The Canadian province of Quebec has prevalence rates of cystic fibrosis (CF) that are among the highest in the world, with an average of 1 in 2,500 newborns (
1;
http://www.cysticfibrosis.ca), and up to 1 in 902 in the region of Saguenay–Lac-Saint-Jean (
2–4). Still, unlike in other provinces (
5–7), molecular epidemiology data are not available for the most common respiratory pathogen associated with this disease,
Pseudomonas aeruginosa (
8). A recent national molecular typing study included isolates from two clinics in Montreal, the largest city in Quebec (
9), but analyses were not directed toward investigating each province individually. Here, we sought to describe the population structure of
P. aeruginosa in Quebec to improve the epidemiological basis for infection control and patient management. We were mainly interested in the prevalences of epidemic strains, which have been reported in the Prairie Provinces and Ontario and are generally associated with worse clinical prognoses (
7,
9,
10).
We selected all sequenced Quebec isolates from the International
Pseudomonas Consortium Database (
http://ipcd.ibis.ulaval.ca) (
11) and 11 reference strains (Data Set S1). The final data set of 298 genomes comprised isolates from five CF clinics scattered across southern Quebec, as well as from environmental sources. We performed a core genome phylogenetic analysis with SaturnV (
https://github.com/ejfresch/saturnV) (
12), and produced
in silico molecular typing using Short Read Sequence Typing for Bacterial Pathogens (SRST2) v0.2.0 (
13).
No geographic structure emerged from the five CF clinics represented (
Fig. 1). However, multiple clones were shared among two or more clinics. Based on molecular sequence typing (
14;
https://pubmlst.org/), the most pervasive clones (sequence type 17 [ST17], ST155, and ST179), including well-characterized clone C (
15), are all widely distributed around the world and likely reflect environmental abundance rather than patient-to-patient transmission (
16). This is further supported by the presence of environmental isolates, which incidentally came from hospital sinks (Data Set S1), within ST155 and ST179. Encouragingly, not a single isolate in this study corresponded to epidemic strains identified in Ontario (Liverpool epidemic strain and epidemic strain B [
7]) or the Prairies (Prairie epidemic strain [PES; ST192] [
5]). It is not clear whether this is due to differences in infection control, human population demographics, or environmental
P. aeruginosa populations among Canadian provinces. Australian studies provide evidence that, except for known epidemic strains (
17), CF strains are a sample of the environmental
P. aeruginosa population (
18,
19). More in-depth analyses are forthcoming for CF clinics where genomic data can be associated with patient identifier (ID), age, study time point, etc. Unfortunately, this type of information, although essential to direct further investigation of genomic data, proved extremely difficult to obtain.
Heterogeneity in
P. aeruginosa population structure across Canada alone emphasizes the need for more customized patient care in the context of CF respiratory infections. This, of course, only adds to the great variability in antimicrobial resistance among
P. aeruginosa isolates (
11,
20). Canadian molecular epidemiology of
P. aeruginosa may benefit from similar nationwide data from the United States. But, as mentioned in a recent review (
16), there is a void to be filled in the literature in this regard.