Laboratory diagnosed microbial infection in English UK Biobank participants in comparison to the general population

Understanding the genetic and environmental risk factors for serious bacterial infections in ageing populations remains incomplete. Utilising the UK Biobank (UKB), a prospective cohort study of 500,000 adults aged 40-69 years at recruitment (2006-2010), can help address this. Partial implementation of such a system helped groups around the world make rapid progress understanding risk factors for SARS-CoV-2 infection and COVID-19, with insights appearing as early as May 2020. In principle, such approaches could also to be used for bacterial isolations. Here we report feasibility testing of linking an England-wide dataset of microbial reporting to UKB participants, to enable characterisation of microbial infections within the UKB Cohort. These records pertain mainly to bacterial isolations; SARS-CoV-2 isolations were not included. Microbiological infections occurring in patients in England, as recorded in the Public Health England second generation surveillance system (SGSS), were linked to UKB participants using pseudonymised identifiers. By January 2015, ascertainment of laboratory reports from UKB participants by SGSS was estimated at 98%. 4.5% of English UKB participants had a positive microbiological isolate in 2015. Half of UKB isolates came from 12 laboratories, and 70% from 21 laboratories. Incidence rate ratios for microbial isolation, which is indicative of serious infection, from the UKB cohort relative to the comparably aged general population ranged from 0.6 to 1, compatible with the previously described healthy participant bias in UKB. Data on microbial isolations can be linked to UKB participants from January 2015 onwards. This linked data would offer new opportunities for research into the role of bacterial agents on health and disease in middle to-old age.

Epidemiology of carbapenemase-producing Enterobacterales in England, May 2015-March 2019: national enhanced surveillance findings and approach

Background

In response to increasing numbers of carbapenemase-producing Enterobacterales (CPE) in England, Public Health England (PHE) launched an electronic reporting system (ERS) for the enhanced surveillance of carbapenemase-producing Gram-negative bacteria. Our study aimed to describe system engagement and the epidemiology of CPE in England.

Methods

Engagement with the ERS was assessed by calculating the proportion of referrals submitted this system. ERS data were extracted and cases defined as patients with CPE isolated from a screening or clinical specimen in England between 1^st May 2015 to 31^st March 2019. Descriptive summary statistics for each variable were prepared.

Results

The ERS processed 12,656 suspected CPE reports. Uptake of the ERS by local microbiology laboratories varied, with approximately 70% of referrals made via the ERS by April 2016; this steadily decreased after March 2018. Six-thousand eight-hundred and fifty-seven cases were included in the analysis. Most cases were from colonised patients (80.6%) rather than infected, and the majority were inpatients in acute hospital settings (87.3%). Carbapenemases were most frequently detected in Klebsiella pneumoniae (39.1%) and Escherichia coli (30.3%). The most frequently identified carbapenemase families were OXA-48-like (45.1%) and KPC (26.4%). Enhanced data variables were poorly completed.

Conclusions

The ERS has provided some insight into the epidemiology of CPE in England. An increasing number of routine diagnostic laboratories have introduced methods to routinely identify acquired carbapenemases and PHE has modified its approach to ensure robust surveillance, which is an essential aspect of an effective response to prevent and control the spread of CPE.

Effect of general practice characteristics and antibiotic prescribing on Escherichia coli antibiotic non-susceptibility in the West Midlands region of England: a 4 year ecological study

Objectives

To assess the effect of general practice characteristics and antibiotic prescribing on the number of non-susceptible Escherichia coli isolated from urine specimens submitted from community settings, we undertook an ecological study of the general practice population in the West Midlands.

Methods

Descriptive analysis and multilevel modelling of temporal trends in antibiotic prescribing and non-susceptibility of E. coli urine isolates to a range of antibiotics prescribed in the community over a 4 year period.

Results

Nine of the 16 antibiotic prescribing/non-susceptibility combinations demonstrated a significant statistical linear correlation with non-susceptibility either for prescribing in a quarter or for prescribing within the previous 12 months. The magnitude of the effect varied, from a 0.3% increase in the odds of non-susceptibility to ampicillin/amoxicillin (when prescribing ampicillin/amoxicillin) to a 6.3% increase in the odds of non-susceptibility to nitrofurantoin (when prescribing nitrofurantoin) for an increase of 50 DDDs per 1000 practice population within a quarter (equivalent to ∼10 courses of antibiotics). In all 16 models, single-handed general practices were shown to have a significant association with increased numbers of non-susceptible E. coli urine isolates (adjusted ORs 1.083-1.657). Increased prescribing of ampicillin/amoxicillin in winter periods was associated with increased non-susceptibility of E. coli isolated from urine specimens.

Conclusions

Small increases in antibiotic prescribing in individual general practices reduce the number of susceptible bacteria in the practice population. To maintain the effectiveness of available treatment, antibiotic stewardship should be encouraged and supported within each practice.

An evaluation of the electronic reporting system for the enhanced surveillance of carbapenemase-producing Gram-negative bacteria in England

BACKGROUND

An electronic reporting system (ERS) for the enhanced surveillance of carbapenemase-producing Gram-negative bacteria (CPGNB) was launched by Public Health England in May 2015.

AIM

This evaluation aimed to assess uptake, timeliness and completeness of data provided and explore potential barriers and facilitators to adopting the system.

METHODS

The evaluation comprised a retrospective analysis of surveillance data and semi-structured interviews with ERS users.

FINDINGS

The proportion of organisms referred for investigation of carbapenem resistance via ERS increased over the first 12 months post-implementation from 35% to 73%; uptake varied widely across regions of England. Completeness of enhanced data fields was poor in 78% of submitted isolates. The median number of days to report confirmatory test results via ERS was 1 day for the regional service and nine days for the national reference laboratory, which additionally conducts phenotypic testing to confirm carbapenemase negativity. Hindrances to ERS utility included: a lack of designated, ongoing resource for system maintenance, technical support and development; uncertainty about how and when to use ERS and workload. Incomplete data prevented gaining a better understanding of important risk factors and transmission routes of CPGNB in England.

CONCLUSION

The ERS is the only surveillance system in England with the potential to gather intelligence on important risk factors for CPGNB to inform public health measures to control their spread. Although the ERS captures more information on CPGNB than other surveillance systems, timeliness and completeness of the enhanced data require substantial improvements in order to deliver the desired health benefits.

Impact of long-term care facility residence on the antibiotic resistance of urinary tract Escherichia coli and Klebsiella

Background

Long-term care facilities (LTCFs) are thought to be important reservoirs of antimicrobial-resistant (AMR) bacteria; however, there is no routine surveillance of resistance in LTCF residents, or large population-based studies comparing AMR in LTCFs with the community, so the relative burden of AMR in LTCFs remains unknown.

Objectives

To compare the frequency of antibiotic resistance of urinary tract bacteria from residents of LTCFs for the elderly and adults aged 70 years or older living in the community.

Methods

Positive urine specimens reported to any diagnostic microbiology laboratory in the West Midlands region (England) from 1 April 2010 to 31 March 2014 collected from individuals aged 70 years or older were analysed. The resistance of Escherichia coli and Klebsiella to trimethoprim, nitrofurantoin, third-generation cephalosporins and ciprofloxacin and the rate of laboratory-confirmed E. coli and Klebsiella urinary tract infection (UTI) were assessed in LTCF residents and in the community.

Results

LTCF residents had a laboratory-confirmed E. coli and Klebsiella UTI rate of 21 per 100 person years compared with 8 per 100 person years in the elderly living in the community [rate ratio (RR)=2.66, 95% CI = 2.58-2.73] and a higher rate of developing E. coli and Klebsiella UTIs caused by bacteria resistant to trimethoprim (RR = 4.41, 95% CI = 4.25-4.57), nitrofurantoin (RR = 4.38, 95% CI = 3.98-4.83), ciprofloxacin (RR = 5.18, 95% CI = 4.82-5.57) and third-generation cephalosporins (RR = 4.49, 95% CI = 4.08-4.94).

Conclusions

Residents of LTCFs for the elderly had more than double the rate of E. coli and Klebsiella UTI and more than four times the rate of E. coli and Klebsiella UTI caused by antibiotic-resistant bacteria compared with those living in the community.

Use of antimicrobial resistance information and prescribing guidance for management of urinary tract infections: survey of general practitioners in the West Midlands

BACKGROUND

There is a marked variation in both antibiotic prescribing practice and urine sampling rates for diagnostic microbiology across general practices in England. To help understand factors driving this variation, we undertook a survey in 2012/13 to determine sampling protocols and antibiotic formularies used by general practitioners (GPs) for managing urinary tract infections (UTIs) in the West Midlands region of England.

METHOD

Cross-sectional survey of all eligible general practices in the West Midlands region of England undertaken in November 2012. GPs were invited to complete an online survey questionnaire to gather information on policies used within the practice for urine sampling for microbiological examination, and the source of antibiotic formularies used to guide treatment of UTIs. The questionnaire also gathered information on how they would manage five hypothetical clinical scenarios encountered in the community.

RESULTS

The response rate was 11.3 % (409/3635 GPs), equivalent to a practice response rate of 26 % (248/950). Only 50 % of GPs reported having a practice policy for urine sampling. Although there was good agreement from GPs regarding collecting specimens in scenarios symbolising treatment failure (98 %), UTI in an adult male (98 %) and asymptomatic UTI in pregnancy (97 %), there was variation in GPs requesting a specimen for the scenarios involving a suspected uncomplicated urinary tract infection (UTI) and an asymptomatic catheterised elderly patient; with 40 and 38 % respectively indicating they would collect a specimen for microbiological examination.

CONCLUSION

Standardised evidence based clinical management policies and antibiotic formularies for GPs should be readily available. This will promote the rational use of diagnostic microbiology services, improve antimicrobial stewardship and aid the interpretation of ongoing antimicrobial resistance surveillance.

Surveillance of antibiotic susceptibility of urinary tract pathogens for a population of 5.6 million over 4 years

OBJECTIVES

To retrospectively analyse routine susceptibility testing data to describe antimicrobial non-susceptibility trends in isolates of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa from urine samples in a population of 5.6 million people over a 4 year period.

METHODS

De-duplicated laboratory data submitted to the AmSurv surveillance system from the West Midlands region of England and results of submissions to the Antimicrobial Resistance and Healthcare Associated Infections Reference Unit were extracted for the period 2010-13. Descriptive analysis of the non-susceptibility of selected Gram-negative organisms to key antibiotics, as recommended for monitoring in the UK Five Year Antimicrobial Resistance Strategy, was undertaken.

RESULTS

During the study period, there were 431 461 reports for E. coli, 23 786 for K. pneumoniae and 6985 for P. aeruginosa from urine specimens. These represented 61%, 3% and 1%, respectively, of all organisms isolated from urine specimens. There was a linear increase in non-susceptibility to third-generation cephalosporins for E. coli and K. pneumoniae, and to ciprofloxacin for E. coli, in specimens from both hospital and community settings (P < 0.001). The proportions of E. coli and K. pneumoniae reported non-susceptible to meropenem and/or imipenem remained low during the study period, with no evidence of linear trend (P ≥ 0.05).

CONCLUSIONS

Automated antimicrobial resistance surveillance enabled, for the first time in England, the systematic monitoring of resistance in bacteria responsible for urinary tract infections in a defined population, and thereby provided a representative indication of the burden of resistance in Gram-negative bacteria in hospital and community settings.

AmWeb: a novel interactive web tool for antimicrobial resistance surveillance, applicable to both community and hospital patients

BACKGROUND

Antimicrobial resistance (AMR) is recognized as one of the most significant threats to human health. Local and regional AMR surveillance enables the monitoring of temporal changes in susceptibility to antibiotics and can provide prescribing guidance to healthcare providers to improve patient management and help slow the spread of antibiotic resistance in the community. There is currently a paucity of routine community-level AMR surveillance information.

METHODS

The HPA in England sponsored the development of an AMR surveillance system (AmSurv) to collate local laboratory reports. In the West Midlands region of England, routine reporting of AMR data has been established via the AmSurv system from all diagnostic microbiology laboratories. The HPA Regional Epidemiology Unit developed a web-enabled database application (AmWeb) to provide microbiologists, pharmacists and other stakeholders with timely access to AMR data using user-configurable reporting tools.

RESULTS

AmWeb was launched in the West Midlands in January 2012 and is used by microbiologists and pharmacists to monitor resistance profiles, perform local benchmarking and compile data for infection control reports. AmWeb is now being rolled out to all English regions.

CONCLUSIONS

It is expected that AmWeb will become a valuable tool for monitoring the threat from newly emerging or currently circulating resistant organisms and helping antibiotic prescribers to select the best treatment options for their patients.