ATCC, a premier global biological materials and information resource and standards organization, presented data on ATCC's efforts to provide scientists with fully authenticated and sequenced reference standards for microbiology research. ATCC believes these standards will enhance the quality, integrity, and reproducibility of research. These findings, presented at American Society of Microbiology (ASM) Microbe 2019, include data on the development and application of new authenticated standards for microbiome research, the characterization of 57 drug-resistant priority pathogens, and the phylogenomic reclassification of several genera.
According to a recent study, approximately $28 billion is spent annually on irreproducible biomedical research. A major limitation in microbiology research is the lack of the reliable reference materials needed for optimizing assay performance and controlling the biases that arise during different steps of the workflow--from sample preparation to data analysis. To address this issue, ATCC presented an array of research findings that demonstrate the enhanced credibility and reliability of ATCC's standards.
"While improved research standards will not guarantee reproducibility on their own, the irreproducibility crisis won't go away without them," says Dr. Raymond Cypess, CEO and President of ATCC. "Getting the research right from the beginning with credible starting materials is imperative for scientific progress and an essential foundation for global health research."
One highlight of ATCC's efforts to provide authenticated standards is its research on the human mycobiome. While a wealth of research on the human microbiome currently focuses on bacteria, researchers are now more deeply studying the role of the mycobiome--particularly with regard to human health and disease. With recent advancements in sequencing technologies, community profiling of fungi is possible, but metagenomics sequence analyses still have several challenges to overcome in assay standardization.
At ASM Microbe, ATCC presented data on the development of two mock fungal communities containing 10 diverse, clinically relevant, fully sequenced fungal strains. The researchers then demonstrated the use of these standards in evaluating DNA extraction efficiency, sequencing methods and technologies, and data analysis platforms. This proof-of-concept data demonstrates the utility of these standards for evaluating run-to-run variability and optimizing assay performance at each stage of the mycobiome analysis workflow.
In addition to mycobiome standards for microbiome research, ATCC also showcased spike-in controls comprising bacterial strains containing unique synthetic DNA tags and presented data on the applications of site-specific microbiome standards for studies on the human oral, gut, skin, and vaginal microbiomes.
At ASM, ATCC also debuted its new next-generation sequencing and genome assembly workflow that is designed to further authenticate its microbial products. As an example, the organization presented findings that it has successfully sequenced and characterized 57 priority drug-resistant pathogens as part of the recently announced expansion of its Global Priority Superbugs portfolio. At a time when these strains continue to spread and put the health of millions at risk, these genomes provide critical information to help tackle antimicrobial resistance (AMR).
ATCC analyzed bacterial strains by sequencing their DNA via a hybrid-assembly process using short-read and long-read sequencing platforms. This method achieved high-quality sequence data while reducing next-generation sequencing (NGS) biases. A proprietary automated pipeline generated and annotated contigs--or genetic sequences that overlap--to characterize the sequences of AMR genes, virulence factors, and metabolic pathways from each strain. Finally, ATCC analyzed genomic maps to reveal the specific location of AMR genes and neighbors in bacterial chromosomes and plasmids.
With the availability of phenotypically characterized strains and high-quality and complete genome sequences, it is possible to study regulatory elements and the complete repertoire of AMR genes expressed in these bacteria. It is also possible to study the interactions of drug-resistant bacterial strains with known and in-development antimicrobial drugs. The process will facilitate drug discovery efforts as well as diagnostic and treatment development.
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