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1.
J Rehabil Med ; 56: jrm39946, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38742877

ABSTRACT

OBJECTIVE: To assess the preliminary effectiveness of three-dimensional printed orthoses compared with conventionally custom-fabricated orthoses in persons with chronic hand conditions on performance of daily activities, hand function, quality of life, satisfaction, and production time and costs. DESIGN: Interventional feasibility study. SUBJECTS: Chronic hand orthotic users (n = 21). METHODS: Participants received a new three-dimensional printed orthosis according to the same type as their current orthosis, which served as the control condition. Primary outcome was performance of daily activities (Patient-Reported Outcomes Measurement Information System-Upper Extremity; Michigan Hand Questionnaire). Secondary outcomes were hand function, quality of life, and satisfaction. Furthermore, production time and costs were recorded. RESULTS: At 4 months' follow-up, no significant differences were found between three-dimensional printed orthoses and participants' existing conventional orthoses on activity performance, hand function, and quality of life. Satisfaction with the three-dimensional printed orthosis was significantly higher and the production time and costs for three-dimensional printed orthoses were significantly lower compared with conventional orthoses. The three-dimensional printed orthosis was preferred by 79% of the participants. CONCLUSIONS: This feasibility study in chronic hand conditions suggests that three-dimensional printed orthoses are similar to conventional orthoses in terms of activity performance, hand function, and quality of life. Satisfaction, and production time and costs favoured the three-dimensional printed hand orthoses.


Subject(s)
Activities of Daily Living , Feasibility Studies , Orthotic Devices , Printing, Three-Dimensional , Quality of Life , Humans , Male , Female , Middle Aged , Adult , Chronic Disease , Patient Satisfaction , Hand , Aged
2.
Article in English | MEDLINE | ID: mdl-38546394

ABSTRACT

BACKGROUND: High-risk human papillomavirus (hrHPV)-based cervical cancer screening in the Netherlands led to a substantial increase in number of colposcopy referrals and low-grade lesions detected. Genotyping strategies may be employed to lower the screening-related burden. METHODS: We evaluated fourteen triage strategies with genotyping (HPV16/18 or HPV16/18/31/33/45/52/58) for hrHPV-positive borderline or mild dyskaryosis (BMD) or normal cytology, using data from a population-based hrHPV-based screening trial with 5-year interval (POBASCAM). We considered colposcopy referral at baseline, after 6-month repeat cytology and after 5-year hrHPV testing. Performance was evaluated by one-round positive and negative predictive value (PPV and NPV) for CIN3+ and by two-round colposcopy referral rate. To identify efficient strategies, they were ordered by the one-round colposcopy referral rate. Adjacent strategies were compared by the marginal PPV for detecting one additional CIN3+ (mPPV). RESULTS: The most conservative strategy (repeat cytology after BMD and HPV16/18/31/33/45/52/58-positive normal cytology, next round otherwise) yielded an mPPV of 28%, NPV of 98.2%, and colposcopy rate of 47.2%. Adding direct referral after BMD or genotype-positive BMD yielded an mPPV≤8.2%, NPV≥98.5% and an increase in colposcopy rate of 1.9-6.5%. Adding direct referral after HPV16/18-positive normal cytology yielded an mPPV≤3.5%, NPV≥99.5% and an increase in colposcopy rate of 13.9%. CONCLUSIONS: Direct colposcopy referral of women with BMD or normal cytology is unlikely to be efficient, but genotype-guided direct referral after BMD may be considered because the increase in colposcopies is limited. IMPACT: HrHPV screening programs can become very efficient when immediate colposcopy referral is limited to women at highest CIN3+ risk.

3.
Gut Microbes ; 16(1): 2292239, 2024.
Article in English | MEDLINE | ID: mdl-38105519

ABSTRACT

The multi-factorial involvement of gut microbiota with Crohn's disease (CD) necessitates robust analysis to uncover possible associations with particular microbes. CD has been linked to specific bacteria, but reported associations vary widely across studies. This inconsistency may result from heterogeneous associations across individual patients, resulting in no apparent or only weak relationships with the means of bacterial abundances. We investigated the relationship between bacterial relative abundances and disease activity in a longitudinal cohort of CD patients (n = 57) and healthy controls (n = 15). We applied quantile regression, a statistical technique that allows investigation of possible relationships outside the mean response. We found several significant and mostly negative associations with CD, especially in lower quantiles of relative abundance on family or genus level. Associations found by quantile regression deviated from the mean response in relative abundances of Coriobacteriaceae, Pasteurellaceae, Peptostreptococcaceae, Prevotellaceae, and Ruminococcaceae. For the family Streptococcaceae we found a significant elevation in relative abundance for patients experiencing an exacerbation relative to those who remained without self-reported symptoms or measurable inflammation. Our analysis suggests that specific bacterial families are related to CD and exacerbation, but associations vary between patients due to heterogeneity in disease course, medication history, therapy response, gut microbiota composition and historical contingency. Our study underscores that microbial diversity is reduced in the gut of CD patients, but suggests that the process of diversity loss is rather irregular with respect to specific taxonomic groups. This novel insight may advance our ecological understanding of this complex disease.


Subject(s)
Crohn Disease , Gastrointestinal Microbiome , Humans , Crohn Disease/microbiology , Inflammation , Bacteria/genetics , Bacteroidetes
4.
BMJ Glob Health ; 8(11)2023 11.
Article in English | MEDLINE | ID: mdl-37931940

ABSTRACT

BACKGROUND: Cervical cancer is a major public health problem in India, where access to prevention programmes is low. The WHO-Strategic Advisory Group of Experts recently updated their recommendation for human papillomavirus (HPV) vaccination to include a single-dose option in addition to the two-dose option, which could make HPV vaccination programmes easier to implement and more affordable. METHODS: We combined projections from a type-specific HPV transmission model and a cancer progression model to assess the health and economic effects of HPV vaccination at national and state level in India. The models used national and state-specific Indian demographic, epidemiological and cost data, and single-dose vaccine efficacy and immunogenicity data from the International Agency for Research on Cancer India vaccine trial with 10-year follow-up. We compared single-dose and two-dose HPV vaccination for a range of plausible scenarios regarding single-dose vaccine protection, coverage and catch-up. We used a healthcare sector payer perspective with a time horizon of 100 years. RESULTS: Under the base-case scenario of lifelong protection of single-dose vaccination in 10-year-old girls with 90% coverage, the discounted incremental cost-effectiveness ratio (ICER) of nationwide vaccination relative to no vaccination was US$406 (₹INR30 000) per DALY (disability-adjusted life-years) averted. This lay below an opportunity-cost-based threshold of 30% Indian gross domestic product per capita in each Indian state (state-specific ICER range: US$67-US$593 per DALY averted). The ICER of two-dose vaccination versus no vaccination vaccination was US$1404 (₹INR104 000). The ICER of two-dose vaccination versus single-dose vaccination, assuming lower initial efficacy and waning of single-dose vaccination, was at least US$2282 (₹INR169 000) per DALY averted. CONCLUSIONS: Nationwide introduction of single-dose HPV vaccination at age 10 in India is highly likely to be cost-effective whereas extending the number of doses from one to two would have a less favourable profile.


Subject(s)
Papillomavirus Infections , Papillomavirus Vaccines , Uterine Cervical Neoplasms , Female , Humans , Child , Papillomavirus Vaccines/therapeutic use , Papillomavirus Infections/prevention & control , Human Papillomavirus Viruses , Cost-Benefit Analysis , Vaccination , Uterine Cervical Neoplasms/prevention & control
5.
J R Soc Interface ; 20(205): 20220912, 2023 08.
Article in English | MEDLINE | ID: mdl-37553995

ABSTRACT

Infectious diseases often involve multiple pathogen species or multiple strains of the same pathogen. As such, knowledge of how different pathogens interact is key to understand and predict the outcome of interventions targeting only a subset of species or strains involved in disease. Population-level data may be useful to infer pathogen strain interactions, but most previously used inference methods only consider uniform interactions between all strains or focus on marginal pairwise interactions. As such, these methods are prone to bias induced by indirect interactions through other strains. Here, we evaluated statistical network inference for reconstructing heterogeneous interactions from cross-sectional surveys detecting joint presence/absence patterns of pathogen strains within hosts. We applied various network models to simulated survey data, representing endemic infection states of multiple pathogen strains with potential interactions in acquisition or clearance of infection. Satisfactory performance was demonstrated by the estimators converging to the true interactions. Accurate reconstruction of interaction networks was achieved by regularization or penalization for sample size. Although performance deteriorated in the presence of host heterogeneity, this was overcome by correcting for individual-level risk factors. Our work demonstrates how statistical network inference could prove useful for detecting multi-strain pathogen interactions and may have applications beyond epidemiology.


Subject(s)
Host-Pathogen Interactions , Cross-Sectional Studies
6.
BMJ Open ; 13(7): e067435, 2023 07 10.
Article in English | MEDLINE | ID: mdl-37429682

ABSTRACT

INTRODUCTION: For idiopathic inflammatory myopathies (IIM) ('myositis') standard initial treatment is high-dosed glucocorticoids, which results in relatively slow improvement of muscle strength. Early immunosuppression or modulation by intensive treatment ('hit-early, hit-hard') may induce faster reduction of disease activity and prevent chronic disability due to disease-induced structural muscle damage. Intravenous immunoglobulin (IVIg) in addition to standard glucocorticoid treatment may be promising in this regard as was shown in various studies: add-on IVIg improved symptoms and muscle strength in refractory myositis patients and monotherapy IVIg improved outcomes after 9 weeks, in about half of treatment-naive patients. HYPOTHESIS: We hypothesise that early add-on IVIg leads to a greater clinical response after 12 weeks in patients with newly diagnosed myositis, in comparison to prednisone monotherapy. Second, we expect that early treatment with add-on IVIg leads to a faster time to improvement and sustained positive effects on multiple secondary outcomes. METHODS: The Time Is Muscle trial is a phase-2 double-blind placebo-controlled randomised trial. Forty-eight patients with IIM will be treated with IVIg or placebo at baseline (within 1 week after diagnosis) and after 4 and 8 weeks, in addition to standard therapy with prednisone. The primary outcome is the Total Improvement Score (TIS) of the myositis response criteria at 12 weeks. At baseline, and after 4, 8, 12, 26 and 52 weeks, relevant secondary outcomes will be assessed, including time to moderate improvement (TIS≥40), mean daily prednisone dosage, physical activity, health-related quality of life, fatigue and MRI muscle imaging parameters. ETHICS AND DISSEMINATION: Ethical approval was obtained from the medical ethics committee of the Academic Medical Centre, University of Amsterdam, the Netherlands (2020_180; including a first amendment approval at the 12 April 2023; A2020_180_0001). The results will be distributed through conference presentations and peer-reviewed publications. TRIAL REGISTRATION NUMBER: EU Clinical trials register (2020-001710-37).


Subject(s)
Immunoglobulins, Intravenous , Myositis , Humans , Immunoglobulins, Intravenous/therapeutic use , Prednisone/therapeutic use , Quality of Life , Muscles , Myositis/drug therapy , Glucocorticoids/therapeutic use , Disease Progression , Randomized Controlled Trials as Topic , Clinical Trials, Phase II as Topic
7.
Sci Rep ; 13(1): 8042, 2023 05 17.
Article in English | MEDLINE | ID: mdl-37198426

ABSTRACT

Human microbiome research is helped by the characterization of microbial networks, as these may reveal key microbes that can be targeted for beneficial health effects. Prevailing methods of microbial network characterization are based on measures of association, often applied to limited sampling points in time. Here, we demonstrate the potential of wavelet clustering, a technique that clusters time series based on similarities in their spectral characteristics. We illustrate this technique with synthetic time series and apply wavelet clustering to densely sampled human gut microbiome time series. We compare our results with hierarchical clustering based on temporal correlations in abundance, within and across individuals, and show that the cluster trees obtained by using either method are significantly different in terms of elements clustered together, branching structure and total branch length. By capitalizing on the dynamic nature of the human microbiome, wavelet clustering reveals community structures that remain obscured in correlation-based methods.


Subject(s)
Gastrointestinal Microbiome , Microbiota , Humans , Wavelet Analysis , Microbial Consortia , Cluster Analysis
8.
Cancer Med ; 12(10): 11786-11794, 2023 05.
Article in English | MEDLINE | ID: mdl-36965085

ABSTRACT

BACKGROUND: The first HPV-vaccine eligible cohorts in the Netherlands will enter the cervical screening program in 2023. However, a substantial number of young women already have had a cervical sample taken before entry into the regular screening program. This study was initiated to explore early effects of HPV vaccination on detection of cytological abnormalities in cervical samples of women younger than the screening age. METHODS: Results of cervical samples were obtained from the Dutch National Pathology Databank (PALGA) and were linked to the women's HPV vaccination status from the national vaccination registry (Praeventis) (N = 42,171). Occurrence of low-grade and high-grade squamous intraepithelial lesions or worse (LSIL and HSIL+) and high-risk HPV positive tests (hrHPV) in the first cervical sample were compared between vaccinated and unvaccinated women by multivariable logistic regression analysis, corrected for age at cervical sampling and age of vaccination (12/13 years, ≥ = 14 years). RESULTS: For fully vaccinated women (three- or two-dose schedule), statistically significant reductions were seen for all outcomes compared to unvaccinated women (hrHPV: adjusted OR, 0.70, 95% CI, 0.63-0.79; LSIL: 0.70, 0.61-0.80; HSIL+: 0.39, 0.30-0.51). CONCLUSIONS: By linking nation-wide registries on pathology and vaccination, we show significant beneficial early effects of HPV-vaccination on LSIL, HSIL+, CIN3/AIS/carcinoma and hrHPV detection in young women upto 24 years of age who have a cervical sample taken before entry into the cervical cancer screening program.


Subject(s)
Papillomavirus Infections , Papillomavirus Vaccines , Squamous Intraepithelial Lesions of the Cervix , Uterine Cervical Dysplasia , Uterine Cervical Neoplasms , Female , Humans , Child , Uterine Cervical Neoplasms/diagnosis , Uterine Cervical Neoplasms/epidemiology , Uterine Cervical Neoplasms/prevention & control , Papillomavirus Infections/epidemiology , Papillomavirus Infections/prevention & control , Early Detection of Cancer/methods , Human Papillomavirus Viruses , Netherlands/epidemiology , Papillomavirus Vaccines/therapeutic use , Vaccination , Squamous Intraepithelial Lesions of the Cervix/epidemiology , Squamous Intraepithelial Lesions of the Cervix/pathology , Papillomaviridae
9.
Liver Int ; 43(5): 1056-1067, 2023 05.
Article in English | MEDLINE | ID: mdl-36779848

ABSTRACT

BACKGROUND & AIMS: Data regarding health-related quality of life (HRQoL) in primary sclerosing cholangitis (PSC) are sparse and have only been studied cross-sectionally in a disease which runs a fluctuating and unpredictable course. We aim to describe HRQoL longitudinally by using repeated measurements in a population-based cohort. METHODS: Every 3 months from May 2017 up to August 2020, patients received digital questionnaires at home. These included the EQ-5D, 5-D Itch, patient-based SCCAI and patient-based HBI. The SF-36, measuring HRQoL over eight dimensions as well as a physical component summary (PCS) and mental component summary (MCS) score, was sent annually. Data were compared with Dutch reference data and a matched IBD disease control from the population-based POBASIC cohort. Mixed-effects modelling was performed to identify factors associated with HRQoL. RESULTS: Three hundred twenty-eight patients completed 2576 questionnaires. A significant reduction of small clinical relevance in several mean HRQoL scores was found compared with the Dutch reference population: 46.4 versus 48.0, p = .018 for PCS and 47.5 versus 50.5, p = .004 for MCS scores. HRQoL outcomes were significantly negatively associated with coexisting active IBD (PCS -12.2, p < .001 and MCS -12.0, p < .001), which was not the case in case of quiescent IBD. Decreasing HRQoL scores were also negatively associated with increasing age (PCS -0.1 per 10 years, p = .002), female sex (PCS -2.8, p < .001), diagnosis of AIH overlap (PCS -3.7, p = .059), end-stage liver disease (PCS -3.7, p = .015) and presence of itch (PCS -9.2, p < .001 and MCS -3.1, p = .078). The odds of reporting a clinically relevant reduction in EQ-5D scores showed seasonal variation, being lowest in summer (OR = 0.48 relative to spring, p = .037). In patients with liver transplant, HRQoL outcomes were comparable to the Dutch general population. CONCLUSIONS: PSC patients report impaired HRQoL of small clinical relevance compared with the general population. After liver transplantation, HRQoL scores are at comparable levels to the general population. HRQoL scores are associated with potentially modifiable factors such as itch and IBD activity.


Subject(s)
Cholangitis, Sclerosing , Inflammatory Bowel Diseases , Humans , Female , Child , Quality of Life , Cohort Studies , Cholangitis, Sclerosing/epidemiology , Cholangitis, Sclerosing/complications , Surveys and Questionnaires , Inflammatory Bowel Diseases/complications
10.
Epidemiol Infect ; 151: e31, 2023 02 02.
Article in English | MEDLINE | ID: mdl-36727199

ABSTRACT

Genital human papillomavirus (HPV) infections are caused by a broad diversity of genotypes. As available vaccines target a subgroup of these genotypes, monitoring transmission dynamics of nonvaccine genotypes is essential. After reviewing the epidemiological literature on study designs aiming to monitor those dynamics, we evaluated their abilities to detect HPV-prevalence changes following vaccine introduction. We developed an agent-based model to simulate HPV transmission in a heterosexual population under various scenarios of vaccine coverage and genotypic interaction, and reproduced two study designs: post-vs.-prevaccine and vaccinated-vs.-unvaccinated comparisons. We calculated the total sample size required to detect statistically significant prevalence differences at the 5% significance level and 80% power. Although a decrease in vaccine-genotype prevalence was detectable as early as 1 year after vaccine introduction, simulations indicated that the indirect impact on nonvaccine-genotype prevalence (a decrease under synergistic interaction or an increase under competitive interaction) would only be measurable after >10 years whatever the vaccine coverage. Sample sizes required for nonvaccine genotypes were >5 times greater than for vaccine genotypes and tended to be smaller in the post-vs.-prevaccine than in the vaccinated-vs.-unvaccinated design. These results highlight that previously published epidemiological studies were not powerful enough to efficiently detect changes in nonvaccine-genotype prevalence.


Subject(s)
Papillomavirus Infections , Papillomavirus Vaccines , Humans , Papillomavirus Infections/epidemiology , Vaccination , Epidemiologic Studies , Genotype , Prevalence , Papillomaviridae
11.
Sex Transm Infect ; 99(3): 149-155, 2023 05.
Article in English | MEDLINE | ID: mdl-35584898

ABSTRACT

BACKGROUND: In many countries, HIV pre-exposure prophylaxis (PrEP) users are screened quarterly for STIs. We assessed the consequences of less frequent STI testing. We also assessed determinants of asymptomatic STI and potential for onward transmission. METHODS: Using data from the AMPrEP study, we assessed the proportion of syphilis, and genital, anal, and pharyngeal chlamydia and gonorrhoea diagnoses which would have been delayed with biannual versus quarterly screening. We assessed the potential for onward transmission by examining reported condomless anal sex (CAS) in periods after to-be-omitted visits when screening biannually. We assessed determinants of incident asymptomatic STIs using Poisson regression and calculated individual risk scores on the basis of the coefficients from this model. RESULTS: We included 366 participants. Median follow-up was 47 months (IQR 43-50). 1,183STIs were diagnosed, of which 932(79%) asymptomatic. With biannual screening, 483 asymptomatic STIs (52%) diagnoses would have been delayed at 364 study visits. Of these visits, 129 (35%), 240 (66%) and 265 (73%) were followed by periods of CAS with steady, known casual or unknown casual partners, respectively. Older participants had a lower risk of asymptomatic STI (incidence rate ratio (IRR) 0.86/10-year increase, 95% CI 0.80 to 0.92), while CAS with known (IRR 1.36, 95% CI 1.10 to 1.68) and unknown (IRR 1.86, 95% CI 1.48 to 2.34) casual partners and chemsex (IRR 1.51, 95% CI 1.28 to 1.78) increased the risk. The individual risk scores had limited predictive value (sensitivity=0.70 (95% CI 0.66 to 0.74), specificity=0.50 (95% CI 0.48 to 0.51)). CONCLUSION: Reducing the STI screening frequency to biannually among PrEP users will likely result in delayed diagnoses, potentially driving onward transmission. Although determinants for asymptomatic STIs were identified, predictive power was low.


Subject(s)
Gonorrhea , HIV Infections , Pre-Exposure Prophylaxis , Sexual and Gender Minorities , Sexually Transmitted Diseases , Syphilis , Humans , Male , HIV Infections/diagnosis , HIV Infections/epidemiology , HIV Infections/prevention & control , Sexually Transmitted Diseases/diagnosis , Sexually Transmitted Diseases/epidemiology , Sexually Transmitted Diseases/prevention & control , Gonorrhea/diagnosis , Gonorrhea/epidemiology , Sexual Behavior , Homosexuality, Male
12.
Lancet Oncol ; 23(11): 1419-1429, 2022 11.
Article in English | MEDLINE | ID: mdl-36174583

ABSTRACT

BACKGROUND: Despite the high burden of cervical cancer, access to preventive measures remains low in India. A single-dose immunisation schedule could facilitate the scale-up of human papillomavirus (HPV) vaccination, contributing to global elimination of cervical cancer. We projected the effect of single-dose quadrivalent HPV vaccination in India in comparison with no vaccination or to a two-dose schedule. METHODS: In this modelling study, we adapted an HPV transmission model (EpiMetHeos) to Indian data on sexual behaviour (from the Demographic and Health Survey and the Indian National AIDS Control Organisation), HPV prevalence data (from two local surveys, from the states of Tamil Nadu and West Bengal), and cervical cancer incidence data (from Cancer Incidence in Five Continents for the period 2008-12 [volume XI], and the Indian National Centre for Disease Informatics and Research for the period 2012-16). Using the model, we projected the nationwide and state-specific effect of HPV vaccination on HPV prevalence and cervical cancer incidence, and lifetime risk of cervical cancer, for 100 years after the introduction of vaccination or in the first 50 vaccinated birth cohorts. Projections were derived under a two-dose vaccination scenario assuming life-long protection and under a single-dose vaccination scenario with protection duration assumptions derived from International Agency for Research on Cancer (IARC) India vaccine trial data, in combination with different vaccination coverages and catch-up vaccination age ranges. We used two thresholds to define cervical cancer elimination: an age-standardised incidence rate of less than 4 cases per 100 000 woman-years, and standardised lifetime risk of less than 250 cases per 100 000 women born. FINDINGS: Assuming vaccination in girls aged 10 years, with 90% coverage, and life-long protection by two-dose or single-dose schedule, HPV vaccination could reduce the prevalence of HPV16 and HPV18 infection by 97% (80% UI 96-99) in 50 years, and the lifetime risk of cervical cancer by 71-78% from 1067 cases per 100 000 women born under a no vaccination scenario to 311 (80% UI 284-339) cases per 100 000 women born in the short term and 233 (219-252) cases per 100 000 women born in the long term in vaccinated cohorts. Under this scenario, we projected that the age-standardised incidence rate threshold for elimination could be met across India (range across Indian states: 1·6 cases [80% UI 1·5-1·7] to 4·0 cases [3·8-4·4] per 100 000 woman-years), while the complementary threshold based on standardised lifetime risk was attainable in 17 (68%) of 25 states, but not nationwide (range across Indian states: 207 cases [80% UI 194-223] to 477 cases [447-514] per 100 000 women born). Under the considered assumptions of waning vaccine protection, single-dose vaccination was projected to have a 21-100% higher per-dose efficiency than two-dose vaccination. Single-dose vaccination with catch-up for girls and women aged 11-20 years was more impactful than two-dose vaccination without catch-up, with reduction of 39-65% versus 38% in lifetime risk of cervical cancer across the ten catch-up birth cohorts and the first ten routine vaccination birth cohorts. INTERPRETATION: Our evidence-based projections suggest that scaling up cervical cancer prevention through single-dose HPV vaccination could substantially reduce cervical cancer burden in India. FUNDING: The Bill & Melinda Gates Foundation.


Subject(s)
Papillomavirus Infections , Papillomavirus Vaccines , Uterine Cervical Neoplasms , Female , Humans , Papillomavirus Infections/epidemiology , Papillomavirus Infections/prevention & control , Papillomavirus Infections/drug therapy , Uterine Cervical Neoplasms/epidemiology , Uterine Cervical Neoplasms/prevention & control , India/epidemiology , Human papillomavirus 16
13.
PLoS Comput Biol ; 18(9): e1010491, 2022 09.
Article in English | MEDLINE | ID: mdl-36084152

ABSTRACT

Unraveling the network of interactions in ecological communities is a daunting task. Common methods to infer interspecific interactions from cross-sectional data are based on co-occurrence measures. For instance, interactions in the human microbiome are often inferred from correlations between the abundances of bacterial phylogenetic groups across subjects. We tested whether such correlation-based methods are indeed reliable for inferring interaction networks. For this purpose, we simulated bacterial communities by means of the generalized Lotka-Volterra model, with variation in model parameters representing variability among hosts. Our results show that correlations can be indicative for presence of bacterial interactions, but only when measurement noise is low relative to the variation in interaction strengths between hosts. Indication of interaction was affected by type of interaction network, process noise and sampling under non-equilibrium conditions. The sign of a correlation mostly coincided with the nature of the strongest pairwise interaction, but this is not necessarily the case. For instance, under rare conditions of identical interaction strength, we found that competitive and exploitative interactions can result in positive as well as negative correlations. Thus, cross-sectional abundance data carry limited information on specific interaction types. Correlations in abundance may hint at interactions but require independent validation.


Subject(s)
Microbial Interactions , Microbiota , Bacteria , Cross-Sectional Studies , Humans , Phylogeny
14.
Tumour Virus Res ; 14: 200240, 2022 12.
Article in English | MEDLINE | ID: mdl-35640823

ABSTRACT

Little is known about the long-term association between high-risk human papillomavirus (hrHPV) test results in women participating in a hrHPV-based cervical cancer screening program. To address this question, we collected data of 2217 women who participated in the POBASCAM hrHPV-based screening trial (enrolment 1999/2002) and also attended the Dutch hrHPV-based screening program between January 2017 and March 2018. Among 143 women who tested hrHPV-positive in 1999/2002, 45 (31.5%) had ≥ CIN2 or hysterectomy before 2017 and 17 (11.9%) tested hrHPV-positive at the 2017/2018 screen. In comparison, among 2074 women who tested hrHPV-negative in 1999/2002, 10 (0.5%) had ≥ CIN2 or hysterectomy before 2017 and 119 (5.7%) tested hrHPV-positive at the 2017/2018 screen. It follows that in the group of women who were not treated for ≥ CIN2 or had a hysterectomy in between the two screens 15 years apart (N = 2162), women who were hrHPV-positive in 1999/2002 had a higher risk of being hrHPV-positive in 2017/2018 than those who were hrHPV-negative in 1999/2002 (OR 3.4, 95% CI 1.8-6.1). A similar association was found at the genotype level for genotype-concordant results (5.1, 1.0-11.3) and for genotype non-concordant results (3.7, 1.6-6.7). Women who were hrHPV-positive in 2017/2018 had a higher risk of CIN3 after a hrHPV-positive result in 1999/2002 than after a hrHPV-negative result (5.8, 1.0-27.8). In conclusion, a positive hrHPV result in screening gives a long-term increased risk of a hrHPV-positive result, also for different genotypes, and a long-term increased risk of CIN3. This supports the concept of risk-stratification in hrHPV-based cervical cancer screening where previous hrHPV results are included in screening recommendations.


Subject(s)
Papillomavirus Infections , Uterine Cervical Dysplasia , Uterine Cervical Neoplasms , Female , Humans , Papillomavirus Infections/diagnosis , Uterine Cervical Neoplasms/diagnosis , Human Papillomavirus Viruses , Early Detection of Cancer/methods , Uterine Cervical Dysplasia/diagnosis
15.
Stat Med ; 41(6): 981-993, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35083763

ABSTRACT

While the serotypes of Streptococcus pneumoniae are known to compete during colonization in human hosts, our knowledge of how competition occurs is still incomplete. New insights of pneumococcal between-type competition could be generated from carriage data obtained by molecular-based detection methods, which record more complete sets of serotypes involved in co-carriage than when detection is done by culture. Here, we develop a Bayesian estimation method for inferring between-type interactions from longitudinal data recording the presence/absence of the types at discrete observation times. It allows inference from data containing co-carriage of two or more serotypes, which is often the case when pneumococcal presence is determined by molecular-based methods. The computational burden posed by the increased number of types detected in co-carriage is addressed by approximating the likelihood under a multi-state model with the likelihood of only those trajectories with minimum number of acquisition and clearance events between observation times. The proposed method's performance was validated on simulated data. The estimates of the interaction parameters of acquisition and clearance were unbiased in settings with short sampling intervals between observation times. With less frequent sampling, the estimates of the interaction parameters became more biased, but their ratio, which summarizes the total interaction, remained unbiased. Confounding due to unobserved heterogeneity in exposure could be corrected by including individual-level random effects. In an application to empirical data about pneumococcal carriage in infants, we found new evidence for between-serotype competition in clearance, although the effect size was small.


Subject(s)
Pneumococcal Infections , Streptococcus pneumoniae , Bayes Theorem , Carrier State , Humans , Infant , Likelihood Functions
16.
J Infect Dis ; 226(4): 634-643, 2022 09 04.
Article in English | MEDLINE | ID: mdl-33964158

ABSTRACT

BACKGROUND: In the Netherlands, the bivalent human papillomavirus (HPV) vaccine has been offered to preadolescent girls via the National Immunization Program in a 2-dose schedule since 2014. The current study estimates vaccine effectiveness (VE) against HPV infections up to 4 years postvaccination among girls eligible for routine 2-dose immunization. METHODS: A cohort study (HAVANA2) was used in which participants annually filled out an online questionnaire and provided a vaginal self-sample for determination of HPV by the SPF10-LiPA25 assay, able to detect 25 HPV types. VE against incident type-specific infections and pooled outcomes was estimated by a Cox proportional hazards model with shared frailty between the HPV types. RESULTS: In total, 2027 girls were included in the study, 1098 (54.2%) of whom were vaccinated with 2 doses. Highest incidence rate was 5.0/1000 person-years (HPV-51) among vaccinated participants and 9.1/1000 person-years (HPV-74) among unvaccinated participants. Adjusted pooled VE was 84.0% (95% confidence interval [CI], 27.0%-96.5%) against incident HPV-16/18 infections and 86.5% (95% CI, 39.5%-97.08%) against cross-protective types HPV-31/33/45. CONCLUSIONS: Four years postvaccination, 2 doses of bivalent HPV vaccine were effective in the prevention of incident HPV-16/18 infections and provided cross-protection to HPV-31/33/45. Our VE estimates rival those from 3-dose schedules, indicating comparable protection by 2-dose schedules.


Subject(s)
Papillomavirus Infections , Papillomavirus Vaccines , Sexually Transmitted Diseases , Cohort Studies , Female , Human papillomavirus 16 , Human papillomavirus 18 , Humans , Immunization Schedule , Papillomaviridae , Papillomavirus Infections/epidemiology , Papillomavirus Infections/prevention & control , Vaccination , Vaccine Efficacy , Vagina
17.
Int J Cancer ; 148(2): 320-328, 2021 01 15.
Article in English | MEDLINE | ID: mdl-32663316

ABSTRACT

Birth cohorts vaccinated against human papillomavirus (HPV) are now entering cervical cancer screening. Assessment of (pre)cancer (CIN3+) risk is needed to assess the residual screening need in vaccinated women. We estimated the lifetime (screen-detected) CIN3+ risk under five-yearly primary HPV screening between age 30 and 60, using HPV genotyping and histology data of 21,287 women participating in a screening trial with two HPV-based screening rounds, 5 years apart. The maximum follow-up after an HPV-positive test was 9 years. We re-estimated the CIN3+ risk after projecting direct vaccine efficacy for the bivalent and the nonavalent HPV vaccines, assuming life-long protection. The lifetime CIN3+ risk was 4.1% (95% confidence interval 3.5-4.9) and declined by 53.5% and 70.5% after bivalent vaccination without and with cross-protection, respectively, translating into a residual lifetime CIN3+ risk of 1.9% (1.4-2.4) and 1.2% (0.9-1.5). The CIN3+ risk declined by 88.5% after nonavalent vaccination, translating into a residual lifetime CIN3+ risk of 0.5% (0.2-0.7). The latter risk increased to 1.6% when vaccine protection only lasted until the first screening round at age 30. Among HPV-positive women with abnormal adjunct cytology, the nine-year CIN3+ risk was 16.9% (8.7-32.4) after nonavalent vaccination. In conclusion, HPV vaccination will lead to a strong decline in the lifetime CIN3+ risk and the remaining absolute CIN3+ risk will be very low. Primary HPV testing combined with adjunct cytology at five-year intervals still seems feasible even after nonavalent vaccination, although unlikely to be cost-effective. Our results support a de-intensification of screening programs in settings with high vaccination coverage.


Subject(s)
Papillomavirus Infections/epidemiology , Papillomavirus Vaccines/administration & dosage , Precancerous Conditions/epidemiology , Uterine Cervical Dysplasia/epidemiology , Uterine Cervical Neoplasms/epidemiology , Adult , Aged , Cohort Studies , Early Detection of Cancer , Female , Humans , Middle Aged , Netherlands/epidemiology , Papillomaviridae/immunology , Papillomaviridae/isolation & purification , Papillomavirus Infections/prevention & control , Precancerous Conditions/prevention & control , Randomized Controlled Trials as Topic , Risk , Uterine Cervical Neoplasms/prevention & control , Vaccination/statistics & numerical data , Uterine Cervical Dysplasia/prevention & control
18.
Clin Infect Dis ; 73(2): 291-297, 2021 07 15.
Article in English | MEDLINE | ID: mdl-32421775

ABSTRACT

BACKGROUND: There is ongoing debate about the possible protective effect of the bivalent human papillomavirus (2vHPV) vaccine, targeting oncogenic types HPV-16/18, against anogenital warts (AGWs), commonly attributed to HPV-6/11. We performed a retrospective registry-based open cohort study to assess the effect of 2vHPV vaccination on AGWs. METHODS: We linked general practice (ie, primary care) data from women born between 1993 and 2002, who had been eligible for HPV vaccination in the Netherlands, to the Dutch national immunization registry on an individual level. Women were followed until their first AGW diagnosis or end of follow-up. Adjusted incidence rate ratios (aIRRs) were estimated using Poisson regression with vaccination status as a time-dependent exposure. RESULTS: We linked data of 96 468 women with a total of 328 019 years observation time and 613 AGW diagnoses (incidence: 1.87/1000 person-years). At the end of follow-up, 61% were 2vHPV vaccinated (≥ 1 dose) of whom 91% were fully vaccinated. The AGW incidence was lower among those with ≥ 1 dose vs 0 doses (aIRR, 0.75 [95% confidence interval {CI}, .64-.88]). The effect of vaccination was stronger after full vaccination (aIRR, 0.72 [95% CI, .61-.86]) and for women who were offered vaccination at 12-13 years of age (aIRR, 0.69 [95% CI, .51-.93]) vs those at 13-16 years of age (aIRR, 0.77 [95% CI, .64-.93]). CONCLUSIONS: This is the largest population-based study so far to examine the effect of 2vHPV vaccination on AGWs, with reliable individual information on AGW diagnoses and vaccination status. The results indicate that 2vHPV vaccination partially protects against AGWs, especially when administered in early adolescence.


Subject(s)
Condylomata Acuminata , Papillomavirus Infections , Papillomavirus Vaccines , Adolescent , Cohort Studies , Condylomata Acuminata/epidemiology , Condylomata Acuminata/prevention & control , Female , Human papillomavirus 16 , Human papillomavirus 18 , Humans , Netherlands/epidemiology , Papillomavirus Infections/epidemiology , Papillomavirus Infections/prevention & control , Primary Health Care , Retrospective Studies , Vaccination
19.
J Infect Dis ; 224(3): 481-491, 2021 08 02.
Article in English | MEDLINE | ID: mdl-31985011

ABSTRACT

BACKGROUND: Although human papillomavirus (HPV) vaccines are highly efficacious in protecting against HPV infections and related diseases, vaccination may trigger replacement by nontargeted genotypes if these compete with the vaccine-targeted types. HPV genotype replacement has been deemed unlikely, based on the lack of systematic increases in the prevalence of nonvaccine-type (NVT) infection in the first decade after vaccination, and on the presence of cross-protection for some NVTs. METHODS: To investigate whether type replacement can be inferred from early postvaccination surveillance, we constructed a transmission model in which a vaccine type and an NVT compete through infection-induced cross-immunity. We simulated scenarios of different levels of cross-immunity and vaccine-induced cross-protection to the NVT. We validated whether commonly used measures correctly indicate type replacement in the long run. RESULTS: Type replacement is a trade-off between cross-immunity and cross-protection; cross-immunity leads to type replacement unless cross-protection is strong enough. With weak cross-protection, NVT prevalence may initially decrease before rebounding into type replacement, exhibiting a honeymoon period. Importantly, vaccine effectiveness for NVTs is inadequate for indicating type replacement. CONCLUSIONS: Although postvaccination surveillance thus far is reassuring, it is still too early to preclude type replacement. Monitoring of NVTs remains pivotal in gauging population-level impacts of HPV vaccination.


Subject(s)
Alphapapillomavirus , Papillomavirus Infections , Papillomavirus Vaccines , Alphapapillomavirus/genetics , Genotype , Humans , Papillomaviridae/genetics , Papillomaviridae/immunology , Papillomavirus Infections/epidemiology , Papillomavirus Infections/prevention & control , Vaccine Efficacy
20.
Clin Infect Dis ; 72(5): e103-e111, 2021 03 01.
Article in English | MEDLINE | ID: mdl-33249475

ABSTRACT

BACKGROUND: Human papillomavirus (HPV) vaccination programs achieve substantial population-level impact, with effects extending beyond protection of vaccinated individuals. We assessed trends in HPV prevalence up to 8 years postvaccination among men and women in the Netherlands, where bivalent HPV vaccination, targeting HPV types 16/18, has been offered to (pre)adolescent girls since 2009 with moderate vaccination coverage. METHODS: We used data from the PASSYON study, a survey initiated in 2009 (prevaccination) and repeated biennially among 16- to 24-year-old visitors of sexual health centers. We studied genital HPV positivity from 2009 to 2017 among women, heterosexual men, and unvaccinated women using Poisson generalized estimating equation models, adjusted for individual- and population-level confounders. Trends were studied for 25 HPV types detected by the SPF10-LiPA25 platform. RESULTS: A total of 6354 women (64.7% self-reported unvaccinated) and 2414 heterosexual men were included. Percentual declines in vaccine types HPV-16/18 were observed for all women (12.6% per year [95% confidence interval {CI}, 10.6-14.5]), heterosexual men (13.0% per year [95% CI, 8.3-17.5]), and unvaccinated women (5.4% per year [95% CI, 2.9-7.8]). We observed significant declines in HPV-31 (all women and heterosexual men), HPV-45 (all women), and in all high-risk HPV types pooled (all women and heterosexual men). Significant increases were observed for HPV-56 (all women) and HPV-52 (unvaccinated women). CONCLUSIONS: Our results provide evidence for first-order herd effects among heterosexual men against HPV-16/18 and cross-protective types. Additionally, we show second-order herd effects against vaccine types among unvaccinated women. These results are promising regarding population-level and clinical impact of girls-only bivalent HPV vaccination in a country with moderate vaccine uptake.


Subject(s)
Papillomavirus Infections , Papillomavirus Vaccines , Adolescent , Adult , Cross-Sectional Studies , Female , Human papillomavirus 16 , Human papillomavirus 18 , Humans , Male , Netherlands/epidemiology , Papillomavirus Infections/epidemiology , Papillomavirus Infections/prevention & control , Prevalence , Vaccination , Young Adult
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