Last data update: Jan 27, 2025. (Total: 48650 publications since 2009)
Records 1-30 (of 214 Records) |
Query Trace: Rogers S[original query] |
---|
Nirsevimab effectiveness against medically attended respiratory syncytial virus illness and hospitalization among Alaska native children - Yukon-Kuskokwim Delta Region, Alaska, October 2023-June 2024
Lefferts B , Bressler S , Keck JW , Desnoyers C , Hodges E , January G , Morris K , Herrmann L , Singleton R , Aho S , Rogers J , Newell K , Ohlsen E , Link-Gelles R , Dawood FS , Bruden D , Fischer M , Klejka J , Scobie HM . MMWR Morb Mortal Wkly Rep 2024 73 (45) 1015-1021 Respiratory syncytial virus (RSV) is a leading cause of hospitalization among young children. Historically, American Indian and Alaska Native (AI/AN) children have experienced high rates of RSV-associated hospitalization. In August 2023, a preventive monoclonal antibody (nirsevimab) was recommended for all infants aged <8 months (born during or entering their first RSV season) and for children aged 8-19 months (entering their second RSV season) who have increased risk for severe RSV illness, including all AI/AN children. This evaluation in Alaska's Yukon-Kuskokwim Delta region estimated nirsevimab effectiveness among AI/AN children in their first or second RSV seasons during 2023-2024. Among 472 children with medically attended acute respiratory illness (ARI), 48% overall had received nirsevimab ≥7 days earlier (median = 91 days before the ARI-related visit). For children in their first RSV season (292), nirsevimab effectiveness was 76% (95% CI = 42%-90%) against medically attended RSV illness and 89% (95% CI = 32%-98%) against RSV hospitalization. For children in their second RSV season (180), effectiveness against medically attended RSV illness was 88% (95% CI = 48%-97%). Nirsevimab is effective for preventing severe RSV illness among infants entering their first RSV season and children entering their second season with increased risk for severe RSV, including all AI/AN children. |
Correction: An observational analysis of the impact of deltamethrin + piperonyl butoxide insecticide-treated nets on malaria case incidence and entomological indicators in Ebonyi State, Nigeria, 2017-2021
Davis KM , Okoko OO , Oduola AO , Inyama PU , Uneke CJ , Ambrose K , Seyoum A , Uhomoibhi P , Rhoda DA , Clary CB , Millar J , Littrell M , Rogers JH , Yoshimizu M , Inyang U , Maire M , Burnett SM . Malar J 2024 23 (1) 349 |
Fatal borealpox in an immunosuppressed patient treated with antivirals and vaccinia immunoglobulin - Alaska, 2023
Rogers JH , Westley B , Mego T , Newell KG , Laurance J , Smith L , Parker J , Park SY , Venkatasubrahmanyam S , Noll N , Bercovici S , Rao AK , McCollum AM , Davidson W , Carson WC , Townsend MB , Doty JB , Hutson C , Li Y , Wilkins K , Deng J , Gigante CM , Satheshkumar PS , Tuttle A , Villalba JA , Bhatnagar J , Reagan-Steiner S , Castrodale LJ , McLaughlin JB . Clin Infect Dis 2024 BACKGROUND: Borealpox virus (BRPV, formerly known as Alaskapox virus) is a zoonotic member of the Orthopoxvirus genus first identified in a person in 2015. In the six patients with infection previously observed BRPV involved mild, self-limiting illness. We report the first fatal BRPV infection in an immunosuppressed patient. METHODS: A man aged 69 years from Alaska's Kenai Peninsula was receiving anti-CD20 therapy for chronic lymphocytic leukemia. He presented to care for a tender, red papule in his right axilla with increasing induration and pain. The patient failed to respond to multiple prescribed antibiotic regimens and was hospitalized 65 days postsymptom onset for progression of presumed infectious cellulitis. BRPV was eventually detected through orthopoxvirus real-time polymerase chain reaction testing of mucosal swabs. He received combination antiviral therapy, including 21 days of intravenous tecovirimat, intravenous vaccinia immunoglobulin, and oral brincidofovir. Serial serology was conducted on specimens obtained posttreatment initiation. FINDINGS: The patient's condition initially improved with plaque recession, reduced erythema, and epithelization around the axillary lesion beginning one-week post-therapy. He later exhibited delayed wound healing, malnutrition, acute renal failure, and respiratory failure. He died 138 days postsymptom onset. Serologic testing revealed no evidence the patient generated a humoral immune response. No secondary cases were detected. CONCLUSION: This report demonstrates that BRPV can cause overwhelming disseminated infection in certain immunocompromised patients. Based on the patient's initial response, early BRPV identification and antiviral therapies might have been beneficial. These therapies, in combination with optimized immune function, should be considered for patients at risk for manifestations of BRPV. |
An observational analysis of the impact of deltamethrin + piperonyl butoxide insecticide-treated nets on malaria case incidence and entomological indicators in Ebonyi State, Nigeria, 2017-2021
Davis KM , Okoko OO , Oduola AO , Inyama PU , Uneke CJ , Ambrose K , Seyoum A , Uhomoibhi P , Rhoda DA , Clary CB , Millar J , Littrell M , Rogers JH , Yoshimizu M , Inyang U , Maire M , Burnett SM . Malar J 2024 23 (1) 317 BACKGROUND: Intense pyrethroid resistance threatens the effectiveness of the primary vector control intervention, insecticide-treated nets (ITNs), in Nigeria, the country with the largest malaria burden globally. In this study, the epidemiological and entomological impact of a new type of ITN (piperonyl-butoxide [PBO] ITNs) distributed in Ebonyi State were evaluated. The epidemiological impact was also compared to the impact of standard pyrethroid-only ITNs in Cross River State. METHODS: A controlled interrupted time series analysis was conducted on monthly malaria incidence data collected at the health facility level, using a multilevel mixed-effects negative binomial model. Data were analysed two years before and after the PBO ITN campaign in Ebonyi State (December 2017 to November 2021). A pre-post analysis, with no comparison group, was used to assess the impact of PBO ITNs on human biting rates and indoor resting density in Ebonyi during the high transmission season immediately before and after the PBO ITN campaign. RESULTS: In Ebonyi, PBO ITNs were associated with a 46.7% decrease (95%CI: -51.5, -40.8%; p < 0.001) in malaria case incidence in the 2 years after the PBO ITN distribution compared to a modelled scenario of no ITNs distributed, with a significant decrease from 269.6 predicted cases per 1000 population to 143.6. In Cross River, there was a significant 28.6% increase (95%CI: -10.4, 49.1%; p < 0.001) in malaria case incidence following the standard ITN distribution, with an increase from 71.2 predicted cases per 1000 population to 91.6. In Ebonyi, the human biting rate was 72% lower (IRR: 0.28; 95%CI 0.21, 0.39; p < 0.001) and indoor resting density was 73% lower (IRR: 0.27; 95%CI 0.21, 0.35; p < 0.001) after the PBO ITNs were distributed. CONCLUSIONS: The epidemiological and entomological impact of the PBO ITNs underscore the impact of these ITNs in areas with confirmed pyrethroid resistance. These findings contribute to ongoing research on the impact of new types of ITNs in Nigeria, providing critical evidence for the Nigeria National Malaria Elimination Programme and other countries for future ITN procurement decisions as part of mass ITN campaign planning and malaria programming. |
Population structure and antimicrobial resistance in Campylobacter jejuni and C. coli isolated from humans with diarrhea and from poultry, East Africa
French NP , Thomas KM , Amani NB , Benschop J , Bigogo GM , Cleaveland S , Fayaz A , Hugho EA , Karimuribo ED , Kasagama E , Maganga R , Melubo ML , Midwinter AC , Mmbaga BT , Mosha VV , Mshana FI , Munyua P , Ochieng JB , Rogers L , Sindiyo E , Swai ES , Verani JR , Widdowson MA , Wilkinson DA , Kazwala RR , Crump JA , Zadoks RN . Emerg Infect Dis 2024 30 (10) 2079-2089 ![]() Campylobacteriosis and antimicrobial resistance (AMR) are global public health concerns. Africa is estimated to have the world's highest incidence of campylobacteriosis and a relatively high prevalence of AMR in Campylobacter spp. from humans and animals. Few studies have compared Campylobacter spp. isolated from humans and poultry in Africa using whole-genome sequencing and antimicrobial susceptibility testing. We explored the population structure and AMR of 178 Campylobacter isolates from East Africa, 81 from patients with diarrhea in Kenya and 97 from 56 poultry samples in Tanzania, collected during 2006-2017. Sequence type diversity was high in both poultry and human isolates, with some sequence types in common. The estimated prevalence of multidrug resistance, defined as resistance to >3 antimicrobial classes, was higher in poultry isolates (40.9%, 95% credible interval 23.6%-59.4%) than in human isolates (2.5%, 95% credible interval 0.3%-6.8%), underlining the importance of antimicrobial stewardship in livestock systems. |
Semi-automated nonresponse detection for open-text survey data
Cibelli Hibben K , Smith Z , Rogers B , Ryan V , Scanlon P , Hoppe T . Soc Sci Comput Rev 2024 ![]() Open-ended survey questions can enable researchers to gain insights beyond more commonly used closed-ended question formats by allowing respondents an opportunity to provide information with few constraints and in their own words. Open-ended web probes are also increasingly used to inform the design and evaluation of survey questions. However, open-ended questions are more susceptible to insufficient or irrelevant responses that can be burdensome and time-consuming to identify and remove manually, often resulting in underuse of open-ended questions and, when used, potential inclusion of poor-quality data. To address these challenges, we developed and publicly released the Semi-Automated Nonresponse Detection for Survey text (SANDS), an item nonresponse detection approach based on a Bidirectional Transformer for Language Understanding model, fine-tuned using Simple Contrastive Sentence Embedding and targeted human coding, to categorize open-ended text data as valid or likely nonresponse. This approach is powerful in that it uses natural language processing as opposed to existing nonresponse detection approaches that have relied exclusively on rules or regular expressions or used bag-of-words approaches that tend to perform less well on short pieces of text, typos, or uncommon words, often prevalent in open-text survey data. This paper presents the development of SANDS and a quantitative evaluation of its performance and potential bias using open-text responses from a series of web probes as case studies. Overall, the SANDS model performed well in identifying a dataset of likely valid results to be used for quantitative or qualitative analysis, particularly on health-related data. Developed for generalizable use and accessible to others, the SANDS model can greatly improve the efficiency of identifying inadequate and irrelevant open-text responses, offering expanded opportunities for the use of open-text data to inform question design and improve survey data quality. © The Author(s) 2024. |
Social and structural drivers of HIV vulnerability among a respondent-driven sample of feminine and non-feminine presenting transgender women who have sex with men in Zimbabwe
Parmley LE , Miller SS , Chingombe I , Mapingure M , Mugurungi O , Rogers JH , Musuka G , Samba C , Hakim AJ , Harris TG . J Int AIDS Soc 2024 27 (4) e26231 INTRODUCTION: We sought to characterize social and structural drivers of HIV vulnerability for transgender women (TGW) in Zimbabwe, where TGW are not legally recognized, and explore differences in vulnerability by feminine presentation. METHODS: A secondary analysis was conducted with a sub-sample of participants recruited from a 2019 respondent-driven sampling survey that comprised men who have sex with men, TGW and genderqueer individuals assigned male sex at birth, from two cities in Zimbabwe. Survey questionnaires captured information related to socio-demographics, sexual and substance use behaviours, and social and structural barriers to HIV services. Secondary analyses were restricted to participants who identified as female, transfemale or transwomen (236/1538) and were unweighted. Descriptive statistics were used to calculate sample estimates and chi-square and Fisher's exact tests were used to assess differences in vulnerability by feminine presentation. RESULTS: Among 236 TGW, almost half (45.3%) presented as feminine in the 6 months preceding the survey and 8.5% had ever used hormones to affirm their gender identities. Median age among TGW was 23 years (interquartile range: 20-26). Feminine presenting TGW in our sample had higher prevalence of arrest (15.9% vs. 3.9%), rejection by family/friends (38.3% vs. 14.0%), employment termination (11.2% vs. 3.9%), employment refusal (14.0% vs. 3.9%), denial of healthcare (16.8% vs. 2.3%), physical, sexual or verbal harassment or abuse (59.8% vs. 34.1%), alcohol dependence (32.7% vs. 12.4%), recent transactional sex with a male or TGW partner (30.8% vs. 13.3%) and recent non-injection drug use (38.3% vs. 20.2%) than non-feminine presenting TGW (all p-value <0.05). CONCLUSIONS: Findings suggest that TGW, particularly feminine presenting TGW, experience social and structural inequities which may contribute to HIV vulnerability. Interventions aimed at addressing inequities, including trans competency training for providers and gender-affirming, psychosocial and legal support services for TGW, might mitigate risk. |
Missed opportunities for TB diagnostic testing among people living with HIV in Zimbabwe: Cross-sectional analysis of the Zimbabwe Population-based HIV Impact Assessment (ZIMPHIA) survey 2015-16
Takamiya M , Takarinda K , Balachandra S , Musuka G , Radin E , Hakim A , Pearson ML , Choto R , Sandy C , Maphosa T , Rogers JH . J Clin Tuberc Other Mycobact Dis 2024 35 100427 BACKGROUND: Using data from the Zimbabwe Population-based HIV Impact Assessment survey 2015-2016, we examined the TB care cascade and factors associated with not receiving TB diagnostic testing among adult PLHIV with TB symptoms. METHODS: Statistical Analysis was limited to PLHIV aged 15 years and older in HIV care. Weighted logistic regression with not receiving TB testing as outcome was adjusted for covariates with crude odd ratios (ORs) with p < 0.25. All analyses accounted for multistage survey design. RESULTS: Among 3507 adult PLHIV in HIV care, 2288 (59.7 %, 95 % CI:58.1-61.3) were female and 2425 (63.6 %, 95 % CI:61.1-66.1) lived in rural areas. 1197(48.7 %, 95 % CI:46.5-51.0) reported being screened for TB symptoms at their last HIV care visit. In the previous 12 months, 639 (26.0 %, 95 % CI:23.9-28.1) reported having symptoms and of those, 239 (37.8 %, 95 % CI:33.3-42.2) received TB testing. Of PLHIV tested for TB, 36 (49.5 %, 95 % CI:35.0-63.1) were diagnosed with TB; 32 (90.3 %, 95 % CI:78.9-100) of those diagnosed with TB received treatment. Never having used IPT was associated with not receiving TB testing. CONCLUSION: The results suggest suboptimal utilization of TB screening and diagnostic testing among PLHIV. New approaches are needed to reach opportunities missed in the HIV/TB integrated services. |
Developing and validating a screening tool for female genital schistosomiasis in urban Zambia
Rogers EQ , Mwangelwa S , Kabengele C , Kilembe W , Vwalika B , Inambao M , Mumba K , Chanda C , Secor WE , Musale V , Himukumbwa C , Parker R , Tichacek A , Bougouma K , Allen S , Wall KM . Front Trop Dis 2023 4 Background: The World Health Organization estimates that 56 million women and girls live with female genital schistosomiasis (FGS) in sub-Saharan Africa. FGS is often confused with symptoms of other genital abnormalities, and gold standard diagnosis with colposcopy is infeasible in most health facilities. Schistosomiasis haematobium is endemic in Zambia, yet routine screening or diagnostic efforts for FGS remain unavailable. Our study aimed to develop and pilot test a feasible FGS screening algorithm to implement in Zambian government clinics. Methodology/Principal Findings: We recruited 499 women from a longitudinal cohort of HIV-negative adult women in Lusaka and Ndola, Zambia. We used demographic, risk factor, and symptom data collected from standardized surveys, gynecological exams, and laboratory tests to develop a screening algorithm for FGS among a derivation cohort (n=349). After cross-validation using 5-fold iterative resampling, the algorithm was applied in a holdout sample of the cohort (n=150). The prevalence of FGS (ascertained by expert review) was 23.4% in the study population. The screening algorithm included childhood and travel exposure to rivers and streams; testing positive for visual inspection of the cervix with acetic acid; hematuria; reporting less than the median average age at sexual debut (<17 years); when asked what diseases can be transmitted via freshwater exposure, reporting ‘none’; being born outside of Lusaka or Copperbelt Province; and reporting occupation as ‘Housekeeper’. The screening algorithm had reasonable discrimination in the derivation cohort (area under the curve [AUC]=0.69, 95% confidence interval [CI]: 0.66-0.79, p-value<0.001). Using a score cut off ≥ 2 the risk algorithm in the derivation cohort had 77% sensitivity, 48% specificity, 35% positive predictive value, and 85% negative predictive value. Conclusions/Significance: Given the prevalence of FGS and associated morbidities, improved screening for FGS is imperative. We developed a simple screening algorithm to improve the diagnosis and treatment of FGS among adult women in Zambian government clinics. Copyright © 2024 Rogers, Mwangelwa, Kabengele, Kilembe, Vwalika, Inambao, Mumba, Chanda, Secor, Musale, Himukumbwa, Parker, Tichacek, Bougouma, Allen and Wall. |
Hepatitis B virus infection (HBV) and HIV-HBV coinfection among men who have sex with men, transgender women, and genderqueer individuals in Harare and Bulawayo Zimbabwe, 2019
Breen RWB , Parmley LE , Mapingure MP , Chingombe I , Mugurungi O , Musuka G , Hakim AJ , Rogers JH , Moyo B , Samba C , Miller SS , Lamb MR , Harris TG . Heliyon 2024 10 (3) e25790 OBJECTIVES: To measure HIV and Hepatitis B virus (HBV) prevalence and associated risk behaviors among men who have sex with men (MSM) and transgender women/genderqueer individuals (TGW/GQ) in Zimbabwe. METHODS: We conducted a biobehavioral survey using respondent-driven sampling (RDS) among adult MSM and TGW/GQ in Harare and Bulawayo, Zimbabwe in 2019. Participants completed a questionnaire and underwent testing for HIV and HBV. RESULTS: Overall, 1,510 (Harare: 694, Bulawayo 816) participants were enrolled and consented to testing; 3.8 % (58) tested positive for HBV, 22.5 % (339) tested positive for HIV, and 2.2 % (33) tested positive for both HIV and HBV. HBV prevalence was higher among participants with HIV compared to HIV-negative participants (9.7 % vs. 2.1 %, p < 0.0001). Overall, HBV prevalence was not statistically different between MSM and TGW/GQ (3.7 % vs 4.5 %, p = 0.49) nor between Harare and Bulawayo (3.3 % vs 4.3 %, p = 0.33). CONCLUSIONS: Our survey demonstrates the prevalence of HBV among MSM and TGW/GQ is lower than other estimates of HBV among MSM in Africa but remains high among our survey population living with HIV highlighting the need to expand HBV testing and treatment services, especially among people with HIV in Zimbabwe. |
Surveillance for acute flaccid myelitis - United States, 2018-2022
Whitehouse ER , Lopez A , English R , Getachew H , Ng TFF , Emery B , Rogers S , Kidd S . MMWR Morb Mortal Wkly Rep 2024 73 (4) 70-76 Acute flaccid myelitis (AFM) is a serious neurologic condition primarily affecting children; AFM can cause acute respiratory failure and permanent paralysis. AFM is a rare but known complication of various viral infections, particularly those of enteroviruses (EVs). Increases in AFM cases during 2014, 2016, and 2018 were associated with EV-D68 infection. This report examines trends in confirmed AFM cases during 2018-2022 and patients' clinical and laboratory characteristics. The number of AFM cases was low during 2019-2022 (28-47 cases per year); the number of cases remained low in 2022 despite evidence of increased EV-D68 circulation in the United States. Compared with cases during the most recent peak year (2018), fewer cases during 2019-2021 had upper limb involvement, prodromal respiratory or febrile illness, or cerebrospinal fluid pleocytosis, and more were associated with lower limb involvement. It is unclear why EV-D68 circulation in 2022 was not associated with an increase in AFM cases or when the next increase in AFM cases will occur. Nonetheless, clinicians should continue to suspect AFM in any child with acute flaccid limb weakness, especially those with a recent respiratory or febrile illness. |
Factors associated with having both male and female recent sexual partnerships among men who have sex with men in Harare and Bulawayo, Zimbabwe
Davis M , Musuka G , Mapingure MP , Hakim A , Parmley LE , Mugurungi O , Chingombe I , Miller SS , Rogers JH , Lamb MR , Samba C , Harris TG . AIDS Behav 2024 To better understand male and female sexual partnerships among men who have sex with men (MSM), we used data from a 2019 biobehavioral survey among MSM in Harare and Bulawayo, Zimbabwe to conduct bivariate analyses and multivariable logistic regression to determine whether sociodemographic characteristics and HIV-related factors were associated with having both male and female sexual partnerships within the last 6 months. Of included MSM (N = 1143), 31% reported both male and female partnerships in the last 6 months. Being married/cohabiting (adjusted odds ratio (aOR) = 8.58, 95% confidence interval (CI) = 4.92-14.95) or separated/divorced/widowed (aOR = 1.96, 95% CI = 1.24-3.08) vs. being single, and hazardous alcohol consumption (aOR = 1.58, 95% CI 1.19-2.09) were associated with higher odds of having both male and female recent partnerships. Being aged 35 + vs. 18-24 (aOR = 0.50, 95% CI = 0.31-0.81), condomless receptive anal intercourse at last sex with the main male partner (aOR = 0.43, 95% CI = 0.26-0.74), and positive HIV status (aOR = 0.46, 95% CI = 0.31-0.67) were associated with lower odds of recent male and female partnerships. MSM in Harare who reported harassment/abuse (aOR = 3.16, 95% CI = 1.72-5.79) had higher odds of both male and female partnerships than MSM in Bulawayo reporting harassment/abuse. The prevalence of both male and female recent partnerships (31%) was lower among MSM in this survey than in other biobehavioral surveys of MSM in sub-Saharan Africa. Findings suggest that MSM with recent male and female partnerships compared to MSM with only male recent partners have lower odds of positive HIV status and participate in behaviors that lower HIV risk; however, the direction of these relationships cannot be determined due to the cross-sectional nature of the data. The findings also suggest a possible connection between experiences of stigma of MSM behavior and not having both male and female partnerships that warrants further exploration. Accessible, stigma-free HIV testing and education programming that considers the potential overlap between the MSM and general populations via both male and female partnerships and the associated behaviors could be a key component of HIV elimination in Zimbabwe. |
Advanced child tax credit payments and national child abuse hotline contacts, 2019-2022
Merrill-Francis M , Chen MS , Dunphy C , Swedo EA , Zhang Kudon H , Metzler M , Mercy JA , Zhang X , Rogers TM , Wu Shortt J . Inj Prev 2024 BACKGROUND: Children in households experiencing poverty are disproportionately exposed to maltreatment. Income support policies have been associated with reductions in child abuse and neglect. The advance child tax credit (CTC) payments may reduce child maltreatment by improving the economic security of some families. No national studies have examined the association between advance CTC payments and child abuse and neglect. This study examines the association between the advance CTC payments and child abuse and neglect-related contacts to the Childhelp National Child Abuse Hotline. METHODS: A time series study of contacts to the Childhelp National Child Abuse Hotline between January 2019 and December 2022 was used to examine the association between the payments and hotline contacts. An interrupted time series (ITS) exploiting the variation in the advance CTC payments was estimated using fixed effects. RESULTS: The CTC advance payments were associated with an immediate 13.8% (95% CI -17.5% to -10.0%) decrease in contacts to the hotline in the ITS model. Following the expiration of the advance CTC payments, there was a significant and gradual 0.1% (95% CI +0.0% to +0.2%) daily increase in contacts. Sensitivity analyses found significant reductions in contacts following each payment, however, the reductions were associated with the last three of the six total payments. CONCLUSION: These findings suggest the advance CTC payments may reduce child abuse and neglect-related hotline contacts and continue to build the evidence base for associations between income-support policies and reductions in child abuse and neglect. |
Etiology of acute lower respiratory illness hospitalizations among infants in 4 countries
Kubale J , Kujawski S , Chen I , Wu Z , Khader IA , Hasibra I , Whitaker B , Gresh L , Simaku A , Simões EAF , Al-Gazo M , Rogers S , Gerber SI , Balmaseda A , Tallo VL , Al-Sanouri TM , Porter R , Bino S , Azziz-Baumgartner E , McMorrow M , Hunt D , Thompson M , Biggs HM , Gordon A . Open Forum Infect Dis 2023 10 (12) ofad580 ![]() BACKGROUND: Recent studies explored which pathogens drive the global burden of pneumonia hospitalizations among young children. However, the etiology of broader acute lower respiratory tract infections (ALRIs) remains unclear. METHODS: Using a multicountry study (Albania, Jordan, Nicaragua, and the Philippines) of hospitalized infants and non-ill community controls between 2015 and 2017, we assessed the prevalence and severity of viral infections and coinfections. We also estimated the proportion of ALRI hospitalizations caused by 21 respiratory pathogens identified via multiplex real-time reverse transcription polymerase chain reaction with bayesian nested partially latent class models. RESULTS: An overall 3632 hospitalized infants and 1068 non-ill community controls participated in the study and had specimens tested. Among hospitalized infants, 1743 (48.0%) met the ALRI case definition for the etiology analysis. After accounting for the prevalence in non-ill controls, respiratory syncytial virus (RSV) was responsible for the largest proportion of ALRI hospitalizations, although the magnitude varied across sites-ranging from 65.2% (95% credible interval, 46.3%-79.6%) in Albania to 34.9% (95% credible interval, 20.0%-49.0%) in the Philippines. While the fraction of ALRI hospitalizations caused by RSV decreased as age increased, it remained the greatest driver. After RSV, rhinovirus/enterovirus (range, 13.4%-27.1%) and human metapneumovirus (range, 6.3%-12.0%) were the next-highest contributors to ALRI hospitalizations. CONCLUSIONS: We observed substantial numbers of ALRI hospitalizations, with RSV as the largest source, particularly in infants aged <3 months. This underscores the potential for vaccines and long-lasting monoclonal antibodies on the horizon to reduce the burden of ALRI in infants worldwide. |
Duration of enterovirus d68 RNA shedding in the upper respiratory tract and transmission among household contacts, Colorado, USA
Nguyen-Tran H , Thompson C , Butler M , Miller KR , Pyle L , Jung S , Rogers S , Ng TFF , Routh J , Dominguez SR , Messacar K . Emerg Infect Dis 2023 29 (11) 2315-2324 ![]() Enterovirus D68 (EV-D68) causes cyclical outbreaks of respiratory disease and acute flaccid myelitis. EV-D68 is primarily transmitted through the respiratory route, but the duration of shedding in the respiratory tract is unknown. We prospectively enrolled 9 hospitalized children with EV-D68 respiratory infection and 16 household contacts to determine EV-D68 RNA shedding dynamics in the upper respiratory tract through serial midturbinate specimen collections and daily symptom diaries. Five (31.3%) household contacts, including 3 adults, were EV-D68-positive. The median duration of EV-D68 RNA shedding in the upper respiratory tract was 12 (range 7-15) days from symptom onset. The most common symptoms were nasal congestion (100%), cough (92.9%), difficulty breathing (78.6%), and wheezing (57.1%). The median illness duration was 20 (range 11-24) days. Understanding the duration of RNA shedding can inform the expected rate and timing of EV-D68 detection in associated acute flaccid myelitis cases and help guide public health measures. |
Human salmonellosis outbreak linked to salmonella typhimurium epidemic in wild songbirds, United States, 2020-2021
Patel K , Stapleton GS , Trevejo RT , Tellier WT , Higa J , Adams JK , Hernandez SM , Sanchez S , Nemeth NM , Debess EE , Rogers KH , Mete A , Watson KD , Foss L , Low MSF , Gollarza L , Nichols M . Emerg Infect Dis 2023 29 (11) 2298-2306 ![]() Salmonella infection causes epidemic death in wild songbirds, with potential to spread to humans. In February 2021, public health officials in Oregon and Washington, USA, isolated a strain of Salmonella enterica serovar Typhimurium from humans and a wild songbird. Investigation by public health partners ultimately identified 30 illnesses in 12 states linked to an epidemic of Salmonella Typhimurium in songbirds. We report a multistate outbreak of human salmonellosis associated with songbirds, resulting from direct handling of sick and dead birds or indirect contact with contaminated birdfeeders. Companion animals might have contributed to the spread of Salmonella between songbirds and patients; the outbreak strain was detected in 1 ill dog, and a cat became ill after contact with a wild bird. This outbreak highlights a One Health issue where actions like regular cleaning of birdfeeders might reduce the health risk to wildlife, companion animals, and humans. |
Impact of SARS-CoV-2 infection on the association between laboratory tests and severe outcomes among hospitalized children
Xie J , Kuppermann N , Florin TA , Tancredi DJ , Funk AL , Kim K , Salvadori MI , Yock-Corrales A , Shah NP , Breslin KA , Chaudhari PP , Bergmann KR , Ahmad FA , Nebhrajani JR , Mintegi S , Gangoiti I , Plint AC , Avva UR , Gardiner MA , Malley R , Finkelstein Y , Dalziel SR , Bhatt M , Kannikeswaran N , Caperell K , Campos C , Sabhaney VJ , Chong SL , Lunoe MM , Rogers AJ , Becker SM , Borland ML , Sartori LF , Pavlicich V , Rino PB , Morrison AK , Neuman MI , Poonai N , Simon NE , Kam AJ , Kwok MY , Morris CR , Palumbo L , Ambroggio L , Navanandan N , Eckerle M , Klassen TP , Payne DC , Cherry JC , Waseem M , Dixon AC , Ferre IB , Freedman SB . Open Forum Infect Dis 2023 10 (10) ofad485 BACKGROUND: To assist clinicians with identifying children at risk of severe outcomes, we assessed the association between laboratory findings and severe outcomes among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected children and determined if SARS-CoV-2 test result status modified the associations. METHODS: We conducted a cross-sectional analysis of participants tested for SARS-CoV-2 infection in 41 pediatric emergency departments in 10 countries. Participants were hospitalized, had laboratory testing performed, and completed 14-day follow-up. The primary objective was to assess the associations between laboratory findings and severe outcomes. The secondary objective was to determine if the SARS-CoV-2 test result modified the associations. RESULTS: We included 1817 participants; 522 (28.7%) SARS-CoV-2 test-positive and 1295 (71.3%) test-negative. Seventy-five (14.4%) test-positive and 174 (13.4%) test-negative children experienced severe outcomes. In regression analysis, we found that among SARS-CoV-2-positive children, procalcitonin ≥0.5 ng/mL (adjusted odds ratio [aOR], 9.14; 95% CI, 2.90-28.80), ferritin >500 ng/mL (aOR, 7.95; 95% CI, 1.89-33.44), D-dimer ≥1500 ng/mL (aOR, 4.57; 95% CI, 1.12-18.68), serum glucose ≥120 mg/dL (aOR, 2.01; 95% CI, 1.06-3.81), lymphocyte count <1.0 × 10(9)/L (aOR, 3.21; 95% CI, 1.34-7.69), and platelet count <150 × 10(9)/L (aOR, 2.82; 95% CI, 1.31-6.07) were associated with severe outcomes. Evaluation of the interaction term revealed that a positive SARS-CoV-2 result increased the associations with severe outcomes for elevated procalcitonin, C-reactive protein (CRP), D-dimer, and for reduced lymphocyte and platelet counts. CONCLUSIONS: Specific laboratory parameters are associated with severe outcomes in SARS-CoV-2-infected children, and elevated serum procalcitonin, CRP, and D-dimer and low absolute lymphocyte and platelet counts were more strongly associated with severe outcomes in children testing positive compared with those testing negative. |
Outbreak of locally acquired mosquito-transmitted (autochthonous) malaria - Florida and Texas, May-July 2023
Blackburn D , Drennon M , Broussard K , Morrison AM , Stanek D , Sarney E , Ferracci C , Huard S , Brennan W , Eaton J , Nealeigh S , Barber N , Zimler RA , Adams JN , Blackmore C , Gordillo M , Mercado R , Vore H , Scanlan K , Motie I , Stanfield L , Farooq A , Widel K , Tomson K , Kerr N , Nasir J , Cone M , Rice C , Larkin T , Hernandez E , Bencie J , Lesser CR , Dersch M , Ramirez-Lachmann S , Clark M , Rollo S , Bashadi A , Tyler R , Bolling B , Moore B , Sullivan B , Fonken E , Castillo R , Gonzalez Y , Olivares G , Mace KE , Sayre D , Lenhart A , Sutcliffe A , Dotson E , Corredor C , Rogers E , Raphael BH , Sapp SGH , Qvarnstrom Y , Ridpath AD , McElroy PD . MMWR Morb Mortal Wkly Rep 2023 72 (36) 973-978 Eight cases of locally acquired, mosquito-transmitted (i.e., autochthonous) Plasmodium vivax malaria, which has not been reported in the United States since 2003, were reported to CDC from state health departments in Florida and Texas during May 18-July 17, 2023. As of August 4, 2023, case surveillance, mosquito surveillance and control activities, and public outreach and education activities continue in both states. U.S. clinicians need to consider a malaria diagnosis in patients with unexplained fever, especially in areas where autochthonous malaria has been recently reported, although the risk for autochthonous malaria in the United States remains very low. Prompt diagnosis and treatment of malaria can prevent severe disease or death and limit ongoing transmission to local Anopheles mosquitoes and other persons. Preventing mosquito bites and controlling mosquitoes at home can prevent mosquitoborne diseases, including malaria. Before traveling internationally to areas with endemic malaria, travelers should consult with a health care provider regarding recommended malaria prevention measures, including potentially taking malaria prophylaxis. Malaria is a nationally notifiable disease; continued reporting of malaria cases to jurisdictional health departments and CDC will also help ensure robust surveillance to detect and prevent autochthonous malaria in the United States. |
Review of intervention products for use in the prevention and control of anemia
Lopez de Romaña D , Mildon A , Golan J , Jefferds MED , Rogers LM , Arabi M . Ann N Y Acad Sci 2023 1529 (1) 42-60 Anemia remains a major public health problem, especially in low- and middle-income countries. The World Health Organization recommends several interventions to prevent and manage anemia in vulnerable population groups, including young children, menstruating adolescent girls and women, and pregnant and postpartum women. Daily iron supplementation reduces the risk of anemia in infants, children, and pregnant women, and intermittent iron supplementation reduces anemia risk in menstruating girls and women. Micronutrient powders reduce the risk of anemia in children. Fortifying wheat flour with iron reduces the risk of anemia in the overall population, whereas the effect of fortifying maize flour and rice is still uncertain. Regarding non-nutrition-related interventions, malaria treatment and deworming have been reported to decrease anemia prevalence. Promising interventions to prevent anemia include vitamin A supplementation, multiple micronutrient supplementation for pregnant women, small-quantity lipid-based supplements, and fortification of salt with iodine and iron. Future research could address the efficacy and safety of different iron supplementation formulations, identify the most bioavailable form of iron for fortification, examine adherence to supplementation regimens and fortification standards, and investigate the effectiveness of integrating micronutrient, helminth, and malaria control programs. |
Consensus-based framework for evaluating data modernization initiatives: the case of cancer registration and electronic reporting
Subramanian S , Tangka FKL , Pordell P , Beizer J , Wilson R , Jones SF , Rogers JD , Benard VB , Richardson LC . JAMIA Open 2023 6 (3) ooad060 As part of its data modernization initiative (DMI), the Centers for Disease Control and Prevention, Division of Cancer Prevention and Control is testing and implementing innovative solutions to improve cancer surveillance data quality and timeliness. We describe a consensus-based effort to create a framework to guide the evaluation of cancer surveillance modernization efforts by addressing specific context, processes, and costs related to cancer registration. We drew on prior theories, consulted with experts, and sought feedback from cancer registry staff. We developed the cancer surveillance systems, context, outcomes, and process evaluation (CS-SCOPE) framework to explain the ways in which cancer registry data quality, timeliness, and efficiency are impacted by external and internal contextual factors and interrelated process and content factors. The framework includes implementation measures to understand acceptability of process changes along with outcome measures to assess DMI initiation and ongoing sustainability. The framework's components and structures can be tailored for use in other DMI evaluations. |
Perspective: Emerging evidence and critical issues with the use of single-drop capillary blood for the measurement of hemoglobin concentration in population-level anemia surveys
Karakochuk CD , Dary O , Flores-Urrutia MC , Garcia-Casal MN , Hayashi C , Jefferds MED , Johnston R , Larson LM , Mapango C , Mazariegos Cordero DI , Moorthy D , Namaste S , Rogers LM , Saha K , Wuehler S . Adv Nutr 2024 100290 Accurate and precise measurement of hemoglobin concentration is critical for reliable estimations of anemia prevalence at the population-level. When systematic and/or random error are introduced in hemoglobin measurement, estimates of anemia prevalence might be significantly erroneous and, hence, limit their usefulness. For decades, single-drop capillary blood has been the most common blood source used for the measurement of hemoglobin concentration in surveys, especially in low- and middle-income countries. Here, we highlight historical and emerging evidence that single-drop capillary blood introduces a high degree of random error (variability) to hemoglobin estimates, leading to less reliable estimates of anemia prevalence at the population-level. At present, the best practice is to collect and use venous blood for measurement of hemoglobin with an automated hematology analyzer, following standard operating procedures and quality assurance measures. Where use of an automated analyzer is not possible, the analysis of venous blood in a point-of-care hemoglobinometer by trained phlebotomists or specimen collectors should be considered. A forthcoming systematic review will provide additional evidence on the accuracy and precision of single-drop capillary blood for hemoglobin assessment. In the meantime, we raise caution when using single-drop capillary blood for hemoglobin measurement as it can result in inaccurate hemoglobin estimates and less reliable anemia prevalence estimates. |
Risk of subsequent respiratory virus detection after primary virus detection in a community household study - King County, Washington 2019-2021
Heimonen J , Chow EJ , Wang Y , Hughes JP , Rogers J , Emanuels A , O'Hanlon J , Han PD , Wolf CR , Logue JK , Ogokeh CE , Rolfes MA , Uyeki TM , Starita L , Englund JA , Chu HY . J Infect Dis 2023 ![]() BACKGROUND: The epidemiology of respiratory viral infections is complex. How infection with one respiratory virus affects risk of subsequent infection with the same or another respiratory virus is not well described. METHODS: We retrospectively analyzed data from a longitudinal household cohort study from October 2019-June 2021. Enrolled households completed active surveillance for acute respiratory illness (ARI), and participants with ARI self-collected nasal swabs; after April 2020, participants with ARI or laboratory-confirmed SARS-CoV-2 and their household members self-collected nasal swabs. Specimens were tested via multiplex RT-PCR for respiratory viruses. A Cox regression model with a time-dependent covariate examined risk of subsequent detections following a specific primary viral detection. RESULTS: Rhinovirus was the most frequently detected pathogen in study specimens (n=406, 9.5%). Among 51 participants with multiple viral detections, rhinovirus to seasonal coronavirus (8, 14.8%) was the most common viral detection pairing. Relative to no primary detection, there was a 1.03-2.06-fold increase in risk of subsequent virus detection in the 90 days following primary detection; risk varied by primary virus: parainfluenza, rhinovirus, and respiratory syncytial virus were statistically significant. CONCLUSIONS: Primary virus detection was associated with higher risk of subsequent virus detection within the first 90 days after primary detection. |
Prevalence of Nonsuppressed Viral Load and Associated Factors Among Adults Receiving Antiretroviral Therapy in Eswatini, Lesotho, Malawi, Zambia, and Zimbabwe (2015-2017): Results from Population-Based Nationally-Representative Surveys (preprint)
Haas AD , Radin E , Hakim AJ , Jahn A , Philip NM , Jonnalagadda S , Saito S , Low A , Patel H , Schwitters AM , Rogers JH , Frederix K , Kim E , Bello G , Williams DB , Parekh B , Sachathep K , Barradas DT , Kalua T , Birhanu S , Musuka G , Mugurungi O , Tippett Barr BA , Sleeman K , Mulenga LB , Thin K , Ao TT , Brown K , Voetsch AC , Justman JE . medRxiv 2020 2020.07.13.20152553 Introduction The Joint United Nations Programme on HIV/AIDS (UNAIDS) has set a target of ≥90% of people living with HIV (PLHIV) receiving antiretroviral therapy (ART) to have viral load suppression (VLS). We examined factors associated with nonsuppressed viral Load (NVL).Methods We included PLHIV receiving ART aged 15–59 years from Eswatini, Lesotho, Malawi, Zambia, and Zimbabwe. Blood samples from PLHIV were analyzed for HIV RNA and recent exposure to antiretroviral drugs (ARVs). Outcomes were NVL (viral load ≥1000 copies/mL), virologic failure (VF; ARVs present and viral load ≥1000 copies/mL), interrupted ART (ARVs absent and viral load ≥1000 copies/mL), and receiving second-line ART. We calculated odds ratios and incidence rate ratios for factors associated with NVL, VF, interrupted ART, and switching to second-line ART.Results The prevalence of NVL was 11.2%: 8.2% experienced VF, and 3.0% interrupted ART. Younger age, male gender, less education, suboptimal adherence, receiving nevirapine, HIV non-disclosure, never having married, and residing in Zimbabwe, Lesotho, or Zambia were associated with higher odds of NVL. Among people with NVL, marriage, female gender, shorter ART duration, higher CD4 count, and alcohol use were associated with higher odds for interrupted ART and lower odds for VF. Many people with VF (44.8%) had CD4 counts <200 cells/µL, but few (0.31% per year) switched to second-line ART.Conclusions Countries are approaching UNAIDS VLS targets for adults. Treatment support for people initiating ART with asymptomatic HIV infection, scale-up of viral load monitoring, and optimized ART regimens may further reduce NVL prevalence.Competing Interest StatementThe authors have declared no competing interest.Funding StatementFunding: This research has been supported by the President's Emergency Plan for AIDS Relief (PEPFAR) through the Centers for Disease Control and Prevention (CDC) under the terms of grant number U2GGH001226. ADH was supported by a Swiss National Science Foundation (SNF) Early Postdoc Mobility Fellowship (grant number: P2BEP3_178602). Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the funding agencies. Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The Eswatini Scientific and Ethics Committee, the National Health Science Research Committee Malawi, the National Health Research Ethics Committee Lesotho, the National Health Research Ethics Committee Lesotho, the Tropical Diseases Research Centre Ethics Review Committee, Zambia, the Medical Research Council of Zimbabwe, and the Institutional Review Boards at the Centers for Disease Control and Prevention (CDC; Atlanta, GA) and Columbia University Medical Center (New York, NY) approved the PHIA surveys.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).Yes I 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.YesPublic datasets for Eswatini, Malawi, and Zambia are available. Public datasets for Lesotho and Zimbabwe will be made available soon. For more information see: https://phia-data.icap.columbia.edu/ https://phia-data.icap.columbia.edu/ |
Mutations in TAC1B: a novel genetic determinant of clinical fluconazole resistance in C. auris (preprint)
Rybak JM , Munoz JF , Barker KS , Parker JE , Esquivel BD , Berkow EL , Lockhart SR , Gade L , Palmer GE , White TC , Kelly SL , Cuomo CA , Rogers PD . bioRxiv 2020 2020.02.18.955534 Candida auris has emerged as a multidrug-resistant pathogen of great clinical concern. Approximately 90% of clinical C. auris isolates are resistant to fluconazole, the most commonly prescribed antifungal agent, yet it remains unknown what mechanisms underpin this fluconazole resistance. To identify novel mechanisms contributing to fluconazole resistance in C. auris, the fluconazole-susceptible C. auris clinical isolate AR0387 was passaged in media supplemented with fluconazole to generate derivative strains which had acquired increased fluconazole resistance in vitro. Comparative analysis of comprehensive sterol profiles, [3H]-fluconazole uptake, sequencing of C. auris genes homologous to genes known to contribute to fluconazole resistance in other species of Candida, and the relative expression of C. auris ERG11, CDR1, and MDR1 were performed. All fluconazole-evolved derivative strains were found to have acquired mutations in the zinc-cluster transcription factor-encoding gene, TAC1B, and a corresponding increase in CDR1 expression relative to the parental clinical isolate, AR0387. Mutations in TAC1B were also identified in a set of 304 globally distributed C. auris clinical isolates representing each of the four major clades. Introduction of the most common mutation found among fluconazole-resistant clinical isolates of C. auris into the fluconazole-susceptible isolate AR0387, was confirmed to increase fluconazole resistance by 8-fold, and the correction of the same mutation in a fluconazole-resistant isolate, AR0390, decreased fluconazole MIC by 16-fold. Taken together, these data demonstrate that C. auris can rapidly acquire resistance to fluconazole in-vitro, and that mutations in TAC1B significantly contribute to clinical fluconazole resistance.IMPORTANCE Candida auris is an emerging multidrug-resistant pathogen of global concern, known to be responsible for outbreaks on six continents and commonly resistant to antifungals. While the vast majority of clinical C. auris isolates are highly resistant to fluconazole, an essential part of the available antifungal arsenal, very little is known about the mechanisms contributing to resistance. In this work, we show that mutations in the transcription factor TAC1B significantly contribute to clinical fluconazole resistance. These studies demonstrate that mutations in TAC1B can arise rapidly in vitro upon exposure to fluconazole, and that a multitude of resistance-associated TAC1B mutations are present among the majority of fluconazole-resistant C. auris isolates from a global collection and appear specific to a subset of lineages or clades. Thus, identification of this novel genetic determinant of resistance significantly adds to the understanding of clinical antifungal resistance in C. auris. |
Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study
Rogers JH , Cox SN , Link AC , Nwanne G , Han PD , Pfau B , Chow EJ , Wolf CR , Boeckh M , Hughes JP , Halloran ME , Uyeki TM , Shim MM , Duchin J , Englund JA , Mosites E , Rolfes MA , Starita LA , Chu HY . Epidemiol Infect 2023 151 1-48 Homeless shelter residents and staff may be at higher risk of SARS-CoV-2 infection. However, | 34 SARS-CoV-2 infection estimates in this population have been reliant on cross-sectional or | 35 outbreak investigation data. We conducted routine surveillance and outbreak testing in 23 | 36 homeless shelters in King County, Washington to estimate the occurrence of laboratory37 confirmed SARS-CoV-2 infection and risk factors during 1/1/2020 -5/31/2021. Symptom surveys | 38 and nasal swabs were collected for SARS-CoV-2 testing by RT-PCR for residents aged ≥3 | 39 months and staff. We collected 12,915 specimens from 2,930 unique participants. We identified | 40 4.74 (95% CI 4.00 – 5.58) SARS-CoV-2 infections per 100 individuals (residents: 4.96, 95% CI | 41 4.12 – 5.91; staff: 3.86, 95% CI 2.43 – 5.79). Most infections were asymptomatic at time of | 42 detection (74%) and detected during routine surveillance (73%). Outbreak testing yielded higher | 43 test positivity compared to routine surveillance (2.7% vs. 0.9%). Among those infected, | 44 residents were less likely to report symptoms than staff. Participants who were vaccinated | 45 against seasonal influenza and were current smokers had lower odds of having an infection | 46 detected. Active surveillance that includes SARS-CoV-2 testing of all persons is essential in | 47 ascertaining the true burden of SARS-CoV-2 infections among residents and staff of congregate | 48 settings. |
Incidence of SARS-CoV-2 infection and associated risk factors among staff and residents at homeless shelters in King County, Washington: an active surveillance study (preprint)
Rogers JH , Cox SN , Link AC , Nwanne G , Han PD , Pfau B , Chow EJ , Wolf CR , Boeckh M , Hughes JP , Halloran ME , Uyeki TM , Shim MM , Duchin J , Englund JA , Mosites E , Rolfes MA , Starita LA , Chu HY . medRxiv 2023 30 Homeless shelter residents and staff may be at higher risk of SARS-CoV-2 infection. However, SARS-CoV-2 infection estimates in this population have been reliant on cross-sectional or outbreak investigation data. We conducted routine surveillance and outbreak testing in 23 homeless shelters in King County, Washington to estimate the occurrence of laboratory-confirmed SARS-CoV-2 infection and risk factors during 1/1/2020 -5/31/2021. Symptom surveys and nasal swabs were collected for SARS-CoV-2 testing by RT-PCR for residents aged >=3 months and staff. We collected 12,915 specimens from 2,930 unique participants. We identified 4.74 (95% CI 4.00 - 5.58) SARS-CoV-2 infections per 100 individuals (residents: 4.96, 95% CI 4.12 - 5.91; staff: 3.86, 95% CI 2.43 - 5.79). Most infections were asymptomatic at time of detection (74%) and detected during routine surveillance (73%). Outbreak testing yielded higher test positivity compared to routine surveillance (2.7% vs. 0.9%). Among those infected, residents were less likely to report symptoms than staff. Participants who were vaccinated against seasonal influenza and were current smokers had lower odds of having an infection detected. Active surveillance that includes SARS-CoV-2 testing of all persons is essential in ascertaining the true burden of SARS-CoV-2 infections among residents and staff of congregate settings. 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. |
Type-specific EV-D68 real-time RT-PCR assay for the detection of all extant enterovirus D68 strains (preprint)
Ng TFF , Nix WA , Rogers SL , Emery B , Chern SW , Butler K , Oberste MS . bioRxiv 2022 06 Enterovirus D68 (EV-D68) has caused recurring respiratory disease outbreaks in the United States since 2014. The dominant circulating EV-D68 strain has evolved from clade B1 to the more recent B2 and B3 clades. As recurrent outbreaks and continued virus evolution are expected for EV-D68, a robust real-time PCR assay that detects known strains as well as potential emerging strains is critical for national surveillance and clinical diagnostics. We describe a type-specific EV-D68 real-time RT-PCR (rRT-PCR) assay termed CDC2022, which targets sequences encoding conserved amino acid regions of all extant EV-D68 strains. We targeted three motifs conserved among all strains in the last 60 years. The assay achieved 100% (270/270) sensitivity and 100% (344/344) specificity when tested with a collection of 613 respiratory specimens, compared to the gold-standard EV semi-nested VP1 PCR and sequencing assay (snPCR/Seq). CDC2022 gave negative results with 289/289 non-target viruses, including 104 EV A-D isolates, 165 rhinovirus (RV) isolates or clinical specimens, and 14 other common respiratory viruses. The assay can detect as few as 0.28 CCID<inf>50</inf> per reaction. An in silico "phylo-primer-mismatch" analysis was performed to visualize primer/probe mismatches and to compare CDC2022 with other EV-D68 rRT-PCR assays, including the previous CDC assay (CDC2015) developed in 2014 for clade B1 strains. It showed that CDC2022 has the fewest primer/probe mismatches among all assays analyzed and is suitable for all clades. We additionally tested 11 EV-D68-positive clinical specimens from 2022 that were confirmed by snPCR/Seq, and all were detected. CDC2022 assay could provide a critical tool for molecular surveillance of EV-D68. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv 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. |
Expression-based diagnosis, treatment selection, and drug development for breast cancer
Ye Q , Wang J , Ducatman B , Raese RA , Rogers JL , Wan YW , Dong C , Padden L , Pugacheva EN , Qian Y , Guo NL . Int J Mol Sci 2023 24 (13) ![]() There is currently no gene expression assay that can assess if premalignant lesions will develop into invasive breast cancer. This study sought to identify biomarkers for selecting patients with a high potential for developing invasive carcinoma in the breast with normal histology, benign lesions, or premalignant lesions. A set of 26-gene mRNA expression profiles were used to identify invasive ductal carcinomas from histologically normal tissue and benign lesions and to select those with a higher potential for future cancer development (ADHC) in the breast associated with atypical ductal hyperplasia (ADH). The expression-defined model achieved an overall accuracy of 94.05% (AUC = 0.96) in classifying invasive ductal carcinomas from histologically normal tissue and benign lesions (n = 185). This gene signature classified cancer development in ADH tissues with an overall accuracy of 100% (n = 8). The mRNA expression patterns of these 26 genes were validated using RT-PCR analyses of independent tissue samples (n = 77) and blood samples (n = 48). The protein expression of PBX2 and RAD52 assessed with immunohistochemistry were prognostic of breast cancer survival outcomes. This signature provided significant prognostic stratification in The Cancer Genome Atlas breast cancer patients (n = 1100), as well as basal-like and luminal A subtypes, and was associated with distinct immune infiltration and activities. The mRNA and protein expression of the 26 genes was associated with sensitivity or resistance to 18 NCCN-recommended drugs for treating breast cancer. Eleven genes had significant proliferative potential in CRISPR-Cas9/RNAi screening. Based on this gene expression signature, the VEGFR inhibitor ZM-306416 was discovered as a new drug for treating breast cancer. |
Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic
Bennett JC , Emanuels A , Heimonen J , O'Hanlon J , Hughes JP , Han PD , Chow EJ , Ogokeh CE , Rolfes MA , Lockwood CM , Pfau B , Uyeki TM , Shendure J , Hoag S , Fay K , Lee J , Sibley TR , Rogers JH , Starita LM , Englund JA , Chu HY . Front Pediatr 2023 11 1198278 ![]() ![]() BACKGROUND: Respiratory viruses might influence Streptococcus pneumoniae nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative S. pneumoniae nasal carriage density in a household setting before and during the COVID-19 pandemic. METHODS: From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including S. pneumoniae, rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative S. pneumoniae nasal carriage density, estimated by the inverse of S. pneumoniae relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of S. pneumoniae Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households. RESULTS: We collected 346 swabs from 239 individuals in 151 households that tested positive for S. pneumoniae (n = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative S. pneumoniae nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus (P < 0.01 for each). When stratified by age, semiquantitative S. pneumoniae nasal carriage density was significantly greater with viral co-detection among children aged <5 (P = 0.002) and 5-17 years (P = 0.005), but not among adults aged 18-64 years (P = 0.29). CONCLUSION: Detection of common respiratory viruses was associated with greater concurrent S. pneumoniae semiquantitative nasal carriage density in a household setting among children, but not adults. |
Previous health care experiences' influence on health care perceptions among residents of six homeless shelters in Seattle, Washington, July-October 2021
Meehan AA , Cox SN , Thuo NB , Rogers JH , Link AC , Martinez MA , Lo NK , Manns BJ , Rolfes MA , Chow EJ , Chu HY , Mosites E , Al Achkar M . J Patient Cent Res Rev 2023 10 (3) 111-120 PURPOSE: The study purpose was to learn and describe 1) where homeless shelter residents receive health care, 2) what contributes to positive or negative health care experiences among shelter residents, and 3) shelter resident perceptions toward health care. METHODS: Semi-structured interviews (SSIs) utilizing purposive sampling and focus group discussions (FGDs) utilizing convenience sampling were conducted at 6 homeless shelters in Seattle-King County, Washington, during July-October 2021. All residents (age ≥18) were eligible to participate. SSIs were conducted with 25 residents, and 8 FGDs were held. Thematic analysis was conducted using Dedoose. RESULTS: Participants received health care in settings ranging from no regular care to primary care providers. Four elements emerged as contributing positively and negatively to health care experiences: 1) ability to access health care financially, physically, and technologically; 2) clarity of communication from providers and staff about appointment logistics, diagnoses, and treatment options; 3) ease of securing timely follow-up services; and 4) respect versus stigma and discrimination from providers and staff. Participants who felt positively toward health care found low- or no-cost care to be widely available and encouraged others to seek care. However, some participants described health care in the United States as greedy, classist, discriminatory, and untrustworthy. Participants reported delaying care and self-medicating in anticipation of discrimination. CONCLUSIONS: Findings demonstrate that while people experiencing homelessness can have positive experiences with health care, many have faced negative interactions with health systems. Improving the patient experience for those experiencing homelessness can increase engagement and improve health outcomes. |
- Page last reviewed:Feb 1, 2024
- Page last updated:Jan 27, 2025
- Content source:
- Powered by CDC PHGKB Infrastructure