Biology subjects

Gorzalski, A.

Publications and source records attributed to Gorzalski, A..

3 recordsLinked to original sources

bioRxiv2025

Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh

BackgroundThe gram-negative bacterium Burkholderia gladioli can cause diseases in a wide range of hosts, including humans and plants. In rice, it produces Bacterial Panicle Blight (BPB), an emerging disease that is threatening the production of this staple food worldwide. Recently, BPB has affected several rice fields in Bangladesh, and B. gladioli has been reported as the causative agent in one of these fields, raising questions about how the pathogen was introduced into the country. Understanding the introduction routes into Bangladesh and the pathogenicity mechanisms of B. gladioli is essential to develop sustainable management strategies to control BPB. ResultsTo investigate the origin of pathogenic B. gladioli strains and their introduction routes into Bangladesh, we sequenced the complete genomes of 19 strains isolated from symptomatic rice panicles from four major rice-growing districts of the country (Rangpur, Faridpur, Natore, and Mymensingh). A phylogenetic analysis encompassing all 320 publicly available B. gladioli genomes along with the 19 newly sequenced genomes revealed five independent introduction events into Bangladesh--four of which showed close phylogenetic links to clinical isolates from the USA--and no evidence of inter-district dissemination within the country. Many host transitions (35 human-to-plant and 1 plant-to-human) were inferred across the phylogeny, highlighting the pathogens versatile and cross-kingdom transmission dynamics. Analysis of the presence/absence patterns of 37 virulence-related genes across all 339 B. gladioli strains indicated that human-to-plant host transitions often coincided with loss of the tsr and motB genes--which are associated with bacterial motility--, suggesting convergent adaptive shifts in response to host switches. ConclusionOur findings shed light on the introduction pathways of pathogenic B. gladioli strains into Bangladesh and highlight specific virulence-related genes as potentially responsible for cross-kingdom host shifts.

genomics↗

bioRxiv2023

Public Health Response to Pan-Resistant Pseudomonas aeruginosa Sequence Type 309 with Tandem Guiana Extended Spectrum Beta Lactamases Genetic Characterization and In Vivo Efficacy Assessment using Translational Murine Model.

Through phenotypic and genetic profiling, we identified the first pan resistant Pseudomonas aeruginosa high-risk sequence type 309 (ST-309) with Guiana Extended Spectrum {beta}-Lactamase (GES) in California, prior to a national outbreak of VIM-GES Pseudomonas aeruginosa (1). Our findings highlight detection and use of the translational murine model provide treatment implications for this emerging Pseudomonas aeruginosa.

microbiology↗

bioRxiv2022

GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification

Whole genome sequencing of clinical bacterial isolates has the potential to transform the fields of medicine and public health, with particular impact on molecular epidemiology, infection control and assessing the spread of antibiotic resistance. To realize this potential, bioinformatic software needs to be developed that meets the quality standards of a diagnostic test to allow the reporting of identification results. Our research group has developed a methodology (GAMBIT: Genomic Approximation Method for Bacterial Identification and Tracking) using k-mer based strategies for identification of bacteria based on whole genome sequence reads. GAMBIT incorporates this algorithm with a highly curated searchable database of genomes, which is a subset of the NCBI RefSeq assembly database. In this manuscript, we describe the validation of the scoring methodology, robustness to chosen parameters, establishment of confidence thresholds and the curation of the reference database. We discuss a validation set with GAMBIT deployed as a laboratory-developed test at the Alameda County Public Health Laboratory in Oakland, California. Three advancements were required to build upon existing k-mer based strategies to allow GAMBIT to possess the quality control parameters desired for its use as a diagnostic laboratory-developed test. Firstly, we innovated the data structure used to store the database of known bacterial genomes. This allowed us to store 48,224 bacterial genomes in a k-mer based database--a majority of the bacterial genomes in the NCBI RefSeq database at the time of development. Secondly, curation of the NCBI RefSeq database was required to remove ambiguous or potentially incorrectly labeled bacterial genomes to greatly increase confidence in positive matches. Lastly, we used this curated version of the NCBI RefSeq database and our scoring method to generate confidence thresholds for identification. Thus, the end-user does not rely simply on the closest match, but is informed whether that closest match exceeds a threshold for highly confident identification. This method greatly reduces or eliminates false identifications which are often detrimental in a clinical setting.

bioinformatics↗