Biochemical Phenotypes to Discriminate Microbial Subpopulations and Improve Outbreak Detection

Background: Clinical microbiology laboratories worldwide constitute an invaluable resource for monitoring emerging threats and the spread of antimicrobial resistance. We studied the growing number of biochemical tests routinely performed on clinical isolates to explore their value as epidemiological markers. Methodology/Principal Findings Microbiology laboratory results from January 2009 through December 2011 from a 793-bed hospital stored in WHONET were examined. Variables included patient location, collection date, organism, and 47 biochemical and 17 antimicrobial susceptibility test results reported by Vitek 2. To identify biochemical tests that were particularly valuable (stable with repeat testing, but good variability across the species) or problematic (inconsistent results with repeat testing), three types of variance analyses were performed on isolates of K. pneumonia: descriptive analysis of discordant biochemical results in same-day isolates, an average within-patient variance index, and generalized linear mixed model variance component analysis. Results: 4,200 isolates of K. pneumoniae were identified from 2,485 patients, 32% of whom had multiple isolates. The first two variance analyses highlighted SUCT, TyrA, GlyA, and GGT as “nuisance” biochemicals for which discordant within-patient test results impacted a high proportion of patient results, while dTAG had relatively good within-patient stability with good heterogeneity across the species. Variance component analyses confirmed the relative stability of dTAG, and identified additional biochemicals such as PHOS with a large between patient to within patient variance ratio. A reduced subset of biochemicals improved the robustness of strain definition for carbapenem-resistant K. pneumoniae. Surveillance analyses suggest that the reduced biochemical profile could improve the timeliness and specificity of outbreak detection algorithms. Conclusions: The statistical approaches explored can improve the robust recognition of microbial subpopulations with routinely available biochemical test results, of value in the timely detection of outbreak clones and evolutionarily important genetic events

Nosocomial Methicillin-resistant Staphylococcus aureus: Acquisition, Infection and Decolonization

Methicillin-resistant Staphylococcus aureus (MRSA), an antibiotic-resistant bacteria, is often carried asymptomatically, but can cause severe disease. In this thesis, I present three retrospective cohort studies conducted in Toronto, Canada, which examine risk factors for infection or acquisition. In a study of 1,125 adult MRSA carriers at a tertiary hospital, risk factors for subsequent MRSA-positive clinically-indicated specimens were recent identification of carriage, older age, male gender, nosocomial acquisition, carriage detection in ICU, and underlying liver conditions. In a study of pairs of patients at two hospitals who shared a room for ≥48 hours, each pair included a MRSA-index case and a patient at risk of acquisition. Fluoroquinolone receipt by either patient increased the probability of MRSA transmission. Nearly half of identified acquisitions in the year following shared occupancy were unrelated to the MRSA-index case. In a study of 62,552 patient admissions, receipt of fluoroquinolone(s) and exposure to high MRSA colonization pressure in the prior week were significant risk factors for MRSA acquisition. The results of the cohort studies suggest that MRSA control should involve consideration of antibiotic exposures among those colonized and those at risk of acquisition. Antimicrobial stewardship and interventions that identify carriers could reduce disease burden.Ph.D.2020-11-19 00:00:0

Effectiveness of an outbreak dose of mumps-containing vaccine in two First Nations communities in Northern Ontario, Canada

Between 18 Dec 2017 and 27 June 2018, a mumps outbreak occurred in two Canadian Indigenous communities. An outbreak dose of mumps-containing vaccine was offered as part of control measures. We conducted a cohort study and survival analysis to describe the outbreak and evaluate the outbreak dose, extracting vaccination information on all community members (n = 3,135) from vaccination records. There were 70 mumps cases; 56% had received two pre-outbreak vaccine doses. Those who received a pre-outbreak dose more distantly had higher rates of mumps compared to those with more recent doses (adjusted hazard ratio = 3.4 (95%CI: 0.7–20.6) for receipt >20 years before vs. receipt ≤3 years). During the outbreak, 33% (1,010/3,080) of eligible individuals received an outbreak dose. The adjusted hazard ratio for no outbreak dose receipt was 2.7 (95%CI: 1.0–10.1). Our results suggest that an outbreak dose of mumps-containing vaccine may be an effective public health intervention, but further study is warranted

Heterogeneity analysis in patients with large numbers of repeat isolates of <i>Klebsiella pneumoniae</i>.

<p>Columns in gray represent the four biochemicals removed to create the reduced biochemical phenotype. Removal of these test results facilitates conclusions about the relatedness of patient isolates.</p

Comparison of the WHONET-SaTScan cluster findings when utilizing full (F) and reduced (R) biochemical phenotypes of <i>Klebsiella pneumoniae</i>.

<p>RI = Recurrence Interval in days.</p

Frequency of bionumbers of <i>Klebsiella pneumoniae</i> isolated from specimens collected January 2009–December 2011, considering the biochemical phenotype without 4 biochemical tests (GGT, TyrA, SUCT and GlyA).

<p>The column Discordance indicates the biochemical tests which distinguish each phenotype from the most common phenotype observed.</p

Frequency of bionumbers of <i>Klebsiella pneumoniae</i> isolated from specimens collected January 2009-December 2011 considering the full biochemical phenotype.

<p>The column Discordance indicates the biochemical tests which distinguish each phenotype from the most common phenotype observed.</p

Frequency of positive test results for patient first isolates of <i>Klebsiella pneumoniae</i> considering the 47 biochemical tests and negative control included in the Vitek 2 ID-GNB Panel.

<p>¹ Clopper-Pearson 95% Confidence Interval calculated with SAS.</p><p>² Covariance Parameter Estimates (CPE), n/c = not convergence.</p

Covariance Parameter Estimate compared with observed weighted average within-patient variance.

<p>Covariance Parameter Estimate compared with observed weighted average within-patient variance.</p

Biochemical and resistance phenotypes of imipenem-resistant <i>K. pneumoniae.</i>

<p>Number of patients  = 13, Number of isolates  = 24. The antibiotic code indicates that the organism is non-susceptible to the indicated agent. AMP = Ampicillin, CAZ = Ceftazidime, CRO = Ceftriaxone, ETP = Ertapanem, IPM = Imipenem, GEN = Gentamicin, AMK =  Amikacin, CIP = Ciprofloxacin, SXT = Trimethoprim/Sulfamethoxazole.</p