27 Genomic Identification of a Cluster of Burkholderia pyrrocinia Bloodstream Infections in Noncystic Fibrosis Patients

Abstract

Background and Case Descriptions: Burkholderia cepacia complex (BCC) constitutes a growing and diverse group of Gram-negative, nonfermenting, and highly drug-resistant environmental bacterial species, frequently isolated from cystic fbrosis (CF) patients. BCC has also been reported as contaminants in materials widely used medically, including saline line flushes, leading to severe sepsis in immunocompromised patients. While particular BCC species are more commonly isolated in clinical settings, the species Burkholderia pyrrocinia is rarely associated with human infections. Here, we present a cluster of B pyrrocinia cases found in blood cultures of three non-CF patients admitted to the same hospital within a period of three weeks. The frst patient was a 63-year-old man with advanced pancreatic cancer who presented with diarrhea, fevers, and hypotension after chemotherapy infusion. The second patient was a 41-year-old woman with metastatic adrenal cancer admitted with acute hypoxemic respiratory failure, who arrived at the hospital 17 days later. The third patient was a 65-year-old man found unconscious at home, who arrived at the hospital four days after the second patient. All three patients were found to have multiple positive blood cultures within days of arriving at the hospital. Methods: Standard microbiological techniques along with matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) were used to initially characterize the isolates. Further speciation was performed at the Cystic Fibrosis Foundation Burkholderia cepacia Research Laboratory and Repository using repetitive extragenic palindromic PCR (rep-PCR). For whole genome sequencing, we utilized the multihospital prospective genomic surveillance program run by the Massachusetts Host-Microbiome Center. Brierry, genomic libraries were prepared from total DNA extracted from each isolate using the Nextera library and sequenced by Illumina MiSeq using PE 2.5 kits. An internally developed computational pipeline of open source tools and custom scripts, deployed to the Partners ERIS cluster, was used to perform genomic assemblies, and annotate individual genes and mobile vectors, as well as for SNP-calling and tree visualization to assess strain relatedness. Results: All three isolates demonstrated similar phenotypic characteristics and antibiotic susceptibility profles, and were identifed using standard microbiology techniques and MALDI-TOF MS as B cepacia complex. Rep-PCR identifed all three isolates as B pyrrocinia, and strongly suggested they were the same strain. Bacterial whole genome sequencing found these isolates to have greater than 99.9% homology, providing further evidence of their relatedness. Conclusion: Although extensive investigation by our laboratory and infection control has yet to identify a common source, the phenotypic and genomic similarity of these isolates, and the infrequency of B pyrrocinia bloodstream infections, coupled with their temporal association strongly suggest a common environmental source and route of exposure prior to their presentation.