Population-based genomic surveillance of Pseudomonas aeruginosa causing bloodstream infections in a large Canadian health region.

PURPOSE: Population-based surveillance was undertaken to determine clinical factors, susceptibility patterns, and incidence rates (IR) of Pseudomonas aeruginosa causing bloodstream infections (BSIs) in a Canadian region (2010-2018). METHODS: We combined clinical data with genomics to characterize P. aeruginosa (BSIs) (n = 167) in a well-defined Canadian (Calgary) human population over a 9-year period (2010-2018). RESULTS: The annual population IR per 100,000 patient years increased from 3.4/100,000 in 2010 to 5.9/100,000 in 2018, with the highest IRs in elderly males from the hospital setting. Over a quarter of patients presented with febrile neutropenia, followed by urinary tract infections and pneumonia. Antimicrobial resistance (AMR) rates and determinants were rare. The P. aeruginosa population was polyclonal consisting of three dominant sequence types (STs), namely ST244, ST111, and ST17. Antimicrobial-susceptible ST244 was the most common clone and belonged to three clades (A, B, C). The ST244 IR/100,000 increased over time due to the expansion of clade C. Multidrug-resistant ST111 was the second most common clone and IR/100,000 decreased over time. ST111 belonged to three clades (A, B, C) with clade C containing blaVIM-2. Different serotypes were linked to various STs. The IR/100,000 of P. aeruginosa that belonged to serotypes O6 increased significantly over time. CONCLUSION: An effective multivalent vaccine consisting of five serotypes (O1, O3, O5, O6, O11) would confer protection to > 70% of Calgary residents with P. aeruginosa BSIs. This study has provided a unique perspective of the population dynamics over time of P. aeruginosa STs, clades, and serotypes responsible for BSIs.

Population-based surveillance of Enterobacter cloacae complex causing blood stream infections in a centralized Canadian region.

Active population-based surveillance determined clinical factors, susceptibility patterns, incidence rates (IR), and genomics among Enterobacter cloacae complex (n = 154) causing blood stream infections in a centralized Canadian region (2015-2017). The annual population IR was 1.2/100,000 (95% CI 0.9-16) in 2015, 1.4/100,000 (95% CI 1.1-1.9) in 2016, and 1.5/100,000 (95% CI 1.2-2.0) in 2017, affecting mainly elderly males with underlying comorbid conditions in the hospital setting. E. cloacae complex was dominated by polyclonal subspecies (i.e., E. hormaechei subsp. steigerwaltii, subsp. hoffmanni and subsp. xiangfangesis). Antimicrobial resistant determinants were rare. This study provided novel information about Enterobacter genomics in a well-defined human population.

Population-based epidemiology of Escherichia coli ST1193 causing blood stream infections in a centralized Canadian region.

Escherichia coli ST1193 is an emerging global clone associated with fluoroquinolone resistance. A population-based study described genomics, clinical factors, susceptibility patterns, and incidence rates of ST1193 (n = 69) causing incident blood stream infections in a centralized Canadian region 2016-18. ST1193 was responsible for community-acquired upper urinary tract infections among the elderly. The incidence rate (IR) per 100,000 person-years among Calgary residents increased from 1.0 (95%confidence interval [95%CI] 0.7-1.5) in 2016, to 1.7 (95%CI 1.3-2.3) in 2018 (p = 0.05). This was mainly due to the significant increase of ST1193 blood stream infections among female long-term care (LTC) residents. ST1193 IR with blaCTX-Ms was 3.18 times higher in 2018 than in 2016 (CI 95% 0.98-13.49). We identified a ST1193 isolate with only a parC S80I mutation that is different from previously published data. The population-based study identified a significant increase over a 2-year period of E. coli ST1193 blood stream infections among elderly females residing in LTC centers. There was also a notable increase of ST1193 with bla CTX-Ms in 2018. The rapid emergence of ST1193 is concerning and adding to the public health burden of multidrug resistant E. coli blood stream infections in Calgary.

Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006-20161.

Global expansion of antimicrobial drug-resistant Escherichia coli sequence type (ST) 131 is unrivaled among human bacteria. Understanding trends among ST131 clades will help with designing prevention strategies. We screened E. coli from blood samples (n = 1,784) obtained in Calgary, Alberta, Canada, during 2006, 2012, and 2016 by PCR for ST131 and positive samples (n = 344) underwent whole-genome sequencing. The incidence rate per 100,000 residents increased from 4.91 during 2006 to 12.35 during 2012 and 10.12 during 2016. ST131 belonged to clades A (10%), B (9%), and C (81%). Clades C1-nonM27 and B were common during 2006, and C2 containing blaCTX-M-15, C1-M27 containing blaCTX-M-27, and A were responsible for the increase of ST131 during 2012 and 2016. C2 was the most antimicrobial drug-resistant subclade and increased exponentially over time. Eradicating ST131, more specifically the C2 subclade, will lead to considerable public health benefits for persons in Calgary.