Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
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Epidemiology of human seasonal coronaviruses among people with mild and severe acute respiratory illness in Blantyre, Malawi, 2011-2017
Kovacs D , Mambule I , Read JM , Kiran A , Chilombe M , Bvumbwe T , Aston S , Menyere M , Masina M , Kamzati M , Ganiza TN , Iuliano D , McMorrow M , Bar-Zeev N , Everett D , French N , Ho A . J Infect Dis 2024 BACKGROUND: The aim of this study was to characterize the epidemiology of human seasonal coronaviruses (HCoVs) in southern Malawi. METHODS: We tested for HCoVs 229E, OC43, NL63, and HKU1 using real-time polymerase chain reaction (PCR) on upper respiratory specimens from asymptomatic controls and individuals of all ages recruited through severe acute respiratory illness (SARI) surveillance at Queen Elizabeth Central Hospital, Blantyre, and a prospective influenza-like illness (ILI) observational study between 2011 and 2017. We modeled the probability of having a positive PCR for each HCoV using negative binomial models, and calculated pathogen-attributable fractions (PAFs). RESULTS: Overall, 8.8% (539/6107) of specimens were positive for ≥1 HCoV. OC43 was the most frequently detected HCoV (3.1% [191/6107]). NL63 was more frequently detected in ILI patients (adjusted incidence rate ratio [aIRR], 9.60 [95% confidence interval {CI}, 3.25-28.30]), while 229E (aIRR, 8.99 [95% CI, 1.81-44.70]) was more frequent in SARI patients than asymptomatic controls. In adults, 229E and OC43 were associated with SARI (PAF, 86.5% and 89.4%, respectively), while NL63 was associated with ILI (PAF, 85.1%). The prevalence of HCoVs was similar between children with SARI and controls. All HCoVs had bimodal peaks but distinct seasonality. CONCLUSIONS: OC43 was the most prevalent HCoV in acute respiratory illness of all ages. Individual HCoVs had distinct seasonality that differed from temperate settings. |
Immunological response to fractional-dose yellow fever vaccine administered during an outbreak in Kinshasa, Democratic Republic of the Congo: results 5 years after vaccination from a prospective cohort study
Doshi RH , Mukadi PK , Casey RM , Kizito GM , Gao H , Nguete UB , Laven J , Sabi L , Kaba DK , Muyembe-Tamfum JJ , Hyde TB , Ahuka-Mundeke S , Staples JE . Lancet Infect Dis 2024 BACKGROUND: In 2016, outbreaks of yellow fever in Angola and the Democratic Republic of the Congo led to a global vaccine shortage. A fractional dose of 17DD yellow fever vaccine (containing one-fifth [0·1 ml] of the standard dose) was used during a pre-emptive mass campaign in August, 2016, in Kinshasa, Democratic Republic of the Congo among children aged 2 years and older and non-pregnant adults (ie, those aged 18 years and older). 1 year following vaccination, 97% of participants were seropositive; however, the long-term durability of the immune response is unknown. We aimed to conduct a prospective cohort study and invited participants enrolled in the previous evaluation to return 5 years after vaccination to assess durability of the immune response. METHODS: Participants returned to one of six health facilities in Kinshasa in 2021, where study staff collected a brief medical history and blood specimen. We assessed neutralising antibody titres against yellow fever virus using a plaque reduction neutralisation test with a 50% cutoff (PRNT(50)). Participants with a PRNT(50) titre of 10 or higher were considered seropositive. The primary outcome was the proportion of participants seropositive at 5 years. FINDINGS: Among the 764 participants enrolled, 566 (74%) completed the 5-year visit. 5 years after vaccination, 539 (95·2%, 95% CI 93·2-96·7) participants were seropositive, including 361 (94·3%, 91·5-96·2) of 383 who were seronegative and 178 (97·3%, 93·8-98·8) of 183 who were seropositive at baseline. Geometric mean titres (GMTs) differed significantly across age groups for those who were initially seronegative with the lowest GMT among those aged 2-5 years and highest among those aged 13 years and older. INTERPRETATION: A fractional dose of the 17DD yellow fever vaccine induced an immunologic response with detectable titres at 5 years among the majority of participants in the Democratic Republic of the Congo. These findings support the use of fractional-dose vaccination for outbreak prevention with the potential for sustained immunity. FUNDING: Gavi, the Vaccine Alliance through the CDC Foundation. TRANSLATION: For the French translation of the abstract see Supplementary Materials section. |
A diverse group of small circular ssDNA viral genomes in human and non-human primate stools.
Ng TF , Zhang W , Sachsenröder J , Kondov NO , da Costa AC , Vega E , Holtz LR , Wu G , Wang D , Stine CO , Antonio M , Mulvaney US , Muench MO , Deng X , Ambert-Balay K , Pothier P , Vinjé J , Delwart E . Virus Evol 2015 1 (1) vev017 Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication initiator protein (Rep). Viral genomes were ∼2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstream of Rep. Several genomes showed evidence of recombination. By digital screening of an in-house virome database (1.04 billion reads) using BLAST, we identified closely related sequences from cases of unexplained diarrhea in France. Deep sequencing and PCR detected such genomes in 7 of 25 US (28 percent) and 14 of 21 French outbreaks (67 percent). One of eighty-five sporadic diarrhea cases in the Gambia was positive by PCR. Twenty-two complete genomes were characterized showing that viruses from patients in the same outbreaks were closely related suggesting common origins. Similar genomes were also characterized from the stools of captive chimpanzees, a gorilla, a black howler monkey, and a lemur that were more diverse than the human stool-associated genomes. The name smacovirus is proposed for this monophyletic viral clade. Possible tropism include mammalian enteric cells or ingested food components such as infected plants. No evidence of viral amplification was found in immunodeficient mice orally inoculated with smacovirus-positive stool supernatants. A role for smacoviruses in diarrhea, if any, remains to be demonstrated. |
Phylogeny of Zika Virus in Western Hemisphere, 2015.
Lanciotti RS , Lambert AJ , Holodniy M , Saavedra S , Signor Ldel C . Emerg Infect Dis 2016 22 (5) 933-5 Zika virus belongs to the genus Flavivirus, family Flaviviridae, and is transmitted by Aedes spp. mosquitoes. Clinical signs and symptoms of human infection include fever, headache, malaise, maculopapular rash, and conjunctivitis. | | Zika virus was first isolated in 1947 from the blood of a febrile sentinel rhesus monkey during a study of yellow fever in the Zika Forest of Uganda (1). During the next 20 years, Zika virus isolates were obtained primarily from East and West Africa during arbovirus surveillance studies in the absence of epidemics. During those 20 years, cases of Zika virus infection were detected sporadically; however, given the clinical similarity of Zika virus and dengue virus infections and the extensive cross-reactivity of Zika virus antibodies with dengue viruses, it is possible that Zika virus was associated with epidemics that were incorrectly attributed to dengue viruses. Beginning in 2007, substantial Zika virus outbreaks were reported first in Yap Island (Federated States of Micronesia), then in French Polynesia, and then in other Pacific Islands (2–4). |
The One Health High-Level Expert Panel (OHHLEP)
Mettenleiter TC , Markotter W , Charron DF , Adisasmito WB , Almuhairi S , Behravesh CB , Bilivogui P , Bukachi SA , Casas N , Becerra NC , Chaudhary A , Zanella JRC , Cunningham AA , Dar O , Debnath N , Dungu B , Farag E , Gao GF , Hayman DTS , Khaitsa M , Koopmans MPG , Machalaba C , Mackenzie JS , Morand S , Smolenskiy V , Zhou L . One Health Outlook 2023 5 (1) 18 One Health is an integrative and systemic approach to health, based on the understanding that human, animal and ecosystem health are inextricably linked. These interconnections and vulnerabilities were once more clearly demonstrated by the COVID-19 pandemic. This led the heads of the United Nations Food and Agriculture Organization (FAO), the United Nations Environment Programme (UNEP), the World Health Organization (WHO), and the World Organization for Animal Health (WOAH; founded as OIE), to enhance their science-based cross-sectoral collaboration by creating a multidisciplinary One Health High-Level Expert Panel (OHHLEP) to provide technical and scientific advice on One Health issues. Out of over 700 applications from all over the world, the four international partners FAO, WHO, WOAH and UNEP selected 26 experts from 24 countries as members of the OHHLEP. The multisectoral and transdisciplinary expertise present in OHHLEP members covers a wide range including animal, human and environmental health, biodiversity conservation and social sciences. The panel was conceived following a proposal by the French and German governments at the Paris Peace Forum in November 2020. It drew on the already existing FAO-OIE-WHO Tripartite intersectoral cooperation on One Health issues. In 2021, UNEP joined to form the Tripartite plus UNEP which was formally transformed into the ‘Quadripartite Collaboration for One Health’ in March 2022 and which now acts as the partner for engaging with OHHLEP. This is the first time that a global advisory panel on One Health has been created as a centre for expert advice. |
Global and regional estimates of genital human papillomavirus prevalence among men: a systematic review and meta-analysis
Bruni L , Albero G , Rowley J , Alemany L , Arbyn M , Giuliano AR , Markowitz LE , Broutet N , Taylor M . Lancet Glob Health 2023 11 (9) e1345-e1362 BACKGROUND: The epidemiology of human papillomavirus (HPV) in women has been well documented. Less is known about the epidemiology of HPV in men. We aim to provide updated global and regional pooled overall, type-specific, and age-specific prevalence estimates of genital HPV infection in men. METHODS: We conducted a systematic review and meta-analysis to assess the prevalence of genital HPV infection in the general male population. We searched Embase, Ovid MEDLINE, and the Global Index Medicus for studies published between Jan 1, 1995, and June 1, 2022. Inclusion criteria were population-based surveys in men aged 15 years or older or HPV prevalence studies with a sample size of at least 50 men with no HPV-related pathology or known risk factors for HPV infection that collected samples from anogenital sites and used PCR or hybrid capture 2 techniques for HPV DNA detection. Exclusion criteria were studies conducted among populations at increased risk of HPV infection, exclusively conducted among circumcised men, and based on urine or semen samples. We screened identified reports and extracted summary-level data from those that were eligible. Data were extracted by two researchers independently and reviewed by a third, and discrepancies were resolved by consensus. We extracted only data on mucosal α-genus HPVs. Global and regional age-specific prevalences for any HPV, high-risk (HR)-HPV, and individual HPV types were estimated using random-effects models for meta-analysis and grouped by UN Sustainable Development Goals geographical classification. FINDINGS: We identified 5685 publications from database searches, of which 65 studies (comprising 44 769 men) were included from 35 countries. The global pooled prevalence was 31% (95% CI 27-35) for any HPV and 21% (18-24) for HR-HPV. HPV-16 was the most prevalent HPV genotype (5%, 95% CI 4-7) followed by HPV-6 (4%, 3-5). HPV prevalence was high in young adults, reaching a maximum between the ages of 25 years and 29 years, and stabilised or slightly decreased thereafter. Pooled prevalence estimates were similar for the UN Sustainable Development Goal geographical regions of Europe and Northern America, Sub-Saharan Africa, Latin America and the Caribbean, and Australia and New Zealand (Oceania). The estimates for Eastern and South-Eastern Asia were half that of the other regions. INTERPRETATION: Almost one in three men worldwide are infected with at least one genital HPV type and around one in five men are infected with one or more HR-HPV types. Our findings show that HPV prevalence is high in men over the age of 15 years and support that sexually active men, regardless of age, are an important reservoir of HPV genital infection. These estimates emphasise the importance of incorporating men in comprehensive HPV prevention strategies to reduce HPV-related morbidity and mortality in men and ultimately achieve elimination of cervical cancer and other HPV-related diseases. FUNDING: Instituto de Salud Carlos III, European Regional Development Fund, Secretariat for Universities and Research of the Department of Business and Knowledge of the Government of Catalonia, and Horizon 2020. TRANSLATIONS: For the Spanish and French translations of the abstract see Supplementary Materials section. |
Notes from the field: Measles outbreak - central Ohio, 2022-2023
Tiller EC , Masters NB , Raines KL , Mathis AD , Crooke SN , Zwickl RC , French GK , Alexy ER , Koch EM , Tucker NE , Wilson EM , Krauss TS , Leasure E , Budd J , Billing LM , Dewart C , Tarter K , Dickerson K , Iyer R , Jones AN , Halabi KC , Washam MC , Sugerman DE , Roberts MW . MMWR Morb Mortal Wkly Rep 2023 72 (31) 847-849 On November 5, 2022, Columbus Public Health, Ohio and the Ohio Department of Health were notified of two children aged 2 years who were admitted to a central Ohio hospital with rash, fever, cough, and congestion, suggestive of measles. Both children were undergoing medical evaluation and treatment for other etiologies before measles was considered in the differential diagnosis. Neither child had received measles, mumps, and rubella (MMR) vaccine, and neither had known contact with a person with measles. Each patient subsequently received a positive measles real-time reverse transcription–polymerase chain reaction (RT-PCR) test result. Neither child had traveled internationally, but during June 12–October 8, 2022, four internationally imported measles cases had been confirmed among unvaccinated Franklin County, Ohio residents who had traveled to areas in East Africa where measles outbreaks were ongoing (1). Investigation of the U.S.-acquired measles cases identified additional measles cases, and local and state health departments confirmed a community outbreak on November 9, 2022. During this community measles outbreak in central Ohio, 85 locally acquired measles cases were confirmed with rash onsets during October 22–December 24, 2022; however, no definitive link to the previous international importations was established. The outbreak was declared over on February 4, 2023, 42 days (two measles incubation periods) after the last reported case. |
Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016-2018: A hidden Markov modelling study (preprint)
Thindwa D , Wolter N , Pinsent A , Carrim M , Ojal J , Tempia S , Moyes J , McMorrow M , Kleynhans J , Gottberg AV , French N , Cohen C , Flasche S . medRxiv 2021 2021.05.21.21257622 Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for 10 months for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant’s age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (<5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (≥18 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9-80.5%) than older children (5-17 years-old) (31.7-50.0%) or adults (11.5-23.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7-15.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91-1.01). Longer average carriage duration (11.4 days, 95%CI: 10.2-12.8 vs 6.0 days, 95%CI: 5.6 - 6.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507-714 vs 389, 95%CI: 311.1-435.5) were estimated in HIV-infected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission.Author summary We assessed the contribution of HIV-infected adults to household pneumococcal transmission by applying a hidden Markov model to pneumococcal cohort data comprising 115,595 nasopharyngeal samples from 1,684 individuals in rural and urban settings in South Africa. We estimated 14.4% of sample misclassifications (false negatives), representing 85.6% sensitivity of a test that was used to detect pneumococcus. Pneumococcal carriage prevalence and acquisition rates, and average duration were usually higher in younger or older children than adults. The use of ART and antibiotics reduced the average carriage duration across all age and HIV groups, and carriage acquisition risks increased in larger household sizes. Despite the longer average carriage duration and higher median carriage density in HIV-infected than HIV-uninfected adults, we found similar carriage acquisition and onward transmission risks in the dual groups. These findings suggest that vaccinating HIV-infected adults on ART with PCV would reduce their risk for pneumococcal disease but may add little to the indirect protection against carriage of the rest of the population.Competing Interest StatementThe authors have declared no competing interest.Clinical TrialNCT02519803Clinical Protocols https://www.medrxiv.org/content/10.1101/2021.01.06.21249313v1.full.pdf Funding StatementThis research was commissioned by the National Institute for Health Research (NIHR) Global Health Research Unit on Mucosal Pathogens under the UK Government. PHIRST study was funded by a cooperative agreement with the United States Centers for Disease Control and Prevention (grant number 1U01IP001048) (https://www.cdc.gov) and the Bill and Melinda Gates Foundation (Grant number: OPP1164778) (https://www.gatesfoundation.org). DT, OJ are supported by th National Institute for Health Research (NIHR) Global Health Research Unit on Mucosal Pathogens (MPRU) using UK aid from the UK Government (16/136/46) (https://www.mpru.org). AP is supported by the Bill and Melinda Gates Foundation (https://www.gatesfoundation.org). SF is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant number 208812/Z/17/Z) (https://wellcome.org). CC and AvG receive grant support through their institution from Sanofi Pasteur (https://www.sanofi.com/en). The funders had no involvement in the study design; collection, analysis and interpretation of data; writing of the report; or decision to submit the article for publication.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The longitudinal pneumococcal carriage data described in this study were obtained from consenting South African children and adults as part of the PHIRST study. The use of data was granted by the University of Witwatersrand, Human Research Ethics Committee (HREC) and the Protocol Review Committee (PRC) under approval 150808, the US CDC Institutional Review Board relied on the local review (6840), and the London School of Hygiene and Tropical Medicine Observational Research Ethics Committee under approval 17902.All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData cannot be shared publicly because of confidentiality. Data are available from the National Institute of Communicable Disease (NICD) if authorised by Institutional Data Access / Ethics Committee (contact via Professor Cherly Cohen, cherylc@nicd.ac.za) for researchers who meet the criteria for access to confidential data. The code underlying the results presented in the study are available from GitHub through the following link (https://github.com/deusthindwa/hmm.pneumococcus.hiv.south-africa) or contact Deus Thindwa through email: deus.thindwa@gmail.com |
Evaluation of the Abbott ARCHITECT HIV Ag/Ab Combo Assay for Determining Recent HIV-1 Infection (preprint)
Curtis KA , Rudolph DL , Pan Y , Delaney K , Anastos K , DeHovitz J , Kassaye SG , Hanson CV , French AL , Golub E , Adimora AA , Ofotokun I , Bolivar H , Kempf MC , Peters PJ , Switzer WM . bioRxiv 2020 2020.11.09.374017 Background Given the challenges and costs associated with implementing HIV-1 incidence assay testing, there is great interest in evaluating the use of commercial HIV diagnostic tests for determining recent HIV infection. A diagnostic test with the capability of providing reliable data for the determination of recent HIV infection without substantial modifications to the test protocol would have a significant impact on HIV surveillance. The Abbott ARCHITECT HIV Ag/Ab Combo Assay is an antigen/antibody immunoassay, which meets the criteria as the first screening test in the recommended HIV laboratory diagnostic algorithm for the United States.Methods In this study, we evaluated the performance characteristics of the ARCHITECT HIV Ag/Ab Combo signal-to-cutoff ratio (S/Co) for determining recent infection, including estimation of the mean duration of recent infection (MDRI) and false recent rate (FRR), and selection of recency cutoffs.Results The MDRI estimates for the S/Co recency cutoff of 400 is within the 4 to 12 months range recommended for HIV incidence assays, and the FRR rate for this cutoff was 1.5%. Additionally, ARCHITECT Combo S/Co values were compared relative to diagnostic test results from two prior prospective HIV-1 diagnostic studies in order to validate the use of the S/Co for both diagnostic and recency determination.Conclusion Dual-use of the ARCHITECT Combo assay data for diagnostic and incidence purposes would reduce the need for separate HIV incidence testing and allow for monitoring of recent infection for incidence estimation and other public health applications. |
The NDV-3A vaccine protects mice from multidrug resistant Candida auris infection (preprint)
Singh S , Uppuluri P , Alqarihi A , Elhassan H , French S , Lockhart SR , Chiller T , Edwards JE Jr , Ibrahim AS . bioRxiv 2018 465096 Candida auris is an emerging, multi-drug resistant, health care-associated fungal pathogen. Its predominant prevalence in hospitals and nursing homes indicates its ability to adhere to and colonize the skin, or persist in an environment outside the host - a trait unique from other Candida species. Besides being associated globally with life-threatening disseminated infections, C. auris also poses significant clinical challenges due to its ability to adhere to polymeric surfaces and form highly drug-resistant biofilms. Here, we performed bioinformatic studies to identify the presence of adhesin proteins in C. auris, with sequence as well as 3-D structural homologies to the major adhesin/invasin of C. albicans, Als3. Anti-Als3p antibodies generated by vaccinating mice with NDV-3A (a vaccine based on the N-terminus of Als3 protein formulated with alum) recognized C. auris in vitro, blocked its ability to form biofilms and enhanced macrophage-mediated killing of the fungus. Furthermore, NDV-3A vaccination induced significant levels of C. auris cross-reactive humoral and cellular immune responses, and protected immunosuppressed mice from lethal C. auris disseminated infection, compared to the control alum-vaccinated mice. Finally, NDV-3A potentiated the protective efficacy of the antifungal drug micafungin, against C. auris candidemia. Identification of Als3-like adhesins in C. auris makes it a target for immunotherapeutic strategies using NDV-3A, a vaccine with known efficacy against other Candida species and safety as well as efficacy in clinical trials. Considering that C. auris can be resistant to almost all classes of antifungal drugs, such an approach has profound clinical relevance.Author Summary Candida auris has emerged as a major health concern to hospitalized patients and nursing home subjects. C. auris strains display multidrug resistance to current antifungal therapy and cause lethal infections. We have determined that C. auris harbors homologs of C. albicans Als cell surface proteins. The C. albicans NDV-3A vaccine, harboring the N-terminus of Als3p formulated with alum, generates cross-reactive antibodies against C. auris clinical isolates and protects neutropenic mice from hematogenously disseminated C. auris infection. Importantly, the NDV-3A vaccine displays an additive protective effect in neutropenic mice when combined with micafungin. Due to its proven safety and efficacy in humans against C. albicans infection, our studies support the expedited testing of the NDV-3A vaccine against C. auris in future clinical trials. |
Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data (preprint)
Chaguza C , Heinsbroek E , Gladstone RA , Tafatatha T , Alaerts M , Peno C , Cornick JE , Musicha P , Bar-Zeev N , Kamng'ona A , Kadioglu A , McGee L , Hanage WP , Breiman RF , Heyderman RS , French N , Everett DB , Bentley SD . bioRxiv 2018 459693 Pneumococcal conjugate vaccines (PCV) have reduced pneumococcal diseases globally. Despite this, much remains to be learned about their effect on pathogen population structure. Here we undertook whole genome sequencing of 660 pneumococcal strains from asymptomatic carriers to investigate population restructuring in pneumococcal strains sampled before and after PCV13 introduction in a previously vaccine-naïve setting. We show substantial decreasing frequency of vaccine-type (VT) strains and their strain diversity post-vaccination in the vaccinated but not unvaccinated age groups indicative of direct but limited or delayed indirect effect of vaccination. Clearance of identical VT serotypes associated with multiple lineages occurred regardless of their genetic background. Interestingly, despite the increasing frequency of non-vaccine type (NVT) strains through serotype replacement, the serotype diversity was not fully restored to the levels observed prior to vaccination implying limited serotype replacement. The frequency of antibiotic resistant strains was low and remained largely unchanged post-vaccination but intermediate-penicillin-resistant lineages were reduced in the post vaccine population. Significant perturbations marked by changing frequency of accessory genes associated with diverse functions especially mobile genetic elements and bacteriocin activity were detected. This phylogenomic analysis demonstrates early vaccine-induced pneumococcal population restructuring not only at serotype but also accessory genome level.Author summary Different formulations of PCVs have been effective in reducing the invasive pneumococcal disease burden globally. Clinical trials have started to indicate high impact and effectiveness of PCV13 in Sub Saharan Africa (SSA) but there is limited understanding of how the introduction of PCVs alters the population structure of pneumococcal strains at serotype and genomic level. Here we investigated this using pneumococcal strains sampled pre‐ and post-PCV13 introduction from a previously vaccine naïve setting in Northern Malawi. Our findings reveal decrease in frequency of VT serotypes and their associated lineages in the largely vaccinated under-five population but not older individuals indicating a direct but limited or delayed indirect protection. The diversity of serotypes also decreased post-vaccination in VT strains in the under-fives but there was no change in NVT strains suggesting incomplete serotype replacement. At the genomic level, logistic regression revealed changing frequency of accessory genes largely associated with mobile genetic elements but such changes did not include any antibiotic resistance genes. These findings show significant perturbations at serotype and accessory genome level in carried pneumococcal population after two years from PCV13 introduction but the pneumococcal population was still perturbed and had not returned to a new equilibrium state. |
Report of the Science Community Workshop on the proposed first sample depot for the Mars sample return campaign
Czaja AD , Zorzano MP , Kminek G , Meyer MA , Beaty DW , Sefton-Nash E , Carrier BL , Thiessen F , Haltigin T , Bouvier A , Dauphas N , French KL , Hallis LJ , Harris RL , Hauber E , Rodriguez LE , Schwenzer SP , Steele A , Tait KT , Thorpe MT , Usui T , Vanhomwegen J , Velbel MA , Edwin S , Farley KA , Glavin DP , Harrington AD , Hays LE , Hutzler A , Wadhwa M . Meteorit Planet Sci 2023 The Mars 2020/Mars Sample Return (MSR) Sample Depot Science Community Workshop was held on September 28 and 30, 2022, to assess the Scientifically-Return Worthy (SRW) value of the full collection of samples acquired by the rover Perseverance at Jezero Crater, and of a proposed subset of samples to be left as a First Depot at a location within Jezero Crater called Three Forks. The primary outcome of the workshop was that the community is in consensus on the following statement: The proposed set of ten sample tubes that includes seven rock samples, one regolith sample, one atmospheric sample, and one witness tube constitutes a SRW collection that: (1) represents the diversity of the explored region around the landing site, (2) covers partially or fully, in a balanced way, all of the International MSR Objectives and Samples Team scientific objectives that are applicable to Jezero Crater, and (3) the analyses of samples in this First Depot on Earth would be of fundamental importance, providing a substantial improvement in our understanding of Mars. At the conclusion of the meeting, there was overall community support for forming the First Depot as described at the workshop and placing it at the Three Forks site. The community also recognized that the diversity of the Rover Cache (the sample collection that remains on the rover after placing the First Depot) will significantly improve with the samples that are planned to be obtained in the future by the Perseverance rover and that the Rover Cache is the primary target for MSR to return to Earth. © 2023 His Majesty the King in Right of Canada, Royal Ontario Museum, Jet Propulsion Laboratory, California Institute of Technology and The Authors. Government sponsorship acknowledged. Meteoritics & Planetary Science published by Wiley Periodicals LLC on behalf of The Meteoritical Society. Reproduced with the permission of the Minister of Canadian Space Agency. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. |
Completion, safety, and efficacy of tuberculosis preventive treatment regimens containing rifampicin or rifapentine: an individual patient data network meta-analysis
Winters N , Belknap R , Benedetti A , Borisov A , Campbell JR , Chaisson RE , Chan PC , Martinson N , Nahid P , Scott NA , Sizemore E , Sterling TR , Villarino ME , Wang JY , Menzies D . Lancet Respir Med 2023 11 (9) 782-790 BACKGROUND: 3 months of weekly rifapentine plus isoniazid (3HP) and 4 months of daily rifampicin (4R) are recommended for tuberculosis preventive treatment. As these regimens have not been compared directly, we used individual patient data and network meta-analysis methods to compare completion, safety, and efficacy between 3HP and 4R. METHODS: We conducted a network meta-analysis of individual patient data by searching PubMed for randomised controlled trials (RCTs) published between Jan 1, 2000, and Mar 1, 2019. Eligible studies compared 3HP or 4R to 6 months or 9 months of isoniazid and reported treatment completion, adverse events, or incidence of tuberculosis disease. Deidentified individual patient data from eligible studies were provided by study investigators and outcomes were harmonised. Methods for network meta-analysis were used to generate indirect adjusted risk ratios (aRRs) and risk differences (aRDs) with their 95% CIs. FINDINGS: We included 17 572 participants from 14 countries in six trials. In the network meta-analysis, treatment completion was higher for people on 3HP than for those on 4R (aRR 1·06 [95% CI 1·02-1·10]; aRD 0·05 [95% CI 0·02-0·07]). For treatment-related adverse events leading to drug discontinuation, risks were higher for 3HP than for 4R for adverse events of any severity (aRR 2·86 [2·12-4·21]; aRD 0·03 [0·02-0·05]) and for grade 3-4 adverse events (aRR 3·46 [2·09-6·17]; aRD 0·02 [0·01-0·03]). Similar increased risks with 3HP were observed with other definitions of adverse events and were consistent across age groups. No difference in the incidence of tuberculosis disease between 3HP and 4R was found. INTERPRETATION: In the absence of RCTs, our individual patient data network meta-analysis indicates that 3HP provided an increase in treatment completion over 4R, but was associated with a higher risk of adverse events. Although findings should be confirmed, the trade-off between completion and safety must be considered when selecting a regimen for tuberculosis preventive treatment. FUNDING: None. TRANSLATIONS: For the French and Spanish translations of the abstract see Supplementary Materials section. |
One Health: A new definition for a sustainable and healthy future.
Adisasmito WB , Almuhairi S , Behravesh CB , Bilivogui P , Bukachi SA , Casas N , Cediel Becerra N , Charron DF , Chaudhary A , Ciacci Zanella JR , Cunningham AA , Dar O , Debnath N , Dungu B , Farag E , Gao GF , Hayman DTS , Khaitsa M , Koopmans MPG , Machalaba C , Mackenzie JS , Markotter W , Mettenleiter TC , Morand S , Smolenskiy V , Zhou L . PLoS Pathog 2022 18 (6) e1010537 The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic once more demonstrated the close connection between humans, animals, and the shared environment. Although still under investigation, the closest relatives of this virus exist in animals, and the factors leading to spillover remain to be fully understood. This interconnectedness again highlighted the need for a One Health approach. Although the One Health concept is not new and has been at the forefront of interdisciplinary and multisectoral discussions for years, there is now an increased interest for this approach to be applied and translated into action. Following a proposal made by the French and German Ministers for Foreign Affairs at the November 2020 Paris Peace Forum, 4 global partners, the Food and Agriculture Organization (FAO), the World Organization for Animal Health (OIE), the United Nations Environment Programme (UNEP), and the World Health Organization (WHO), in May 2021 established the interdisciplinary One Health High-Level Expert Panel (OHHLEP) (https://www.who.int/groups/one-health-high-level-expert-panel) to enhance their cross-sectoral collaboration. The creation of OHHLEP represents a recognition at the highest level of the urgency and complexities surrounding One Health and the intent to take this concept forward into policies and concrete actions. |
Vaccine Effectiveness against DS-1-Like Rotavirus Strains in Infants with Acute Gastroenteritis, Malawi, 2013-2015
Jere KC , Bar-Zeev N , Chande A , Bennett A , Pollock L , Sanchez-Lopez PF , Nakagomi O , Tate JE , Parashar UD , Heyderman RS , French N , Iturriza-Gomara M , Cunliffe NA . Emerg Infect Dis 2019 25 (9) 1734-1737 Atypical DS-1-like G1P[8] rotaviruses emerged in 2013 in Malawi after rotavirus vaccine introduction. Vaccine effectiveness among infants hospitalized with acute DS-1-like G1P[8] rotavirus gastroenteritis was 85.6% (95% CI 34.4%-96.8%). These findings suggest that vaccine provides protection against these strains despite their emergence coinciding with vaccine introduction. |
Status of malaria in pregnancy services in Madagascar 2010-2021: a scoping review
Malpass A , Hansen N , Dentinger CM , Youll S , Cotte A , Mattern C , Ravaoarinosy A . Malar J 2023 22 (1) 59 BACKGROUND: Malaria in pregnancy (MIP) increases the risk of poor maternal and infant outcomes. To reduce these risks, WHO recommends insecticide-treated net (ITN) use, intermittent preventive treatment during pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP), and prompt case management. However, uptake of these interventions remains sub-optimal in Madagascar. A scoping review was conducted to determine the breadth and depth of information available during 2010-2021 about Madagascar's MIP activities and to identify barriers and facilitators to MIP interventions uptake. METHODS: PubMed, Google Scholar, and USAID's files (Development Experience Catalog) were searched using the terms "Madagascar AND pregnancy AND malaria," and reports and materials from stakeholders were collected. Documents in English and French from 2010 to 2021 with data regarding MIP were included. Documents were systematically reviewed and summarized; results were captured in an Excel database. RESULTS: Of 91 project reports, surveys and published articles, 23 (25%) fell within the stated time period and contained relevant data on MIP activities in Madagascar and were categorized accordingly: eight (35%) quality of care, including health facility readiness, provider knowledge and commodity availability; nine (39%) care-seeking behaviour; and, six (26%) prevention of MIP. Key barriers were identified: nine articles mentioned SP stockouts; seven found limitations of provider knowledge, attitudes, and behaviours (KAB) regarding MIP treatment and prevention; and, one reported limited supervision. MIP care seeking and prevention barriers and facilitators included women's KAB regarding MIP treatment and prevention, distance, wait times, poor service quality, cost, and/or unwelcoming providers. A 2015 survey of 52 health facilities revealed limited client access to antenatal care due to financial and geographic barriers; two 2018 surveys revealed similar findings. Self-treatment and care-seeking delays were reported even when distance was not a barrier. CONCLUSION: Among the studies and reports on MIP in Madagascar, the scoping review frequently noted barriers that could be mitigated by reducing stockouts, improving provider knowledge and attitudes, refining MIP communication, and improving service access. There is a need for coordinated efforts to address the identified barriers is the key implication of the findings. |
Capacity building at points of entry during COVID-19 pandemic: harmonising training curriculum for Economic Community of West African States
Usman AB , Lokossou VK , Sawadogo K , Ward S , Umeokonkwo CD , Sawadogo B , Hanlon C , Kayita G , Balogun MS , Antara S , Merrill R , Nguku PM , Issiaka S , Jc Aïssi MA . BMJ Glob Health 2023 8 (1) This paper describes the process for developing, validating and disseminating through a train-the-trainer (TOT) event a standardised curriculum for public health capacity building for points of entry (POE) staff across the 15-member state Economic Community of West African States (ECOWAS) that reflects both international standards and national guidelines.A five-phase process was used in developing the curriculum: phase (1) assessment of existing materials developed by the US Centers for Disease Control and Prevention (CDC), Africa CDC and the West African Economic and Monetary Union, (2) design of retained and new, harmonised content, (3) validation by the national leadership to produce final content, (4) implementation of the harmonised curriculum during a regional TOT, and (5) evaluation of the curriculum.Of the nine modules assessed in English and French, the technical team agreed to retain six harmonised modules providing materials for 10 days of intensive training. Following the TOT, most participants (n=28/30, 93.3%) indicated that the International Health Regulations and emergency management modules were relevant to their work and 96.7% (n=29/30) reported that the training should be cascaded to POE staff in their countries.The ECOWAS harmonised POE curriculum provides a set of training materials and expectations for national port health and POE staff to use across the region. This initiative contributes to reducing the effort required by countries to identify emergency preparedness and response capacity-building tools for border health systems in the Member States in a highly connected region. |
Zika virus as a cause of birth defects: Were the teratogenic effects of Zika virus missed for decades?
Gilbert RK , Petersen LR , Honein MA , Moore CA , Rasmussen SA . Birth Defects Res 2022 115 (3) 265-274 Zika virus (ZIKV) was identified as a teratogen in 2016 when an increase in severe microcephaly and other brain defects was observed in fetuses and newborns following outbreaks in French Polynesia (2013-2014) and Brazil (2015-2016) and among travelers to other countries experiencing outbreaks. Some have questioned why ZIKV was not recognized as a teratogen before these outbreaks: whether novel genetic changes in ZIKV had increased its teratogenicity or whether its association with birth defects had previously been undetected. Here we examine the evidence for these two possibilities. We describe evidence for specific mutations that arose before the French Polynesia outbreak that might have increased ZIKV teratogenicity. We also present information on children born with findings consistent with congenital Zika syndrome (CZS) as early as 2009 and epidemiological evidence that suggests increases in CZS-type birth defects before 2013. We also explore reasons why a link between ZIKV and birth defects might have been missed, including issues with surveillance of ZIKV infections and of birth defects, challenges to ZIKV diagnostic testing, and the susceptibility of different populations to ZIKV infection at the time of pregnancy. Although it is not possible to prove definitively that ZIKV had teratogenic properties before 2013, several pieces of evidence support the hypothesis that its teratogenicity had been missed in the past. These findings emphasize the need for further investments in global surveillance for emerging infections and for birth defects so that infectious teratogens can be identified more expeditiously in the future. |
A multilingual tool for standardized laboratory biosafety and biosecurity assessment and monitoring
Orelle A , Nikiema A , Zakaryan A , Albetkova AA , Keita MS , Rayfield MA , Peruski LF , Pierson A . Health Secur 2022 20 (6) 488-496 Control of infectious diseases requires the handling of infectious materials by both clinical and public health laboratories with exposure risks for laboratory personnel and environment. A comprehensive tool for assessing the capacity to manage these risks could enable the development of action plans for mitigation. Under the framework of the Global Health Security Agenda action package for biosafety and biosecurity, the authors developed a tool dedicated to assessing laboratory biosafety and biosecurity. The Biosafety and Biosecurity Laboratory Assessment Tool (BSS LAT) assesses the status of all laboratory biosafety core requirements across 10 different modules. It consists of a standardized spreadsheet-based tool that provides automatic scoring. It is designed to support national, regional, and global efforts to strengthen biosafety in clinical, public health, and veterinary laboratories. The BSS LAT was first used in Burkina Faso in collaboration with the African Society for Laboratory Medicine and the US Centers for Disease Control and Prevention to support the country in strengthening their biorisk management system. Since then, it has been successfully used in other countries (ie, Armenia, Burundi, Cameroon, Ghana, Guinea, Kazakhstan, Liberia), various settings (medical and veterinary laboratories), and translated into several languages (eg, English, French, Russian). The BSS LAT is a multipurpose tool that assists with standardization of biosafety and biosecurity requirements for all laboratories working with infectious materials, serves as a self-assessment guide for laboratories to develop improvement plans and reinforce capacities, and serves as a training guide for individual laboratories and networks or at the national level. The BSS LAT can also be used as a monitoring tool for the assessment of biosafety and biosecurity across all laboratories working with infectious materials at the national, regional, and global levels. |
Comprehensive vaccine-preventable disease surveillance in the Western Pacific Region: A literature review on integration of surveillance functions, 2000-2021
Donadel M , Scobie HM , Pastore R , Grabovac V , Batmunkh N , O'Connor S , Dahl BA , Murrill CS . Glob Health Sci Pract 2022 10 (5) INTRODUCTION: A strategic framework for 2021-2030 developed by the World Health Organization (WHO) Regional Office for the Western Pacific emphasizes the need for high-quality and integrated vaccine-preventable disease (VPD) surveillance. We conducted a literature review to document the barriers, enabling factors, and innovations for integrating surveillance functions for VPDs and other communicable diseases in Western Pacific Region (WPR) countries. METHODS: We searched published and gray literature on integrated VPD surveillance from 2000 to 2021. Articles in English, Spanish, or French were screened to identify those relating to VPD surveillance in a WPR country and not meeting defined exclusion criteria. We categorized articles using the 8 WHO surveillance support functions and abstracted data on the country; type of surveillance; and reported barriers, enabling factors, and best practices for integration. RESULTS: Of the 3,137 references screened, 87 met the eligibility criteria. Of the 8 surveillance support functions, the proportion of references that reported integration related to the laboratory was 56%, followed by workforce capacity (54%), governance (51%), data management and use (47%), field logistics and communication (47%), coordination (15%), program management (13%), and supervision (9%). Several references noted fragmented systems and a lack of coordination between units as barriers to integration, highlighting the importance of engagement across public health units and between the public and private sectors. The literature also indicated a need for interoperable information systems and revealed the use of promising new technologies for data reporting and laboratory testing. In some WPR countries, workforce capacity was strengthened at all administrative levels by the implementation of integrated trainings on data monitoring and use and on laboratory techniques applicable to multiple VPDs. CONCLUSION: This literature review supports integrating VPDs into broader communicable disease surveillance systems in WPR countries while ensuring that the minimal WHO-recommended standards for VPD surveillance are met. |
Defining elimination as a public health problem for schistosomiasis control programmes: beyond prevalence of heavy-intensity infections
Wiegand RE , Fleming FM , deVlas SJ , Odiere MR , Kinung'hi S , King CH , Evans D , French MD , Montgomery SP , Straily A , Utzinger J , Vounatsou P , Secor WE . Lancet Glob Health 2022 10 (9) e1355-e1359 WHO's 2021-30 road map for neglected tropical diseases (NTDs) outlines disease-specific and cross-cutting targets for the control, elimination, and eradication of NTDs in affected countries. For schistosomiasis, the criterion for elimination as a public health problem (EPHP) is defined as less than 1% prevalence of heavy-intensity infections (ie, 50 Schistosoma haematobium eggs per 10 mL of urine or 400 Schistosoma mansoni eggs per g of stool). However, we believe the evidence supporting this definition of EPHP is inadequate and the shifting distribution of schistosomiasis morbidity towards more subtle, rather than severe, morbidity in the face of large-scale control programmes requires guidelines to be adapted. In this Viewpoint, we outline the need for more accurate measures to develop a robust evidence-based monitoring and evaluation framework for schistosomiasis. Such a framework is crucial for achieving the goal of widespread EPHP of schistosomiasis and to meet the WHO road map targets. We encourage use of overall prevalence of schistosome infection (instead of the prevalence of heavy-intensity infections), development of species-dependent and age-dependent morbidity markers, and construction of a standardised monitoring and evaluation protocol. |
The Amazonian Tropical Bites Research Initiative, a hope for resolving zoonotic neglected tropical diseases in the One Health era
Taylor E , Aguilar-Ancori EG , Banyard AC , Abel I , Mantini-Briggs C , Briggs CL , Carrillo C , Gavidia CM , Castillo-Neyra R , Parola AD , Villena FE , Prada JM , Petersen BW , FalconPerez N , CabezasSanchez C , Sihuincha M , Streicker DG , MaguinaVargas C , NavarroVela AM , Vigilato MAN , WenFan H , Willoughby R , Horton DL , Recuenco SE . Int Health 2022 15 (2) 216-223 BACKGROUND: Neglected tropical diseases (NTDs) disproportionately affect populations living in resource-limited settings. In the Amazon basin, substantial numbers of NTDs are zoonotic, transmitted by vertebrate (dogs, bats, snakes) and invertebrate species (sand flies and triatomine insects). However, no dedicated consortia exist to find commonalities in the risk factors for or mitigations against bite-associated NTDs such as rabies, snake envenoming, Chagas disease and leishmaniasis in the region. The rapid expansion of COVID-19 has further reduced resources for NTDs, exacerbated health inequality and reiterated the need to raise awareness of NTDs related to bites. METHODS: The nine countries that make up the Amazon basin have been considered (Bolivia, Brazil, Colombia, Ecuador, French Guiana, Guyana, Peru, Surinam and Venezuela) in the formation of a new network. RESULTS: The Amazonian Tropical Bites Research Initiative (ATBRI) has been created, with the aim of creating transdisciplinary solutions to the problem of animal bites leading to disease in Amazonian communities. The ATBRI seeks to unify the currently disjointed approach to the control of bite-related neglected zoonoses across Latin America. CONCLUSIONS: The coordination of different sectors and inclusion of all stakeholders will advance this field and generate evidence for policy-making, promoting governance and linkage across a One Health arena. |
Pairing Project ECHO and patient navigation as an innovative approach to improving the health and wellness of cancer survivors in rural settings
Rohan E , Kuiper N , Bowen SA , Mast DK , House M , French C , Tharpe FS , Henley SJ , Wanliss E , Puckett M . J Rural Health 2022 38 (4) 855-864 PURPOSE: We conducted a 12-month pilot study of 2 complementary strategies for improving rural cancer survivorship outcomes: (1) Project ECHO, a telementoring model to increase knowledge and skills about cancer survivorship among multidisciplinary health care provider teams in rural areas and (2) patient navigation (PN) services to connect rural cancer survivors with resources for enhancing health and wellness. METHODS: We recruited 4 CDC-funded National Comprehensive Cancer Control Program sites to implement Project ECHO and PN interventions for a defined rural population in each of their jurisdictions. Sites received ongoing technical assistance and a stipend to support implementation. We conducted a mixed-methods evaluation consisting of quantitative performance monitoring data and qualitative interviews with site staff to assess implementation. FINDINGS: Site teams delivered 21 cancer survivorship ECHO sessions to rural providers resulting in 329 participant encounters. Almost all (93%) ECHO participants reported enhanced knowledge of cancer survivorship issues, and 80% reported intent to apply learnings to their practices. Site teams engaged 16 patient navigators who navigated 164 cancer survivors during the study period. Successful implementation required strong partnerships, clear avenues for recruitment of rural providers and cancer survivors, and activities tailored to local needs. Fostering ongoing relationships among sites through community of practice calls also enhanced implementation. CONCLUSIONS: Sites successfully implemented a novel approach for enhancing care for cancer survivors in rural communities. Pairing Project ECHO to address structural barriers and PN to address individual factors affecting survivorship may help bridge the health equity gap experienced by cancer survivors in rural communities. |
The contribution of discrete vegetables, mixed dishes, and other foods to total vegetable consumption: US ages 2 years and over, 2017-2018
Wambogo EA , Ansai N , Ahluwalia N , Ogden CL . J Acad Nutr Diet 2022 122 (11) 2115-2126 e2 BACKGROUND: The 2020-2025 Dietary Guidelines for Americans (DGAs) recommend intake of a variety of vegetables, including dark green, red and orange, starchy, and other vegetables. OBJECTIVES: This study aims to describe sociodemographic differences in the contribution of different categories of vegetables, and the form in which they are consumed, i.e., discrete vegetables, mixed dishes, and other foods such as savory snacks to total vegetables intake on a given day. DESIGN: This is a cross-sectional, secondary analysis of the 2017-2018 National Health and Nutrition Examination Survey (NHANES). PARTICIPANTS: /Setting: This study included the data of 7122 persons aged 2 years with reliable day 1 24-hour dietary recalls. MAIN OUTCOME MEASURES: Serving equivalents of vegetables from 20 discrete categories of vegetables, and from mixed dishes and other foods as a percentage of total vegetables. STATISTICAL ANALYSES: Pairwise differences by age, sex, and race and Hispanic origin, and family income were examined using univariate t statistics, and trends by age and income examined using orthogonal polynomials. RESULTS: Mean serving equivalents of vegetables was 1.4 cups. The serving equivalents increased with age among youth, was higher among non-Hispanic Asian (NHA) persons than other subgroups and increased with increasing family income. Overall, discrete vegetables contributed 55.2% of total vegetable intake and the contribution increased with age in adults, and with increasing family income. The top five discrete vegetable contributors were other vegetables and combinations, French fries and other fried white potatoes, lettuce and lettuce salads, mashed potatoes and white potato mixtures, and baked or boiled white potatoes. Non-starchy discrete vegetables contributed more to total vegetables for adults (37.6%) than youth (28.0%), and the contribution increased with increasing family income. On the other hand, the contribution of mixed dishes and other foods decreased with increasing family income. CONCLUSIONS: Discrete vegetables only contributed 55.2% of total vegetables intake, and the top sources were not varied, three of them potato-based, which may explain the reported low vegetables intake, relative to the DGAs. More than one-third of vegetables consumed were non-starchy discrete vegetables, many of which are high in vitamins. Non-starchy discrete vegetable intake was higher in adults than youth and increased with family income. |
Clinical characteristics, risk factors and outcomes in patients with severe COVID-19 registered in the International Severe Acute Respiratory and Emerging Infection Consortium WHO clinical characterisation protocol: a prospective, multinational, multicentre, observational study.
Reyes LF , Murthy S , Garcia-Gallo E , Irvine M , Merson L , Martin-Loeches I , Rello J , Taccone FS , Fowler RA , Docherty AB , Kartsonaki C , Aragao I , Barrett PW , Beane A , Burrell A , Cheng MP , Christian MD , Cidade JP , Citarella BW , Donnelly CA , Fernandes SM , French C , Haniffa R , Harrison EM , Ho AYW , Joseph M , Khan I , Kho ME , Kildal AB , Kutsogiannis D , Lamontagne F , Lee TC , Bassi GL , LopezRevilla JW , Marquis C , Millar J , Neto R , Nichol A , Parke R , Pereira R , Poli S , Povoa P , Ramanathan K , Rewa O , Riera J , Shrapnel S , Silva MJ , Udy A , Uyeki T , Webb SA , Wils EJ , Rojek A , Olliaro PL . ERJ Open Res 2022 8 (1) Due to the large number of patients with severe coronavirus disease 2019 (COVID-19), many were treated outside the traditional walls of the intensive care unit (ICU), and in many cases, by personnel who were not trained in critical care. The clinical characteristics and the relative impact of caring for severe COVID-19 patients outside the ICU is unknown. This was a multinational, multicentre, prospective cohort study embedded in the International Severe Acute Respiratory and Emerging Infection Consortium World Health Organization COVID-19 platform. Severe COVID-19 patients were identified as those admitted to an ICU and/or those treated with one of the following treatments: invasive or noninvasive mechanical ventilation, high-flow nasal cannula, inotropes or vasopressors. A logistic generalised additive model was used to compare clinical outcomes among patients admitted or not to the ICU. A total of 40440 patients from 43 countries and six continents were included in this analysis. Severe COVID-19 patients were frequently male (62.9%), older adults (median (interquartile range (IQR), 67 (55-78) years), and with at least one comorbidity (63.2%). The overall median (IQR) length of hospital stay was 10 (5-19)days and was longer in patients admitted to an ICU than in those who were cared for outside the ICU (12 (6-23) days versus 8 (4-15) days, p<0.0001). The 28-day fatality ratio was lower in ICU-admitted patients (30.7% (5797 out of 18831) versus 39.0% (7532 out of 19295), p<0.0001). Patients admitted to an ICU had a significantly lower probability of death than those who were not (adjusted OR 0.70, 95% CI 0.65-0.75; p<0.0001). Patients with severe COVID-19 admitted to an ICU had significantly lower 28-day fatality ratio than those cared for outside an ICU. |
Cross-border malaria in the triple border region between Brazil, Venezuela and Guyana
Abdallah R , Louzada J , Carlson C , Ljolje D , Udhayakumar V , Oliveira-Ferreira J , Lucchi NW . Sci Rep 2022 12 (1) 1200 The state of Roraima, in Brazil, has recently seen an increase in the number of reported Plasmodium falciparum infections believed to be imported from neighboring countries. The objective of this study was to determine the prevalence of Plasmodium species among patients attending malaria health posts in Roraima and quantify the infections attributable to imported malaria. This cross-sectional case study was carried out between March 2016 and September 2018. Study participants were recruited as they exited the malaria health post. Information about residence, occupation and travel history was collected using a questionnaire. A dried blood spot was collected and used for malaria diagnosis by PCR. A total of 1222 patients were enrolled. Of the 80% Plasmodium positive samples, 50% were P. falciparum, 34% P. vivax, 8% mixed P. falciparum/P. vivax and 0.2% mixed P. falciparum/P. ovale infections and 8% tested positive for Plasmodium, but the species could not be identified. 80% of the malaria patients likely acquired infections in Venezuela and the remaining 20% acquired in Guyana, Brazil, Suriname and French Guyana. 50% of the study participants reported to be working in a mine. Results from this study support the hypothesis that imported malaria contribute to the bulk of malaria diagnosed in Roraima. These findings are in keeping with previous findings and should be considered when developing malaria control interventions. |
Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016-2018: A hidden Markov modelling study.
Thindwa D , Wolter N , Pinsent A , Carrim M , Ojal J , Tempia S , Moyes J , McMorrow M , Kleynhans J , Gottberg AV , French N , Cohen C , Flasche S . PLoS Comput Biol 2021 17 (12) e1009680 Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for approximately 10 months each year during a three-year study period for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant's age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (<5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (≥18 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9-80.5%) than older children (5-17 years-old) (31.7-50.0%) or adults (11.5-23.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7-15.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91-1.01). Longer average carriage duration (11.4 days, 95%CI: 10.2-12.8 vs 6.0 days, 95%CI: 5.6-6.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507-714 vs 389, 95%CI: 311.1-435.5) were estimated in HIV-infected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission. |
Orbiting Sample Tiger Team Recommendation on Orbiting Sample Cleanliness
Cockell CS , Chatale R , Clement B , Davila AF , Freeman KH , French K , Glavin DP , Hays LE , Hummel K , Meyer MA , Pratt L , Salvo C , Seasly E , Tsang W . Astrobiology 2021 22 S238-S241 The National Aeronautics and Space Administration-European Space Agency (NASA-ESA) Mars Sample Return (MSR) campaign involves the collection of samples on Mars by the Perseverance (Mars 2020) rover and their return to Earth. To accomplish this, the Orbiting Sample container (OS) will be sent to Mars to accommodate the collected samples then launched from Mars and returned to Earth, where the samples will be removed for examination in the Sample Return Facility (SRF). Crucial to this entire sequence will be establishment of the required level of cleanliness inside the OS. In February 2021, the NASA Headquarters' Mars Sample Return Program and Office of Planetary Protection assembled an MSR OS Tiger Team (OSTT) to discuss the appropriate cleanliness level options of the interior of the OS. The team's remit was primarily focused on evaluating the trade-offs between Planetary Protection cleanliness levels 4a and 4b. These cleanliness levels are determined by the Committee on Space Research (COSPAR) planetary protection regulations, where 4a requires < 300 bacterial spores/m2 and < 3 x 105 bacterial spores on the spacecraft (in this case, the interior of the OS) and 4b mandates the more stringent requirement of < 30 bacterial spores on the spacecraft. This report documents the consensus opinion submitted by the OSTT that recommended the interior of the OS be cleaned to a 4a requirement with any feasible added effort toward 4b. This report provides, as well, the rationale for that decision. |
Pregnancy exposure to synthetic phenols and placental DNA methylation - An epigenome-wide association study in male infants from the EDEN cohort.
Jedynak P , Tost J , Calafat AM , Bourova-Flin E , Busato F , Forhan A , Heude B , Jakobi M , Rousseaux S , Schwartz J , Slama R , Vaiman D , Philippat C , Lepeule J . Environ Pollut 2021 290 118024 In utero exposure to environmental chemicals, such as synthetic phenols, may alter DNA methylation in different tissues, including placenta - a critical organ for fetal development. We studied associations between prenatal urinary biomarker concentrations of synthetic phenols and placental DNA methylation. Our study involved 202 mother-son pairs from the French EDEN cohort. Nine phenols were measured in spot urine samples collected between 22 and 29 gestational weeks. We performed DNA methylation analysis of the fetal side of placental tissues using the IlluminaHM450 BeadChips. We evaluated methylation changes of individual CpGs in an adjusted epigenome-wide association study (EWAS) and identified differentially methylated regions (DMRs). We performed mediation analysis to test whether placental tissue heterogeneity mediated the association between urinary phenol concentrations and DNA methylation. We identified 46 significant DMRs (≥5 CpGs) associated with triclosan (37 DMRs), 2,4-dichlorophenol (3), benzophenone-3 (3), methyl- (2) and propylparaben (1). All but 2 DMRs were positively associated with phenol concentrations. Out of the 46 identified DMRs, 7 (6 for triclosan) encompassed imprinted genes (APC, FOXG1, GNAS, GNASAS, MIR886, PEG10, SGCE), which represented a significant enrichment. Other identified DMRs encompassed genes encoding proteins responsible for cell signaling, transmembrane transport, cell adhesion, inflammatory, apoptotic and immunological response, genes encoding transcription factors, histones, tumor suppressors, genes involved in tumorigenesis and several cancer risk biomarkers. Mediation analysis suggested that placental cell heterogeneity may partly explain these associations. This is the first study describing the genome-wide modifications of placental DNA methylation associated with pregnancy exposure to synthetic phenols or their precursors. Our results suggest that cell heterogeneity might mediate the effects of triclosan exposure on placental DNA methylation. Additionally, the enrichment of imprinted genes within the DMRs suggests mechanisms by which certain exposures, mainly to triclosan, could affect fetal development. |
Development and implementation of the Ebola exposure window calculator: A tool for Ebola virus disease outbreak field investigations
Whitesell A , Bustamante ND , Stewart M , Freeman J , Dismer AM , Alarcon W , Kofman A , Ben Hamida A , Nichol ST , Damon I , Haberling DL , Keita M , Mbuyi G , Armstrong G , Juang D , Dana J , Choi MJ . PLoS One 2021 16 (8) e0255631 During an Ebola virus disease (EVD) outbreak, calculating the exposure window of a confirmed case can assist field investigators in identifying the source of infection and establishing chains of transmission. However, field investigators often have difficulty calculating this window. We developed a bilingual (English/French), smartphone-based field application to assist field investigators in determining the exposure window of an EVD case. The calculator only requires the reported date of symptoms onset and the type of symptoms present at onset or the date of death. Prior to the release of this application, there was no similar electronic capability to enable consistent calculation of EVD exposure windows for field investigators. The Democratic Republic of the Congo Ministry of Health endorsed the application and incorporated it into trainings for field staff. Available for Apple and Android devices, the calculator continues to be downloaded even as the eastern DRC outbreak resolved. We rapidly developed and implemented a smartphone application to estimate the exposure window for EVD cases in an outbreak setting. |
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