Distinguishing virulent from harmless bacteria to help biological surveillance

“Our work shows that of the more than 120 Francisella genomes that have been sequenced, only a few contain plasmids. This becomes a really useful signpost for researchers, adding genomic features that can prevent misidentification of bacterial relatives that happen to share an otherwise similar genetic profile,” she said. Environmental surveys indicate that F. novicida and similar strains are widely distributed and abundant in diverse environments across the United States, and most importantly, this group appears likely to be a source of environmental false positives forF. tularensis that have occurred in surveillance systems.

To accomplish the analysis, the team sequenced genomes from samples of seawater in the area of Galveston Bay, Texas (F. novicida-like), some human clinical samples (F. novicida AZ06-7470 and F. opportunistica), water from a warm spring (F. novicida) and a form isolated from an air conditioning system (F. frigiditurris). Several of the plasmid-containing Francisella strains were sequenced by the Genome Sciences group in the Bioscience Division at Los Alamos.

“Only a few members of the Francisella genus carry plasmids; these include several F. novicida strains, and we found that all of the plasmids were apparently cryptic, encoding functions potentially involved in replication, conjugal transfer and partitioning, a few functions that could be important to environmental survival, and some hypothetical proteins to which a function could not be assigned,” Challacombe said.

According to the published conclusion by Challacombe and her coauthors Cheryl Kuske and Segaran Pillai, “While bacterial plasmids can carry traits that enhance the survival of host cells and influence bacterial evolution, cryptic plasmids encode few functions other than those needed to replicate and mobilize. With no obvious benefit to the host cells that carry them, cryptic plasmids are somewhat of an enigma… Our results comparing the cryptic plasmids in diverse Francisella genomes show that they are also found in clinical isolates. These results provide a new understanding of the phenotypic variability and complex taxonomic relationships among the known Francisella species, and also give us new plasmid features to use in characterizing related species groups.”

There are many cultured Francisella isolates for which we still have no genomic sequence, the researchers point out. It will only be through the sequencing and comparison of many more environmental and near neighbor Francisella isolates that researchers will be able to identify additional genomic features that enable accurately discriminating among the various species groups.

LANL says that biosciences have been a strong focus at Los Alamos ever since the early radiation-dose measurement efforts of the Manhattan Project, and the Lab’s Bioscience Division has long been closely involved in biohazard analysis, genetic research and development of such tools and techniques as flow cytometry.

— Read more in Jean F. Challacombe et al., “Shared Features of Cryptic Plasmids from Environmental and Pathogenic Francisella Species,” PLOS ONE (24 August 2017) (doi:org/10.1371/journal.pone.0183554