Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
Records 1-30 (of 150 Records) |
Query Trace: Cruz K [original query] |
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Assessing the impact of the 2020 Council of State and Territorial Epidemiologists case definition for pertussis on reported pertussis cases
Rubis AB , Cole M , Tondella ML , Pawloski LC , Youngkin E , Firmender P , Aden V , Cruz V , Stanislawski E , Wester R , Cieslak PR , Acosta AM , Skoff TH . Clin Infect Dis 2024 BACKGROUND: In 2020, the Council of State and Territorial Epidemiologists (CSTE) pertussis case definition was modified; the main change was classifying PCR-positive cases as confirmed, regardless of cough duration. Pertussis data reported through Enhanced Pertussis Surveillance (EPS) in seven sites and the National Notifiable Diseases Surveillance System (NNDSS) were used to evaluate the impact of the new case definition. METHODS: We compared the number of EPS cases with cough onset in 2020 to the number that would have been reported based on the prior (2014) CSTE case definition. To assess the impact of the change nationally, the proportion of EPS cases newly reportable under the 2020 CSTE case definition was applied to 2020 NNDSS data to estimate how many additional cases were captured nationally. RESULTS: Among 442 confirmed and probable cases reported to EPS states in 2020, 42 (9.5%) were newly reportable according to the 2020 case definition. Applying this proportion to the 6,124 confirmed and probable cases reported nationally in 2020, we estimated that the new definition added 582 cases. Had the case definition not changed, reported cases in 2020 would have decreased by 70% from 2019; the observed decrease was 67%. CONCLUSIONS: Despite a substantial decrease in reported pertussis cases in the setting of COVID-19, our data show that the 2020 pertussis case definition change resulted in additional case reporting compared with the previous case definition, providing greater opportunities for public health interventions such as prophylaxis of close contacts. |
Multistate outbreak of Salmonella Oranienburg infections linked to bulb onions imported from Mexico – United States, 2021
Mitchell MR , Kirchner M , Schneider B , McClure M , Neil KP , Madad A , Jemaneh T , Tijerina M , Nolte K , Wellman A , Neises D , Pightling A , Swinford A , Piontkowski A , Sexton R , McKenna C , Cornell J , Sandoval AL , Wang H , Bell RL , Stager C , Zamora Nava MC , Lara de la Cruz JL , Sánchez Córdova LI , Galván PR , Ortiz JA , Flowers S , Grisamore A , Gieraltowski L , Bazaco M , Viazis S . Food Control 2024 160 In 2021, the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and state and local health and regulatory partners investigated an outbreak of Salmonella enterica serovar Oranienburg infections linked to bulb onions from Mexico, resulting in 1040 illnesses and 260 hospitalizations across 39 states, the District of Columbia, and Puerto Rico. The Kansas Department of Agriculture recovered the outbreak strain of Salmonella Oranienburg from a sample of condiment collected from an ill person's home. The condiment was made with cilantro, lime, and onions, but, at the time of collection, there were no onions remaining in it. FDA conducted traceback investigations for white, yellow, and red bulb onions, cilantro, limes, tomatoes, and jalapeño peppers. Growers in the state of Chihuahua, Mexico, were identified as supplying the implicated onions that could account for exposure to onions for all illnesses included in the traceback investigation, but investigators could not determine a single source or route of contamination. FDA collected product and environmental samples across the domestic supply chain but did not recover the outbreak strain of Salmonella. Binational collaboration and information sharing supported Mexican authorities in collecting environmental samples from two packing plants and onion, water, and environmental samples from 15 farms and firms in Chihuahua, Mexico identified through FDA's traceback investigation, but did not recover the outbreak strain. Distributors of the implicated onions issued voluntary recalls of red, yellow, and white whole, fresh onions imported from the state of Chihuahua, Mexico. This outbreak showcased how investigators overcame significant traceback and epidemiologic challenges, the need for strengthening the ongoing collaboration between U.S. and Mexican authorities and highlighted the need for identifying practices across the supply chain that can help improve the safety of onions. © 2024 |
Author Correction: Ultra-long-acting in-situ forming implants with cabotegravir protect female macaques against rectal SHIV infection
Young IC , Massud I , Cottrell ML , Shrivastava R , Maturavongsadit P , Prasher A , Wong-Sam A , Dinh C , Edwards T , Mrotz V , Mitchell J , Seixas JN , Pallerla A , Thorson A , Schauer A , Sykes C , De la Cruz G , Montgomery SA , Kashuba ADM , Heneine W , Dobard CW , Kovarova M , Garcia JV , Garcίa-Lerma JG , Benhabbour SR . Nat Commun 2024 15 (1) 1054 |
Assessing the living environment of persons displaced following a strong earthquake sequence in Puerto Rico, 2020
Cruz MA , Garfield R , Irizarry J , Torres-Delgado NI , Rodriguez-Rivera MZ , Montoya-Zavala M , Cortes LM , Algarín G , Bayleyegn T , Funk RH , Rodriguez-Orengo JF , Zavala DE . J Emerg Manag 2023 21 (6) 487-495 In the public health portfolio of disaster tools, rapid needs assessments are essential intelligence data mining resources that can assess immediate needs in almost all hazard scenarios. Following prolonged and unusual seismic activity that caused significant structural damage, mainly in the southwest part of the island of Puerto Rico, thousands of area residents were forced to leave their homes and establish improvised camps. The austere environmental exposure and limited access to safety and hygiene services prompted public health authorities to request assistance with conducting a rapid needs assessment of those encampments. This report summarizes the design, organization, and execution of a rapid needs assessment of improvised camps following a strong sequence of earthquakes in Puerto Rico. |
Using regional sero-epidemiology SARS-CoV-2 Anti-S antibodies in the Dominican Republic to inform targeted public health response
Mario Martin B , Cadavid Restrepo A , Mayfield HJ , Then Paulino C , De St Aubin M , Duke W , Jarolim P , Zielinski Gutiérrez E , Skewes Ramm R , Dumas D , Garnier S , Etienne MC , Peña F , Abdalla G , Lopez B , de la Cruz L , Henríquez B , Baldwin M , Sartorius B , Kucharski A , Nilles EJ , Lau CL . Trop Med Infect Dis 2023 8 (11) Incidence of COVID-19 has been associated with sociodemographic factors. We investigated variations in SARS-CoV-2 seroprevalence at sub-national levels in the Dominican Republic and assessed potential factors influencing variation in regional-level seroprevalence. Data were collected in a three-stage cross-sectional national serosurvey from June to October 2021. Seroprevalence of antibodies against the SARS-CoV-2 spike protein (anti-S) was estimated and adjusted for selection probability, age, and sex. Multilevel logistic regression was used to estimate the effect of covariates on seropositivity for anti-S and correlates of 80% protection (PT(80)) against symptomatic infection for the ancestral and Delta strains. A total of 6683 participants from 134 clusters in all 10 regions were enrolled. Anti-S, PT80 for the ancestral and Delta strains odds ratio varied across regions, Enriquillo presented significant higher odds for all outcomes compared with Yuma. Compared to being unvaccinated, receiving ≥2 doses of COVID-19 vaccine was associated with a significantly higher odds of anti-S positivity (OR 85.94, [10.95-674.33]) and PT(80) for the ancestral (OR 4.78, [2.15-10.62]) and Delta strains (OR 3.08, [1.57-9.65]) nationally and also for each region. Our results can help inform regional-level public health response, such as strategies to increase vaccination coverage in areas with low population immunity against currently circulating strains. |
The Human Phenotype Ontology in 2024: phenotypes around the world
Gargano MA , Matentzoglu N , Coleman B , Addo-Lartey EB , Anagnostopoulos AV , Anderton J , Avillach P , Bagley AM , Bakštein E , Balhoff JP , Baynam G , Bello SM , Berk M , Bertram H , Bishop S , Blau H , Bodenstein DF , Botas P , Boztug K , Čady J , Callahan TJ , Cameron R , Carbon SJ , Castellanos F , Caufield JH , Chan LE , Chute CG , Cruz-Rojo J , Dahan-Oliel N , Davids JR , de Dieuleveult M , de Souza V , de Vries BBA , de Vries E , DePaulo JR , Derfalvi B , Dhombres F , Diaz-Byrd C , Dingemans AJM , Donadille B , Duyzend M , Elfeky R , Essaid S , Fabrizzi C , Fico G , Firth HV , Freudenberg-Hua Y , Fullerton JM , Gabriel DL , Gilmour K , Giordano J , Goes FS , Moses RG , Green I , Griese M , Groza T , Gu W , Guthrie J , Gyori B , Hamosh A , Hanauer M , Hanušová K , He YO , Hegde H , Helbig I , Holasová K , Hoyt CT , Huang S , Hurwitz E , Jacobsen JOB , Jiang X , Joseph L , Keramatian K , King B , Knoflach K , Koolen DA , Kraus ML , Kroll C , Kusters M , Ladewig MS , Lagorce D , Lai MC , Lapunzina P , Laraway B , Lewis-Smith D , Li X , Lucano C , Majd M , Marazita ML , Martinez-Glez V , McHenry TH , McInnis MG , McMurry JA , Mihulová M , Millett CE , Mitchell PB , Moslerová V , Narutomi K , Nematollahi S , Nevado J , Nierenberg AA , Čajbiková NN , Nurnberger JI Jr , Ogishima S , Olson D , Ortiz A , Pachajoa H , Perez de Nanclares G , Peters A , Putman T , Rapp CK , Rath A , Reese J , Rekerle L , Roberts AM , Roy S , Sanders SJ , Schuetz C , Schulte EC , Schulze TG , Schwarz M , Scott K , Seelow D , Seitz B , Shen Y , Similuk MN , Simon ES , Singh B , Smedley D , Smith CL , Smolinsky JT , Sperry S , Stafford E , Stefancsik R , Steinhaus R , Strawbridge R , Sundaramurthi JC , Talapova P , Tenorio Castano JA , Tesner P , Thomas RH , Thurm A , Turnovec M , van Gijn ME , Vasilevsky NA , Vlčková M , Walden A , Wang K , Wapner R , Ware JS , Wiafe AA , Wiafe SA , Wiggins LD , Williams AE , Wu C , Wyrwoll MJ , Xiong H , Yalin N , Yamamoto Y , Yatham LN , Yocum AK , Young AH , Yüksel Z , Zandi PP , Zankl A , Zarante I , Zvolský M , Toro S , Carmody LC , Harris NL , Munoz-Torres MC , Danis D , Mungall CJ , Köhler S , Haendel MA , Robinson PN . Nucleic Acids Res 2023 52 D1333-D1346 The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs. |
Trade-offs between individual and ensemble forecasts of an emerging infectious disease (preprint)
Oidtman RJ , Omodei E , Kraemer MUG , Castañeda-Orjuela CA , Cruz-Rivera E , Misnaza-Castrillón S , Cifuentes MP , Rincon LE , Cañon V , Alarcon P , España G , Huber JH , Hill SC , Barker CM , Johansson MA , Manore CA , Reiner RC Jr , Rodriguez-Barraquer I , Siraj AS , Frias-Martinez E , García-Herranz M , Perkins TA . medRxiv 2021 2021.02.25.21252363 When new pathogens emerge, numerous questions arise about their future spread, some of which can be addressed with probabilistic forecasts. The many uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among model structures and assumptions, however. To assess the potential for uncertainties about emerging pathogens to affect forecasts of their spread, we evaluated the performance of a suite of 16 forecasting models in the context of the 2015-2016 Zika epidemic in Colombia. Each model featured a different combination of assumptions about the role of human mobility in driving transmission, spatiotemporal variation in transmission potential, and the number of times the virus was introduced. All models used the same core transmission model and the same iterative data assimilation algorithm to generate forecasts. By assessing forecast performance through time using logarithmic scoring with ensemble weighting, we found that which model assumptions had the most ensemble weight changed through time. In particular, spatially coupled models had higher ensemble weights in the early and late phases of the epidemic, whereas non-spatial models had higher ensemble weights at the peak of the epidemic. We compared forecast performance of the equally-weighted ensemble model to each individual model and identified a trade-off whereby certain individual models outperformed the ensemble model early in the epidemic but the ensemble model outperformed all individual models on average. On balance, our results suggest that suites of models that span uncertainty across alternative assumptions are necessary to obtain robust forecasts in the context of emerging infectious diseases.Competing Interest StatementThe authors have declared no competing interest.Funding StatementRJO acknowledges support from an Eck Institute for Global Health Fellowship, GLOBES grant, Arthur J. Schmitt Fellowship, and the UNICEF Office of Innovation. MUGK is supported by The Branco Weiss Fellowship - Society in Science, administered by the ETH Zurich and acknowledges funding from the Oxford Martin School and the European Union Horizon 2020 project MOOD (\#874850). SCH is supported by the Wellcome Trust (220414/Z/20/Z).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:No IRB approvals were necessary.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.YesThe mobile phone data set used in this study is proprietary and subject to strict privacy regulations. The access to this data set was granted after reaching a non-disclosure agreement with the proprietor, who anonymized and aggregated the original data before giving access to the authors. The mobile phone is available on request after negotiation of a non-disclosure agreement with the company. The contact person is Enrique Frias-Martinez (efm{at}tid.es). Epidemiological, meteorological, and demographic data are available from Siraj et al.2018 and additionally available on https://github.com/roidtman/eid_ensemble_forecasting. https://www.github.com/roidtman/eid_ensemble_forecasting |
COPLA, a taxonomic classifier of plasmids (preprint)
Redondo-Salvo S , Bartomeus-Peñalver R , Vielva L , Tagg KA , Webb HE , Fernández-López R , de la Cruz F . bioRxiv 2020 2020.12.15.422809 The Plasmid Taxonomic Unit (PTU) concept is an initial step for a natural classification of plasmids. Here we present COPLA, a software for plasmid assignation to existing PTUs. To assess its performance, we used a sample of 1,000 plasmids missing from its current database. Overall, 41% of samples could be assigned an existing PTU (63% within the most abundant order, Enterobacterales), while 4% of samples could help to define new PTUs once COPLA database was updated.Competing Interest StatementThe authors have declared no competing interest. |
Comparative genomics of the major parasitic worms (preprint)
International Helminth Genomes Consortium , Coghlan Avril , Tyagi Rahul , Cotton James A , Holroyd Nancy , Rosa Bruce A , Tsai Isheng Jason , Laetsch Dominik R , Beech Robin N , Day Tim A , Hallsworth-Pepin Kymberlie , Ke Huei-Mien , Kuo Tzu-Hao , Lee Tracy J , Martin John , Maizels Rick M , Mutowo Prudence , Ozersky Philip , Parkinson John , Reid Adam J , Rawlings Neil D , Ribeiro Diogo M , Seshadri Swapna Lakshmipuram , Stanley Eleanor , Taylor David W , Wheeler Nicolas J , Zamanian Mostafa , Zhang Xu , Allan Fiona , Allen Judith E , Asano Kazuhito , Babayan Simon A , Bah Germanus , Beasley Helen , Bennett Hayley M , Bisset Stewart A , Castillo Estela , Cook Joseph , Cooper Philip J , Cruz-Bustos Teresa , Cuéllar Carmen , Devaney Eileen , Doyle Stephen R , Eberhard Mark L , Emery Aidan , Eom Keeseon S , Gilleard John S , Gordon Daria , Harcus Yvonne , Harsha Bhavana , Hawdon John M , Hill Dolores E , Hodgkinson Jane , Horák Petr , Howe Kevin L , Huckvale Thomas , Kalbe Martin , Kaur Gaganjot , Kikuchi Taisei , Koutsovoulos Georgios , Kumar Sujai , Leach Andrew R , Lomax Jane , Makepeace Benjamin , Matthews Jacqueline B , Muro Antonio , O’Boyle Noel Michael , Olson Peter D , Osuna Antonio , Partono Felix , Pfarr Kenneth , Rinaldi Gabriel , Foronda Pilar , Rollinson David , Gomez Samblas Mercedes , Sato Hiroshi , Schnyder Manuela , Scholz Tomáš , Shafie Myriam , Tanya Vincent N , Toledo Rafael , Tracey Alan , Urban Joseph F , Wang Lian-Chen , Zarlenga Dante , Blaxter Mark L , Mitreva Makedonka , Berriman Matthew . bioRxiv 2017 236539 Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we compare the genomes of 81 nematode and platyhelminth species, including those of 76 parasites. From 1.4 million genes, we identify gene family births and hundreds of large expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We use a wide-ranging in silico screen to identify and prioritise new potential drug targets and compounds for testing. We also uncover lineage-specific differences in core metabolism and in protein families historically targeted for drug development. This is the broadest comparative study to date of the genomes of parasitic and non-parasitic worms. It provides a transformative new resource for the research community to understand and combat the diseases that parasitic worms cause. |
High Burden of COVID-19 among Unvaccinated Law Enforcement Officers and Firefighters (preprint)
Caban-Martinez AJ , Gaglani M , Olsho LEW , Grant L , Schaefer-Solle N , Louzado-Feliciano P , Tyner HL , Yoon SK , Naleway AL , Smith M , Sokol BE , Lutrick K , Fowlkes AL , Meece J , Noriega R , Odean M , Phillips AL , Groom HC , Murthy K , Edwards LJ , Ellingson KD , Yoo YM , Cruz A , Respet K , Thiese MS , Kuntz JL , Rose S , Hadden LS , Gerald JK , Mak J , Gallimore-Wilson D , Lundgren J , Hegmann KT , Dunnigan K , Wesley MG , Bedrick EJ , Lamberte JM , Jones JM , Hunt A , Bruner MM , Groover K , Kutty PK , Testoff AC , LeClair LB , Etolue JM , Thompson MG , Burgess JL . medRxiv 2021 26 Law Enforcement Officers (LEOs), firefighters, and other first responders are at increased risk of SARS-CoV-2 infection compared to healthcare personnel but have relatively low COVID-19 vaccine uptake. Resistance to COVID-19 vaccine mandates among first responders has the potential to disrupt essential public services and threaten public health and safety. Using data from the HEROES-RECOVER prospective cohorts, we report on the increased illness burden of COVID-19 among unvaccinated first responders. From January to September 2021, first responders contributed to weekly active surveillance for COVID-19-like illness (CLI). Self-collected respiratory specimens collected weekly, irrespective of symptoms, and at the onset CLI were tested by Reverse Transcription Polymerase Chain Reaction (RT-PCR) assay for SARSCoV-2. Among 1415 first responders, 17% were LEOs, 68% firefighters, and 15% had other first responder occupations. Unvaccinated (41%) compared to fully vaccinated (59%) first responders were less likely to believe COVID-19 vaccines are very or extremely effective (17% versus 54%) or very or extremely safe (15% versus 54%). From January through September 2021, among unvaccinated LEOs, the incidence of COVID-19 was 11.9 per 1,000 person-weeks (95%CI=7.0-20.1) compared to only 0.6 (95%CI=0.2-2.5) among vaccinated LEOs. Incidence of COVID-19 was also higher among unvaccinated firefighters (9.0 per 1,000 person-weeks; 95%CI=6.4-12.7) compared to those vaccinated (1.8 per 1,000; 95%CI=1.1-2.8). Once they had laboratory-confirmed COVID-19, unvaccinated first responders were sick for a mean+/-SD of 14.7+/-21.7 days and missed a mean of 38.0+/-46.0 hours of work. These findings suggest that state and local governments with large numbers of unvaccinated first responders may face major disruptions in their workforce due to COVID-19 illness. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. |
Integrated SARS-CoV-2 serological and virological screening across an acute fever surveillance platform to monitor temporal changes in anti-spike antibody levels and risk of infection during sequential waves of variant transmission - Dominican Republic, March 2021 to August 2022 (preprint)
Nilles EJ , Aubin MDSt , Dumas D , Duke W , Etienne MC , Abdalla G , Jarolim P , Oasan T , Garnier S , Iihoshi N , Lopez B , de la Cruz L , Puello YC , Baldwin M , Roberts KW , Pena F , Durski K , Sanchez IM , Gunter SM , Kneubehl AR , Murray KO , Lino A , Strobel S , Baez AA , Lau CL , Kucharski A , Gutierrez EZ , Skewes-Ramm R , Vasquez M , Paulino CT . medRxiv 2022 26 The global SARS-CoV-2 immune landscape and population protection against emerging variants is largely unknown. We assessed SARS-CoV-2 antibody changes in the Dominican Republic and implications for immunological protection against variants of concern. Between March 2021 and August 2022, 2,300 patients with undifferentiated febrile illnesses were prospectively enrolled. Sera was tested for total anti-spike antibodies and simultaneously collected nasopharyngeal samples for acute SARSCoV-2 infection with RT-PCR. Geometric mean anti-spike titers increased from 6.6 BAU/ml (95% CI 5.1-8.7) to 1,332 BAU/ml (1055-1,682). Multivariable binomial odds ratios for acute SARS-CoV-2 infection were 0.55 (0.40-0.74), 0.38 (0.27-0.55), and 0.27 (0.18-0.40) for the second, third, and fourth versus the first anti-S quartile, with similar findings by viral strain. Integrated serological and virological screening can leverage existing acute fever surveillance platforms to monitor population-level immunological markers and concurrently characterize implications for emergent variant transmission in near real-time. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Reemergence of Dengue Virus Serotype 3, Brazil, 2023
Naveca FG , Santiago GA , Maito RM , Ribeiro Meneses CA , do Nascimento VA , de Souza VC , do Nascimento FO , Silva D , Mejía M , Gonçalves L , de Figueiredo RMP , Ribeiro Cruz AC , Diniz Nunes BT , Presibella MM , Quallio Marques NF , Riediger IN , de Mendonça MCL , de Bruycker-Nogueira F , Sequeira PC , de Filippis AMB , Resende P , Campos T , Wallau GL , Gräf T , Delatorre E , Kopp E , Morrison A , Muñoz-Jordán JL , Bello G . Emerg Infect Dis 2023 29 (7) 1482-1484 We characterized 3 autochthonous dengue virus serotype 3 cases and 1 imported case from 2 states in the North and South Regions of Brazil, 15 years after Brazil's last outbreak involving this serotype. We also identified a new Asian lineage recently introduced into the Americas, raising concerns about future outbreaks. |
Reemergence of Dengue Virus Serotype 3, Brazil, 2023 (preprint)
Naveca FG , Santiago GA , Maito RM , Meneses CAR , do Nascimento VA , de Souza VC , do Nascimento FO , Silva D , Mejia M , Goncalves L , de Figueiredo RMP , Cruz ACR , Nunes BTD , Presibella MM , Marques NFQ , Riediger IN , de Mendonca MCL , de Bruycker-Nogueira F , Sequeira PC , de Filippis AMB , Resende P , Campos T , Wallau GL , Graf T , Delatorre E , Kopp E , Morrison A , Munoz-Jordan JL , Bello G . medRxiv 2023 05 (7) 1482-1484 In 2023, three autochthonous DENV-3 cases were detected in Roraima and one imported case in Parana, fifteen years after the last DENV-3 outbreak in Brazil. Phylogenetic analyses confirmed all belonging to a new Asian lineage recently introduced in the Americas, raising concerns about future large dengue outbreaks in this region. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. |
Vaccine effectiveness of CanSino (Adv5-nCoV) COVID-19 vaccine among childcare workers - Mexico, March-December 2021 (preprint)
Richardson VL , Franco MAC , Marquez AB , Valdez LM , Ceronio LEC , Cruz VC , Gharpure R , Lafond KE , Yau TS , Azziz-Baumgartner E , Avila MH . medRxiv 2022 17 Background: Beginning in March 2021, Mexico vaccinated childcare workers with a single-dose CanSino Biologics (Adv5-nCoV) COVID-19 vaccine. Although CanSino is currently approved for use in 10 Latin American, Asian, and European countries, little information is available about its vaccine effectiveness (VE). Method(s): We evaluated CanSino VE within a childcare worker cohort that included 1,408 childcare facilities. Participants were followed during March-December 2021 and tested through SARS-CoV-2 RT-PCR or rapid antigen test if they developed any symptom compatible with COVID-19. Vaccination status was obtained through worker registries. VE was calculated as 100% x (1-hazard ratio for SARS-CoV-2 infection in fully vaccinated vs. unvaccinated participants), using an Andersen-Gill model adjusted for age, sex, state, and local viral circulation. Result(s): The cohort included 43,925 persons who were mostly (96%) female with a median age of 32 years; 37,646 (86%) were vaccinated with CanSino. During March-December 2021, 2,250 (5%) participants had laboratory-confirmed COVID-19, of whom 25 were hospitalized and 6 died. Adjusted VE was 20% (95% CI = 10-29%) against illness, 76% (42-90%) against hospitalization, and 94% (66-99%) against death. VE against illness declined from 48% (95% CI = 33-61) after 14-60 days following full vaccination to 20% (95% CI = 9-31) after 61-120 days. Conclusion(s): CanSino vaccine was effective at preventing COVID-19 illness and highly effective at preventing hospitalization and death. It will be useful to further evaluate duration of protection and assess the value of booster doses to prevent COVID-19 and severe outcomes. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Antiviral susceptibility of clade 2.3.4.4b highly pathogenic avian influenza A(H5N1) viruses isolated from birds and mammals in the United States, 2022
Nguyen HT , Chesnokov A , De La Cruz J , Pascua PNQ , Mishin VP , Jang Y , Jones J , Di H , Ivashchenko AA , Killian ML , Torchetti MK , Lantz K , Wentworth DE , Davis CT , Ivachtchenko AV , Gubareva LV . Antiviral Res 2023 217 105679 Clade 2.3.4.4 b highly pathogenic avian influenza (HPAI) A (H5N1) viruses that are responsible for devastating outbreaks in birds and mammals pose a potential threat to public health. Here, we evaluated their susceptibility to influenza antivirals. Of 1015 sequences of HPAI A (H5N1) viruses collected in the United States during 2022, eight viruses (∼0.8%) had a molecular marker of drug resistance to an FDA-approved antiviral: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T). Additionally, 31 viruses contained mutations that may reduce susceptibility to inhibitors of neuraminidase (NA) (n = 20) or cap-dependent endonuclease (CEN) (n = 11). A panel of 22 representative viruses was tested phenotypically. Overall, clade 2.3.4.4 b A (H5N1) viruses lacking recognized resistance mutations were susceptible to FDA-approved antivirals. Oseltamivir was least potent at inhibiting NA activity, while the investigational NA inhibitor AV5080 was most potent, including against NA mutants. A novel NA substitution T438N conferred 12-fold reduced inhibition by zanamivir, and in combination with the known marker N295S, synergistically affected susceptibility to all five NA inhibitors. In cell culture-based assays HINT and IRINA, the PA-I38T virus displayed 75- to 108-fold and 37- to 78-fold reduced susceptibility to CEN inhibitors baloxavir and investigational AV5116, respectively. Viruses with PA-I38M or PA-A37T showed 5- to 10-fold reduced susceptibilities. As HPAI A (H5N1) viruses continue to circulate and evolve, close monitoring of drug susceptibility is needed for risk assessment and to inform decisions regarding antiviral stockpiling. |
Insecticide resistance levels and associated mechanisms in three Aedes aegypti populations from Venezuela
Rubio-Palis Y , Dzuris N , Sandi C , Vizcaino-Cabarrus RL , Corredor-Medina C , González JA , Lenhart AE . Mem Inst Oswaldo Cruz 2023 118 e220210 BACKGROUND: The massive use of insecticides in public health has exerted selective pressure resulting in the development of resistance in Aedes aegypti to different insecticides in Venezuela. Between 2010 and 2020, the only insecticides available for vector control were the organophosphates (Ops) fenitrothion and temephos which were focally applied. OBJECTIVES: To determine the state of insecticide resistance and to identify the possible biochemical and molecular mechanisms involved in three populations of Ae. aegypti from Venezuela. METHODS: CDC bottle bioassays were conducted on Ae. aegypti collected between October 2019 and February 2020 in two hyperendemic localities for dengue in Aragua State and in a malaria endemic area in Bolívar State. Insecticide resistance mechanisms were studied using biochemical assays and polymerase chain reaction (PCR) to detect kdr mutations. FINDINGS: Bioassays showed contrasting results among populations; Las Brisas was resistant to malathion, permethrin and deltamethrin, Urbanización 19 de Abril was resistant to permethrin and Nacupay to malathion. All populations showed significantly higher activity of mixed function oxidases and glutathione-S-transferases (GSTs) in comparison with the susceptible strain. The kdr mutations V410L, F1534C, and V1016I were detected in all populations, with F1534C at higher frequencies. MAIN CONCLUSION: Insecticide resistance persists in three Ae. aegypti populations from Venezuela even in the relative absence of insecticide application. |
High post-exposure prophylaxis (PEP) uptake among household contacts of pertussis patients enrolled in a PEP effectiveness evaluation - United States, 2015-2017
McNamara LA , Rubis AB , Pawloski L , Briere E , Misegades L , Brusseau AA , Peña S , Edge K , Wester R , Burzlaff K , Cruz V , Tondella L , Skoff TH . PLoS One 2023 18 (5) e0285953 BACKGROUND: Post-exposure prophylaxis (PEP) for pertussis is recommended for household contacts of pertussis cases in the United States within 21 days of exposure, but data on PEP effectiveness for prevention of secondary cases in the setting of widespread pertussis vaccination are limited. We implemented a multi-state evaluation of azithromycin PEP use and effectiveness among household contacts. METHODS: Culture- or PCR-confirmed pertussis cases were identified through surveillance. Household contacts were interviewed within 7 days of case report and again 14-21 days later. Interviewers collected information on exposure, demographics, vaccine history, prior pertussis diagnosis, underlying conditions, PEP receipt, pertussis symptoms, and pertussis testing. A subset of household contacts provided nasopharyngeal and blood specimens during interviews. RESULTS: Of 299 household contacts who completed both interviews, 12 (4%) reported not receiving PEP. There was no evidence of higher prevalence of cough or pertussis symptoms among contacts who did not receive PEP. Of 168 household contacts who provided at least one nasopharyngeal specimen, four (2.4%) were culture or PCR positive for B. pertussis; three of these received PEP prior to their positive test result. Of 156 contacts with serologic results, 14 (9%) had blood specimens that were positive for IgG anti-pertussis toxin (PT) antibodies; all had received PEP. CONCLUSIONS: Very high PEP uptake was observed among household contacts of pertussis patients. Although the number of contacts who did not receive PEP was small, there was no difference in prevalence of pertussis symptoms or positive laboratory results among these contacts compared with those who did receive PEP. |
Emergence of influenza B/Victoria in the Micronesian US-affiliated Pacific Islands, spring 2019
O'Connor S , Hancock WT , Ada E , Anzures E , Baza C , Aguon AL , Cruz D , Johnson E , Mallari AJ , McCready JA , Niedenthal J , Pobutsky A , Santos AM , Santos JV , Sasamoto J , Tomokane P , Villagomez W , White P . Western Pac Surveill Response J 2021 12 (4) 1-9 Data collected through routine syndromic surveillance for influenza-like illness in the Micronesian United States-affiliated Pacific Islands highlighted out-of-season influenza outbreaks in the spring of 2019. This report describes the data collected through the World Health Organization's Pacific Syndromic Surveillance System for the Commonwealth of the Northern Mariana Islands (CNMI), Guam, the Federated States of Micronesia (FSM) and the Republic of the Marshall Islands (RMI). Compared with historical data, more cases of influenza-like illness were observed in all four islands described here, with the highest number reported in Guam in week 9, CNMI and FSM in week 15, and RMI in week 19. The outbreaks predominantly affected those aged < 20 years, with evidence from CNMI and RMI suggesting higher attack rates among those who were unvaccinated. Cases confirmed by laboratory testing suggested that influenza B was predominant, with 83% (99/120) of subtyped specimens classified as influenza B/Victoria during January-May 2019. These outbreaks occurred after the usual influenza season and were consistent with transmission patterns in Eastern Asia rather than those in Oceania or the United States of America, the areas typically associated with the United States-affiliated Pacific Islands due to their geographical proximity to Oceania and political affiliation with the United States of America. A plausible epidemiological route of introduction may be the high levels of international tourism from Eastern Asian countries recorded during these periods of increased influenza B/Victoria circulation. This report demonstrates the value of year-round surveillance for communicable diseases and underscores the importance of seasonal influenza vaccination, particularly among younger age groups. |
Tuberculosis Infection in Children
Stewart RJ , Wortham J , Parvez F , Bamrah Morris S , Kirking HL , Hatzenbuehler Cameron L , Cruz AT . J Nurse Pract 2020 16 (9) 673-678 Globally, tuberculosis (TB) is the leading cause of infectious disease mortality; however, clinicians in the United States are increasingly unfamiliar with TB and the recommended tests and treatment for latent TB infection. Compared with adults, children who develop TB more often develop severe disease, and children < 2 years are particularly susceptible to developing TB disease after initial infection. Nurse practitioners who work in primary care are on the front lines of identifying children at high risk and obtaining testing and treatment. This article reviews the clinical course for identifying children at risk for TB and provides updated guidelines for testing and treatment. |
Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium , Coghlan Avril , Tyagi Rahul , Cotton James A , Holroyd Nancy , Rosa Bruce A , Tsai Isheng Jason , Laetsch Dominik R , Beech Robin N , Day Tim A , Hallsworth-Pepin Kymberlie , Ke Huei-Mien , Kuo Tzu-Hao , Lee Tracy J , Martin John , Maizels Rick M , Mutowo Prudence , Ozersky Philip , Parkinson John , Reid Adam J , Rawlings Neil D , Ribeiro Diogo M , Seshadri Swapna Lakshmipuram , Stanley Eleanor , Taylor David W , Wheeler Nicolas J , Zamanian Mostafa , Zhang Xu , Allan Fiona , Allen Judith E , Asano Kazuhito , Babayan Simon A , Bah Germanus , Beasley Helen , Bennett Hayley M , Bisset Stewart A , Castillo Estela , Cook Joseph , Cooper Philip J , Cruz-Bustos Teresa , Cuéllar Carmen , Devaney Eileen , Doyle Stephen R , Eberhard Mark L , Emery Aidan , Eom Keeseon S , Gilleard John S , Gordon Daria , Harcus Yvonne , Harsha Bhavana , Hawdon John M , Hill Dolores E , Hodgkinson Jane , Horák Petr , Howe Kevin L , Huckvale Thomas , Kalbe Martin , Kaur Gaganjot , Kikuchi Taisei , Koutsovoulos Georgios , Kumar Sujai , Leach Andrew R , Lomax Jane , Makepeace Benjamin , Matthews Jacqueline B , Muro Antonio , O’Boyle Noel Michael , Olson Peter D , Osuna Antonio , Partono Felix , Pfarr Kenneth , Rinaldi Gabriel , Foronda Pilar , Rollinson David , Gomez Samblas Mercedes , Sato Hiroshi , Schnyder Manuela , Scholz Tomáš , Shafie Myriam , Tanya Vincent N , Toledo Rafael , Tracey Alan , Urban Joseph F , Wang Lian-Chen , Zarlenga Dante , Blaxter Mark L , Mitreva Makedonka , Berriman Matthew . Nat Genet 2019 51 (1) 163-174 Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritized new potential drug targets and compounds for testing. This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms. |
Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.
Allix-Béguec C , Arandjelovic I , Bi L , Beckert P , Bonnet M , Bradley P , Cabibbe AM , Cancino-Muñoz I , Caulfield MJ , Chaiprasert A , Cirillo DM , Clifton DA , Comas I , Crook DW , De Filippo MR , de Neeling H , Diel R , Drobniewski FA , Faksri K , Farhat MR , Fleming J , Fowler P , Fowler TA , Gao Q , Gardy J , Gascoyne-Binzi D , Gibertoni-Cruz AL , Gil-Brusola A , Golubchik T , Gonzalo X , Grandjean L , He G , Guthrie JL , Hoosdally S , Hunt M , Iqbal Z , Ismail N , Johnston J , Khanzada FM , Khor CC , Kohl TA , Kong C , Lipworth S , Liu Q , Maphalala G , Martinez E , Mathys V , Merker M , Miotto P , Mistry N , Moore DAJ , Murray M , Niemann S , Omar SV , Ong RT , Peto TEA , Posey JE , Prammananan T , Pym A , Rodrigues C , Rodrigues M , Rodwell T , Rossolini GM , Sánchez Padilla E , Schito M , Shen X , Shendure J , Sintchenko V , Sloutsky A , Smith EG , Snyder M , Soetaert K , Starks AM , Supply P , Suriyapol P , Tahseen S , Tang P , Teo YY , Thuong TNT , Thwaites G , Tortoli E , van Soolingen D , Walker AS , Walker TM , Wilcox M , Wilson DJ , Wyllie D , Yang Y , Zhang H , Zhao Y , Zhu B . N Engl J Med 2018 379 (15) 1403-1415 BACKGROUND: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.). |
SARS-CoV-2 seroprevalence, cumulative infections, and immunity to symptomatic infection - A multistage national household survey and modelling study, Dominican Republic, June-October 2021.
Nilles EJ , Paulino CT , de St Aubin M , Restrepo AC , Mayfield H , Dumas D , Finch E , Garnier S , Etienne MC , Iselin L , Duke W , Jarolim P , Oasan T , Yu J , Wan H , Peña F , Iihoshi N , Abdalla G , Lopez B , Cruz L , Henríquez B , Espinosa-Bode A , Puello YC , Durski K , Baldwin M , Baez AA , Merchant RC , Barouch DH , Skewes-Ramm R , Gutiérrez EZ , Kucharski A , Lau CL . Lancet Reg Health Am 2022 16 100390 BACKGROUND: Population-level SARS-CoV-2 immunological protection is poorly understood but can guide vaccination and non-pharmaceutical intervention priorities. Our objective was to characterise cumulative infections and immunological protection in the Dominican Republic. METHODS: Household members ≥5 years were enrolled in a three-stage national household cluster serosurvey in the Dominican Republic. We measured pan-immunoglobulin antibodies against the SARS-CoV-2 spike (anti-S) and nucleocapsid glycoproteins, and pseudovirus neutralising activity against the ancestral and B.1.617.2 (Delta) strains. Seroprevalence and cumulative prior infections were weighted and adjusted for assay performance and seroreversion. Binary classification machine learning methods and pseudovirus neutralising correlates of protection were used to estimate 50% and 80% protection against symptomatic infection. FINDINGS: Between 30 Jun and 12 Oct 2021 we enrolled 6683 individuals from 3832 households. We estimate that 85.0% (CI 82.1-88.0) of the ≥5 years population had been immunologically exposed and 77.5% (CI 71.3-83) had been previously infected. Protective immunity sufficient to provide at least 50% protection against symptomatic SARS-CoV-2 infection was estimated in 78.1% (CI 74.3-82) and 66.3% (CI 62.8-70) of the population for the ancestral and Delta strains respectively. Younger (5-14 years, OR 0.47 [CI 0.36-0.61]) and older (≥75-years, 0.40 [CI 0.28-0.56]) age, working outdoors (0.53 [0.39-0.73]), smoking (0.66 [0.52-0.84]), urban setting (1.30 [1.14-1.49]), and three vs no vaccine doses (18.41 [10.69-35.04]) were associated with 50% protection against the ancestral strain. INTERPRETATION: Cumulative infections substantially exceeded prior estimates and overall immunological exposure was high. After controlling for confounders, markedly lower immunological protection was observed to the ancestral and Delta strains across certain subgroups, findings that can guide public health interventions and may be generalisable to other settings and viral strains. FUNDING: This study was funded by the US CDC. |
Monitoring temporal changes in SARS-CoV-2 spike antibody levels and variant-specific risk for infection, Dominican Republic, March 2021-August 2022
Nilles EJ , de St Aubin M , Dumas D , Duke W , Etienne MC , Abdalla G , Jarolim P , Oasan T , Garnier S , Iihoshi N , Lopez B , de la Cruz L , Puello YC , Baldwin M , Roberts KW , Peña F , Durski K , Sanchez IM , Gunter SM , Kneubehl AR , Murray KO , Lino A , Strobel S , Baez AA , Lau CL , Kucharski A , Gutiérrez EZ , Skewes-Ramm R , Vasquez M , Paulino CT . Emerg Infect Dis 2023 29 (4) 723-733 To assess changes in SARS-CoV-2 spike binding antibody prevalence in the Dominican Republic and implications for immunologic protection against variants of concern, we prospectively enrolled 2,300 patients with undifferentiated febrile illnesses in a study during March 2021-August 2022. We tested serum samples for spike antibodies and tested nasopharyngeal samples for acute SARS-CoV-2 infection using a reverse transcription PCR nucleic acid amplification test. Geometric mean spike antibody titers increased from 6.6 (95% CI 5.1-8.7) binding antibody units (BAU)/mL during March-June 2021 to 1,332 (95% CI 1,055-1,682) BAU/mL during May-August 2022. Multivariable binomial odds ratios for acute infection were 0.55 (95% CI 0.40-0.74), 0.38 (95% CI 0.27-0.55), and 0.27 (95% CI 0.18-0.40) for the second, third, and fourth versus the first anti-spike quartile; findings were similar by viral strain. Combining serologic and virologic screening might enable monitoring of discrete population immunologic markers and their implications for emergent variant transmission. |
Ultra-long-acting in-situ forming implants with cabotegravir protect female macaques against rectal SHIV infection
Young IC , Massud I , Cottrell ML , Shrivastava R , Maturavongsadit P , Prasher A , Wong-Sam A , Dinh C , Edwards T , Mrotz V , Mitchell J , Seixas JN , Pallerla A , Thorson A , Schauer A , Sykes C , De la Cruz G , Montgomery SA , Kashuba ADM , Heneine W , Dobard CW , Kovarova M , Garcia JV , García-Lerma JG , Benhabbour SR . Nat Commun 2023 14 (1) 708 Ultra-long-acting delivery platforms for HIV pre-exposure prophylaxis (PrEP) may increase adherence and maximize public health benefit. We report on an injectable, biodegradable, and removable in-situ forming implant (ISFI) that is administered subcutaneously and can release the integrase inhibitor cabotegravir (CAB) above protective benchmarks for more than 6 months. CAB ISFIs are well-tolerated in female mice and female macaques showing no signs of toxicity or chronic inflammation. In macaques, median plasma CAB concentrations exceed established PrEP protection benchmarks within 3 weeks and confer complete protection against repeated rectal SHIV challenges. Implant removal via a small incision in 2 macaques at week 12 results in a 7- to 48-fold decrease in plasma CAB levels within 72 hours. Modeling to translate CAB ISFI dosing suggests that a 3 mL injection would exceed protective benchmarks in humans for over 5 months post administration. Our results support the clinical advancement of CAB ISFIs for ultra-long-acting PrEP in humans. |
High Level of Pretreatment and Acquired Human Immunodeficiency Virus Drug Resistance in El Salvador: A Nationally Representative Survey, 2018-2019.
Girón-Callejas A , García-Morales C , Mendizabal-Burastero R , Quezada A , Ruiz L , Arguera N , Sorto S , Nieto AI , Tapia-Trejo D , López-Sánchez DM , Pérez-García M , Cruz L , Andino R , Sajquim E , Juárez SI , Farach N , Ravasi G , Northbrook S , Reyes-Terán G , Ávila-Ríos S . Open Forum Infect Dis 2022 9 (11) ofac580 BACKGROUND: Human immunodeficiency virus drug resistance (HIVDR) can negatively impact the effectiveness of antiretroviral therapy (ART). We aimed to estimate the prevalence of pretreatment HIVDR (PDR) among ART initiators and the prevalence of viral load (VL) suppression and acquired HIVDR among individuals receiving ART for 12 ± 3 months (ADR12) and ≥48 months (ADR48) in El Salvador. METHODS: Nationally representative cross-sectional PDR, ADR12 and ADR48 surveys were conducted among adults with HIV from October 2018 to August 2019, following World Health Organization-recommended methods. Demographic and clinic data and blood specimens were collected. RESULTS: Two hundred sixty participants were enrolled in the PDR survey, 230 in ADR12 and 425 in ADR48. Twenty-seven percent (95% confidence interval [CI], 17.1%-39.9%) of ART initiators had PDR to efavirenz or nevirapine. The prevalence of VL suppression was 88.8% (95% CI, 83.1%-92.8%) in ADR12 and 80.5% (95% CI, 76.6%-84.0%) in ADR48 surveys. Among people with HIV receiving a first-line nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART regimens and with unsuppressed VL, the prevalence of ADR to efavirenz or nevirapine was 72.0% (95% CI, 32.3%-93.3%) and 95.0% (68.5%-99.4%) in the ADR12 and ADR28 surveys, respectively. ADR12 to boosted protease inhibitors (PI/r) or integrase strand transfer inhibitors (INSTIs) was not observed. ADR48 was 1.3% (95% CI, 0.2%-9.6%) and 2.1% (0.3%-13.7%), respectively. CONCLUSIONS: Programmatic improvements in ART delivery are urgently needed in El Salvador to address the high levels of resistance to efavirenz or nevirapine among ART initiators and the low VL suppression prevalence among individuals on treatment. |
Assessing changes in insurance status and access to care among patients attending Chicago STI specialty clinics from 2013-2019
Korban C , Tabidze I , Broussard D , Cruz Y , Kern D , Mehta SD . Sex Transm Dis 2022 50 (3) 161-166 BACKGROUND: Public STI clinics are safety net providers for uninsured and underinsured individuals but are at risk for closure due to declining budgets and shifting priorities. This study sought to assess changes in insurance status and access to preventive care among public STI clinic patients following immediate and long-term implementation of the Affordable Care Act (ACA). MATERIALS AND METHODS: Patients receiving care in STI clinics administered by Chicago Department of Public Health were asked to complete an anonymous survey in 2013, 2014, and 2019. We estimated the prevalence rate ratio (PRR) of (1) being insured and (2) having access to preventive care over time, adjusted for age, race, and gender/sexual orientation, and employment status. RESULTS: Among 1,711 respondents, compared to 2013 patients, patients were 1.41 (adjusted PRR) times more likely to report being insured in 2014 (95% CI: 1.11-1.77), and 1.24 (aPRR) times more likely to report being insured in 2019 (95% CI: 0.99-1.55). After adjusting for other significant variables (age, sex and orientation, and insurance status), reported access to preventive care increased by 34% among respondents in 2019 as compared to 2013 (aPRR = 1.34). Unsurprisingly, being insured was associated with increased preventive care access (aPRR = 1.78). CONCLUSIONS: Even after implementation of the ACA, survey of public STI clinic patients in Chicago found a sizeable proportion of individuals without insurance, and many lacked access to preventive care, highlighting the continued need for these safety net clinics to provide STI care. |
Diagnostics to support mycetoma management - Development of two Target Product Profiles
Fongwen N , Asiedu KB , Bakhiet S , Bonifaz A , Cruz I , Argaw D , Estrada-Chavez G , Fahal AH , Litvintseva A , Marks M , Salinas-Carmona MC , Sow D , vandeSande WWJ . Trop Med Int Health 2022 27 (12) 1059-1064 OBJECTIVE: Mycetoma is a neglected tropical disease caused by more than 70 different micro-organisms and identified by WHO as one of the high-priority diseases for developing diagnostic tests. To ensure production of diagnostic assays for use by clinical staff in endemic regions, Target Product Profiles (TPP) were designed. METHODS: We describe the development of two TPPs: one for a diagnostic test able to identify the causative agent of mycetoma and another which would determine when treatment could be stopped. The TPPs were developed by considering product use, design, performance, product configuration and costs. RESULTS: Version 1.0 TPPs for two uses were posted by WHO for a one-month online public consultation on 25 October 2021 and the final TPP was posted online on 05 May 2022. CONCLUSION: A major difficulty encountered in developing both TPPs was the large number of agents able to cause mycetoma and the lack of specific biomarkers for most of them. |
Genome Sequences of 18 Salmonella enterica Serotype Hadar Strains Collected from Patients in the United States.
Webb HE , Kim JY , Tagg KA , de la Cruz F , Peñil-Celis A , Tolar B , Ellison Z , Schwensohn C , Brandenburg J , Nichols M , Folster JP . Microbiol Resour Announc 2022 11 (10) e0052222 Despite being linked to a number of recent poultry-associated outbreaks in the United States, few reference genomes are available for Salmonella enterica serotype Hadar. Here, we address this need by reporting 18 Salmonella Hadar genomes from samples collected from patients in the United States between 2014 and 2020. |
Five Complete Salmonella enterica Serotype Reading Genomes Recovered from Patients in the United States.
Webb HE , Tagg KA , Kim JY , Miller EA , Johnson TJ , Peñil-Celis A , de la Cruz F , Folster JP . Microbiol Resour Announc 2022 11 (7) e0038822 Between 2018 and 2019, Salmonella enterica serotype Reading caused a large, multistate outbreak linked to contact with raw turkey products in the United States. Here, we provide five Salmonella Reading reference genomes collected from US patients between 2016 and 2018. |
Vaccine effectiveness of CanSino (Adv5-nCoV) COVID-19 vaccine among childcare workers - Mexico, March-December 2021.
Richardson VL , Franco MAC , Márquez AB , Valdez LM , Ceronio LEC , Cruz VC , Gharpure R , Lafond KE , Yau TS , Azziz-Baumgartner E , Ávila MH . Clin Infect Dis 2022 75 S167-S173 BACKGROUND: Beginning in March 2021, Mexico vaccinated childcare workers with a single-dose CanSino Biologics (Adv5-nCoV) COVID-19 vaccine. Although CanSino is currently approved for use in 10 Latin American, Asian, and European countries, little information is available about its vaccine effectiveness (VE). METHODS: We evaluated CanSino VE within a childcare worker cohort that included 1,408 childcare facilities. Participants were followed during March-December 2021 and tested through SARS-CoV-2 RT-PCR or rapid antigen test if they developed any symptom compatible with COVID-19. Vaccination status was obtained through worker registries. VE was calculated as 100% × (1-hazard ratio for SARS-CoV-2 infection in fully vaccinated vs. unvaccinated participants), using an Andersen-Gill model adjusted for age, sex, state, and local viral circulation. RESULTS: The cohort included 43,925 persons who were mostly (96%) female with a median age of 32 years; 37,646 (86%) were vaccinated with CanSino. During March-December 2021, 2,250 (5%) participants had laboratory-confirmed COVID-19, of whom 25 were hospitalized and 6 died. Adjusted VE was 20% (95% CI = 10-29%) against illness, 76% (42-90%) against hospitalization, and 94% (66-99%) against death. VE against illness declined from 48% (95% CI = 33-61) after 14-60 days following full vaccination to 20% (95% CI = 9-31) after 61-120 days. CONCLUSIONS: CanSino vaccine was effective at preventing COVID-19 illness and highly effective at preventing hospitalization and death. It will be useful to further evaluate duration of protection and assess the value of booster doses to prevent COVID-19 and severe outcomes. |
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