Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-30 (of 501 Records) |
Query Trace: Katz L[original query] |
---|
Interpreter usage and associations with latent tuberculosis infection treatment acceptance and completion in the USA among non-U.S.-born persons, 2012-2017
Gonzalez-Reyes R , Katz D , Lambert L , Sorri Y , Narita M , Horne DJ . PLoS One 2024 19 (4) e0298628 BACKGROUND: Latent tuberculosis infection (LTBI) screening and treatment interventions that are tailored to optimize acceptance among the non-U.S.-born population are essential for U.S. tuberculosis elimination. We investigated the impact of medical interpreter use on LTBI treatment acceptance and completion among non-U.S.-born persons in a multisite study. METHODS: The Tuberculosis Epidemiologic Studies Consortium was a prospective cohort study that enrolled participants at high risk for LTBI at ten U.S. sites with 18 affiliated clinics from 2012 to 2017. Non-U.S.-born participants with at least one positive tuberculosis infection test result were included in analyses. Characteristics associated with LTBI treatment offer, acceptance, and completion were evaluated using multivariable logistic regression with random intercepts to account for clustering by enrollment site. Our primary outcomes were whether use of an interpreter was associated with LTBI treatment acceptance and completion. We also evaluated whether interpreter usage was associated treatment offer and whether interpreter type was associated with treatment offer, acceptance, or completion. RESULTS: Among 8,761 non-U.S.-born participants, those who used an interpreter during the initial interview had a significantly greater odds of accepting LTBI treatment than those who did not use an interpreter. There was no association between use of an interpreter and a clinician's decision to offer treatment or treatment completion once accepted. Characteristics associated with lower odds of treatment being offered included experiencing homelessness and identifying as Pacific Islander persons. Lower treatment acceptance was observed in Black and Latino persons and lower treatment completion by participants experiencing homelessness. Successful treatment completion was associated with use of shorter rifamycin-based regimens. Interpreter type was not associated with LTBI treatment offer, acceptance, or completion. CONCLUSIONS: We found greater LTBI treatment acceptance was associated with interpreter use among non-U.S.-born individuals. |
Farmworker mobility and COVID-19 vaccination strategies: Yuma County, Arizona, 2021
Franc KA , Phippard AE , Ruedas P , Pinto SJ , Mehta K , Montiel S , Contreras S , Katz H , McIntyre E , Lopez B , Kreutzberg-Martinez M , Steiner D , Gomez D , Merrill R . Am J Trop Med Hyg 2024 Farmworkers, a group of essential workers, experience a disproportionately high burden of COVID-19 due to their living and working conditions. This project characterized farmworker mobility in and around Yuma County, Arizona, to identify opportunities to improve farmworker access to COVID-19 vaccination. We collected qualitative and geospatial data through a series of in-person and virtual focus group discussions, key informant interviews, and intercept interviews with participatory mapping. Participants included farmworkers, employers, and representatives of local institutions who serve or interact with farmworkers. We identified participants through purposive and referential sampling and grouped people by sociodemographic characteristics for interviews. We used qualitative and geospatial analyses to identify common themes and mobility patterns. The team interviewed 136 people from February 26 to April 2, 2021. Common themes emerged about how farmworkers have little or no access to COVID-19 vaccination unless offered at their workplaces or at locations where they congregate at convenient times. Further, farmworkers described how their demanding work schedules, long commute times, and caretaker commitments make it challenging to access vaccination services. Geospatial analyses identified three geographic areas in Yuma County where farmworkers reported living and working that did not have a COVID-19 vaccine clinic within walking distance. Coordination between local public health authorities and key partners, including employers and trusted representatives from local community-based organizations or the Mexican consulate, to offer vaccination at worksites or other locations where farmworkers congregate can help improve access to COVID-19 vaccines and booster doses for this population. |
Correction: Behavior change among HIV-negative men who have sex with men not using PrEP in the United States
Goodreau SM , Barry MP , Hamilton DT , Williams AM , Wang LY , Sanchez TH , Katz DA , Delaney KP . AIDS Behav 2024 |
Age-group associations of schistosomiasis prevalence from trial data, Côte d'Ivoire, Kenya and the United Republic of Tanzania
Wiegand RE , Odiere MR , Kinung'hi S , N'Goran EK , Mwinzi P , Secor WE . Bull World Health Organ 2024 102 (4) 265-275 OBJECTIVE: To determine if the prevalence of schistosomiasis in children aged 9-12 years is associated with the prevalence in 5-8-year-olds and adults after preventive chemotherapy in schools or the community. METHODS: We combined data from four community-randomized, preventive chemotherapy trials in treatment-naïve populations in Côte d'Ivoire, Kenya and the United Republic of Tanzania during 2010-2016 according to the number of praziquantel treatments and the delivery method. Schistosoma mansoni infection was sought on two slides prepared from each participant's first stool using the Kato-Katz technique. We assessed associations between S. mansoni prevalence in 9-12-year-olds and 5-8-year-olds and adults in the community before and after treatment using Bayesian regression models. FINDINGS: Stool samples from 47 985 5-8-year-olds, 81 077 9-12-year-olds and 20 492 adults were analysed. We found associations between the prevalence in 9-12-year-olds and that in 5-8-year-olds and adults after preventive treatment, even when only school-age children were treated. When the prevalence in 9-12-year-olds was under 10%, the prevalence in 5-8-year-olds was consistently under 10%. When the prevalence in 9-12-year-olds was under 50%, the prevalence in adults after two or four rounds of preventive chemotherapy was 10%-15% lower than before chemotherapy. Post-chemotherapy age-group associations were consistent with pre-chemotherapy associations in this analysis and previous studies. CONCLUSION: The prevalence of S. mansoni infection in 9-12-year-olds was associated with the prevalence in other age groups and could be used to guide community treatment decisions. |
Clinical and laboratory characteristics of patients hospitalized with severe COVID-19 in New Orleans, August 2020 to September 2021
Drouin A , Plumb ID , McCullough M , James Gist J , Liu S , Theberge M , Katz J , Moreida M , Flaherty S , Chatwani B , Briggs Hagen M , Midgley CM , Fusco D . Sci Rep 2024 14 (1) 6539 Louisiana experienced high morbidity and mortality from COVID-19. To assess possible explanatory factors, we conducted a cohort study (ClinSeqSer) of patients hospitalized with COVID-19 in New Orleans during August 2020-September 2021. Following enrollment, we reviewed medical charts, and performed SARS-CoV-2 RT-PCR testing on nasal and saliva specimens. We used multivariable logistic regression to assess associations between patient characteristics and severe illness, defined as ≥ 6 L/min oxygen or intubation. Among 456 patients, median age was 56 years, 277 (60.5%) were Black non-Hispanic, 436 (95.2%) had underlying health conditions, and 358 were unvaccinated (92.0% of 389 verified). Overall, 187 patients (40.1%) had severe illness; 60 (13.1%) died during admission. In multivariable models, severe illness was associated with age ≥ 65 years (OR 2.08, 95% CI 1.22-3.56), hospitalization > 5 days after illness onset (OR 1.49, 95% CI 1.01-2.21), and SARS CoV-2 cycle threshold (Ct) result of < 32 in saliva (OR 4.79, 95% CI 1.22-18.77). Among patients who were predominantly Black non-Hispanic, unvaccinated and with underlying health conditions, approximately 1 in 3 patients had severe COVID-19. Older age and delayed time to admission might have contributed to high case-severity. An association between case-severity and low Ct value in saliva warrants further investigation. |
Animal vaccine strain Brucella abortus infection in a plateletpheresis donor: A case report
Parsons MG , Hermelin D , Hennenfent A , Tiller RV , Annambhotla P , Negrón ME , Basavaraju SV , Katz LM . Transfusion 2024 |
Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics
Lindsey RL , Gladney LM , Huang AD , Griswold T , Katz LS , Dinsmore BA , Im MS , Kucerova Z , Smith PA , Lane C , Carleton HA . Front Microbiol 2023 14 1225207 Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods. |
Economic insecurities and patient-reported outcomes in patients with systemic lupus erythematosus in the USA: a cross-sectional analysis of data from the California Lupus Epidemiology Study
Sandoval-Heglund D , Roberts E , Park J , Dall'Era M , Lanata C , Barbour KE , Greenlund KJ , Gordon C , Katz PP , Yazdany J . Lancet Rheumat 2023 Background: Social determinants of health are consistently associated with systemic lupus erythematosus (SLE) outcomes. However, social determinants of health are typically measured with conventional socioeconomic status factors such as income or education. We assessed the association of economic insecurities (ie, food, housing, health care, and financial insecurity) with patient-reported outcomes in a cohort of patients with SLE. Methods: In this cross-sectional analysis, data were derived from the California Lupus Epidemiology Study based in the San Francisco Bay Area, CA, USA. Participants were recruited between Feb 25, 2015, and Jan 10, 2018, from rheumatology clinics. Inclusion criteria were Bay Area residency; oral fluency in English, Spanish, Cantonese, or Mandarin; 18 years or older; ability to provide informed consent; and a physician confirmed SLE diagnosis. Food, housing, health care, and financial economic insecurities were assessed by validated screening tools. Patient-reported outcomes were obtained using PROMIS, Quality of Life in Neurological Disorders (known as Neuro-QoL) Cognitive Function short form, Patient Health Questionnaire (PHQ)-8, and General Anxiety Disorder (GAD)-7 instruments. Poverty was defined as household income of 125% or less of the federal poverty limit. Lower education was defined as less than college-graduate education. The association of economic insecurities with patient-reported outcomes was assessed by multivariable linear regression models adjusting for demographics, SLE disease characteristics, and comorbidities. We tested for interactions of insecurities with poverty and education. Findings: The final cohort included 252 participants. Mean age was 49·7 (SD 13·4) years, 228 (90%) of 252 were women and 24 (10%) were men. 80 (32%) individuals self-identified as Asian, 26 (10%) as Black, 101 (40%) as White, eight (3%) as mixed race, and 37 (15%) as other race; 59 (23%) self-identified as Hispanic. 135 (54%) individuals had at least one insecurity. Insecurities were highly prevalent, and more common in those with poverty and lower education. Adjusted multivariate analyses revealed that participants with any insecurity had significantly worse scores across all measured patient-reported outcomes. For physical function, no insecurity had an adjusted mean score of 48·9 (95% CI 47·5–50·3) and any insecurity had 45·7 (44·3–47·0; p=0·0017). For pain interference, no insecurity was 52·0 (50·5–53·5) and any insecurity was 54·4 (53·0–55·8; p=0·031). For fatigue, no insecurity was 50·5 (48·8–52·3) and any insecurity was 54·9 (53·3–56·5; p=0·0005). For sleep disturbance, no insecurity was 49·9 (48·3–51·6) and any insecurity was 52·9 (51·4–54·5; p=0·012). For cognitive function, no insecurity was 49·3 (47·7–50·9) and any insecurity was 45·6 (44·1–47·0; p=0·0011). For PHQ-8, no insecurity was 4·4 (3·6–5·1) and any insecurity was 6·1 (5·4–6·8; p=0·0013). For GAD-7, no insecurity was 3·3 (2·6–4·1) and any insecurity was 5·2 (4·5–5·9; p=0·0008). Individuals with more insecurities had worse patient-reported outcomes. There were no statistically significant interactions between insecurities and poverty or education. Interpretation: Having any economic insecurity was associated with worse outcomes for people with SLE regardless of poverty or education. The findings of this study provide insight into the relationship between economic insecurities and SLE outcomes and underscore the need to assess whether interventions that directly address these insecurities can reduce health disparities in SLE. Funding: US Centers for Disease Control, Rheumatology Research Foundation, and National Institute of Arthritis and Musculoskeletal and Skin Diseases. © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license |
Surveillance for soil-transmitted helminths in high-risk county, Mississippi, USA
Bradbury RS , Martin L , Malloch L , Martin M , Williams JM , Patterson K , Sanders C , Singh G , Arguello I , Rodriguez E , Byers P , Haynie L , Qvarnstrom Y , Hobbs CV . Emerg Infect Dis 2023 29 (12) 2533-2537 Recent reports of hookworm infection in Alabama, USA, has prompted surveillance in Mississippi, given the states' similar environmental conditions. We collected stool specimens from 277 children in Rankin County, Mississippi. Kato-Katz microscopic smear, agar plate culture, and quantitative PCR indicated no soil-transmitted helminths. Nevertheless, further surveillance in other high-risk Mississippi counties is warranted. |
Use of a reduced (4-dose) vaccine schedule for postexposure prophylaxis to prevent human rabies: recommendations of the advisory committee on immunization practices
Rupprecht CE , Briggs D , Brown CM , Franka R , Katz SL , Kerr HD , Lett SM , Levis R , Meltzer MI , Schaffner W , Cieslak PR . MMWR Recomm Rep 2010 59 1-9 This report summarizes new recommendation and updates previous recommendations of the Advisory Committee on Immunization Practices (ACIP) for postexposure prophylaxis (PEP) to prevent human rabies (CDC. Human rabies prevention---United States, 2008: recommendations of the Advisory Committee on Immunization Practices. MMWR 2008;57[No. RR-3]). Previously, ACIP recommended a 5-dose rabies vaccination regimen with human diploid cell vaccine (HDCV) or purified chick embryo cell vaccine (PCECV). These new recommendations reduce the number of vaccine doses to four. The reduction in doses recommended for PEP was based in part on evidence from rabies virus pathogenesis data, experimental animal work, clinical studies, and epidemiologic surveillance. These studies indicated that 4 vaccine doses in combination with rabies immune globulin (RIG) elicited adequate immune responses and that a fifth dose of vaccine did not contribute to more favorable outcomes. For persons previously unvaccinated with rabies vaccine, the reduced regimen of 4 1-mL doses of HDCV or PCECV should be administered intramuscularly. The first dose of the 4-dose course should be administered as soon as possible after exposure (day 0). Additional doses then should be administered on days 3, 7, and 14 after the first vaccination. ACIP recommendations for the use of RIG remain unchanged. For persons who previously received a complete vaccination series (pre- or postexposure prophylaxis) with a cell-culture vaccine or who previously had a documented adequate rabies virus-neutralizing antibody titer following vaccination with noncell-culture vaccine, the recommendation for a 2-dose PEP vaccination series has not changed. Similarly, the number of doses recommended for persons with altered immunocompetence has not changed; for such persons, PEP should continue to comprise a 5-dose vaccination regimen with 1 dose of RIG. Recommendations for pre-exposure prophylaxis also remain unchanged, with 3 doses of vaccine administered on days 0, 7, and 21 or 28. Prompt rabies PEP combining wound care, infiltration of RIG into and around the wound, and multiple doses of rabies cell-culture vaccine continue to be highly effective in preventing human rabies. |
Leveraging donor populations to study the epidemiology and pathogenesis of transfusion-transmitted and emerging infectious diseases
Bloch EM , Busch MP , Corash LM , Dodd R , Hailu B , Kleinman S , O'Brien S , Petersen L , Stramer SL , Katz L . Transfus Med Rev 2023 37 (4) 150769 The tragedy of transfusion-associated hepatitis and HIV spurred a decades-long overhaul of the regulatory oversight and practice of blood transfusion. Consequent to improved donor selection, testing, process control, clinical transfusion practice and post-transfusion surveillance, transfusion in the United States and other high-income countries is now a very safe medical procedure. Nonetheless, pathogens continue to emerge and threaten the blood supply, highlighting the need for a proactive approach to blood transfusion safety. Blood donor populations and the global transfusion infrastructure are under-utilized resources for the study of infectious diseases. Blood donors are large, demographically diverse subsets of general populations for whom cross-sectional and longitudinal samples are readily accessible for serological and molecular testing. Blood donor collection networks span diverse geographies, including in low- and middle-income countries, where agents, especially zoonotic pathogens, are able to emerge and spread, given limited tools for recognition, surveillance and control. Routine laboratory storage and transportation, coupled with data capture, afford access to rich epidemiological data to assess the epidemiology and pathogenesis of established and emerging infections. Subsequent to the State of the Science in Transfusion Medicine symposium in 2022, our working group (WG), "Emerging Infections: Impact on Blood Science, the Blood Supply, Blood Safety, and Public Health" elected to focus on "leveraging donor populations to study the epidemiology and pathogenesis of transfusion-transmitted and emerging infectious diseases." The 5 landmark studies span (1) the implication of hepatitis C virus in post-transfusion hepatitis, (2) longitudinal evaluation of plasma donors with incident infections, thus informing the development of a widely used staging system for acute HIV infection, (3) explication of the dynamics of early West Nile Virus infection, (4) the deployment of combined molecular and serological donor screening for Babesia microti, to characterize its epidemiology and infectivity and facilitate routine donor screening, and (5) national serosurveillance for SARS-CoV-2 during the COVID-19 pandemic. The studies highlight the interplay between infectious diseases and transfusion medicine, including the imperative to ensure blood transfusion safety and the broader application of blood donor populations to the study of infectious diseases. |
Modeling the impact of changing sexual behaviors with opposite-sex partners and STI testing among women and men ages 15–44 on STI diagnosis rates in the United States 2012–2019
Hamilton DT , Katz DA , Haderxhanaj LT , Copen CE , Spicknall IH , Hogben M . Infect Dis Model 2023 8 (4) 1169-1176 Objective: To estimate the potential contributions of reported changes in frequency of penile-vaginal sex (PVS), condom use and STI screening to changes in gonorrhea and chlamydial diagnoses from 2012 to 2019. Methods: An agent-based model of the heterosexual population in the U.S. simulated the STI epidemics. Baseline was calibrated to 2012 diagnosis rates, testing, condom use, and frequency of PVS. Counterfactuals used behaviors from the 2017-2019 NSFG, and we evaluated changes in diagnosis and incidence rates in 2019. Results: Higher testing rates increased gonorrhea and chlamydia diagnosis by 14% and 13%, respectively, but did not reduce incidence. Declining frequency of PVS reduced the diagnosis rate for gonorrhea and chlamydia 6% and 3% respectively while reducing incidence by 10% and 9% respectively. Declining condom use had negligible impact on diagnosis and incidence. Conclusion: Understanding how changing behavior drives STI incidence is essential to addressing the growing epidemics. Changes in testing and frequency of PVS likely contributed to some, but not all, of the changes in diagnoses. More research is needed to understand the context within which changing sexual behavior and testing are occurring. © 2023 The Authors |
Primary series and booster coronavirus disease 2019 vaccine effectiveness in a cohort of healthcare workers in Albania during a BA.1 and BA.2 variant period, January-May 2022
Finci I , Rojas Castro MY , Hasibra I , Sulo J , Fico A , Daja R , Vasili A , Kota M , Preza I , Mühlemann B , Drosten C , Pebody R , Lafond KE , Kissling E , Katz MA , Bino S . Open Forum Infect Dis 2023 10 (10) ofad479 BACKGROUND: Healthcare workers (HCWs) have experienced high rates of coronavirus disease 2019 (COVID-19) morbidity and mortality. We estimated COVID-19 2-dose primary series and monovalent booster vaccine effectiveness (VE) against symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron (BA.1 and BA.2) infection among HCWs in 3 Albanian hospitals during January-May 2022. METHODS: Study participants completed weekly symptom questionnaires, underwent polymerase chain reaction (PCR) testing when symptomatic, and provided quarterly blood samples for serology. We estimated VE using Cox regression models (1 - hazard ratio), with vaccination status as the time-varying exposure and unvaccinated HCWs as the reference group, adjusting for potential confounders: age, sex, prior SARS-CoV-2 infection (detected by PCR, rapid antigen test, or serology), and household size. RESULTS: At the start of the analysis period, 76% of 1462 HCWs had received a primary series, 10% had received a booster dose, and 9% were unvaccinated; 1307 (89%) HCWs had evidence of prior infection. Overall, 86% of primary series and 98% of booster doses received were BNT162b2. The median time interval from the second dose and the booster dose to the start of the analysis period was 289 (interquartile range [IQR], 210-292) days and 30 (IQR, 22-46) days, respectively. VE against symptomatic PCR-confirmed infection was 34% (95% confidence interval [CI], -36% to 68%) for the primary series and 88% (95% CI, 39%-98%) for the booster. CONCLUSIONS: Among Albanian HCWs, most of whom had been previously infected, COVID-19 booster dose offered improved VE during a period of Omicron BA.1 and BA.2 circulation. Our findings support promoting booster dose uptake among Albanian HCWs, which, as of January 2023, was only 20%. Clinical Trials Registration. NCT04811391. |
P-BB-3 | a case of brucella abortus RB51-positive platelet unit culture
Parsons M , Hermelin D , Tiller R , Hennenfent A , Negrón Sureda M , Annambhotla P , Basavaraju S , Katz L . Transfusion 2023 63 91A-92A |
Coding-complete genome sequences of rotavirus A reference strains EDIM, Ph158, and CC425
Casey-Moore MC , Katz E , Mijatovic-Rustempasic S , Jaimes J , Gautam R , Bowen MD . Microbiol Resour Announc 2023 12 (11) e0063023 This study reports the coding-complete genome sequences of three rotavirus A (RVA) reference strains previously adapted in tissue culture: RVA/Mouse-tc/USA/EDIM/XXXX/G16P[16] with a G16-P[16]-I7-R7-C7-M8-A7-N7-T10-E7-H9 genotype constellation, RVA/Human-tc/USA/Ph158/1998/G9P[6] with a G9-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genotype constellation, and RVA/Human-tc/USA/CC425/1998/G3P[9] with a G3-P[9]-I2-R2-C2-M2-A3-N2-T1-E2-H3 genotype constellation. |
Changes in oral and anal sex with opposite-sex partners among sexually active females and males ages 15-44 in the United States: National Survey of Family Growth, 2011-2019
Katz DA , Copen CE , Haderxhanaj LT , Hogben M , Goodreau SM , Spicknall IH , Hamilton DT . Sex Transm Dis 2023 50 (11) 713-719 BACKGROUND: Oral and anal sex with opposite-sex partners are common and associated with STI transmission. Trends in these behaviors over the last decade, during which bacterial STI diagnoses have reached historic highs while HIV diagnoses have decreased, are not well understood. We examined recent trends in oral and anal sex and associated condom use with opposite-sex partners among females and males. METHODS: We analyzed data from 16,926 female and 13,533 male respondents ages 15-44 who reported sex with an opposite-sex partner in the past 12 months from the National Survey of Family Growth, 2011-2019. We used survey-weighted linear or logistic regression to evaluate linear temporal trends in oral and anal sex behaviors. RESULTS: From 2011-13 to 2017-19, reports of oral sex and number of oral sex partners in the past 12 months increased among females (85.4% in 2011-13 to 89.4% in 2017-19, OR = 1.05, 95%CI = 1.02-1.09; and β = 0.014, 95%CI = 0.005-0.023; respectively) but not males (ranges = 87.9-89.1%; 1.27-1.31). Condom use at last oral sex decreased among both females and males (6.3% to 4.3%, OR = 0.93, 95%CI = 0.88-0.99; 5.9% to 4.4%, OR = 0.95, 95%CI = 0.91-1.00). Anal sex (female range = 21.0-23.3%, male = 23.3-24.6%), number of anal sex partners (females = 0.22-0.25; males = 0.26-0.30), and condom use at last anal sex (females = 15.3-18.2%; males = 27.0-28.7%) remained stable. CONCLUSIONS: The frequency of oral and anal sex with opposite-sex partners among U.S. 15-44-year-olds, paired with limited and - for oral sex - decreasing condom use, demonstrates the need to understand the role of these behaviors in increasing STI diagnosis rates and the potential role of extragenital screening and condoms in reducing STI transmission. |
Reoccurring Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks, 2016-2019
Chen JC , Patel K , Smith PA , Vidyaprakash E , Snyder C , Tagg KA , Webb HE , Schroeder MN , Katz LS , Rowe LA , Howard D , Griswold T , Lindsey RL , Carleton HA . Emerg Infect Dis 2023 29 (9) 1895-1899 Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period. |
Predicting food sources of Listeria monocytogenes based on genomic profiling using random forest model
Gu W , Cui Z , Stroika S , Carleton HA , Conrad A , Katz LS , Richardson LC , Hunter J , Click ES , Bruce BB . Foodborne Pathog Dis 2023 20 (12) 579-586 Listeria monocytogenes can cause severe foodborne illness, including miscarriage during pregnancy or death in newborn infants. When outbreaks of L. monocytogenes illness occur, it may be possible to determine the food source of the outbreak. However, most reported L. monocytogenes illnesses do not occur as part of a recognized outbreak and most of the time the food source of sporadic L. monocytogenes illness in people cannot be determined. In the United States, L. monocytogenes isolates from patients, foods, and environments are routinely sequenced and analyzed by whole genome multilocus sequence typing (wgMLST) for outbreak detection by PulseNet, the national molecular surveillance system for foodborne illnesses. We investigated whether machine learning approaches applied to wgMLST allele call data could assist in attribution analysis of food source of L. monocytogenes isolates. We compiled isolates with a known source from five food categories (dairy, fruit, meat, seafood, and vegetable) using the metadata of L. monocytogenes isolates in PulseNet, deduplicated closely genetically related isolates, and developed random forest models to predict the food sources of isolates. Prediction accuracy of the final model varied across the food categories; it was highest for meat (65%), followed by fruit (45%), vegetable (45%), dairy (44%), and seafood (37%); overall accuracy was 49%, compared with the naive prediction accuracy of 28%. Our results show that random forest can be used to capture genetically complex features of high-resolution wgMLST for attribution of isolates to their sources. |
Next generation 3D-printed intravaginal ring for prevention of HIV and unintended pregnancy
Young IC , Srinivasan P , Shrivastava R , Janusziewicz R , Thorson A , Cottrell ML , Sellers RS , Sykes C , Schauer A , Little D , Kelley K , Kashuba ADM , Katz D , Pyles RB , García-Lerma JG , Vincent KL , Smith J , Benhabbour SR . Biomaterials 2023 301 122260 Globally, there are 20 million adolescent girls and young women living with HIV who have limited access to long-acting, effective, women-controlled preventative methods. Additionally, although there are many contraceptive methods available, globally, half of all pregnancies remain unintended. Here we report the first 3D-printed multipurpose prevention technology (MPT) intravaginal ring (IVR) for HIV prevention and contraception. We utilized continuous liquid interface production (CLIP™) to fabricate MPT IVRs in a biocompatible silicone-based resin. Etonogestrel (ENG), ethinyl estradiol (EE), and islatravir (ISL) were loaded into the silicone poly(urethane) IVR in a controlled single step drug loading process driven by absorption. ENG/EE/ISL IVR promoted sustained release of drugs for 150 days in vitro and 14 days in sheep. There were no adverse MPT IVR-related findings of cervicovaginal toxicity or changes in vaginal biopsies or microbiome community profiles evaluated in sheep. Furthermore, ISL IVR in macaques promoted sustained release for 28 days with ISL-triphosphate levels above the established pharmacokinetic benchmark of 50-100 fmol/10(6) PBMCs. The ISL IVR was found to be safe and well tolerated in the macaques with no observed mucosal cytokine changes or alterations in peripheral CD4 T-cell populations. Collectively, the proposed MPT IVR has potential to expand preventative choices for young women and girls. |
Quality of vital event data for infant mortality estimation in prospective, population-based studies: an analysis of secondary data from Asia, Africa, and Latin America
Erchick DJ , Subedi S , Verhulst A , Guillot M , Adair LS , Barros AJD , Chasekwa B , Christian P , da Silva BGC , Silveira MF , Hallal PC , Humphrey JH , Huybregts L , Kariuki S , Khatry SK , Lachat C , Matijasevich A , McElroy PD , Menezes AMB , Mullany LC , Perez TLL , Phillips-Howard PA , Roberfroid D , Santos IS , Ter Kuile FO , Ravilla TD , Tielsch JM , Wu LSF , Katz J . Popul Health Metr 2023 21 (1) 10 INTRODUCTION: Infant and neonatal mortality estimates are typically derived from retrospective birth histories collected through surveys in countries with unreliable civil registration and vital statistics systems. Yet such data are subject to biases, including under-reporting of deaths and age misreporting, which impact mortality estimates. Prospective population-based cohort studies are an underutilized data source for mortality estimation that may offer strengths that avoid biases. METHODS: We conducted a secondary analysis of data from the Child Health Epidemiology Reference Group, including 11 population-based pregnancy or birth cohort studies, to evaluate the appropriateness of vital event data for mortality estimation. Analyses were descriptive, summarizing study designs, populations, protocols, and internal checks to assess their impact on data quality. We calculated infant and neonatal morality rates and compared patterns with Demographic and Health Survey (DHS) data. RESULTS: Studies yielded 71,760 pregnant women and 85,095 live births. Specific field protocols, especially pregnancy enrollment, limited exclusion criteria, and frequent follow-up visits after delivery, led to higher birth outcome ascertainment and fewer missing deaths. Most studies had low follow-up loss in pregnancy and the first month with little evidence of date heaping. Among studies in Asia and Latin America, neonatal mortality rates (NMR) were similar to DHS, while several studies in Sub-Saharan Africa had lower NMRs than DHS. Infant mortality varied by study and region between sources. CONCLUSIONS: Prospective, population-based cohort studies following rigorous protocols can yield high-quality vital event data to improve characterization of detailed mortality patterns of infants in low- and middle-income countries, especially in the early neonatal period where mortality risk is highest and changes rapidly. |
Primary series and booster COVID-19 vaccine effectiveness in a cohort of healthcare workers in Albania during a BA.1 and BA.2 variant period, January - May 2022 (preprint)
Finci I , Castro MYR , Hasibra I , Sulo J , Fico A , Daja R , Vasili A , Kota M , Preza I , Muhlemann B , Drosten C , Pebody R , Lafond KE , Kissling E , Katz MA , Bino S . medRxiv 2023 05 Background Healthcare workers (HCWs) have experienced high rates of COVID-19 morbidity and mortality. We estimated COVID-19 two-dose primary series and monovalent booster vaccine effectiveness (VE) against symptomatic SARS-CoV-2 Omicron (BA.1 and BA.2) infection among HCWs in three Albanian hospitals during January-May 2022. Methods Study participants completed weekly symptom questionnaires, underwent PCR testing when symptomatic, and provided quarterly blood samples for serology. We estimated VE using Cox regression models (1-hazard ratio), with vaccination status as the time-varying exposure and unvaccinated HCWs as the reference group, adjusting for potential confounders: age, sex, prior SARS-CoV-2 infection (detected by PCR, rapid-antigen test or serology), and household size. Results At the start of the analysis period, 76% of 1,462 HCWs had received a primary series, 10% had received a booster dose, and 9% were unvaccinated; 1,307 (89%) HCWs had evidence of prior infection. Overall, 86% of primary series and 98% of booster doses received were BNT162b2. The median time interval from the second dose and the booster dose to the start of the analysis period was 289 days (IQR:210-292) and 30 days (IQR:22-46), respectively. VE against symptomatic PCR-confirmed infection was 34% (95%CI: -36;68) for the primary series and 88% (95%CI: 38;98) for the booster. Conclusions Among Albanian HCWs, most of whom had been previously infected, COVID-19 booster dose offered improved VE during a period of Omicron BA.1 and BA.2 circulation. Our findings support promoting booster dose uptake among Albanian HCWs, which, as of January 2023, was only 20%. 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. |
Selective whole genome amplification as a tool to enrich specimens with low Treponema pallidum genomic DNA copies for whole genome sequencing (preprint)
Thurlow CM , Joseph SJ , Ganova-Raeva L , Katz SS , Pereira L , Chen C , Debra A , Vilfort K , Workowski K , Cohen SE , Reno H , Sun Y , Burroughs M , Sheth M , Chi KH , Danavall D , Philip SS , Cao W , Kersh EN , Pillay A . bioRxiv 2021 10 Downstream next generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome, and the capture and removal of CpG-methylated host DNA using the NEBNext Microbiome DNA Enrichment Kit followed by MDA with the REPLI-g Single Cell Kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93-98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit propagated isolates, containing >14 T. pallidum genomic copies/ul of sample for SWGA and >129 genomic copies/ul for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens, showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which have been challenging until now. 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. |
Trends in tuberculosis clinicians' adoption of short-course regimens for latent tuberculosis infection
Feng PI , Horne DJ , Wortham JM , Katz DJ . J Clin Tuberc Other Mycobact Dis 2023 33 100382 OBJECTIVE: Little is known about regimen choice for latent tuberculosis infection in the United States. Since 2011, the Centers for Disease Control and Prevention has recommended shorter regimens-12 weeks of isoniazid and rifapentine or 4 months of rifampin-because they have similar efficacy, better tolerability, and higher treatment completion than 6-9 months of isoniazid. The objective of this analysis is to describe frequencies of latent tuberculosis infection regimens prescribed in the United States and assess changes over time. METHODS: Persons at high risk for latent tuberculosis infection or progression to tuberculosis disease were enrolled into an observational cohort study from September 2012-May 2017, tested for tuberculosis infection, and followed for 24 months. This analysis included those with at least one positive test who started treatment. RESULTS: Frequencies of latent tuberculosis infection regimens and 95% confidence intervals were calculated overall and by important risk groups. Changes in the frequencies of regimens by quarter were assessed using the Mann-Kendall statistic. Of 20,220 participants, 4,068 had at least one positive test and started treatment: 95% non-U.S.-born, 46% female, 12% <15 years old. Most received 4 months of rifampin (49%), 6-9 months of isoniazid (32%), or 12 weeks of isoniazid and rifapentine (13%). Selection of short-course regimens increased from 55% in 2013 to 81% in late 2016 (p < 0.001). CONCLUSIONS: Our study identified a trend towards adoption of shorter regimens. Future studies should assess the impact of updated treatment guidelines, which have added 3 months of daily isoniazid and rifampin to recommended regimens. |
Association of Mycobacterium tuberculosis infection test results with risk factors for tuberculosis transmission
Venkatappa T , Shen D , Ayala A , Li R , Sorri Y , Punnoose R , Katz D . J Clin Tuberc Other Mycobact Dis 2023 33 100386 BACKGROUND: Close contacts infected with Mycobacterium tuberculosis are at high risk of tuberculosis (TB) disease and a priority for preventive treatment. Three tests measure infection: two interferon-gamma release assays (IGRAs) and the tuberculin skin test (TST). The objective of our study was to assess the association of positive test results in contacts with infectiousness of the presumed TB source case. METHODS: Contacts in a cohort study at 10 United States sites received both IGRAs (QuantiFERON-TB Gold In-Tube (QFT-GIT) and T-SPOT.TB (T-SPOT)) and TST. We defined test conversion as negative for all tests at baseline and positive for at least one on retest. Risk ratios (RR) and 95% confidence intervals (CI) assessed association of positive test results with increased infectiousness of the TB case-defined as acid-fast bacilli (AFB) on sputum microscopy or cavities on chest radiographs- and contact demographics. RESULTS: Adjusted for contacts' age, nativity, sex, and race, IGRAs (QFT-GIT RR = 6.1, 95% CI 1.7-22.2; T-SPOT RR = 9.4, 95% CI 1.1-79.1), but not TST (RR = 1.7, 95% CI 0.8-3.7), were more likely to convert among contacts exposed to persons with cavitary TB disease. CONCLUSIONS: Because IGRA conversions in contacts are associated with infectiousness of the TB case, their use may improve efficiency of health department contact investigations by focusing efforts on those likely to benefit from preventive treatment in the United States. |
Volunteer-contributed observations of flowering often correlate with airborne pollen concentrations
Crimmins TM , Vogt E , Brown CL , Dalan D , Manangan A , Robinson G , Song Y , Zhu K , Katz DSW . Int J Biometeorol 2023 67 (8) 1363-1372 Characterizing airborne pollen concentrations is crucial for supporting allergy and asthma management; however, pollen monitoring is labor intensive and, in the USA, geographically limited. The USA National Phenology Network (USA-NPN) engages thousands of volunteer observers in regularly documenting the developmental and reproductive status of plants. The reports of flower and pollen cone status contributed to the USA-NPN's platform, Nature's Notebook, have the potential to help address gaps in pollen monitoring by providing real-time, spatially explicit information from across the country. In this study, we assessed whether observations of flower and pollen cone status contributed to Nature's Notebook can serve as effective proxies for airborne pollen concentrations. We compared daily pollen concentrations from 36 National Allergy Bureau (NAB) stations in the USA with flowering and pollen cone status observations collected within 200 km of each NAB station in each year, 2009-2021, for 15 common tree taxa using Spearman's correlations. Of 350 comparisons, 58% of correlations were significant (p < 0.05). Comparisons could be made at the largest numbers of sites for Acer and Quercus. Quercus demonstrated a comparatively high proportion of tests with significant agreement (median ρ = 0.49). Juglans demonstrated the strongest overall coherence between the two datasets (median ρ = 0.79), though comparisons were made at only a small number of sites. For particular taxa, volunteer-contributed flowering status observations demonstrate promise to indicate seasonal patterns in airborne pollen concentrations. The quantity of observations, and therefore, their utility for supporting pollen alerts, could be substantially increased through a formal observation campaign. |
Medication cost concerns and disparities in patient-reported outcomes among a multiethnic cohort of patients with lupus
Aguirre A , DeQuattro K , Shiboski S , Katz P , Greenlund KJ , Barbour KE , Gordon C , Lanata C , Criswel L , Dall'Era M , Yazdany J . J Rheumatol 2023 50 (10) 1302-1309 OBJECTIVE: Concerns about the affordability of medications are common in systemic lupus erythematosus (SLE), but the relationship between medication cost concerns and health outcomes is poorly understood. We assessed the association of self-reported medication cost concerns and patient-reported outcomes (PROs) in a multiethnic lupus cohort. METHODS: The California Lupus Epidemiology Study is a cohort of individuals with physicianconfirmed SLE. Medication cost concerns was defined as having difficulties affording lupus medications, skipping doses, delaying refills, requesting lower cost alternatives, purchasing medications outside the US, or applying for patient assistance programs. Linear regression and mixed effects models assessed the cross-sectional and longitudinal association of medication cost concerns and PROs, respectively, adjusting for age, sex, race and ethnicity, income, principal insurance, immunomodulatory medications, and organ damage. RESULTS: Of 334 participants, medication cost concerns were reported by 91 (27%). Medication cost concerns were associated with worse Systemic Lupus Erythematosus Activity Questionnaire (SLAQ, beta coefficient 5.9, 95% CI 4.3 to 7.6, P<0.001), Patient Health Questionnaire Depression Scale (PHQ-8, beta coefficient 2.7, 95% CI 1.4 to 4.0, P<0.001), and Patient-Reported Outcomes Measurement Information System (PROMIS, beta coefficient for physical function -4.6, 95% CI -6.7 to -2.4, P<0.001) scores after adjusting for covariates. Medication cost concerns were not associated with significant changes in PROs over two-year follow-up. CONCLUSION: More than a quarter of participants reported at least one medication cost concern, which was associated with worse patient-reported outcomes. Our results reveal a potentially modifiable risk factor for poor outcomes rooted in the unaffordability of lupus care. |
Primary series COVID-19 vaccine effectiveness among healthcare workers in Albania, February-December 2021
Rubin-Smith JE , Castro MYR , Preza I , Hasibra I , Sulo J , Fico A , Daja R , Vasili A , Kota M , Schmid A , Sridhar S , Guseinova A , Boshevska G , Bejtja G , Mühlemann B , Drosten C , Jorgensen P , Pebody R , Kissling E , Lafond KE , Katz MA , Bino S . IJID Reg 2023 8 19-27 BACKGROUND: Healthcare workers have experienced high rates of morbidity and mortality from coronavirus disease 2019 (COVID-19). METHODS: A prospective cohort study was conducted in three Albanian hospitals between 19 February and 14 December 2021. All participants underwent polymerase chain reaction (PCR) and serological testing at enrolment, regular serology throughout, and PCR testing when symptomatic.Vaccine effectiveness (VE) against COVID-19 and against all severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections (symptomatic or asymptomatic) was estimated. VE was estimated using a Cox regression model, with vaccination status as a time-varying variable. FINDINGS: In total, 1504 HCWs were enrolled in this study; 70% had evidence of prior SARS-CoV-2 infection. VE was 65.1% [95% confidence interval (CI) 37.7-80.5] against COVID-19, 58.2% (95% CI 15.7-79.3) among participants without prior SARS-CoV-2 infection, and 73.6% (95% CI 24.3-90.8) among participants with prior SARS-CoV-2 infection. For BNT162b2 alone, VE was 69.5% (95% CI 44.5-83.2). During the period when the Delta variant was predominant, VE was 67.1% (95% CI 38.3-82.5). VE against SARS-CoV-2 infection for the full study period was 36.9% (95% CI 15.8-52.7). INTERPRETATION: This study found moderate primary series VE against COVID-19 among healthcare workers in Albania. These results support the continued promotion of COVID-19 vaccination in Albania, and highlight the benefits of vaccination in populations with high levels of prior infection. |
Characterization of a nonagglutinating toxigenic vibrio cholerae isolate
Gladney LM , Griswold T , Turnsek M , Im MS , Parsons MMB , Katz LS , Tarr CL , Lee CC . Microbiol Spectr 2023 11 (3) e0018223 Toxigenic Vibrio cholerae serogroup O1 is the etiologic agent of the disease cholera, and strains of this serogroup are responsible for pandemics. A few other serogroups have been found to carry cholera toxin genes-most notably, O139, O75, and O141-and public health surveillance in the United States is focused on these four serogroups. A toxigenic isolate was recovered from a case of vibriosis from Texas in 2008. This isolate did not agglutinate with any of the four different serogroups' antisera (O1, O139, O75, or O141) routinely used in phenotypic testing and did not display a rough phenotype. We investigated several hypotheses that might explain the recovery of this potential nonagglutinating (NAG) strain using whole-genome sequencing analysis and phylogenetic methods. The NAG strain formed a monophyletic cluster with O141 strains in a whole-genome phylogeny. Furthermore, a phylogeny of ctxAB and tcpA sequences revealed that the sequences from the NAG strain also formed a monophyletic cluster with toxigenic U.S. Gulf Coast (USGC) strains (O1, O75, and O141) that were recovered from vibriosis cases associated with exposures to Gulf Coast waters. A comparison of the NAG whole-genome sequence showed that the O-antigen-determining region of the NAG strain was closely related to those of O141 strains, and specific mutations were likely responsible for the inability to agglutinate. This work shows the utility of whole-genome sequence analysis tools for characterization of an atypical clinical isolate of V. cholerae originating from a USGC state. IMPORTANCE Clinical cases of vibriosis are on the rise due to climate events and ocean warming (1, 2), and increased surveillance of toxigenic Vibrio cholerae strains is now more crucial than ever. While traditional phenotyping using antisera against O1 and O139 is useful for monitoring currently circulating strains with pandemic or epidemic potential, reagents are limited for non-O1/non-O139 strains. With the increased use of next-generation sequencing technologies, analysis of less well-characterized strains and O-antigen regions is possible. The framework for advanced molecular analysis of O-antigen-determining regions presented herein will be useful in the absence of reagents for serotyping. Furthermore, molecular analyses based on whole-genome sequence data and using phylogenetic methods will help characterize both historical and novel strains of clinical importance. Closely monitoring emerging mutations and trends will improve our understanding of the epidemic potential of Vibrio cholerae to anticipate and rapidly respond to future public health emergencies. |
Examining test cutoffs to optimize diagnosis of latent tuberculosis infection in non-US-born people
Zavala S , Winglee K , Ho CS , Pettit AC , Ahmed A , Katz DJ , Belknap RW , Stout JE . Ann Am Thorac Soc 2023 20 (9) 1258-1266 RATIONALE: Detection of latent tuberculosis infection (LTBI) in persons born in high tuberculosis (TB) incidence countries living in low TB incidence countries is key to tuberculosis elimination in low-incidence countries. Optimizing LTBI tests is critical to targeting treatment. OBJECTIVES: To compare the sensitivity/specificity of tuberculin skin test (TST) and two interferon-gamma release assays (IGRA) at different cutoffs, and of a single test versus dual testing. METHODS: We examined a subset (N=14,167) of a prospective cohort of people in the United States tested for LTBI. We included non-US-born, HIV-seronegative people ages 5 years and older with valid TST, QuantiFERON-TB Gold-in-Tube(QFT), and T-SPOT.TB(TSPOT) results. The sensitivity/specificity of different test cutoffs and test combinations, obtained from a Bayesian latent class model, were used to construct receiver operating characteristic (ROC) curves and assess area under the curve (AUC) for each test. The sensitivity/specificity of dual testing were calculated. RESULTS: The AUC of the TST ROC curve was 0.81(95% Credible Interval(CrI) 0.78-0.86), with sensitivity/specificity at cutoffs of 5, 10, and 15mm of 86.5%/61.6%, 81.7%/71.3, and 55.6%/88.0%, respectively. The AUC of the QFT ROC curve was 0.89(95%CrI 0.86-0.93), with sensitivity/specificity at cutoffs of 0.35, 0.7, and 1.0IU/mL of 77.7%/98.3%, 66.9%/99.1%, and 61.5/99.4%. The AUC of the TSPOT ROC curve was 0.92(95%CrI 0.88-0.96) with sensitivity/specificity for 5, 6, 7, and 8 spots of 79.2%/96.7%, 76.8%/97.7%, 74.0%/98.6%, and 71.8%/99.5%. Sensitivity/specificity of TST-QFT, TST-TSPOT and QFT-TSPOT at standard cutoffs were 73.1%/99.4%, 64.8%/99.8%, and 65.3%/100%. CONCLUSION: IGRAs have a better predictive ability than TST in people at high risk of LTBI. |
Mashtree: a rapid comparison of whole genome sequence files
Katz LS , Griswold T , Morrison SS , Caravas JA , Zhang S , den Bakker HC , Deng X , Carleton HA . J Open Source Softw 2019 4 (44) In the past decade, the number of publicly available bacterial genomes has increased dramatically. These genomes have been generated for impactful initiatives, especially in the field of genomic epidemiology (Brown, Dessai, McGarry, & Gerner-Smidt, 2019; Timme et al., 2017). Genomes are sequenced, shared publicly, and subsequently analyzed for phylogenetic relatedness. If two genomes of epidemiological interest are found to be related, further investigation might be prompted. However, comparing the multitudes of genomes for phylogenetic relatedness is computationally expensive and, with large numbers, laborious. Consequently, there are many strategies to reduce the complexity of the data for downstream analysis, especially using nucleotide stretches of length k (kmers). |
- Page last reviewed:Feb 1, 2024
- Page last updated:May 06, 2024
- Content source:
- Powered by CDC PHGKB Infrastructure