A Phylogeny-Informed Proteomics Approach for Species Identification within the Burkholderia cepacia Complex.

Ancestral genetic exchange between members of many important bacterial pathogen groups has resulted in phylogenetic relationships better described as networks than as bifurcating trees. In certain cases, these reticulated phylogenies have resulted in phenotypic and molecular overlap that challenges the construction of practical approaches for species identification in the clinical microbiology laboratory. Burkholderia cepacia complex (Bcc), a betaproteobacteria species group responsible for significant morbidity in persons with cystic fibrosis and chronic granulomatous disease, represents one such group where network-structured phylogeny has hampered the development of diagnostic methods for species-level discrimination. Here, we present a phylogeny-informed proteomics approach to facilitate diagnostic classification of pathogen groups with reticulated phylogenies, using Bcc as an example. Starting with a set of more than 800 Bcc and Burkholderia gladioli whole-genome assemblies, we constructed phylogenies with explicit representation of inferred interspecies recombination. Sixteen highly discriminatory peptides were chosen to distinguish B. cepacia, Burkholderia cenocepacia, Burkholderia multivorans, and B. gladioli and multiplexed into a single, rapid liquid chromatography-tandem mass spectrometry multiple reaction monitoring (LC-MS/MS MRM) assay. Testing of a blinded set of isolates containing these four Burkholderia species demonstrated 50/50 correct automatic negative calls (100% accuracy with a 95% confidence interval [CI] of 92.9 to 100%), and 70/70 correct automatic species-level positive identifications (100% accuracy with 95% CI 94.9 to 100%) after accounting for a single initial incorrect identification due to a preanalytic error, correctly identified on retesting. The approach to analysis described here is applicable to other pathogen groups for which development of diagnostic classification methods is complicated by interspecies recombination.

Optimizing Value of Colon Surgery in Michigan.

OBJECTIVE: To assess the value of bundling perioperative care measures in colon surgery. BACKGROUND: Surgical site infections (SSI) in colectomy are associated with increased morbidity and cost. Perioperative care bundling has been designed to improve processes of care surrounding colectomy operations. METHODS: Retrospective cohort study performed by the Michigan Surgical Quality Collaborative (MSQC) of patients who underwent elective colon surgery from 2012 to 2015. We identified 3,387 patients in the MSQC database who underwent colon surgery. Of these cases, 332 had associated episodic cost data. RESULTS: High compliance (3-6 bundle elements) and low compliance (0-2 bundle elements) had a risk-adjusted SSI rate of 8.2% (95% confidence interval, CI, 7.2-9.2%) and 16.0% (95% CI, 12.9-19.1%), respectively (P < 0.01). When compared with low compliance, the high compliance group had an absolute risk reduction of 3.6% (P < 0.01), 2.9% (P < 0.01) and 1.3% (P < 0.01) for SSI rates in superficial space, deep space, and organ space, respectively. Low compliance had an average episodic cost of $20,046 (95% CI, $17,281-$22,812) whereas high compliance had an episodic cost of $15,272 (95% CI, $14,354-$16,192). This showed a $4,774 (95% CI, $1,859-$7,688) and 23.8% cost reduction (P < 0.01). Facility base payments decreased 14.8% ($13,444; $11,458), professional payments decreased 43.9% ($5,180; $2,906), and other payments decreased 36.2% ($1,422; $908). CONCLUSIONS: A colectomy perioperative care bundle in Michigan is associated with improved value of surgical care. We will expand efforts to implement perioperative care bundles in Michigan to improve outcomes and reduce costs.