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  • 1
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    Online Resource
    Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys
    eLife Sciences Publications, Ltd ; 2021
    In:  eLife Vol. 10 ( 2021-03-05)
    Details
    In: eLife, eLife Sciences Publications, Ltd, Vol. 10 ( 2021-03-05)
    Abstract: Establishing how many people have been infected by SARS-CoV-2 remains an urgent priority for controlling the COVID-19 pandemic. Serological tests that identify past infection can be used to estimate cumulative incidence, but the relative accuracy and robustness of various sampling strategies have been unclear. We developed a flexible framework that integrates uncertainty from test characteristics, sample size, and heterogeneity in seroprevalence across subpopulations to compare estimates from sampling schemes. Using the same framework and making the assumption that seropositivity indicates immune protection, we propagated estimates and uncertainty through dynamical models to assess uncertainty in the epidemiological parameters needed to evaluate public health interventions and found that sampling schemes informed by demographics and contact networks outperform uniform sampling. The framework can be adapted to optimize serosurvey design given test characteristics and capacity, population demography, sampling strategy, and modeling approach, and can be tailored to support decision-making around introducing or removing interventions.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    URL: Article
    DOI: 10.7554/eLife.64206
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2021
    detail.hit.zdb_id: 2687154-3
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  • 2
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    Childhood Respiratory Outpatient Visits Correlate With Socioeconomic Status and Drive Geographic Patterns in Antibiotic Prescribing
    Oxford University Press (OUP) ; 2021
    In:  The Journal of Infectious Diseases Vol. 223, No. 12 ( 2021-06-15), p. 2029-2037
    Details
    In: The Journal of Infectious Diseases, Oxford University Press (OUP), Vol. 223, No. 12 ( 2021-06-15), p. 2029-2037
    Abstract: Reducing geographic disparities in antibiotic prescribing is a central public health priority to combat antibiotic resistance, but drivers of this variation have been unclear. Methods We measured how variation in outpatient visit rates (observed disease) and antibiotic prescribing rates per visit (prescribing practices) contributed to geographic variation in per capita antibiotic prescribing in Massachusetts residents younger than 65 years between 2011 and 2015. Results Of the difference in per capita antibiotic prescribing between high- and low-prescribing census tracts in Massachusetts, 45.2% was attributable to variation in outpatient visit rates, while 25.8% was explained by prescribing practices. Outpatient visits for sinusitis, pharyngitis, and suppurative otitis media accounted for 30.3% of the gap in prescribing, with most of the variation in visit rates concentrated in children younger than 10 years. Outpatient visits for these conditions were less frequent in census tracts with high social deprivation index. Conclusions Interventions aimed at reducing geographic disparities in antibiotic prescribing should target the drivers of outpatient visits for respiratory illness and should account for possible underutilization of health services in areas with the lowest antibiotic consumption. Our findings challenge the conventional wisdom that prescribing practices are the main driver of geographic disparities in antibiotic use.
    Type of Medium: Online Resource
    ISSN: 0022-1899 , 1537-6613
    URL: Article
    DOI: 10.1093/infdis/jiab218
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1473843-0
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  • 3
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    Distinguishing the Roles of Antibiotic Stewardship and Reductions in Outpatient Visits in Generating a 5-Year Decline in Antibiotic Prescribing
    Oxford University Press (OUP) ; 2021
    In:  Clinical Infectious Diseases Vol. 72, No. 9 ( 2021-05-04), p. 1568-1576
    Details
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 72, No. 9 ( 2021-05-04), p. 1568-1576
    Abstract: The mechanisms driving the recent decline in outpatient antibiotic prescribing are unknown. We estimated the extent to which reductions in the number of antibiotic prescriptions filled per outpatient visit (stewardship) and reductions in the monthly rate of outpatient visits (observed disease) for infectious disease conditions each contributed to the decline in outpatient antibiotic prescribing in Massachusetts between 2011 and 2015. Methods Outpatient medical and pharmacy claims from the Massachusetts All-Payer Claims Database were used to estimate rates of antibiotic prescribing and outpatient visits for 20 medical conditions and their contributions to the overall decline in antibiotic prescribing. Trends were compared with those in the National Ambulatory Medical Care Survey (NAMCS). Results Between 2011 and 2015, the January and July antibiotic-prescribing rates per 1000 individuals in Massachusetts declined by 18.9% and 13.6%, respectively. The monthly rate of outpatient visits per 1000 individuals in Massachusetts declined (P  & lt; .05) for respiratory infections and urinary tract infections. Nationally, outpatient visits for antibiotic-meriting medical conditions also declined between 2010 and 2015. Of the estimated 358 antibiotic prescriptions per 1000 individuals averted over the study period in Massachusetts, 59% (95% CI, 54–63%) were attributable to reduced observed disease and 41% (95% CI, 37–46%) to improved stewardship. Conclusions The decline in antibiotic prescribing in Massachusetts was driven both by a decline in observed disease and improved antibiotic stewardship, in agreement with national trends. A focus on infectious disease prevention should be considered alongside antibiotic stewardship as a means to reduce antibiotic prescribing.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    URL: Article
    DOI: 10.1093/cid/ciaa269
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2002229-3
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  • 4
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    242. Seasonality in antibiotic use and resistance across multiple bacterial pathogens and antibiotic classes
    Oxford University Press (OUP) ; 2020
    In:  Open Forum Infectious Diseases Vol. 7, No. Supplement_1 ( 2020-12-31), p. S121-S121
    Details
    In: Open Forum Infectious Diseases, Oxford University Press (OUP), Vol. 7, No. Supplement_1 ( 2020-12-31), p. S121-S121
    Abstract: Antibiotic use is an important driver of antibiotic resistance. Previous studies have shown that this relationship is detectable on a seasonal timescale, where seasonally cycling antibiotic prescribing corresponds with cycling levels of resistance. Here, we evaluated the seasonal relationship between antibiotic use and resistance across multiple species and antibiotic classes in Boston, Massachusetts. Methods To conduct our study, we analyzed antibiotic claims data from the Massachusetts All Payers Claims Database for five antibiotic classes, beta-lactams, macrolides, quinolones, tetracyclines, and nitrofurans, which together account for 74% of the total outpatient antibiotic claims in this dataset. In addition, we analyzed antibiotic susceptibility data for clinical isolates collected from two tertiary care hospitals, focusing on three clinically important bacterial pathogens. Our analysis included a total of 131,815 Escherichia coli, 47,208 Staphylococcus aureus, and 27,237 Klebsiella pneumoniae isolates collected over the years 2007–2019, with susceptibility testing data for 5–6 antibiotics per species. To determine the extent of seasonality in use and resistance, we fit the antibiotic claims data for each antibiotic class and the minimum inhibitory concentration (MIC) data for each species-antibiotic combination to a sinusoidal model with either a 6 or 12-month period. Results We found that use of all 5 antibiotic classes and resistance in 9 out of 15 species-antibiotic combinations showed a significant amplitude of seasonality (p-value & lt; 0.05). Despite different seasonal peaks in antibiotic use across classes, resistance peaked in the winter for almost all species-antibiotic combinations and was most highly correlated with use of winter-peaking antibiotic classes, beta-lactams and macrolides. Conclusion Overall, these results suggest that co-resistance and “bystander” selection – selection for resistance in asymptomatically colonizing and potentially pathogenic bacteria that are not the direct target of treatment – mediate the effects of antibiotic prescribing on the landscape of resistance. Disclosures All Authors: No reported disclosures
    Type of Medium: Online Resource
    ISSN: 2328-8957
    URL: Article
    DOI: 10.1093/ofid/ofaa439.286
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2757767-3
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  • 5
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    Reduction in Antibiotic Prescribing Attainable With a Gonococcal Vaccine
    Oxford University Press (OUP) ; 2021
    In:  Clinical Infectious Diseases Vol. 73, No. 6 ( 2021-09-15), p. e1368-e1371
    Details
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 73, No. 6 ( 2021-09-15), p. e1368-e1371
    Abstract: We estimated the fraction of antibiotic prescribing in the United States attributable to gonorrhea. Gonorrhea contributes to an outsized proportion of antibiotic prescriptions in young adults, males, and in the southern and western United States. A gonococcal vaccine could substantially reduce antibiotic prescribing in these populations.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    URL: Article
    DOI: 10.1093/cid/ciab276
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2002229-3
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  • 6
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    Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study
    eLife Sciences Publications, Ltd ; 2022
    In:  eLife Vol. 11 ( 2022-11-16)
    Details
    In: eLife, eLife Sciences Publications, Ltd, Vol. 11 ( 2022-11-16)
    Abstract: The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. Methods: We characterized 1,280 infections from the National Basketball Association occupational health cohort identified between June 2020 and January 2022 using serial RT-qPCR testing. Logistic regression and semi-mechanistic viral RNA kinetics models were used to quantify the effect of age, variant, symptom status, infection history, vaccination status and antibody titer to the founder SARS-CoV-2 strain on the duration of potential infectiousness and overall viral kinetics. The frequency of viral rebounds was quantified under multiple cycle threshold (Ct) value-based definitions. Results: Among individuals detected partway through their infection, 51.0% (95% credible interval [CrI]: 48.3–53.6%) remained potentially infectious (Ct 〈 30) 5 days post detection, with small differences across variants and vaccination status. Only seven viral rebounds (0.7%; N=999) were observed, with rebound defined as 3+days with Ct 〈 30 following an initial clearance of 3+days with Ct ≥30. High antibody titers against the founder SARS-CoV-2 strain predicted lower peak viral loads and shorter durations of infection. Among Omicron BA.1 infections, boosted individuals had lower pre-booster antibody titers and longer clearance times than non-boosted individuals. Conclusions: SARS-CoV-2 viral kinetics are partly determined by immunity and variant but dominated by individual-level variation. Since booster vaccination protects against infection, longer clearance times for BA.1-infected, boosted individuals may reflect a less effective immune response, more common in older individuals, that increases infection risk and reduces viral RNA clearance rate. The shifting landscape of viral kinetics underscores the need for continued monitoring to optimize isolation policies and to contextualize the health impacts of therapeutics and vaccines. Funding: Supported in part by CDC contract #200-2016-91779, a sponsored research agreement to Yale University from the National Basketball Association contract #21-003529, and the National Basketball Players Association.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    URL: Article
    DOI: 10.7554/eLife.81849
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2022
    detail.hit.zdb_id: 2687154-3
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  • 7
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    Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants
    eLife Sciences Publications, Ltd ; 2020
    In:  eLife Vol. 9 ( 2020-06-30)
    Details
    In: eLife, eLife Sciences Publications, Ltd, Vol. 9 ( 2020-06-30)
    Abstract: Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require surveillance to ensure early detection of novel resistance variants, but efficient strategies to do so remain undefined. We evaluate the efficiency of targeted sampling approaches informed by patient and pathogen characteristics in detecting antibiotic resistance and diagnostic escape variants in Neisseria gonorrhoeae, a pathogen associated with a high burden of disease and antibiotic resistance and the development of genotype-based diagnostics. We show that patient characteristic-informed sampling is not a reliable strategy for efficient variant detection. In contrast, sampling informed by pathogen characteristics, such as genomic diversity and genomic background, is significantly more efficient than random sampling in identifying genetic variants associated with resistance and diagnostic escape.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    URL: Article
    DOI: 10.7554/eLife.56367
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2020
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  • 8
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    Impact of Respiratory Infection and Chronic Comorbidities on Early Pediatric Antibiotic Dispensing in the United States
    Oxford University Press (OUP) ; 2023
    In:  Clinical Infectious Diseases Vol. 76, No. 3 ( 2023-02-08), p. 382-388
    Details
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 76, No. 3 ( 2023-02-08), p. 382-388
    Abstract: In the United States, children aged & lt;5 years receive high volumes of antibiotics, which may contribute to antibiotic resistance. It has been unclear what role preventable illnesses and chronic comorbidities play in prompting antibiotic prescriptions. Methods We conducted an observational study with a cohort of 124 759 children aged & lt;5 years born in the United States between 2008 and 2013 with private medical insurance. Study outcomes included the cumulative number of antibiotic courses dispensed per child by age 5 and the proportion of children for whom at least 1 antibiotic course was dispensed by age 5. We identified which chronic medical conditions predicted whether a child would be among the top 20% of antibiotic recipients. Results Children received a mean of 6.8 (95% confidence interval [CI]: 6.7–6.9) antibiotic courses by age 5, and 91% (95% CI: 90%–92%) of children had received at least 1 antibiotic course by age 5. Most antibiotic courses (71%; 95% CI: 70%–72%) were associated with respiratory infections. Presence of a pulmonary/respiratory, otologic, and/or immunological comorbidity substantially increase a child's odds of being in the top 20% of antibiotic recipients. Children with at least 1 of these conditions received a mean of 10.5 (95% CI: 10.4–10.6) antibiotic courses by age 5. Conclusions Privately insured children in the United States receive many antibiotics early in life, largely due to respiratory infections. Antibiotic dispensing varies widely among children, with more antibiotics dispensed to children with pulmonary/respiratory, otologic, and/or immunological comorbidities.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    URL: Article
    DOI: 10.1093/cid/ciac811
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2002229-3
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  • 9
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    ANTICIPATING RACIAL/ETHNIC MORTALITY DISPLACEMENT FROM COVID-19
    Oxford University Press (OUP) ; 2022
    In:  American Journal of Epidemiology Vol. 191, No. 8 ( 2022-07-23), p. 1519-1520
    Details
    In: American Journal of Epidemiology, Oxford University Press (OUP), Vol. 191, No. 8 ( 2022-07-23), p. 1519-1520
    Type of Medium: Online Resource
    ISSN: 0002-9262 , 1476-6256
    URL: Article
    DOI: 10.1093/aje/kwac079
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2030043-8
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  • 10
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    Spatiotemporal Trends in Group A Streptococcal Pharyngitis in the United States
    Oxford University Press (OUP) ; 2024
    In:  Clinical Infectious Diseases ( 2024-02-19)
    Details
    In: Clinical Infectious Diseases, Oxford University Press (OUP), ( 2024-02-19)
    Abstract: Group A Streptococcus (GAS) causes an estimated 5.2 million outpatient visits for pharyngitis annually in the United States (U.S.) with incidence peaking in winter, but the annual spatiotemporal pattern of GAS pharyngitis across the U.S. is poorly characterized. Methods We used outpatient claims data from individuals with private medical insurance between 2010-2018 to quantify GAS pharyngitis visit rates across U.S. census regions, subregions, and states. We evaluated seasonal and age-based patterns of geographic spread and the association between school start dates and the summertime upward inflection in GAS visits. Results The South had the most visits per person (yearly average 39.11 visits per 1000 people, 95% CI: 36.21-42.01), and the West had the fewest (yearly average 17.63 visits per 1000 people, 95% CI: 16.76-18.49). Visits increased earliest in the South and in school-age children. Differences in visits between the South and other regions were most pronounced in the late summer through early winter. Visits peaked earliest in central southern states, in December to January, and latest on the coasts, in March. The onset of the rise in GAS pharyngitis visits correlated with, but preceded, average school start times. Conclusions The burden and timing of GAS pharyngitis varied across the continental U.S., with the South experiencing the highest overall rates and earliest onset and peak in outpatient visits. Understanding the drivers of these regional differences in GAS pharyngitis will help in identifying and targeting prevention measures.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    URL: Article
    DOI: 10.1093/cid/ciae083
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2002229-3
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