Publications
A Curated, Comprehensive Database of Plasmid Sequences
by L. E. Brooks, M. Kaze, M. Sistrom
Microbiology Resource Announcements (2019)
Plasmid sequences are central to a myriad of microbial functions and processes. Here, we have compiled a database of complete plasmid sequences and associated metadata curated from both NCBI’s recent genome database update, which includes plasmids as organisms, and all available annotated bacterial genomes. The resultant database contains 10,892 complete plasmid sequences and associated metadata.
This GRAS Isn’t Greener: Biopesticides as Unintentional Reservoirs of Antibiotic5 Resistance
by M. Kaze, L. E. Brooks, M. Sistrom
In Review 2020
The crisis of antibiotic resistant bacterial infections is one of the most pressing public health issues we face. Common agricultural practices have been implicated in the generation of antibiotic resistant bacteria. Biopesticides, live bacteria used for pest control, are non-pathogenic and considered safe for consumption. Application of bacteria-based pesticides to crops in high concentrations raises the possibility of unintentional contributions to the movement and generation of Antibiotic Resistance Genes (ARG) in the environment. However, the presence of clinically relevant ARG and their resistance phenotypes are currently unknown. Here we use a combination of multiple bioinformatic and microbiological techniques to define resistomes of widely used biopesticides and determine how the presence of suspected ARG translates to observable resistance phenotypes in several biopesticide products. Our results demonstrate that biopesticide products are reservoirs of clinically relevant antibiotic resistance genes and bear resistance to multiple drug classes. We anticipate that this study is an important starting point for further investigation into the use of biopesticides and the likely role they play as potential vectors of unintended transmission of antibiotic resistance.
WElcome to thunderdome: the resistome and the virome of the plasmidome
by M. Kaze, L. E. Brooks, M. Sistrom
In process 2020
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Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges
by L. E. Brooks, M. Kaze, M. Sistrom
Microbial genomics 5.1 (2019)
Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.
Mixing with a Bad Crowd: ARG exchange between Klebsiella pneumoniae and Bacillus based-Biopesticides Leads to Carbapenem Resistant Phenotypes
by M. Kaze, L. E. Brooks, M. Sistrom
The causes of the global antibiotic resistance crisis are complex and the development of effective responses depends on a comprehensive understanding of these factors. Many agricultural practices have been implicated in the evolution and dissemination of antibiotic resistance genes. Biopesticides - microorganism-based insecticides, are applied globally in large quantities and have recently been connected to the presence of ARG in the environment. An important, multi-drug resistant pathogen that has arisen globally in the last 30 years is Klebsiella pneumoniae. A Gram negative, soil-dwelling bacterium that causes pneumonia, septicemia, and meningitis, and can be both community and hospital-acquired. K. pneumoniae-based pneumonia is a common nosocomial infection often associated with ventilator use. K. pneumoniae and widely-used biopesticide Bacillus thuringiensis both have unusual plasmid permissivity and genomic plasticity, making their potential for exchange an intriguing and important interaction to investigate. This study tests the hypothesis that horizontal gene exchange via plasmid conjugation can occur between commercial, Bacillus-based biopesticide products and a carbapenemase-positive (blaKPC) strain of K. pneumoniae, and that this exchange results in the acquisition of resistant phenotypes by commercial biopesticide strains. We used Hi-C proximity ligation to identify the location - chromosome or plasmid, of specific ARG in biopesticides isolated from commercial products, and MIC tests to determine their resistance phenotypes. We then conducted conjugation pairwise between biopesticide strains and carbapenemase-positive (blaKPC) K. pneumoniae. We demonstrate that K. pneumoniae and Bacillus-based biopesticides can exchange carbapenem antibiotic resistance genes after contact resulting the acquisition of carbapenem resistant phenotypes in biopesticides.
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Add your answer here. Fusce rhoncus vulputate ex, eget lacinia orci. Pellentesque lacinia felis sit amet ex mattis, vitae euismod leo hendrerit. Etiam scelerisque turpis quis sem volutpat, eu scelerisque nisi vehicula.