Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
Records 1-30 (of 135 Records) |
Query Trace: Jenkins E [original query] |
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Patterns of TB transmission in the United States, 2011-2017
Yamkovoy K , Self JL , Jenkins HE , Horsburgh CR , White LF . Int J Tuberc Lung Dis 2024 28 (3) 154-156 |
Notes from the field: Rapidly linking an outbreak of salmonella typhimurium infections to domestically grown cantaloupes through early collaboration - United States, 2022
Schwensohn C , Schneider B , Jenkins E , Wellman A , Federman SS , Oni O , Stone N , Adams J , Gieraltowski L . MMWR Morb Mortal Wkly Rep 2024 73 (5) 114-115 |
Using data-to-care strategies to optimize the HIV care continuum in Connecticut: Results from a randomized controlled trial
Machavariani E , Miceli J , Altice FL , Fanfair RN , Speers S , Nichols L , Jenkins H , Villanueva M . J Acquir Immune Defic Syndr 2024 BACKGROUND: Re-engaging people with HIV (PWH) who are newly out-of-care remains challenging. Data-to-care (D2C) is a potential strategy to re-engage such individuals. METHODS: A prospective randomized controlled trial compared a D2C strategy using a disease intervention specialist (DIS) vs standard-of-care (SOC) where 23 HIV clinics in 3 counties in Connecticut could re-engage clients using existing methods. Using a data reconciliation process to confirm being newly out-of-care, 655 participants were randomized to DIS (N=333) or SOC (N=322). HIV care continuum outcomes included re-engagement at 90 days, retention in care and viral suppression (VS) by 12 months. Multivariable regression models were used to assess factors predictive of attaining HIV care continuum outcomes. RESULTS: Participants randomized to DIS were more likely to be re-engaged at 90 days (aOR=1.42, p=0.045). Independent predictors of re-engagement at 90 days were: age>40 years (aOR=1.84, p=0.012) and peri-natal HIV risk category (aOR=3.19, p=0.030). Predictors of retention at 12 months included: re-engagement at 90 days (aOR=10.31, p<0.001), drug injection HIV risk category (aOR=1.83, p=0.032), detectable HIV-1 RNA before randomization (aOR=0.40, p=0.003) and county (Hartford aOR=1.74, p=0.049; New Haven aOR=1.80, p=0.030). Predictors of VS included: re-engagement at 90 days (aOR=2.85, p<0.001), retention in HIV care (aOR=7.07, p<0.001), and detectable HIV-1 RNA pre-randomization (aOR=0.23, p<0.001). CONCLUSIONS: A D2C strategy significantly improved re-engagement at 90 days. Early re-engagement improved downstream benefits along the HIV care continuum like retention in care and VS at 12 months. Moreover, other factors predictive of care continuum outcomes can be used to improve D2C strategies. |
Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
Njamkepo E , Fawal N , Tran-Dien A , Hawkey J , Strockbine N , Jenkins C , Talukder KA , Bercion R , Kuleshov K , Kolínská R , Russell JE , Kaftyreva L , Accou-Demartin M , Karas A , Vandenberg O , Mather AE , Mason CJ , Page AJ , Ramamurthy T , Bizet C , Gamian A , Carle I , Sow AG , Bouchier C , Wester AL , Lejay-Collin M , Fonkoua MC , Le Hello S , Blaser MJ , Jernberg C , Ruckly C , Mérens A , Page AL , Aslett M , Roggentin P , Fruth A , Denamur E , Venkatesan M , Bercovier H , Bodhidatta L , Chiou CS , Clermont D , Colonna B , Egorova S , Pazhani GP , Ezernitchi AV , Guigon G , Harris SR , Izumiya H , Korzeniowska-Kowal A , Lutyńska A , Gouali M , Grimont F , Langendorf C , Marejková M , Peterson LA , Perez-Perez G , Ngandjio A , Podkolzin A , Souche E , Makarova M , Shipulin GA , Ye C , Žemličková H , Herpay M , Grimont PA , Parkhill J , Sansonetti P , Holt KE , Brisse S , Thomson NR , Weill FX . Nat Microbiol 2016 1 16027 Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease. |
Genomic description of acquired fluconazole- and echinocandin-resistance in patients with serial Candida glabrata isolates
Misas E , Seagle E , Jenkins EN , Rajeev M , Hurst S , Nunnally NS , Bentz ML , Lyman MM , Berkow E , Harrison LH , Schaffner W , Markus TM , Pierce R , Farley MM , Chow NA , Lockhart SR , Litvintseva AP . J Clin Microbiol 2024 e0114023 Candida glabrata is one of the most common causes of systemic candidiasis, often resistant to antifungal medications. To describe the genomic context of emerging resistance, we conducted a retrospective analysis of 82 serially collected isolates from 33 patients from population-based candidemia surveillance in the United States. We used whole-genome sequencing to determine the genetic relationships between isolates obtained from the same patient. Phylogenetic analysis demonstrated that isolates from 29 patients were clustered by patient. The median SNPs between isolates from the same patient was 30 (range: 7-96 SNPs), while unrelated strains infected four patients. Twenty-one isolates were resistant to echinocandins, and 24 were resistant to fluconazole. All echinocandin-resistant isolates carried a mutation either in the FKS1 or FKS2 HS1 region. Of the 24 fluconazole-resistant isolates, 17 (71%) had non-synonymous polymorphisms in the PDR1 gene, which were absent in susceptible isolates. In 11 patients, a genetically related resistant isolate was collected after recovering susceptible isolates, indicating in vivo acquisition of resistance. These findings allowed us to estimate the intra-host diversity of C. glabrata and propose an upper boundary of 96 SNPs for defining genetically related isolates, which can be used to assess donor-to-host transmission, nosocomial transmission, or acquired resistance.IMPORTANCEIn our study, mutations associated to azole resistance and echinocandin resistance were detected in Candida glabrata isolates using a whole-genome sequence. C. glabrata is the second most common cause of candidemia in the United States, which rapidly acquires resistance to antifungals, in vitro and in vivo. |
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Carey ME , Dyson ZA , Ingle DJ , Amir A , Aworh MK , Chattaway MA , Chew KL , Crump JA , Feasey NA , Howden BP , Keddy KH , Maes M , Parry CM , Van Puyvelde S , Webb HE , Afolayan AO , Alexander AP , Anandan S , Andrews JR , Ashton PM , Basnyat B , Bavdekar A , Bogoch II , Clemens JD , da Silva KE , De A , de Ligt J , Diaz Guevara PL , Dolecek C , Dutta S , Ehlers MM , Francois Watkins L , Garrett DO , Godbole G , Gordon MA , Greenhill AR , Griffin C , Gupta M , Hendriksen RS , Heyderman RS , Hooda Y , Hormazabal JC , Ikhimiukor OO , Iqbal J , Jacob JJ , Jenkins C , Jinka DR , John J , Kang G , Kanteh A , Kapil A , Karkey A , Kariuki S , Kingsley RA , Koshy RM , Lauer AC , Levine MM , Lingegowda RK , Luby SP , Mackenzie GA , Mashe T , Msefula C , Mutreja A , Nagaraj G , Nagaraj S , Nair S , Naseri TK , Nimarota-Brown S , Njamkepo E , Okeke IN , Perumal SPB , Pollard AJ , Pragasam AK , Qadri F , Qamar FN , Rahman SIA , Rambocus SD , Rasko DA , Ray P , Robins-Browne R , Rongsen-Chandola T , Rutanga JP , Saha SK , Saha S , Saigal K , Sajib MSI , Seidman JC , Shakya J , Shamanna V , Shastri J , Shrestha R , Sia S , Sikorski MJ , Singh A , Smith AM , Tagg KA , Tamrakar D , Tanmoy AM , Thomas M , Thomas MS , Thomsen R , Thomson NR , Tupua S , Vaidya K , Valcanis M , Veeraraghavan B , Weill FX , Wright J , Dougan G , Argimón S , Keane JA , Aanensen DM , Baker S , Holt KE . Elife 2023 12 BACKGROUND: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. FUNDING: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]). | Salmonella Typhi (Typhi) is a type of bacteria that causes typhoid fever. More than 110,000 people die from this disease each year, predominantly in areas of sub-Saharan Africa and South Asia with limited access to safe water and sanitation. Clinicians use antibiotics to treat typhoid fever, but scientists worry that the spread of antimicrobial-resistant Typhi could render the drugs ineffective, leading to increased typhoid fever mortality. The World Health Organization has prequalified two vaccines that are highly effective in preventing typhoid fever and may also help limit the emergence and spread of resistant Typhi. In low resource settings, public health officials must make difficult trade-off decisions about which new vaccines to introduce into already crowded immunization schedules. Understanding the local burden of antimicrobial-resistant Typhi and how it is spreading could help inform their actions. The Global Typhoid Genomics Consortium analyzed 13,000 Typhi genomes from 110 countries to provide a global overview of genetic diversity and antimicrobial-resistant patterns. The analysis showed great genetic diversity of the different strains between countries and regions. For example, the H58 Typhi variant, which is often drug-resistant, has spread rapidly through Asia and Eastern and Southern Africa, but is less common in other regions. However, distinct strains of other drug-resistant Typhi have emerged in other parts of the world. Resistance to the antibiotic ciprofloxacin was widespread and accounted for over 85% of cases in South Africa. Around 70% of Typhi from Pakistan were extensively drug-resistant in 2020, but these hard-to-treat variants have not yet become established elsewhere. Variants that are resistant to both ciprofloxacin and ceftriaxone have been identified, and azithromycin resistance has also appeared in several different variants across South Asia. The Consortium’s analyses provide valuable insights into the global distribution and transmission patterns of drug-resistant Typhi. Limited genetic data were available fromseveral regions, but data from travel-associated cases helped fill some regional gaps. These findings may help serve as a starting point for collective sharing and analyses of genetic data to inform local public health action. Funders need to provide ongoing supportto help fill global surveillance data gaps. | eng |
Rare variants in CAPN2 increase risk for isolated hypoplastic left heart syndrome
Blue EE , White JJ , Dush MK , Gordon WW , Wyatt BH , White P , Marvin CT , Helle E , Ojala T , Priest JR , Jenkins MM , Almli LM , Reefhuis J , Pangilinan F , Brody LC , McBride KL , Garg V , Shaw GM , Romitti PA , Nembhard WN , Browne ML , Werler MM , Kay DM , Mital S , Chong JX , Nascone-Yoder NM , Bamshad MJ . HGG Adv 2023 4 (4) 100232 Hypoplastic left heart syndrome (HLHS) is a severe congenital heart defect (CHD) characterized by hypoplasia of the left ventricle and aorta along with stenosis or atresia of the aortic and mitral valves. HLHS represents only ∼4%-8% of all CHDs but accounts for ∼25% of deaths. HLHS is an isolated defect (i.e., iHLHS) in 70% of families, the vast majority of which are simplex. Despite intense investigation, the genetic basis of iHLHS remains largely unknown. We performed exome sequencing on 331 families with iHLHS aggregated from four independent cohorts. A Mendelian-model-based analysis demonstrated that iHLHS was not due to single, large-effect alleles in genes previously reported to underlie iHLHS or CHD in >90% of families in this cohort. Gene-based association testing identified increased risk for iHLHS associated with variation in CAPN2 (p = 1.8 × 10(-5)), encoding a protein involved in functional adhesion. Functional validation studies in a vertebrate animal model (Xenopus laevis) confirmed CAPN2 is essential for cardiac ventricle morphogenesis and that in vivo loss of calpain function causes hypoplastic ventricle phenotypes and suggest that human CAPN2(707C>T) and CAPN2(1112C>T) variants, each found in multiple individuals with iHLHS, are hypomorphic alleles. Collectively, our findings show that iHLHS is typically not a Mendelian condition, demonstrate that CAPN2 variants increase risk of iHLHS, and identify a novel pathway involved in HLHS pathogenesis. |
Notes from the field: Cruise ship norovirus outbreak associated with person-to-person transmission - United States Jurisdiction, January 2023
Crisp CA , Jenkins KA , Dunn I , Kupper A , Johnson J , White S , Moritz ED , Rodriguez LO . MMWR Morb Mortal Wkly Rep 2023 72 (30) 833-834 CDC’s Vessel Sanitation Program (VSP) monitors cases of acute gastroenteritis (AGE) on board cruise ships traveling to a U.S. port (1). Persons who have ≥3 loose stools (or more than normal for that person) within a 24-hour period or vomiting plus one other sign or symptom (e.g., fever, diarrhea, bloody stool, myalgia, abdominal cramps, or headache) meet the case definition for reportable AGE (2). When the percentage of passengers or crew members with AGE is ≥2% and the ship is due to arrive at a U.S. port within 15 days, the Maritime Illness Disease Reporting System alerts VSP and activates an investigation (1). During the first week of January 2023, VSP was notified of cases of AGE affecting >2% of passengers on board a ship that had completed three voyages in Europe and was within 15 days of arriving at a U.S. port (voyage 4)* (Figure). Ship medical crew members submitted stool samples from ill travelers for testing. All samples tested positive for norovirus genotype II. While the ship was sailing to a U.S. port, VSP monitored AGE cases on board and reviewed case data. By mid-January, passenger AGE prevalence reached 3.4%. |
What do United States adolescents eat? Food group consumption patterns and dietary diversity from a decade of nationally representative data
Jenkins M , Jefferds MED , Aburto NJ , Ramakrishnan U , Martorell R , Addo OY . Curr Dev Nutr 2023 7 (8) 101968 BACKGROUND: Although the importance of adolescent nutrition has gained attention in the global nutrition community, there is a gap in research focused on adolescent dietary diversity and food group consumption. OBJECTIVES: This study aimed to characterize population-level food group consumption patterns and quantify the extent of dietary diversity among United States adolescents using a large nationally representative sample of adolescents aged 10-19 y. METHODS: We used 24-h dietary recall data from the National Health and Nutrition Examination Survey (NHANES) from 2007 to 2018 to construct the 10 food groups comprising the minimum dietary diversity for women (MDD-W) indicator and estimated the prevalence of intake of each food group. A composite metric adolescent dietary diversity score (ADDS) was derived for each adolescent where 1 point was awarded per food group. Both population scores and the distribution of individual scores were estimated. Differences in proportions of food groups consumed across sociodemographic categories were tested using the Rao-Scott χ(2) test, and pairwise comparisons were expressed as population prevalence differences and prevalence ratios. RESULTS: Food group consumption patterns were very similar across 2 d of dietary recall but varied significantly by sex, race/ethnicity, and income status. The food groups with the highest prevalence of consumption were grains, white, roots, and tubers (∼99%), milk products (∼92%), and meat, poultry, and fish (∼85%), whereas <15% of adolescents consumed key micronutrient-dense foods, such as vitamin A-rich fruits and vegetables and dark green vegetables. The mean ADDS was 4.69, with modest variation across strata. CONCLUSIONS: On average, United States youth consumed fewer than 5 food groups on a given day. The lack of dietary variety and relatively low prevalence of consumption of several micronutrient-rich plant-based foods could pose a risk for adolescents' ability to achieve micronutrient adequacy in the United States. |
One Health Investigation of SARS-CoV-2 Infection and Seropositivity among Pets in Households with Confirmed Human COVID-19 Cases — Utah and Wisconsin, 2020 (preprint)
Goryoka GW , Cossaboom CM , Gharpure R , Dawson P , Tansey C , Rossow J , Mrotz V , Rooney J , Torchetti M , Loiacono CM , Killian ML , Jenkins-Moore M , Lim A , Poulsen K , Christensen D , Sweet E , Peterson D , Sangster AL , Young EL , Oakeson KF , Taylor D , Price A , Kiphibane T , Klos R , Konkle D , Bhattacharyya S , Dasu T , Chu VT , Lewis NM , Queen K , Zhang J , Uehara A , Dietrich EA , Tong S , Kirking HL , Doty JB , Murrell LS , Spengler JR , Straily A , Wallace R , Barton Behravesh C . bioRxiv 2021 2021.04.11.439379 Background Approximately 67% of U.S. households have pets. Limited data are available on SARS-CoV-2 in pets. We assessed SARS-CoV-2 infection in pet cohabitants as a sub-study of an ongoing COVID-19 household transmission investigation.Methods Mammalian pets from households with ≥1 person with laboratory-confirmed COVID-19 were eligible for inclusion from April–May 2020. Demographic/exposure information, oropharyngeal, nasal, rectal, and fur swabs, feces, and blood were collected from enrolled pets and tested by rRT-PCR and virus neutralization assays.Findings We enrolled 37 dogs and 19 cats from 34 of 41 eligible households. All oropharyngeal, nasal, and rectal swabs tested negative by rRT-PCR; one dog’s fur swabs (2%) tested positive by rRT-PCR at the first animal sampling. Among 47 pets with serological results from 30 households, eight (17%) pets (4 dogs, 4 cats) from 6 (20%) households had detectable SARS-CoV-2 neutralizing antibodies. In households with a seropositive pet, the proportion of people with laboratory-confirmed COVID-19 was greater (median 79%; range: 40–100%) compared to households with no seropositive pet (median 37%; range: 13–100%) (p=0.01). Thirty-three pets with serologic results had frequent daily contact (≥1 hour) with the human index patient before the person’s COVID-19 diagnosis. Of these 33 pets, 14 (42%) had decreased contact with the human index patient after diagnosis and none (0%) were seropositive; of the 19 (58%) pets with continued contact, 4 (21%) were seropositive.Interpretations Seropositive pets likely acquired infection from humans, which may occur more frequently than previously recognized. People with COVID-19 should restrict contact with animals.Funding Centers for Disease Control and Prevention, U.S. Department of AgricultureCompeting Interest StatementThe authors have declared no competing interest. |
From people to Panthera: Natural SARS-CoV-2 infection in tigers and lions at the Bronx Zoo (preprint)
McAloose D , Laverack M , Wang L , Killian ML , Caserta LC , Yuan F , Mitchell PK , Queen K , Mauldin MR , Cronk BD , Bartlett SL , Sykes JM , Zec S , Stokol T , Ingerman K , Delaney MA , Fredrickson R , Ivančić M , Jenkins-Moore M , Mozingo K , Franzen K , Bergeson NH , Goodman L , Wang H , Fang Y , Olmstead C , McCann C , Thomas P , Goodrich E , Elvinger F , Smith DC , Tong S , Slavinski S , Calle PP , Terio K , Torchetti MK , Diel DG . bioRxiv 2020 2020.07.22.213959 We describe the first cases of natural SARS-CoV-2 infection detected in animals in the United States. In March 2020, four tigers and three lions at the Bronx Zoo developed mild respiratory signs. SARS-CoV-2 RNA was detected by rRT-PCR in respiratory secretions and/or feces from all seven affected animals; viral RNA and/or antibodies were detected in their keepers. SARS-CoV-2 was isolated from respiratory secretions or feces from three affected animals; in situ hybridization co-localized viral RNA with cellular damage. Whole genome sequence and haplotype network analyses showed tigers and lions were infected with two different SARS-CoV-2 strains, suggesting independent viral introductions. The source of SARS-CoV-2 infection in the lions is unknown. Epidemiological data and genetic similarities between keeper and tiger viruses indicate human to animal transmission.Competing Interest StatementThe authors have declared no competing interest. |
Natural SARS-CoV-2 infections, including virus isolation, among serially tested cats and dogs in households with confirmed human COVID-19 cases in Texas, USA (preprint)
Hamer SA , Pauvolid-Corrêa A , Zecca IB , Davila E , Auckland LD , Roundy CM , Tang W , Torchetti M , Killian ML , Jenkins-Moore M , Mozingo K , Akpalu Y , Ghai RR , Spengler JR , Behravesh CB , Fischer RSB , Hamer GL . bioRxiv 2020 The natural infections and epidemiological roles of household pets in SARS-CoV-2 transmission are not understood. We conducted a longitudinal study of dogs and cats living with at least one SARS-CoV-2 infected human in Texas and found 47.1% of 17 cats and 15.3% of 59 dogs from 25.6% of 39 households were positive for SARS-CoV-2 via RT-PCR and genome sequencing or neutralizing antibodies. Virus was isolated from one cat. The majority (82.4%) of infected pets were asymptomatic. Re-sampling of one infected cat showed persistence of viral RNA at least 32 d-post human diagnosis (25 d-post initial test). Across 15 antibody-positive animals, titers increased (33.3%), decreased (33.3%) or were stable (33.3%) over time. A One Health approach is informative for prevention and control of SARS-CoV-2 transmission. |
Recent O-antigen diversification masks highly pathogenic STEC O104:H4 (preprint)
Lang C , Fruth A , Campbell IW , Jenkins C , Smith P , Strockbine N , Weill FX , Nubel U , Grad YH , Waldor MK , Flieger A . bioRxiv 2022 15 Background: Shiga toxin-producing E. coli (STEC) can give rise to a range of clinical outcomes from diarrhea to the life-threatening systemic condition, hemolytic uremic syndrome (HUS). A major outbreak of HUS occurred in 2011, and was caused by a rare serotype, STEC O104:H4. Prior to 2011 and since the outbreak, STEC O104:H4 were rarely associated with human infections. Method(s): From 2012 to 2020 intensified STEC surveillance was performed in Germany where subtyping of ~8,000 clinical isolates by molecular methods including whole genome sequencing was carried out. Virulence traits and phylogenetic context were investigated for a subset of strains. Result(s): A rare STEC serotype O181:H4 associated with HUS was identified, belonging to sequence type (ST) 678, like the STEC O104:H4 outbreak strain. Virulence and genomic comparisons revealed that the two strains are phylogenetically related and differ principally in the gene cluster encoding their respective lipopolysaccharide O-antigens. In addition, five other serotypes belonging to ST678 from human clinical infection were identified from diverse locations worldwide. Conclusion(s): Our data suggest the high virulence ensemble of STEC O104:H4 remains a global threat, but that horizontal exchange of O-antigen gene clusters has cloaked the pathogen with new O-antigens, confounding interpretation of their potential risk. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. |
An investigation of an outbreak of Salmonella Newport infections linked to melons United States, 2020
Jenkins E , Gardenhire I , Whitney BM , Martin KB , Schwensohn C , Gieraltowski L , Leeper MM , McCurdy V , McClure M , Wellman A , Pightling A , Smith M , Swinford A , Hainstock L , Crosby AJ , Bazaco MC , Viazis S . Food Control 2023 152 The United States are one of the world's leading consumers of melons. In 2020, the Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and state health and regulatory partners investigated an outbreak of Salmonella Newport infections linked to melons from southwest Indiana, resulting in 80 ill persons and 18 hospitalizations reported across 15 states. Epidemiologic and traceback data indicated melons as the vehicle for these infections, but the collinearity of melon varieties purchased and consumed together in combination with the traceback investigation that could not rule out either melon type, did not allow investigators to delineate whether the vehicle was cantaloupe alone or, both cantaloupe and watermelons. Analysis of traceback records for cantaloupe and/or watermelon exposures for 12 ill people indicated convergence on a grower in southwest Indiana which supplied cantaloupe to the nine of eleven points of service where ill people purchased cantaloupe; similar convergence was not observed for watermelon. While Salmonella isolates were recovered from environmental samples collected by FDA throughout the growing operation, they were not highly genetically related to the outbreak strain by whole genome sequencing analyses, i.e. greater than a 20 high quality single nucleotide polymorphisms difference. This outbreak illustrates the need for additional efforts to determine the source and extent of environmental contamination in the melon growing region of southwest Indiana and emphasizes the need for outreach and education efforts to help promote farm practices to reduce pathogen contamination of melons. 2023 |
O-antigen diversification masks identification of highly pathogenic shiga toxin-producing Escherichia coli O104:H4-like strains
Lang C , Fruth A , Campbell IW , Jenkins C , Smith P , Strockbine N , Weill FX , Nübel U , Grad YH , Waldor MK , Flieger A . Microbiol Spectr 2023 11 (3) e0098723 Shiga toxin-producing Escherichia coli (STEC) can give rise to a range of clinical outcomes from diarrhea to the life-threatening systemic condition hemolytic-uremic syndrome (HUS). Although STEC O157:H7 is the serotype most frequently associated with HUS, a major outbreak of HUS occurred in 2011 in Germany and was caused by a rare serotype, STEC O104:H4. Prior to 2011 and since the outbreak, STEC O104:H4 strains have only rarely been associated with human infections. From 2012 to 2020, intensified STEC surveillance was performed in Germany where the subtyping of ~8,000 clinical isolates by molecular methods, including whole-genome sequencing, was carried out. A rare STEC serotype, O181:H4, associated with HUS was identified, and like the STEC O104:H4 outbreak strain, this strain belongs to sequence type 678 (ST678). Genomic and virulence comparisons revealed that the two strains are phylogenetically related and differ principally in the gene cluster encoding their respective lipopolysaccharide O-antigens but exhibit similar virulence phenotypes. In addition, five other serotypes belonging to ST678 from human clinical infection, such as OX13:H4, O127:H4, OgN-RKI9:H4, O131:H4, and O69:H4, were identified from diverse locations worldwide. IMPORTANCE Our data suggest that the high-virulence ensemble of the STEC O104:H4 outbreak strain remains a global threat because genomically similar strains cause disease worldwide but that the horizontal acquisition of O-antigen gene clusters has diversified the O-antigens of strains belonging to ST678. Thus, the identification of these highly pathogenic strains is masked by diverse and rare O-antigens, thereby confounding the interpretation of their potential risk. |
Public Health Approach to Decrease Mortality for Congenital Heart Defects: Dying Too Soon
Jenkins KJ , Honein MA . J Am Coll Cardiol 2018 71 (21) 2447-2449 With advancements in clinical care, it is unquestionable that survival for both children and adults with congenital heart defects has improved significantly (1). In the United States in 2010, there were an estimated 1.4 million adults and 1 million children living with congenital heart defects (2). Some stakeholders have suggested that survival is no longer a concern, based on improving results in surgical registries. However, in this issue of the Journal, the new study by Spector et al. (3) links one of the highest-quality U.S. registries collected for quality improvement to the National Death Index, and demonstrates that despite tremendous advances, people with congenital heart defects are still dying too soon. Even for the most recent time period, the 15-year mortality for those who survived surgery for their congenital heart defects (6.5% had already died before leaving the hospital) was about 10 times higher than for those of the same age and sex in the general population. Surprisingly, the continued excess mortality even among survivors of initial congenital heart surgery was observed not only among those with the most severe defects, like tricuspid atresia or hypoplastic left heart syndrome, but also for those with simple defects, like atrial septal defects, which are frequently viewed as “cured” by surgery (3). To address this early risk for death and improve the health of individuals and families affected by congenital heart defects, a public health approach is essential. |
Maternal mortality in Colombia during the COVID-19 pandemic: time series and social inequities
Castañeda-Orjuela C , Hilarion Gaitan L , Diaz-Jimenez D , Cotes-Cantillo K , Garfield R . BMJ Open 2023 13 (4) e064960 OBJECTIVE: The impact of the COVID-19 pandemic goes beyond morbidity and mortality from that disease. Increases in maternal mortality have also been described but have not been extensively studied to date. This study aimed to examine changes in maternal mortality and identify correlates and predictors of excess maternal mortality in Colombia during the pandemic. SETTING: Analysis of data from the national epidemiological surveillance databases of Colombia (Sivigila). PARTICIPANTS: Deaths among 6342 Colombian pregnant women who experienced complications associated with pregnancy, childbirth or the perperium during 2008-2020 were included in this study. For inequalities analysis, a subsample of 1055 women from this group who died in 2019 or 2020 years were analysed. METHODS: We collected data from the national surveillance system (Sivigila) on maternal mortality. Analysis was carried out in two stages, starting with a time series modelling using the Box-Jenkins approach. Data from Sivigila for 2008-2019 were used to establish a baseline of expected mortality levels. Both simple and complex inequality metrics, with the maternal mortality ratios (MMRs), were then calculated using the Multidimensional Poverty Index as a socioeconomic proxy. RESULTS: Maternal deaths in 2020 were 12.6% (95% CI -21.4% to 95.7%) higher than expected. These excess deaths were statistically significant in elevation for the months of July (97.4%, 95% CI 35.1% to 250.0%) and August (87.8%, 95% CI 30.5% to 220.8%). The MMR was nearly three times higher in the poorest municipalities compared with the most affluent communities in 2020. CONCLUSIONS: The COVID-19 pandemic had considerable impact on maternal health, not only by leading to increased deaths, but also by increasing social health inequity. Barriers to access and usage of essential health services are a challenge to achieving health-related Sustainable Development Goals. |
Exome-wide assessment of isolated biliary atresia: A report from the National Birth Defects Prevention Study using child-parent trios and a case-control design to identify novel rare variants.
Sok P , Sabo A , Almli LM , Jenkins MM , Nembhard WN , Agopian AJ , Bamshad MJ , Blue EE , Brody LC , Brown AL , Browne ML , Canfield MA , Carmichael SL , Chong JX , Dugan-Perez S , Feldkamp ML , Finnell RH , Gibbs RA , Kay DM , Lei Y , Meng Q , Moore CA , Mullikin JC , Muzny D , Olshan AF , Pangilinan F , Reefhuis J , Romitti PA , Schraw JM , Shaw GM , Werler MM , Harpavat S , Lupo PJ . Am J Med Genet A 2023 191 (6) 1546-1556 The etiology of biliary atresia (BA) is unknown, but recent studies suggest a role for rare protein-altering variants (PAVs). Exome sequencing data from the National Birth Defects Prevention Study on 54 child-parent trios, one child-mother duo, and 1513 parents of children with other birth defects were analyzed. Most (91%) cases were isolated BA. We performed (1) a trio-based analysis to identify rare de novo, homozygous, and compound heterozygous PAVs and (2) a case-control analysis using a sequence kernel-based association test to identify genes enriched with rare PAVs. While we replicated previous findings on PKD1L1, our results do not suggest that recurrent de novo PAVs play important roles in BA susceptibility. In fact, our finding in NOTCH2, a disease gene associated with Alagille syndrome, highlights the difficulty in BA diagnosis. Notably, IFRD2 has been implicated in other gastrointestinal conditions and warrants additional study. Overall, our findings strengthen the hypothesis that the etiology of BA is complex. |
The Cooperative Re-Engagement Controlled Trial (CoRECT): Durable viral suppression assessment
O'Shea J , Fanfair RN , Williams T , Khalil G , Brady KA , DeMaria A Jr , Villanueva M , Randall LM , Jenkins H , Altice FL , Camp N , Lucas C , Buchelli M , Samandari T , Weidle PJ . J Acquir Immune Defic Syndr 2023 93 (2) 134-142 BACKGROUND: A collaborative, data-to-care strategy to identify persons with HIV (PWH) newly out-of-care, combined with an active public health intervention, significantly increases the proportion of PWH re-engaged in HIV care. We assessed this strategy's impact on durable viral suppression (DVS). METHODS: A multi-site, prospective randomized controlled trial for out-of-care individuals using a data-to-care strategy and comparing public health field services to locate, contact, and facilitate access to care versus the standard of care (SOC). DVS was defined as the last viral load (VL), the VL at least three months prior, and any VL between the two were all <200 copies/mL during the 18 months post-randomization. Alternative definitions of DVS were also analyzed. RESULTS: Between August 1, 2016 - July 31, 2018, 1,893 participants were randomized from Connecticut (CT) (n=654), Massachusetts (MA) (n=630), and Philadelphia (PHL) (n=609). Rates of achieving DVS were similar in the intervention and SOC arms in all jurisdictions (All sites: 43.4% vs 42.4%, p=0.67; CT: 46.7% vs 45.0%, p=0.67; MA: 40.7 vs 44.4%, p=0.35; PHL: 42.4% vs 37.3%, p=0.20). There was no association between DVS and the intervention (RR:1.01, CI: 0.91-1.12; p=0.85) adjusting for site, age categories, race/ethnicity, birth sex, CD4 categories, and exposure categories. CONCLUSION: A collaborative, data-to-care strategy, and active public health intervention did not increase the proportion of PWH achieving DVS suggesting additional support to promote retention in care and antiretroviral adherence may be needed. Initial linkage and engagement services, through data-to-care or other means, are likely necessary but insufficient for achieving DVS for all PWH. |
Costs and cost-effectiveness of a collaborative data-to-care intervention for HIV treatment and care in the United States
Shrestha RK , Fanfair RN , Randall LM , Lucas C , Nichols L , Camp N , Brady KA , Jenkins H , Altice FL , DeMaria A , Villanueva M , Weidle PJ . J Int AIDS Soc 2023 26 (1) e26040 INTRODUCTION: Data-to-care programmes utilize surveillance data to identify persons who are out of HIV care, re-engage them in care and improve HIV care outcomes. We assess the costs and cost-effectiveness of re-engagement in an HIV care intervention in the United States. METHODS: The Cooperative Re-engagement Control Trial (CoRECT) employed a data-to-care collaborative model between health departments and HIV care providers, August 2016-July 2018. The health departments in Connecticut (CT), Massachusetts (MA) and Philadelphia (PHL) collaborated with HIV clinics to identify newly out-of-care patients and randomize them to receive usual linkage and engagement in care services (standard-of-care control arm) or health department-initiated active re-engagement services (intervention arm). We used a microcosting approach to identify the activities and resources involved in the CoRECT intervention, separate from the standard-of-care, and quantified the costs. The cost data were collected at the start-up and recurrent phases of the trial to incorporate potential variation in the intervention costs. The costs were estimated from the healthcare provider perspective. RESULTS: The CoRECT trial in CT, MA and PHL randomly assigned on average 327, 316 and 305 participants per year either to the intervention arm (n = 166, 159 and 155) or the standard-of-care arm (n = 161, 157 and 150), respectively. Of those randomized, the number of participants re-engaged in care within 90 days in the intervention and standard-of-care arms was 85 and 70 in CT, 84 and 70 in MA, and 98 and 67 in PHL. The additional number of participants re-engaged in care in the intervention arm compared with those in the standard-of-care arm was 15 (CT), 14 (MA) and 31 (PHL). We estimated the annual total cost of the CoRECT intervention at $490,040 in CT, $473,297 in MA and $439,237 in PHL. The average cost per participant enrolled was $2952, $2977 and $2834 and the average cost per participant re-engaged in care was $5765, $5634 and $4482. We estimated an incremental cost per participant re-engaged in care at $32,669 (CT), $33,807 (MA) and $14,169 (PHL). CONCLUSIONS: The costs of the CoRECT intervention that identified newly out-of-care patients and re-engaged them in HIV care are comparable with other similar interventions, suggesting a potential for its cost-effectiveness in the US context. |
Predicted effects of the introduction of long-acting injectable cabotegravir pre-exposure prophylaxis in sub-Saharan Africa: a modelling study
Smith J , Bansi-Matharu L , Cambiano V , Dimitrov D , Bershteyn A , van de Vijver D , Kripke K , Revill P , Boily MC , Meyer-Rath G , Taramusi I , Lundgren JD , van Oosterhout JJ , Kuritzkes D , Schaefer R , Siedner MJ , Schapiro J , Delany-Moretlwe S , Landovitz RJ , Flexner C , Jordan M , Venter F , Radebe M , Ripin D , Jenkins S , Resar D , Amole C , Shahmanesh M , Gupta RK , Raizes E , Johnson C , Inzaule S , Shafer R , Warren M , Stansfield S , Paredes R , Phillips AN . Lancet HIV 2023 10 (4) e254-e265 BACKGROUND: Long-acting injectable cabotegravir pre-exposure prophylaxis (PrEP) is recommended by WHO as an additional option for HIV prevention in sub-Saharan Africa, but there is concern that its introduction could lead to an increase in integrase-inhibitor resistance undermining treatment programmes that rely on dolutegravir. We aimed to project the health benefits and risks of cabotegravir-PrEP introduction in settings in sub-Saharan Africa. METHODS: With HIV Synthesis, an individual-based HIV model, we simulated 1000 setting-scenarios reflecting both variability and uncertainty about HIV epidemics in sub-Saharan Africa and compared outcomes for each with and without cabotegravir-PrEP introduction. PrEP use is assumed to be risk-informed and to be used only in 3-month periods (the time step for the model) when having condomless sex. We consider three groups at risk of integrase-inhibitor resistance emergence: people who start cabotegravir-PrEP after (unknowingly) being infected with HIV, those who seroconvert while on PrEP, and those with HIV who have residual cabotegravir drugs concentrations during the early tail period after recently stopping PrEP. We projected the outcomes of policies of cabotegravir-PrEP introduction and of no introduction in 2022 across 50 years. In 50% of setting-scenarios we considered that more sensitive nucleic-acid-based HIV diagnostic testing (NAT), rather than regular antibody-based HIV rapid testing, might be used to reduce resistance risk. For cost-effectiveness analysis we assumed in our base case a cost of cabotegravir-PrEP drug to be similar to oral PrEP, resulting in a total annual cost of USD$144 per year ($114 per year and $264 per year considered in sensitivity analyses), a cost-effectiveness threshold of $500 per disability-adjusted life years averted, and a discount rate of 3% per year. FINDINGS: Reflecting our assumptions on the appeal of cabotegravir-PrEP, its introduction is predicted to lead to a substantial increase in PrEP use with approximately 2·6% of the adult population (and 46% of those with a current indication for PrEP) receiving PrEP compared with 1·5% (28%) without cabotegravir-PrEP introduction across 20 years. As a result, HIV incidence is expected to be lower by 29% (90% range across setting-scenarios 6-52%) across the same period compared with no introduction of cabotegravir-PrEP. In people initiating antiretroviral therapy, the proportion with integrase-inhibitor resistance after 20 years is projected to be 1·7% (0-6·4%) without cabotegravir-PrEP introduction but 13·1% (4·1-30·9%) with. Cabotegravir-PrEP introduction is predicted to lower the proportion of all people on antiretroviral therapy with viral loads less than 1000 copies per mL by 0·9% (-2·5% to 0·3%) at 20 years. For an adult population of 10 million an overall decrease in number of AIDS deaths of about 4540 per year (-13 000 to -300) across 50 years is predicted, with little discernible benefit with NAT when compared with standard antibody-based rapid testing. AIDS deaths are predicted to be averted with cabotegravir-PrEP introduction in 99% of setting-scenarios. Across the 50-year time horizon, overall HIV programme costs are predicted to be similar regardless of whether cabotegravir-PrEP is introduced (total mean discounted annual HIV programme costs per year across 50 years is $151·3 million vs $150·7 million), assuming the use of standard antibody testing. With antibody-based rapid HIV testing, the introduction of cabotegravir-PrEP is predicted to be cost-effective under an assumed threshold of $500 per disability-adjusted life year averted in 82% of setting-scenarios at the cost of $144 per year, in 52% at $264, and in 87% at $114. INTERPRETATION: Despite leading to increases in integrase-inhibitor drug resistance, cabotegravir-PrEP introduction is likely to reduce AIDS deaths in addition to HIV incidence. Long-acting cabotegravir-PrEP is predicted to be cost-effective if delivered at similar cost to oral PrEP with antibody-based rapid HIV testing. FUNDING: Bill & Melinda Gates Foundation, National Institute of Allergy and Infectious Diseases of the National Institutes of Health. |
State-level metabolic comorbidity prevalence and control among adults age 50-plus with diabetes: estimates from electronic health records and survey data in five states
Mardon R , Campione J , Nooney J , Merrill L , Johnson MJr , Marker D , Jenkins F , Saydah S , Rolka D , Zhang X , Shrestha S , Gregg E . Popul Health Metr 2022 20 (1) 22 BACKGROUND: Although treatment and control of diabetes can prevent complications and reduce morbidity, few data sources exist at the state level for surveillance of diabetes comorbidities and control. Surveys and electronic health records (EHRs) offer different strengths and weaknesses for surveillance of diabetes and major metabolic comorbidities. Data from self-report surveys suffer from cognitive and recall biases, and generally cannot be used for surveillance of undiagnosed cases. EHR data are becoming more readily available, but pose particular challenges for population estimation since patients are not randomly selected, not everyone has the relevant biomarker measurements, and those included tend to cluster geographically. METHODS: We analyzed data from the National Health and Nutritional Examination Survey, the Health and Retirement Study, and EHR data from the DARTNet Institute to create state-level adjusted estimates of the prevalence and control of diabetes, and the prevalence and control of hypertension and high cholesterol in the diabetes population, age 50 and over for five states: Alabama, California, Florida, Louisiana, and Massachusetts. RESULTS: The estimates from the two surveys generally aligned well. The EHR data were consistent with the surveys for many measures, but yielded consistently lower estimates of undiagnosed diabetes prevalence, and identified somewhat fewer comorbidities in most states. CONCLUSIONS: Despite these limitations, EHRs may be a promising source for diabetes surveillance and assessment of control as the datasets are large and created during the routine delivery of health care. TRIAL REGISTRATION: Not applicable. |
Recurrent candidemia: Trends and risk factors among persons residing in 4 US states, 2011-2018
Seagle EE , Jackson BR , Lockhart SR , Jenkins EN , Revis A , Farley MM , Harrison LH , Schaffner W , Markus TM , Pierce RA , Zhang AY , Lyman MM . Open Forum Infect Dis 2022 9 (10) ofac545 BACKGROUND: Candidemia is a common healthcare-associated infection with high mortality. Estimates of recurrence range from 1% to 17%. Few studies have focused on those with recurrent candidemia, who often experience more severe illness and greater treatment failure. We describe recurrent candidemia trends and risk factors. METHODS: We analyzed population-based candidemia surveillance data collected during 2011-2018. Persons with >1 episode (defined as the 30-day period after a positive Candida species) were classified as having recurrent candidemia. We compared factors during the initial episode between those who developed recurrent candidemia and those who did not. RESULTS: Of the 5428 persons identified with candidemia, 326 (6%) had recurrent infection. Recurrent episodes occurred 1.0 month to 7.6 years after any previous episode. In multivariable logistic regression controlling for surveillance site and year, recurrent candidemia was associated with being 19-44 years old (vs ≥65 years; adjusted odds ratio [aOR], 3.05 [95% confidence interval {CI}, 2.10-4.44]), being discharged to a private residence (vs medical facility; aOR, 1.53 [95% CI, 1.12-2.08]), hospitalization in the 90 days prior to initial episode (aOR, 1.66 [95% CI, 1.27-2.18]), receipt of total parenteral nutrition (aOR, 2.08 [95% CI, 1.58-2.73]), and hepatitis C infection (aOR, 1.65 [95% CI, 1.12-2.43]). CONCLUSIONS: Candidemia recurrence >30 days after initial infection occurred in >1 in 20 persons with candidemia. Associations with younger age and hepatitis C suggest injection drug use may play a modifiable role. Prevention efforts targeting central line care and total parenteral nutrition use may help reduce the risk of recurrent candidemia. |
Monkeypox virus infection resulting from an occupational needlestick - florida, 2022
Mendoza R , Petras JK , Jenkins P , Gorensek MJ , Mableson S , Lee PA , Carpenter A , Jones H , de Perio MA , Chisty Z , Brueck S , Rao AK , Salzer JS , Stanek D , Blackmore C . MMWR Morb Mortal Wkly Rep 2022 71 (42) 1348-1349 In August 2022, the Florida Department of Health notified CDC of a nurse who acquired monkeypox through an occupational exposure while providing care to a patient with monkeypox. To date, occupationally acquired Monkeypox virus (MPXV) infections in health care personnel (HCP) have been rarely reported during the 2022 multinational outbreak (1,2). This report describes the first reported U.S. case and recommends approaches for preventing occupationally acquired MPXV infections in HCP. |
Low sensitivity of International Classification of Diseases, Tenth Revision coding for culture-confirmed candidemia cases in an active surveillance system: United States, 2019-2020
Benedict K , Gold JAW , Jenkins EN , Roland J , Barter D , Czaja CA , Johnston H , Clogher P , Farley MM , Revis A , Harrison LH , Tourdot L , Davis SS , Phipps EC , Felsen CB , Tesini BL , Escutia G , Pierce R , Zhang A , Schaffner W , Lyman M . Open Forum Infect Dis 2022 9 (9) ofac461 We evaluated healthcare facility use of International Classification of Diseases, Tenth Revision (ICD-10) codes for culture-confirmed candidemia cases detected by active public health surveillance during 2019-2020. Most cases (56%) did not receive a candidiasis code, suggesting that studies relying on ICD-10 codes likely underestimate disease burden. |
Choosing the emergency department as an alternative for STD care: Potential disparities in access
Pearson WS , Tromble E , Jenkins WD , Solnick R , Gift TL . J Health Care Poor Underserved 2022 33 (3) 1163-1168 This analysis was designed to determine if there existed differences by race in seeking sexually transmitted disease (STD) care in an emergency department (ED). Methods. Data were collected from 4,138 patients attending 26 STD clinics across the United States (U.S.). The questionnaire asked where the patient would have sought care if the STD clinic had not been available that day. Responses were stratified by race and differences were tested for statistical significance. Results. Black/African American patients chose hospital emergency room as an alternative for STD clinic care at a rate approximately 2.5 times that of White patients (15.5% v. 5.8%, p <.05). This difference persisted among Black/African American patients after controlling for demographic variables (adjusted OR 2.91; 2.213.82 95% CI). Discussion. Receiving appropriate care is key to stemming the increases in sexually transmitted infections in the U.S. These findings suggest that disparities in access to STD care exist for Black/African American people. Meharry Medical College Journal of Health Care for the Poor and Underserved. |
A 2019 Outbreak Investigation of Hepatitis A Virus Infections in the United States Linked to Imported Fresh Blackberries.
McClure M , Nsubuga J , Montgomery MP , Jenkins E , Crosby A , Schoelen D , Basler C , Ramachandran S , Lin Y , Xia GL , Khudaykov Y , Suktankar V , Wagley A , Thomas V , Woods J , Hintz L , Oliveira J , Sandoval AL , Frederick J , Hendrickson B , Gieraltowski L , Viazis S . Food Environ Virol 2022 14 (3) 236-245 Globally, hepatitis A virus (HAV) is one of the most common agents of acute viral hepatitis and causes approximately 1.4 million cases and 90,000 deaths annually despite the existence of an effective vaccine. In 2019, federal, state, and local partners investigated a multi-state outbreak of HAV infections linked to fresh blackberries sourced from multiple suppliers in Michoacn, Mexico. A total of 20 individuals with outbreak-related HAV infection were reported in seven states, including 11 hospitalizations, and no deaths. The Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and Nebraska State and Douglas County Health Departments conducted a traceback investigation for fresh blackberries reportedly purchased by 16 ill persons. These individuals reported purchasing fresh blackberries from 11 points of service from September 16 through 29, 2019 and their clinical isolates assessed through next-generation sequencing and phylogenetic analysis were genetically similar. The traceback investigation did not reveal convergence on a common grower or packing house within Mexico, but all of the blackberries were harvested from growers in Michoacn, Mexico. FDA did not detect the pathogen after analyzing fresh blackberry samples from four distributors, one consumer, and from nine importers at the port of entry as a result of increased screening. Challenges included gaps in traceability practices and the inability to recover the pathogen from sample testing, which prohibited investigators from determining the source of the implicated blackberries. This multi-state outbreak illustrated the importance of food safety practices for fresh produce that may contribute to foodborne illness outbreaks. |
Exome sequencing identifies genetic variants in anophthalmia and microphthalmia.
Li J , Yang W , Wang YJ , Ma C , Curry CJ , McGoldrick D , Nickerson DA , Chong JX , Blue EE , Mullikin JC , Reefhuis J , Nembhard WN , Romitti PA , Werler MM , Browne ML , Olshan AF , Finnell RH , Feldkamp ML , Pangilinan F , Almli LM , Bamshad MJ , Brody LC , Jenkins MM , Shaw GM . Am J Med Genet A 2022 188 (8) 2376-2388 Anophthalmia and microphthalmia (A/M) are rare birth defects affecting up to 2 per 10,000 live births. These conditions are manifested by the absence of an eye or reduced eye volumes within the orbit leading to vision loss. Although clinical case series suggest a strong genetic component in A/M, few systematic investigations have been conducted on potential genetic contributions owing to low population prevalence. To overcome this challenge, we utilized DNA samples and data collected as part of the National Birth Defects Prevention Study (NBDPS). The NBDPS employed multi-center ascertainment of infants affected by A/M. We performed exome sequencing on 67 family trios and identified numerous genes affected by rare deleterious nonsense and missense variants in this cohort, including de novo variants. We identified 9 nonsense changes and 86 missense variants that are absent from the reference human population (Genome Aggregation Database), and we suggest that these are high priority candidate genes for A/M. We also performed literature curation, single cell transcriptome comparisons, and molecular pathway analysis on the candidate genes and performed protein structure modeling to determine the potential pathogenic variant consequences on PAX6 in this disease. |
Conceptual framework for understanding incident management systems during public health emergencies
Clark-Ginsberg A , Fisher H , Awan J , Rico A , Thomas T , Rose D , Vagi S , Jenkins L , Nelson C . Disaster Med Public Health Prep 2022 17 1-7 OBJECTIVE: Effective incident management is essential for coordinating efforts of multiple disciplines and stakeholders when responding to emergencies, including public health disasters such as the ongoing coronavirus disease 2019 (COVID-19) pandemic. METHODS: Existing research frameworks tend to focus on formal structures and doctrine (eg, ICS-NIMS); however, organizational processes that underlie incident management have not been systematically assessed and synthesized into a coherent conceptual framework. RESULTS: The lack of a framework has hindered the development of measures of performance that could be used to further develop the evidence base and facilitate process improvement. To address this gap, we present a conceptual framework of incident management drawn from expert feedback and a review of literature on incident management and related fields. The framework features 23 measurement constructs grouped into 5 domains: (1) situational awareness and information sharing, (2) incident action and implementation planning, (3) resource management and mobilization, (4) coordination and collaboration, and (5) feedback and continuous quality improvement. CONCLUSIONS: As such, the article provides a first step toward the development of robust measures for assessing the performance and effectiveness of incident management systems. |
A genome-wide association study of obstructive heart defects among participants in the National Birth Defects Prevention Study.
Rashkin SR , Cleves M , Shaw GM , Nembhard WN , Nestoridi E , Jenkins MM , Romitti PA , Lou XY , Browne ML , Mitchell LE , Olshan AF , Lomangino K , Bhattacharyya S , Witte JS , Hobbs CA . Am J Med Genet A 2022 188 (8) 2303-2314 Obstructive heart defects (OHDs) share common structural lesions in arteries and cardiac valves, accounting for ~25% of all congenital heart defects. OHDs are highly heritable, resulting from interplay among maternal exposures, genetic susceptibilities, and epigenetic phenomena. A genome-wide association study was conducted in National Birth Defects Prevention Study participants (N(discovery) = 3978; N(replication) = 2507), investigating the genetic architecture of OHDs using transmission/disequilibrium tests (TDT) in complete case-parental trios (N(discovery_TDT) = 440; N(replication_TDT) = 275) and case-control analyses separately in infants (N(discovery_CCI) = 1635; N(replication_CCI) = 990) and mothers (case status defined by infant; N(discovery_CCM) = 1703; N(replication_CCM) = 1078). In the TDT analysis, the SLC44A2 single nucleotide polymorphism (SNP) rs2360743 was significantly associated with OHD (p(discovery) = 4.08 × 10(-9) ; p(replication) = 2.44 × 10(-4) ). A CAPN11 SNP (rs55877192) was suggestively associated with OHD (p(discovery) = 1.61 × 10(-7) ; p(replication) = 0.0016). Two other SNPs were suggestively associated (p < 1 × 10(-6) ) with OHD in only the discovery sample. In the case-control analyses, no SNPs were genome-wide significant, and, even with relaxed thresholds ( × (discovery) < 1 × 10(-5) and p(replication) < 0.05), only one SNP (rs188255766) in the infant analysis was associated with OHDs (p(discovery) = 1.42 × 10(-6) ; p(replication) = 0.04). Additional SNPs with p(discovery) < 1 × 10(-5) were in loci supporting previous findings but did not replicate. Overall, there was modest evidence of an association between rs2360743 and rs55877192 and OHD and some evidence validating previously published findings. |
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