals of organism specific host–pathogen interactions and provides opportunities for new diagnostics.
91. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Host-pathogen Interactions: Honing in on enteric fever

    Lyle R McKinnon, Quarraisha Abdool Karim
92. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    A micro-epidemiological analysis of febrile malaria in Coastal Kenya showing hotspots within hotspots

    Philip Bejon, Thomas N Williams ... Steffen Borrmann

    Malaria 'hotspots' can be identified that range in size from a few homesteads to a village, and it will be necessary to eliminate hotspots at varying scales as we progress towards eliminating malaria.
93. 1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

    István Bartha, Jonathan M Carlson ... Jacques Fellay

    An innovative strategy in genome analysis has generated a detailed description of how pathogens mutate when facing human genetic diversity.
94. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Rapid localized spread and immunologic containment define Herpes simplex virus-2 reactivation in the human genital tract

    Joshua T Schiffer, David Swan ... Lawrence Corey

    A combination of detailed sampling and mathematical modeling suggests that the response of immune cells to reactivation of herpes simplex virus 2 is extremely rapid and effective within microscopic areas of genital skin.
95. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Global divergence in critical income for adult and childhood survival: analyses of mortality using Michaelis–Menten

    Ryan J Hum, Prabhat Jha ... Yu-Ling Cheng

    A mathematical model based on enzyme kinetics shows how the relationships between life expectancy, survival rates for children and adults, and national income change over time.
96. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Population Biology: Enzymes provide demographers with food for thought

    Mark Jit, Patrick Gerland