Pertussis is a highly contagious respiratory tract infection caused by the gram negative bacterium Bordetella pertussis or less commonly by B. parapertussis . The disease is classically characterized by three stages : (i) a nonspecific catarrhal stage; (ii) a subsequent spasmodic stage involves the characteristic paroxysmal cough with inspiratory whoop, and lasting two to eight weeks; and (iii) a convalescent phase . The pathogenesis of the disease is not fully understood but involves both direct toxic effects of bacterial endo- and exotoxins, and also indirect effects of toxins on the host immune response, including a reduction in lymphocyte circulation [1, 4, 5]. While children and adults of any age may develop pertussis, severe sequelae (including encephalopathy and pneumonia) are most common in infants aged < 6 months [6–8]. The incidence of pertussis has decreased dramatically in wealthy countries since the implementation of widespread vaccination programs (e.g., from ~170/100 000 in the 1930s to fewer than 20/100 000 in the 1970s in Canada) pertussis is still an important source of mortality worldwide. The disease remains one of the leading causes of infant mortality,[6–8] and causes approximately 300 000 deaths in 50 million cases per year [7, 10].
In high income countries, elimination of pertussis has not occurred despite immunization, and apparent disease incidence has increased in recent decades [3, 6, 11]. Recent outbreaks, some with infant deaths, in Nottingham and Derby (England) , California , Ireland  and New South Wales, Australia  have been a source of considerable concern. It has been suggested, however, that increasingly sensitive PCR methods for the diagnosis of pertussis may have contributed to apparent, rather than real, increases in disease incidence [7, 9, 16–18]. Other factors invoked to explain pertussis increases in countries with high rates of immunization include genetic changes in the pathogen, [19, 20] waning immunity following both vaccination and infection,[1, 3, 7] reduced potency of vaccines following the switch to an acellular vaccine,[21, 22] more widespread laboratory testing due to increased awareness of the disease in adults, and lack of immunity or waning immunity in specific age cohorts . The role played by young adolescents and adults in disease spread, and the recognition of a gradual loss in immunity after natural infection or vaccination, have led several countries to advocate booster dosing of pertussis vaccine for young teens and adults [16, 25–27].
Surveillance of pertussis is complicated by differing manifestations of the disease in infants, adolescents and adults , with the disease presenting as apnea or poor feeding in infants [2, 12], whereas adults and adolescents often present only with prolonged cough , or minimal symptomatology . Nasopharyngeal swab culture is the historical gold-standard diagnostic modality for pertussis, but is sensitive only early in the infection, with a sensitivity < 50% after three weeks of illness or cough . Serology is even less sensitive but can be used to diagnose pertussis late in the course of infection . In recent years, the sensitivity and rapidity of polymerase chain reaction (PCR) have brought this testing modality into widespread use, even if testing is not well-standardized between laboratories [8, 16–18]. The World Health Organization's (WHO) most recent guidelines define a pertussis case as clinically confirmed (without laboratory confirmation) or laboratory confirmed (and meeting the clinical case definition). Prior to 2008, Canadian case definitions permitted the classification of a case of pertussis as "confirmed" based on a positive laboratory test (including PCR) alone [29, 30].
The Greater Toronto Area (GTA) is Canada's largest metropolitan area. All pertussis testing in the GTA is performed in only two laboratories (the Public Health Laboratory--Toronto (PHLT) and the laboratory of the Hospital for Sick Children (HSC), which share strong historical linkages, making it possible to evaluate not only case counts (according to pre-2008 Canadian case definitions) via laboratory data, but also to evaluate the impact that testing volume and testing practice may have had on measured disease epidemiology. The region experienced a documented outbreak of pertussis in 2005-2006 [7, 9, 16], and experienced a prolonged increase in pertussis incidence in association with the introduction of novel testing methodologies. Our objectives were to evaluate changes in pertussis epidemiology in this large urban setting and to define the relative contributions to disease incidence that may be attributable to laboratory testing submission volumes, changing testing technologies and underlying disease epidemiology.