Serratia marcescens Outbreak at a Correctional Facility: Environmental Sampling, Laboratory Analyses and Genomic Characterization to Assess Sources and Persistence

Serratia marcescens is an environmental bacterium and clinical pathogen that can cause an array of infections. We describe an environmental sampling and comparative genomics approach used to investigate a multi-year outbreak of S. marcescens at a correctional facility. Whole genome sequencing analysis revealed a predominant cluster of clonally related S. marcescens from nine patient cases and items associated with illicit drug use. Closely related strains found among items associated with case-patient cells and diluted Cell Block 64 (CB64), a quaternary ammonium disinfectant, and Break Out (BO), a multipurpose cleaner, highlighted their role as environmental reservoirs for S. marcescens in this outbreak. Comparative genomic analysis suggested outbreak strains were both persistent (identical strains found over long periods and in multiple locations of the correctional facility) and diverse (strains clustered with multiple global samples from NCBI database). No correlation was found between antimicrobial resistance (AMR) genes of outbreak strains; NCBI strains have more AMR genes. Principal component analysis (PCA) of virulence factors associated with persistence and infectivity indicated variation based on phylogroups, including the predominant cluster; identifiable variations among environmental versus clinical strains were not observed. Identification of multiple distinct genetic groups highlights the importance of putting epidemiological genomic studies in a proper genetic context

The Genomics of Imidacloprid-Remediating Bacteria

Rain and irrigation can transport pesticides from farmland into surrounding surface waters. Pesticide-contaminated waters are costly to treat and detrimental to public health. Genomic sequencing of pesticide-degrading bacteria can provide insight to using the bacteria as an inexpensive solution for targeted pesticide water treatment. The goal of this project was to generate genome sequences for pesticide-bioremediating bacteria previously isolated from agricultural drainage ditches near Salinas, California using minimal media with the pesticide imidacloprid as the sole carbon source. High quality and high molecular weight DNA from these microbes was used to generate both Oxford Nanopore Technologies MinION and MiSeq sequencing data. This data was then assembled into de novo genome sequences and annotated for likely genetic functions in order to study the molecular mechanism involved in the remediation process and create freely available novel genetic resources. The bacterial strains were most closely related to Microbacterium paraoxydans, Paenarthrobacter aurescens, Microbacterium oxydans. and Pseudarthrobacter phenanthrenivorans. The bacterial genomes include the genes cytochrome P450, ATP-binding cassette (ABC) transporters, and UDP-glycosyltransferase which may be involved in the bacteria’s imidacloprid-bioremediation capabilities

Predicting SARS-CoV-2 Evolution Using Population-Scale Intra-Host Diversity Data Derived from Public SRA Data

VCF Files for Population Genomics: Scaling to Millions of Samples Codeatho