Identifying subtypes of chronic kidney disease with machine learning: development, internal validation and prognostic validation using linked electronic health records in 350,067 individuals.

BACKGROUND: Although chronic kidney disease (CKD) is associated with high multimorbidity, polypharmacy, morbidity and mortality, existing classification systems (mild to severe, usually based on estimated glomerular filtration rate, proteinuria or urine albumin-creatinine ratio) and risk prediction models largely ignore the complexity of CKD, its risk factors and its outcomes. Improved subtype definition could improve prediction of outcomes and inform effective interventions. METHODS: We analysed individuals ≥18 years with incident and prevalent CKD (n = 350,067 and 195,422 respectively) from a population-based electronic health record resource (2006-2020; Clinical Practice Research Datalink, CPRD). We included factors (n = 264 with 2670 derived variables), e.g. demography, history, examination, blood laboratory values and medications. Using a published framework, we identified subtypes through seven unsupervised machine learning (ML) methods (K-means, Diana, HC, Fanny, PAM, Clara, Model-based) with 66 (of 2670) variables in each dataset. We evaluated subtypes for: (i) internal validity (within dataset, across methods); (ii) prognostic validity (predictive accuracy for 5-year all-cause mortality and admissions); and (iii) medications (new and existing by British National Formulary chapter). FINDINGS: After identifying five clusters across seven approaches, we labelled CKD subtypes: 1. Early-onset, 2. Late-onset, 3. Cancer, 4. Metabolic, and 5. Cardiometabolic. Internal validity: We trained a high performing model (using XGBoost) that could predict disease subtypes with 95% accuracy for incident and prevalent CKD (Sensitivity: 0.81-0.98, F1 score:0.84-0.97). Prognostic validity: 5-year all-cause mortality, hospital admissions, and incidence of new chronic diseases differed across CKD subtypes. The 5-year risk of mortality and admissions in the overall incident CKD population were highest in cardiometabolic subtype: 43.3% (42.3-42.8%) and 29.5% (29.1-30.0%), respectively, and lowest in the early-onset subtype: 5.7% (5.5-5.9%) and 18.7% (18.4-19.1%). MEDICATIONS: Across CKD subtypes, the distribution of prescription medication classes at baseline varied, with highest medication burden in cardiometabolic and metabolic subtypes, and higher burden in prevalent than incident CKD. INTERPRETATION: In the largest CKD study using ML, to-date, we identified five distinct subtypes in individuals with incident and prevalent CKD. These subtypes have relevance to study of aetiology, therapeutics and risk prediction. FUNDING: AstraZeneca UK Ltd, Health Data Research UK.

A retrospective cohort study predicting and validating impact of the COVID-19 pandemic in individuals with chronic kidney disease.

Chronic kidney disease (CKD) is associated with increased risk of baseline mortality and severe COVID-19, but analyses across CKD stages, and comorbidities are lacking. In prevalent and incident CKD, we investigated comorbidities, baseline risk, COVID-19 incidence, and predicted versus observed one-year excess death. In a national dataset (NHS Digital Trusted Research Environment [NHSD TRE]) for England encompassing 56 million individuals), we conducted a retrospective cohort study (March 2020 to March 2021) for prevalence of comorbidities by incident and prevalent CKD, SARS-CoV-2 infection and mortality. Baseline mortality risk, incidence and outcome of infection by comorbidities, controlling for age, sex and vaccination were assessed. Observed versus predicted one-year mortality at varying population infection rates and pandemic-related relative risks using our published model in pre-pandemic CKD cohorts (NHSD TRE and Clinical Practice Research Datalink [CPRD]) were compared. Among individuals with CKD (prevalent:1,934,585, incident:144,969), comorbidities were common (73.5% and 71.2% with one or more condition[s] in respective data sets, and 13.2% and 11.2% with three or more conditions, in prevalent and incident CKD), and associated with SARS-CoV-2 infection, particularly dialysis/transplantation (odds ratio 2.08, 95% confidence interval 2.04-2.13) and heart failure (1.73, 1.71-1.76), but not cancer (1.01, 1.01-1.04). One-year all-cause mortality varied by age, sex, multi-morbidity and CKD stage. Compared with 34,265 observed excess deaths, in the NHSD-TRE and CPRD databases respectively, we predicted 28,746 and 24,546 deaths (infection rates 10% and relative risks 3.0), and 23,754 and 20,283 deaths (observed infection rates 6.7% and relative risks 3.7). Thus, in this largest, national-level study, individuals with CKD have a high burden of comorbidities and multi-morbidity, and high risk of pre-pandemic and pandemic mortality. Hence, treatment of comorbidities, non-pharmaceutical measures, and vaccination are priorities for people with CKD and management of long-term conditions is important during and beyond the pandemic.

Geographical variation in rates of surgical treatment for female stress urinary incontinence in England: a national cohort study.

OBJECTIVE: To examine geographic variation in use of surgery for female stress urinary incontinence (SUI), mainly midurethral mesh tape insertions, in the English National Health Service (NHS). DESIGN: National cohort study. SETTING: NHS hospitals. PARTICIPANTS: 27 997 women aged 20 years or older who had a first SUI surgery in an English NHS Hospital between April 2013 and March 2016 and a diagnosis of SUI at the same time as the procedure. METHODS: Multilevel Poisson regression was used to adjust for geographic differences in age, ethnicity, prevalence of long-term illness and socioeconomic deprivation. PRIMARY OUTCOME MEASURE: Rate of surgery for SUI per 100 000 women/year at two geographic levels: Clinical Commissioning Group (CCG; n=209) and Sustainability and Transformation Partnership (STP; n=44). RESULTS: The rate of surgery for SUI was 40 procedures per 100 000 women/year. Risk-adjusted rates ranged from 20 to 106 procedures per 100 000 women/year across CCGs and 24 to 69 procedures per 100 000 women/year across the STP areas. These regional differences were only partially explained by demographic characteristics as adjustment reduced variance of surgery rates by 16% among the CCGs and 35% among the STPs. CONCLUSIONS: Substantial geographic variation exists in the use of surgery for female SUI in the English NHS, suggesting that women in some areas are more likely to be treated compared with women with the same condition in other areas. The variation reflects differences in how national guidelines are being interpreted in the context of the ongoing debate about the safety of SUI surgery.

Long-term Rate of Mesh Sling Removal Following Midurethral Mesh Sling Insertion Among Women With Stress Urinary Incontinence.

Importance: There is concern about outcomes of midurethral mesh sling insertion for women with stress urinary incontinence. However, there is little evidence on long-term outcomes. Objective: To examine long-term mesh removal and reoperation rates in women who had a midurethral mesh sling insertion for stress urinary incontinence. Design, Setting, and Participants: This population-based retrospective cohort study included 95 057 women aged 18 years or older who had a first-ever midurethral mesh sling insertion for stress urinary incontinence in the National Health Service hospitals in England between April 1, 2006, and December 31, 2015. Women were followed up until April 1, 2016. Exposures: Patient and hospital factors and retropubic or transobturator mesh sling insertions. Main Outcomes and Measures: The primary outcome was the risk of midurethral mesh sling removal (partial or total) and secondary outcomes were reoperation for stress urinary incontinence and any reoperation including mesh removal, calculated with death as competing risk. A multivariable Fine-Gray model was used to calculate subdistribution hazard ratios as estimates of relative risk. Results: The study population consisted of 95 057 women (median age, 51 years; interquartile range, 44-61 years) with first midurethral mesh sling insertion, including 60 194 with retropubic insertion and 34 863 with transobturator insertion. The median follow-up time was 5.5 years (interquartile range, 3.2-7.5 years). The rate of midurethral mesh sling removal was 1.4% (95% CI, 1.3%-1.4%) at 1 year, 2.7% (95% CI, 2.6%-2.8%) at 5 years, and 3.3% (95% CI, 3.2%-3.4%) at 9 years. Risk of removal declined with age. The 9-year removal risk after transobturator insertion (2.7% [95% CI, 2.4%-2.9%]) was lower than the risk after retropubic insertion (3.6% [95% CI, 3.5%-3.8%]; subdistribution hazard ratio, 0.72 [95% CI, 0.62-0.84]). The rate of reoperation for stress urinary incontinence was 1.3% (95% CI, 1.3%-1.4%) at 1 year, 3.5% (95% CI, 3.4%-3.6%) at 5 years, and 4.5% (95% CI, 4.3%-4.7%) at 9 years. The rate of any reoperation, including mesh removal, was 2.6% (95% CI, 2.5%-2.7%) at 1 year, 5.5% (95% CI, 5.4%-5.7%) at 5 years, and 6.9% (95% CI, 6.7%-7.1%) at 9 years. Conclusions and Relevance: Among women undergoing midurethral mesh sling insertion, the rate of mesh sling removal at 9 years was estimated as 3.3%. These findings may guide women and their surgeons when making decisions about surgical treatment of stress urinary incontinence.