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Background Widespread testing for chlamydia is expected to result in a reduction in prevalence. In 2008, coverage indicators introduced by the Department of Health (DH) required collection and submission of all tests performed outside of genitourinary medicine clinics. No mechanism existed to collect community-based tests conducted outside of the National Chlamydia Screening Programme. The Health Protection Agency Regional Epidemiology Unit in the East of England (EoE) set up a new system to routinely collect and submit these tests on behalf of the regional Primary Care Organizations (PCOs). Methods Testing data were requested from all laboratories commissioned to undertake chlamydia testing by EoE PCOs. Data were imported into a bespoke Structured Query Language server database and automated data processing routines were run. Data fulfilling national criteria were submitted for inclusion in the DH indicators. Results High-quality data were submitted to set deadlines with minimum impact on laboratories. Completeness of data variables varied by laboratory and by variable type. After complex data processing, 96% of laboratory reported tests in the 15–24 year age range were eligible for submission. Conclusions This centralized method of data collection provides high-quality data, allowing for further analysis, which can be used to inform improvements in health care. These methods could be transferred to any of the hundreds of organisms for which similar laboratory data exist. [ABSTRACT FROM PUBLISHER]

Background: The burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures., Methods: In this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases., Findings: Between March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting., Interpretation: We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings., Funding: COVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute., (Copyright © 2020 Elsevier Ltd. All rights reserved.)