Borrelia maritima sp. nov., a novel species of the Borrelia burgdorferi sensu lato complex, occupying a basal position to North American species.

Borrelia species are vector-borne parasitic bacteria with unusual, highly fragmented genomes that include a linear chromosome and linear as well as circular plasmids that differ numerically between and within various species. Strain CA690T, which was cultivated from a questing Ixodes spinipalpis nymph in the San Francisco Bay area, CA, was determined to be genetically distinct from all other described species belonging to the Borrelia burgdorferi sensu lato complex. The genome, including plasmids, was assembled using a hybrid assembly of short Illumina reads and long reads obtained via Oxford Nanopore Technology. We found that strain CA690T has a main linear chromosome containing 902176 bp with a blast identity ≤91 % compared with other Borrelia species chromosomes and five linear and two circular plasmids. A phylogeny based on 37 single-copy genes of the main linear chromosome and rooted with the relapsing fever species Borrelia duttonii strain Ly revealed that strain CA690T had a sister-group relationship with, and occupied a basal position to, species occurring in North America. We propose to name this species Borrelia maritima sp. nov. The type strain, CA690T, has been deposited in two national culture collections, DSMZ (=107169) and ATCC (=TSD-160).

Borrelia lanei sp. nov. extends the diversity of Borrelia species in California.

The diversity of Borrelia species discovered in California appears to be particularly high. A divergent group of Borrelia strains collected from Ixodes ticks in California was described by Postic and co-workers and designated 'genomospecies 2' (Postic D, Garnier M, Baranton G. Int J Med Microbiol 2007;297:263-271; Postic D, Ras NM, Lane RS, Hendson M, Baranton G. J Clin Microbiol 1998;36:3497-3504). We performed multilocus sequence analysis (MLSA) using eight housekeeping loci (clpA, clpX, nifS, pepX, pyrG, recG, rplB and uvrA) on 12 strains of this Borreliagenospecies to confirm that these strains form a distinct group within the Borreliaburgdorferi s. l. complex (Margos G, Hojgaard A, Lane RS, Cornet M, Fingerle V et al.Ticks Tick Borne Dis 2010;1:151-158). Phylogenetic and genetic distance analyses based on sequences of the MLSA housekeeping genes corroborated the distinctness of this group; genetic distances to all other members of the B. burgdorferi s.l. complex were 96 % or lower. We propose the name Borrelia lanei sp. nov. for this genospecies in honor of Professor Robert S. Lane, University of California Berkeley, for his contributions to Borrelia and tick research. The type strain for Borrelia lanei sp. nov., strain CA28-91T, has been deposited to two culture collections (=DSM 17992T=CIP 109135T).

Detection and Isolation of Rickettsia tillamookensis (Rickettsiales: Rickettsiaceae) From Ixodes pacificus (Acari: Ixodidae) From Multiple Regions of California.

The western black-legged tick (Ixodes pacificus) is the most frequently identified human-biting tick species in the western United States and the principal vector of at least three recognized bacterial pathogens of humans. A potentially pathogenic Rickettsia species, first described in 1978 and recently characterized as a novel transitional group agent designated as Rickettsia tillamookensis, also exists among populations of I. pacificus, although the distribution and frequency of this agent are poorly known. We evaluated DNA extracts from 348 host-seeking I. pacificus nymphs collected from 9 locations in five California counties, and from 916 I. pacificus adults collected from 24 locations in 13 counties, by using a real-time PCR designed specifically to detect DNA of R. tillamookensis. DNA of R. tillamookensis was detected in 10 (2.9%) nymphs (95% CI: 1.6-5.2%) and 17 (1.9%) adults (95% CI: 1.2-3.0%) from 11 counties of northern California. Although site-specific infection rates varied greatly, frequencies of infection remained consistently low when aggregated by stage, sex, habitat type, or geographical region. Four novel isolates of R. tillamookensis were cultivated in Vero E6 cells from individual adult ticks collected from Alameda, Nevada, and Yolo counties. Four historical isolates, serotyped previously as 'Tillamook-like' strains over 40 yr ago, were revived from long-term storage in liquid nitrogen and confirmed subsequently by molecular methods as isolates of R. tillamookensis. The potential public health impact of R. tillamookensis requires further investigation.

Larval keys to the genera of Ixodidae (Acari) and species of Ixodes (Latreille) ticks established in California.

In California, hard (Ixodidae) ticks transmit at least 8 zoonotic disease agents (1 virus, 6 bacteria, 1 protozoan) to humans or other animals. The correct taxonomic identification of all 3 parasitic stages (larvae, nymphs, adults) of ticks is integral to understanding host-tick associations and disease dynamics, but immature ticks, especially the larvae, can be difficult to identify. Here, we present larval keys to the 4 genera of Ixodidae (DermacentorKoch, 1844; HaemaphysalisKoch, 1844; IxodesLatreille, 1795; RhipicephalusKoch, 1844) and to the 18 species of Ixodes known to be established in California. Several new diagnostic features, as well as photographs of microscopic structures, are provided to facilitate identification. Non-exclusive characters are utilized to separate the subgenera IxodiopsisFilippova, 1957 and PholeoixodesSchulze, 1942.

Remarkable diversity of tick or mammalian-associated Borreliae in the metropolitan San Francisco Bay Area, California.

The diversity of Lyme disease (LD) and relapsing fever (RF)-group spirochetes in the metropolitan San Francisco Bay area in northern California is poorly understood. We tested Ixodes pacificus, I. spinipalpis, and small mammals for presence of borreliae in Alameda County in the eastern portion of San Francisco Bay between 2009 and 2012. Analyses of 218 Borrelia burgdorferi sensu lato (Bb sl) culture or DNA isolates recovered from host-seeking I. pacificus ticks revealed that the human pathogen Bb sensu stricto (hereinafter, B. burgdorferi) had the broadest habitat distribution followed by B. bissettii. Three other North American Bb sl spirochetes, B. americana, B. californiensis and B. genomospecies 2, also were detected at lower prevalence. OspC genotyping of the resultant 167 B. burgdorferi isolates revealed six ospC alleles (A, D, E3, F, H and K) in I. pacificus. A novel spirochete belonging to the Eurasian Bb sl complex, designated CA690, was found in a questing I. spinipalpis nymph. Borrelia miyamotoi, a relapsing-fever (RF) group spirochete recently implicated as a human pathogen, was detected in 24 I. pacificus. Three rodent species were infected with Bb sl: the fox squirrel (Sciurus niger) with B. burgdorferi, and the dusky-footed wood rat (Neotoma fuscipes) and roof rat (Rattus rattus) with B. bissettii. Another spirochete that clustered phylogenetically with the Spanish R57 Borrelia sp. in a clade distinct from both the LD and RF groups infected some of the roof rats. Together, eight borrelial genospecies were detected in ticks or small mammals from a single Californian county, two of which were related phylogenetically to European spirochetes.

Eco-epidemiological factors contributing to the low risk of human exposure to ixodid tick-borne borreliae in southern California, USA.

Little is known about the eco-epidemiology of Lyme disease in southern California, a region where the incidence is much lower than it is in northern California. Here, we sought to discover the previously unknown microhabitats of nymphs of the primary vector, the western black-legged tick (Ixodes pacificus), in 3 moderately to heavily-utilized state parks in the Santa Monica Mountains in Los Angeles County; to elucidate the seasonal distribution and abundance of adults of I. pacificus and another human-biter, the Pacific Coast tick (Dermacentor occidentalis); and to determine what Lyme-disease or relapsing-fever group borreliae are present in questing nymphs or adult ticks. I. pacificus nymphs were collected infrequently at various times of day in 2 chaparral or 7 woodland litter areas by dragging (combined mean=0.4 nymphs per hour). The western fence lizard (Sceloporus occidentalis) was a choice sentinel animal for detecting the presence of I. pacificus nymphs (and larvae) in diverse biotopes even when dragging litter in them was fruitless. The abundance and seasonality of I. pacificus and D. occidentalis adults resembled what had been documented previously for these ticks in northern California. Overall, zero of 27 free-living and 118 lizard-infesting I. pacificus nymphs, 7 (0.29%) of 2392 I. pacificus adults and 2 (0.22%) of 896 D. occidentalis adults were infected with Borrelia burgdorferi sensu lato (Bb sl), but none of them harbored B. miyamotoi, a relapsing-fever group spirochete implicated recently as a zoonotic pathogen in Russia. Borrelia americana and the human pathogen B. burgdorferi sensu stricto were each detected in one (0.04%), and uncharacterized Bb sl in 5 adult I. pacificus (0.21%) that clustered with B. americana. Both PCR-positive D. occidentalis adults contained B. burgdorferi sensu stricto. We conclude that the acarologic risk of being bitten by a B. burgdorferi sensu lato-infected ixodid tick in the habitats studied is slight, which offers a plausible explanation for the low reported incidence of Lyme disease in south coastal California.