Pathogen Genomic Surveillance Program

The genomic surveillance program sequences multi-drug resistant isolates from multiple participating hospitals with Partners Healthcare. Isolates with MDR phenotypes are flagged prospectively by the Crimson LIMS per automatic queries against clinical microbiology data from participating labs. MHMC staff receive the isolates, confirm the species microbiologically and perform DNA extraction and genome sequencing by Illumina MiSeq. Fellows in Dr. Bry’s lab, with the BWH Clinical Microbiology residents and fellows, perform bioinformatic and genomic analyses to identify specific resistance genes, their context in mobile elements or on the chromosome, and association with any current or previously sequenced strains, per SNP-based tree and phylogenetic analyses. Findings are discussed with area infection control teams to help inform outbreak investigations and define the genomic landscape of resistance and resistance gene mobilization.


Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System

Nicole D. Pecora, Ning Lia, Marc Allardb, Cong Lib, Esperanza Albanoa, Mary Delaneya, Andrea Duboisa, Andrew B. Onderdonka, Lynn Bry

Services Provided: 

MHMC services that were provided included pulling  isolates as identified by the Crimson LIMS. MHMC staff determined microbiologically if an isolate exists in pure culture and re-streak as needed to obtain a pure culture. Frozen stocks are prepared and MHMC staff perform DNA extraction and genome sequencing using the Illumina Miseq.

Pathogen Genomes Project Services and Costs

Project Setup1each85.16108.15134
Receive and Process Sample-Microbead freeze44each5.116.497.5
Discarded Culture Isolate44per unit21.4527.2430.46
DNA Extraction44per unit24.9831.7235.47
Monthly Sample Storage44each0.070.090.10
Library preparation**, MiSeq sequencing and data QC44each300.00350.00400.00
Total Project Cost***4416,694.2820,03023,141.16
*FY 2018 Fees
**Libraries are aggregated to sequence 12 isolates, per estimated genome size, to at least ~20X median coverage to support adequate analysis of resistance genes and their context in mobile elements, which often contain repetitive regions.
***Approximate cumulative costs reflected over a four year study period.