Optimization is required when using linked hospital and laboratory data to investigate respiratory infections

Record linkage study of the pathogen-specific burden of respiratory viruses in children

Background

Reliance on hospital discharge diagnosis codes alone will likely underestimate the burden of respiratory viruses.

Objectives

To describe the epidemiology of respiratory viruses more accurately, we used record linkage to examine data relating to all children hospitalized in Western Australia between 2000 and 2012.

Patients/Methods

We extracted hospital, infectious disease notification and laboratory data of a cohort of children born in Western Australia between 1996 and 2012. Laboratory records of respiratory specimens collected within 48 hours of admission were linked to hospitalization records. We calculated the frequency and rates of virus detection. To identify groups where under‐ascertainment for respiratory viruses was greatest, we used logistic regression to determine factors associated with failure to test.

Results and conclusions

Nine percentage of 484 992 admissions linked to a laboratory record for respiratory virus testing. While 62% (n = 26 893) of laboratory‐confirmed admissions received respiratory infection diagnosis codes, 38% (n = 16 734) had other diagnoses, notably viral infection of unspecified sites. Of those tested, incidence rates were highest for respiratory syncytial virus (247 per 100 000 child‐years) followed by parainfluenza (63 per 100 000 child‐years). Admissions among older children and those without a respiratory diagnosis were associated with failure to test for respiratory viruses. Linked data can significantly enhance diagnostic codes when estimating the true burden of disease. In contrast to current emphasis on influenza, respiratory syncytial virus and parainfluenza were the most common viral pathogens among hospitalized children. By characterizing those failing to be tested, we can begin to quantify the under‐ascertainment of respiratory viruses.

Using record linkage to validate notification and laboratory data for a more accurate assessment of notifiable infectious diseases

BACKGROUND

Infectious disease burden is commonly assessed using notification data. Using retrospective record linkage in Western Australia, we described how well notification data captures laboratory detections of influenza, pertussis and invasive pneumococcal disease (IPD).

METHODS

We linked data from the Western Australian Notifiable Infectious Diseases Database (WANIDD) and the PathWest Laboratory Database (PathWest) pertaining to the Triple I birth cohort, born in Western Australia in 1996-2012. These were combined to calculate the number of unique cases captured in each dataset alone or in both datasets. To assess the impact of under-ascertainment, we compared incidence rates calculated using WANIDD data alone and using combined data.

RESULTS

Overall, there were 5550 influenza, 513 IPD (2001-2012) and 4434 pertussis cases (2000-2012). Approximately 2% of pertussis and IPD cases and 7% of influenza cases were solely recorded in PathWest. Notification of influenza and pertussis cases to WANIDD improved over time. Overall incidence rates of influenza in children aged <5 years using both datasets was 10% higher than using WANIDD data alone (IRR = 1.1, 95% CI = 1.1-1.2).

CONCLUSIONS

This is the first time WANIDD data have been validated against routinely collected laboratory data. We anticipated all cases would be captured in WANIDD but found additional laboratory-confirmed cases that were not notified. Studies investigating pathogen-specific infectious disease would benefit from using multiple data sources.

Using record linkage to examine testing patterns for respiratory viruses among children born in Western Australia

Changes in respiratory pathogen testing can affect disease burden estimates. Using linked data, we describe changes in respiratory virus testing among children born in Western Australia in 1996-2012. We extracted data on respiratory specimens from these children from birth to age 9 years. We estimated testing rates by age, year, Aboriginal status and geographical location. Predictors of testing among children hospitalised at least once before their 10th birthday were identified using logistic regression. We compared detection methods for respiratory viruses from nasal/nasopharyngeal (NP) specimens by age and year. Of 83 199 virology testing records in 2000-2012, 80% were nasal/NP specimens. Infants aged <1 month had the highest testing rates. Testing rates in all children increased over the study period with considerable yearly fluctuations. Among hospitalised children, premature children <32 weeks gestation had over three times the odds of being tested (95% CI 3·47-4·13) than those born at term. Testing using molecular methods increased from 5% to 87% over the study period. Proportion of positive samples increased from 36·3% to 44·4% (P < 0·01); this change was greatest in children aged 2-9 years. These findings will assist in interpreting results from future epidemiology studies assessing the pathogen-specific burden of disease.

Characterizing the risk of respiratory syncytial virus in infants with older siblings: a population-based birth cohort study

From a population-based birth cohort of 245 249 children born in Western Australia during 1996-2005, we used linkage of laboratory and birth record datasets to obtain data including all respiratory syncytial virus (RSV) detections during infancy from a subcohort of 87 981 singleton children born in the Perth metropolitan area from 2000 to 2004. Using log binomial regression, we found that the risk of infant RSV detection increases with the number of older siblings, with those having ⩾3 older siblings experiencing almost three times the risk (relative risk 2·83, 95% confidence interval 2·46-3·26) of firstborn children. We estimate that 45% of the RSV detections in our subcohort were attributable to infection from an older sibling. The sibling effect was significantly higher for those infants who were younger during the season of peak risk (winter) than those who were older. Although older siblings were present in our cohort, they had very few RSV detections which could be temporally linked to an infant's infection. We conclude that RSV infection in older children leads to less severe symptoms but is nevertheless an important source of infant infection. Our results lend support to a vaccination strategy which includes family members in order to provide maximum protection for newborn babies.

The Role of Clinical Virology Laboratory and the Clinical Virology Laboratorian in Ensuring Effective Surveillance for Influenza and Other Respiratory Viruses: Points to Consider and Pitfalls to Avoid

Influenza and respiratory viruses have a global impact on public health. Clinical virology laboratories and laboratorians play an important role in not only the diagnosis but also the surveillance of these pathogens. Surveillance for influenza and other respiratory pathogens is important, as it informs public health decision making in terms of influenza vaccine and antiviral effectiveness, informs clinicians and public health practitioners about the pathogenicity of specific viral strains, guides clinical practice, and supports laboratory panning activities. Key background issues include the following: the fact that the laboratory is only one of several data providers to a surveillance system, the biologic nature of influenza and respiratory viruses and the laboratory needs to keep up to date on the diagnosis of these agents, the need for laboratorians to be involved in case definition development, the impact of push and pull data flow models on laboratory resources, and the fact that laboratories may be asked to provide more than just test results to surveillance programs. This review also identifies some key issues or questions that arise during the pre-analytic, analytic, and post-analytic phases that could impact on the ability of the laboratory to link to surveillance programs. Finally, issues surrounding virus characterization programs and how they link to surveillance programs are identified and discussed.