Spatial analysis of community-onset Staphylococcus aureus bacteremia in Queensland, Australia

Linking administrative data sets of inpatient infectious diseases diagnoses in far North Queensland: a cohort profile

PURPOSE

To design a linked hospital database using administrative and clinical information to describe associations that predict infectious diseases outcomes, including long-term mortality.

PARTICIPANTS

A retrospective cohort of Townsville Hospital inpatients discharged with an International Classification of Diseases and Related Health Problems 10th Revision Australian Modification code for an infectious disease between 1 January 2006 and 31 December 2016 was assembled. This used linked anonymised data from: hospital administrative sources, diagnostic pathology, pharmacy dispensing, public health and the National Death Registry. A Created Study ID was used as the central identifier to provide associations between the cohort patients and the subsets of granular data which were processed into a relational database. A web-based interface was constructed to allow data extraction and evaluation to be performed using editable Structured Query Language.

FINDINGS TO DATE

The database has linked information on 41 367 patients with 378 487 admissions and 1 869 239 diagnostic/procedure codes. Scripts used to create the database contents generated over 24 000 000 database rows from the supplied data. Nearly 15% of the cohort was identified as Aboriginal or Torres Strait Islanders. Invasive staphylococcal, pneumococcal and Group A streptococcal infections and influenza were common in this cohort. The most common comorbidities were smoking (43.95%), diabetes (24.73%), chronic renal disease (17.93%), cancer (16.45%) and chronic pulmonary disease (12.42%). Mortality over the 11-year period was 20%.

FUTURE PLANS

This complex relational database reutilising hospital information describes a cohort from a single tropical Australian hospital of inpatients with infectious diseases. In future analyses, we plan to explore analyses of risks, clinical outcomes, healthcare costs and antimicrobial side effects in site and organism specific infections.

Incidence of community onset MRSA in Australia: least reported where it is Most prevalent

Background

This is the first review of literature and synthesis of data on community onset methicillin resistant Staphylococcus aureus (CO-MRSA) infections in Australia. Incidence of CO-MRSA varies considerably in Australia, depending on geographic and demographic factors.

Methods

Data for the rates of MRSA infections were collected from articles identified using PubMed, Scopus, the grey literature and data from State and Federal Government Surveillance Systems. We synthesized data and developed a framework for how data was selected, collated, linked, organized and interpreted.

Results

The results of our literature search demonstrates considerable gaps in the reporting of CO-MRSA in Australia. Consequently, total incidences were under reported; however the available data suggests the incidence varied between 44 (Tasmania) and 388 (southern Northern Territory) cases per 100,000 person years. Hospitalised cases of CO-MRSA varied between 3.8 (regional Victoria) and 329 (southern Northern Territory). Taking the median percentage of infections by site for all regions available, skin and soft tissue infections (SSTIs) consisted of 56% of hospitalized CO-MRSA, compared with bacteremias, which represented 14%. No region had a complete data set of CO-MRSA infections treated in out-patient settings and so incidences were underestimates. Nevertheless, estimates of the incidence of CO-MRSA treated outside hospitals varied between 11.3 (Melbourne) and 285 (Northern Territory) per 100,000 person-years. These infections were chiefly SSTIs, although urinary tract infections were also noted.

Incidences of CO-MRSA blood-stream infections and outpatient skin and soft tissue infections have been increasing with time, except in Tasmania. CO-MRSA is observed to affect people living in remote areas and areas of socioeconomic disadvantage disproportionately.

Conclusions

We generated the first estimates of the incidence of CO-MRSA infections in Australia and identified stark regional differences in the nature and frequency of infections. Critically, we demonstrate that there has been a lack of consistency in reporting CO-MRSA and a general dearth of data. The only government in Australia that requires reporting of CO-MRSA is the Tasmanian, where the infection was least prevalent. Some regions of Australia have very high incidences of CO-MRSA. To improve surveillance and inform effective interventions, we recommend a standardized national reporting system in Australia that reports infections at a range of infection sites, has broad geographic coverage and consistent use of terminology. We have identified limitations in the available data that hinder understanding the prevalence of CO-MRSA.

Electronic supplementary material

The online version of this article (10.1186/s13756-019-0485-7) contains supplementary material, which is available to authorized users.