DNA capture and enrichment: a culture-independent approach for characterizing the genomic diversity of pathogenic leptospira species

Authors: STONE, NATHAN - Northern Arizona University; MCDONOUGH, RYELAN - Northern Arizona University; HAMOND, CAMILA - US Department Of Agriculture (USDA); LECOUNT, KAREN - US Department Of Agriculture (USDA); BUSCH, JOSEPH - Northern Arizona University; DIRSMITH, KATHERINE - Animal And Plant Health Inspection Service (APHIS); RIVERA-GARCIA, SARAI - Animal And Plant Health Inspection Service (APHIS); SOLTERO, FRED - Animal And Plant Health Inspection Service (APHIS); ARNOLD, LAURA - University Of Kentucky; WEINER, ZACHARY - Centers For Disease Control And Prevention (CDC) - United States; GALLOWAY, RENEE - Centers For Disease Control And Prevention (CDC) - United States; SCHLATER, LINDA - US Department Of Agriculture (USDA); Nally, Jarlath; SAHL, JASON - Northern Arizona University; WAGNER, DAVID - Northern Arizona University

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/11/2023
Publication Date: 5/14/2023
Citation: Stone, N.E., McDonough, R.F., Hamond, C., LeCount, K., Busch, J.D., Dirsmith, K.L., Rivera-Garcia, S., Soltero, F., Arnold, L.M., Weiner, Z., Galloway, R.L., Schlater, L.K., Nally, J.E., Sahl, J.W., Wagner, D.M. 2023. DNA Capture and Enrichment: A Culture-Independent Approach for Characterizing the Genomic Diversity of Pathogenic Leptospira Species. Microorganisms. 11(5). https://doi.org/10.3390/microorganisms11051282.
DOI: https://doi.org/10.3390/microorganisms11051282

Interpretive Summary: Leptospirosis is a global zoonotic disease, endemic in the U.S.A. and caused by an unusual bacterium, pathogenic Leptospira. There are more than 38 pathogenic species of Leptospira, comprising hundreds of different serovars. To design and apply efficacious diagnostics and vaccines that will prevent disease transmission, it is essential to know what species and serovars are circulating and causing infection in human and animal populations. The definitive method of identifying the species and serovar of Leptospira associated with infection is culture, which provides an isolate that can be comprehensively characterized. However, culture of Leptospira from human and animal samples is inherently difficult and requires the use of specialized media and expertise. Therefore, culture is not routinely practiced. To overcome this limitation, a culture independent method was developed to extract and enrich for the DNA of Leptospira directly from complex diagnostic samples, including blood, urine, and kidney. In this way, a large amount of genomic DNA derived from species and serovars of Leptospira causing infection can be identified and characterized. This, in turn, provides a better understanding of overall genomic diversity and gene content of pathogenic Leptospira associated with infection, without the need for culture.

Technical Abstract: Because they are difficult to culture, obtaining genomic information from Leptospira spp. is challenging, hindering overall understanding of leptospirosis. We designed and validated a culture independent DNA capture and enrichment system for obtaining Leptospira genomic information from complex human and animal samples. It can be utilized with a variety of complex sample types and diverse species as it was designed using the pan genome of all known pathogenic Leptospira spp. This system significantly increases the proportion of Leptospira DNA contained within DNA extracts obtained from complex samples, oftentimes reaching >95% even when some estimated starting proportions were <1%. Sequencing enriched extracts results in genomic coverage similar to sequenced isolates, thereby enabling enriched complex extracts to be analyzed together with whole genome sequences from isolates, which facilitates robust species identification and high-resolution genotyping. The system is flexible and can be readily updated when new genomic information becomes available. Implementation of this DNA capture and enrichment system will improve efforts to obtain genomic data from unculturable Leptospira-positive human and animal samples. This, in turn, will lead to better understanding of overall genomic diversity and gene content of Leptospira spp. that cause leptospirosis, aiding epidemiology and the development of improved diagnostics and vaccines.