Comparative genomics of the Western Hemisphere soft tick-borne relapsing fever borreliae highlights extensive plasmid diversity.

BACKGROUND: Tick-borne relapsing fever (TBRF) is a globally prevalent, yet under-studied vector-borne disease transmitted by soft and hard bodied ticks. While soft TBRF (sTBRF) spirochetes have been described for over a century, our understanding of the molecular mechanisms facilitating vector and host adaptation is poorly understood. This is due to the complexity of their small (~ 1.5 Mb) but fragmented genomes that typically consist of a linear chromosome and both linear and circular plasmids. A majority of sTBRF spirochete genomes' plasmid sequences are either missing or are deposited as unassembled sequences. Consequently, our goal was to generate complete, plasmid-resolved genomes for a comparative analysis of sTBRF species of the Western Hemisphere. RESULTS: Utilizing a Borrelia specific pipeline, genomes of sTBRF spirochetes from the Western Hemisphere were sequenced and assembled using a combination of short- and long-read sequencing technologies. Included in the analysis were the two recently isolated species from Central and South America, Borrelia puertoricensis n. sp. and Borrelia venezuelensis, respectively. Plasmid analyses identified diverse sequences that clustered plasmids into 30 families; however, only three families were conserved and syntenic across all species. We also compared two species, B. venezuelensis and Borrelia turicatae, which were isolated ~ 6,800 km apart and from different tick vector species but were previously reported to be genetically similar. CONCLUSIONS: To truly understand the biological differences observed between species of TBRF spirochetes, complete chromosome and plasmid sequences are needed. This comparative genomic analysis highlights high chromosomal synteny across the species yet diverse plasmid composition. This was particularly true for B. turicatae and B. venezuelensis, which had high average nucleotide identity yet extensive plasmid diversity. These findings are foundational for future endeavors to evaluate the role of plasmids in vector and host adaptation.

Isolation of Rickettsia rickettsii in Rocky Mountain Spotted Fever Outbreak, Panama.

We report new cases of Rocky Mountain spotted fever in patients from Kinkantu, Ngäbe-Bugle indigenous comarca, Panama. We isolated Rickettsia rickettsii in cell culture after intraperitoneal inoculation of guinea pigs with tissues from a deceased patient. Our results indicate that Rocky Mountain spotted fever is emerging in this region.

Morphotype and haplotype identification of Varroa destructor (Acari: Varroidae), and its importance for apiculture in Nicaragua.

The ectoparasite Varroa (Acari: Varroidae) is considered to be the main pest of honey bees (Apis mellifera L.) in Nicaragua. The aim of this study was to determine morphotypes and mitochondrial haplotypes of the Varroa mites, related to infestation levels in A. mellifera hives in Nicaragua in a cross-sectional study (2013-2016). Samples were taken from 34 sentinel apiaries in five geographical zones; from 713 Varroa females collected during the study, 153 were selected for measurement of various morphometric characters for further classification into morphotypes. The mitochondrial haplotype was assigned to one of the two (Korean or Japanese), using the restriction by SacI of the PCR product of a fragment of the gene CO-I. Morphometric measurement and sequencing revealed the affiliation to the species Varroa destructor with a mean (± SD) body width of 1699.1 ± 60.2 µm and a body length of 1161.1 ± 34.9 µm. Body characters were significantly different among the 34 apiaries. Varroa destructor samples were classified into four morphotypes, with no significant differences in the geographical zones. As GAGCTC SacI enzyme cleavage sequences were not observed, all PCR products were identified as V. destructor Korean haplotype. The CO-I gene nucleotide sequences from two samples V. destructor showed both 100% similarity with the Korean haplotype and 99.8% similarity to the Japanese haplotype. Although the V. destructor mite was identified as a Korean haplotype, host-parasite association in 2 decades has led into a balance without entering into severe losses in the Nicaraguan apiculture.

New feather mites of the Nycteridocaulus generic group (Acariformes: Proctophyllodidae) from passerines (Passeriformes) in Panama.

Three new feather mite species of the Nycteridocaulus generic group (Proctophyllodidae: Proctophyllodinae) are described from passerines in Panama: Atrichophyllodes myrmotherulae sp. n. from the Slaty Antwren, Myrmotherula schisticolor (Lawrence) (Thamnophilidae), Nycteridocaulus apanaskevichi sp. n. from the Grey-breasted Wood Wren, Henicorhina leucophrys (Tschudi) (Troglodytidae), and N. empidonicus sp. n. from the Yellowish Flycatcher Empidonax flavescens Lawrence (Tyrannidae). Nycteridocaulus apanaskevichi, presenting the second record of the genus from a host of oscine passerines, differs from N. guaratubensis Hernandes, 2014 in having the anterolateral extensions of the prodorsal shield rounded and the hysteronotal shield lacking any ornamentation. Males of N. empidonicus differ from N. myiobius Mironov, 2017 in having the supranal concavity open posteriorly and tarsus IV with rounded apical process; and females are distinguished by macrosetae h2 having long filiform apices. Males of A. myrmotherulae most clearly differ from A. mentalis Hernandes et al. 2007 in having the terminal lamellae rectangular and tarsus IV with triangular ventral process, and females are distinguished in having a noticeably longer idiosoma, 400-430 µm long. Comments on systematics and host associations of the genera Atrichophyllodes and Nycteridocaulus are provided.

Using DNA-barcoded Malaise trap samples to measure impact of a geothermal energy project on the biodiversity of a Costa Rican old-growth rain forest.

We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rain forest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World Heritage Site, Área de Conservación Guanacaste (ACG), in northwestern Costa Rica. This biomonitoring is part of Costa Rica's ongoing efforts to sustainably retain its wild biodiversity through biodevelopmental integration with its societies. Essential tools are geothermal engineering needs, entomological knowledge, insect species-rich forest, government-NGO integration, common sense, DNA barcoding for species-level identification, and Malaise traps. This research is tailored for integration with its society at the product level. We combine an academic view with on-site engineering decisions. This biomonitoring requires alpha-level DNA barcoding combined with centuries of morphology-based entomological taxonomy and ecology. Not all desired insect community analyses are performed; they are for data from subsequent years combined with this year. We provide enough analysis to be used by both guilds now. This biomonitoring has shown, for the first year, that the geothermal project impacts only the biodiversity within a zone less than 50 m from the project margin.

Wireless Sensor Platform for Cultural Heritage Monitoring and Modeling System.

Results from three years of continuous monitoring of environmental conditions using a wireless sensor platform installed at The Cloisters, the medieval branch of the New York Metropolitan Museum of Art, are presented. The platform comprises more than 200 sensors that were distributed in five galleries to assess temperature and air flow and to quantify microclimate changes using physics-based and statistical models. The wireless sensor network data shows a very stable environment within the galleries, while the dense monitoring enables localized monitoring of subtle changes in air quality trends and impact of visitors on the microclimate conditions. The high spatial and temporal resolution data serves as a baseline study to understand the impact of visitors and building operations on the long-term preservation of art objects.

Ticks and tick-borne pathogens of dogs along an elevational and land-use gradient in Chiriquí province, Panamá.

Systematic acarological surveys are useful tools in assessing risk to tick-borne infections, especially in areas where consistent clinical surveillance for tick-borne disease is lacking. Our goal was to identify environmental predictors of tick burdens on dogs and tick-borne infectious agents in dog-derived ticks in the Chiriquí Province of western Panama to draw inferences about spatio-temporal variation in human risk to tick-borne diseases. We used a model-selection approach to test the relative importance of elevation, human population size, vegetative cover, and change in landuse on patterns of tick parasitism on dogs. We collected 2074 ticks, representing four species (Rhipicephalus sanguineus, R. microplus, Amblyomma ovale, and Ixodes boliviensis) from 355 dogs. Tick prevalence ranged from 0 to 74% among the sites we sampled, and abundance ranged from 0 to 20.4 ticks per dog with R. sanguineus s.l. being the most commonly detected tick species (97% of all ticks sampled). Whereas elevation was the best single determinant of tick prevalence and abundance on dogs, the top models also included predictor variables describing vegetation cover and landuse change. Specifically, low-elevation areas associated with decreasing vegetative cover were associated with highest tick occurrence on dogs, potentially because of the affinity of R. sanguineus for human dwellings. Although we found low prevalence of tick-borne pathogen genera (two Rickettsia-positive ticks, no R. rickettsia or Ehrlichia spp.) in our study, all of the tick species we collected from dogs are known vectors of zoonotic pathogens. In areas where epidemiological surveillance infrastructure is limited, field-based assessments of acarological risk can be useful and cost-effective tools in efforts to identify high-risk environments for tick-transmitted pathogens.

Description of a new species of Ixodes Latreille, 1795 (Acari: Ixodidae) and redescription of I. lasallei Méndez & Ortiz, 1958, parasites of agoutis and pacas (Rodentia: Dasyproctidae, Cuniculidae) in Central and South America.

Ixodes bocatorensis n. sp. (Acari: Ixodidae), is described based on adults ex agoutis (Rodentia: Dasyproctidae), pacas (Rodentia: Cuniculidae) and "tapir and sloth" (Perissodactyla: Tapiridae and Pilosa) from Colombia, Panama and Venezuela. Adults of I. bocatorensis n. sp. are similar to those of I. lasallei Méndez & Ortiz, 1958 but can be distinguished by the scutum dimensions, punctation pattern, gnathosoma and palpi measurements and their ratios, basis capituli anterior angle and shape of the spur of palpal segment I ventrally. For comparative purposes the female of I. lasallei is redescribed and the true male of this species is described for the first time. Studied adults of I. lasallei were found on agoutis, pacas and ocelot (Carnivora: Felidae) in Colombia, Peru and Venezuela.

First description of the male and redescription of the female of Ixodes tapirus Kohls, 1956 (Acari: Ixodidae), a parasite of tapirs (Perissodactyla: Tapiridae) from the mountains of Colombia, Costa Rica and Panama.

The male of Ixodes tapirus Kohls, 1956 (Acari: Ixodidae) is described for the first time and the female is redescribed in greater detail. Adults of I. tapirus are similar to those of Ixodes guatemalensis Kohls, 1956, Ixodes lasallei Méndez & Ortiz, 1958, Ixodes montoyanus Cooley, 1944 and Ixodes venezuelensis Kohls, 1953 but can be distinguished by their overall size, the amount of sclerotisation of the conscutum and accessory plates, the shape of the scutum, the number of punctations and their pattern on the conscutum and scutum, the depth of the punctations on the basis capituli dorsally, the shape and size of the porose areas and the size and shape of the auriculae. Adults of I. tapirus were collected from tapirs and vegetation in the mountains of Colombia, Panama and recorded from Costa Rica for the first time.

Designed Modular Proteins as Scaffolds To Stabilize Fluorescent Nanoclusters.

Proteins have been used as templates to stabilize fluorescent metal nanoclusters thus obtaining stable fluorescent structures, and their fluorescent properties being modulated by the type of protein employed. Designed consensus tetratricopeptide repeat (CTPR) proteins are suited candidates as templates for the stabilization of metal nanoclusters due to their modular structural and functional properties. Here, we have studied the ability of CTPR proteins to stabilize fluorescent gold nanoclusters giving rise to designed functional hybrid nanostructures. First, we have investigated the influence of the number of CTPR units, as well as the presence of cysteine residues in the CTPR protein, on the fluorescent properties of the protein-stabilized gold nanoclusters. Synthetic protocols to retain the protein structure and function have been developed, since the structural and functional integrity of the protein template is critical for further applications. Finally, as a proof-of-concept, a CTPR module with specific binding capabilities has been used to stabilize gold nanoclusters with positive results. Remarkably, the protein-stabilized gold nanocluster obtained combines both the fluorescence properties of the nanoclusters and the functional properties of the protein. The fluorescence changes in nanoclusters fluorescence have been successfully used as a sensor to detect when the specific ligand was recognized by the CTPR module.

Molecular detection of rickettsial agents in Amblyomma maculatum ticks (Ixodida: Ixodidae) from Ecuador.

Rickettsiales are obligate intracellular bacteria that need vertebrates and arthropods to maintain their life cycles. Some species of the genera Anaplasma, Ehrlichia, and Rickettsia are transmitted by ticks to both animals and humans and can cause mild to severe and even fatal cases. In the Americas, there is substantial data on rickettsial agents, encompassing both clinical cases and the detection of these agents in ticks, but in Ecuador, the information about them remains poorly understood. Therefore, the objective of this study was to detect molecularly rickettsial agents in Amblyomma maculatum ticks in both parasitic and free-living phases collected from domestic animals and pasture in five localities across three coastal provinces of Ecuador. Rickettsia parkeri, Candidatus Rickettsia andeanae, and Ehrlichia sp. were recorded in A. maculatum for the first time in Ecuador. These records were made in a region where antibodies to the Spotted Fever Rickettsia Group were detected in humans. Additional studies are needed to characterize Ehrlichia sp. at a specific level. Furthermore, recognizing the specific Rickettsiales species circulating in the ticks and the hosts within a region is crucial for assessing potential contact risks.

Description of a new Dermacentor (Acari: Ixodidae) species, a parasite of wild mammals in Central America.

A new tick species belonging to the genus Dermacentor Koch, 1844, Dermacentor panamensis n. sp., is described. All stages of this species are similar to those of Dermacentor halli McIntosh, 1931, with which it was confused for a long time. Males of D. panamensis can be distinguished from those of D. halli by the following suite of characters: narrower conscutum, broader basis capituli, shorter dorsal cornua, narrower palpi, palpal segment III tapering to its apex, legs poorly ornate: ivory colored patches present only on dorsal aspects of leg segments (mostly on legs III and IV), and internal spur of coxae I narrower and more tapering. Females of D. panamensis can be distinguished from those of D. halli by the following suite of characters: narrower and less ornate scutum, broader basis capituli, shorter dorsal cornua, larger porose areas, narrower palpi, palpal segment III tapering to its apex, legs poorly ornate: ivory colored patches present only on dorsal aspects of leg segments (mostly on legs III and IV), and internal spur of coxae I narrower and more tapering. Nymphs of D. panamensis can be distinguished from those of D. halli by clear posterolateral projections of scutum and by absence of coxal "pore" on coxae I-IV, while larvae of D. panamensis can be distinguished from those ofD. halli by shorter and less sharp lateral projections of basis capituli dorsally and slightly sharp anterior angle of basis capituli. D. panamensis is known from highlands of Costa Rica, Guatemala, Honduras, Nicaragua, and Panama where the adults were collected from porcupines and unidentified sloth and mouse while nymphs and larvae were found on various rodents and a bat.

Description of two new species in the Ixodes ricinus complex from the New World (Acari: Ixodidae), and redescription of Ixodes affinis Neumann, 1899.

Ixodes chacoensis n. sp. is described based on males, females, nymphs and larvae collected from vegetation, ungulates and passerine birds in northeastern Argentina. Ixodes affinis Neumann, 1899 is redescribed based on the original type specimens (females) from Leopardus pardalis, and from recently collected specimens from Costa Rica. Ixodes keiransi n. sp., previously treated as North American populations of Ixodes affinis, is described based on males and females from carnivores and ungulates from the southeastern United States. Concatenated total evidence phylogenetics based on combined DNA sequence analyses from mitochondrial genes (12SrDNA, 16SrDNA and COI) and a nuclear gene (ITS2) corroborate the recognition of these species.

Perception of Ticks and Tick-Borne Diseases Worldwide.

In this comprehensive review study, we addressed the challenge posed by ticks and tick-borne diseases (TBDs) with growing incidence affecting human and animal health worldwide. Data and perspectives were collected from different countries and regions worldwide, including America, Europe, Africa, Asia, and Oceania. The results updated the current situation with ticks and TBD and how it is perceived by society with information bias and gaps. The study reinforces the importance of multidisciplinary and international collaborations to advance in the surveillance, communication and proposed future directions to address these challenges.

One Health Approach to Identify Research Needs on Rhipicephalus microplus Ticks in the Americas.

We aim to provide a harmonized view of the factors that affect the survival and promote the spread of R. microplus in the Neotropics, approaching its different facets of biology, ecology, distribution, and control. We review the interactions among environmental niche, landscape fragmentation, vegetal coverage (abiotic traits), and the biotic aspects of its ecology (abundance of domesticated or wild competent hosts), proposing emerging areas of research. We emphasize a holistic view integrating an economically and ecologically sustainable control of infestations and transmitted pathogens by R. microplus in the Neotropics. Examples of research link the trends of climate, the composition of the community of hosts, the landscape features, and a tailored management based on ecological grounds. Our view is that factors driving the spread of R. microplus are complex and deeply interrelated, something that has been seldom considered in control strategies. The effects of climate may affect the dynamics of wildlife or the landscape composition, promoting new patterns of seasonal activity of the tick, or its spread into currently free areas. In this paper we encourage a One Health approach highlighting the main aspects governing the components of the tick's life cycle and its interactions with livestock and wild animals.

Amplification and sequencing of entire tick mitochondrial genomes for a phylogenomic analysis.

The mitochondrial genome (mitogenome) has proven to be important for the taxonomy, systematics, and population genetics of ticks. However, current methods to generate mitogenomes can be cost-prohibitive at scale. To address this issue, we developed a cost-effective approach to amplify and sequence the whole mitogenome of individual tick specimens. Using two different primer sites, this approach generated two full-length mitogenome amplicons that were sequenced using the Oxford Nanopore Technologies' Mk1B sequencer. We used this approach to generate 85 individual tick mitogenomes from samples comprised of the three tick families, 11 genera, and 57 species. Twenty-six of these species did not have a complete mitogenome available on GenBank prior to this work. We benchmarked the accuracy of this approach using a subset of samples that had been previously sequenced by low-coverage Illumina genome skimming. We found our assemblies were comparable or exceeded the Illumina method, achieving a median sequence concordance of 99.98%. We further analyzed our mitogenome dataset in a mitophylogenomic analysis in the context of all three tick families. We were able to sequence 72 samples in one run and achieved a cost/sample of ~ $10 USD. This cost-effective strategy is applicable for sample identification, taxonomy, systematics, and population genetics for not only ticks but likely other metazoans; thus, making mitogenome sequencing equitable for the wider scientific community.

Free-living hard ticks (Ixodida: Ixodidae) from three different natural environments of Costa Rica.

This paper presents data on free-living ticks collected by flagging and using CO2 traps in three natural areas in Costa Rica: Carara National Park (CNP), Palo Verde National Park (PVNP), and a Private Forest Reserve in Sarapiquí (SPR). Data were analyzed calculating aspects of alpha diversity (species richness, entropy; dominance index, and evenness); and for beta diversity, compositional similarity between communities of ticks was also calculated. We collected 12,795 ticks belonging to 10 species: Amblyomma coelebs, Amblyomma dissimile, Amblyomma mixtum, Amblyomma naponense, Amblyomma cf. oblongoguttatum, Amblyomma cf. parvum, Amblyomma sabanerae, Amblyomma tapirellum, Haemaphysalis juxtakochi and Ixodes affinis. The number of species and individuals varied between sites: 5970 ticks were collected in CNP, 4443 in PVNP, and 2382 in SPR. Amblyomma cf. oblongoguttatum and A. cf. parvum were collected at all three sites, but A. mixtum was the most abundant species, even though it was not collected in SPR. Values of alpha diversity were calculated for CNP and SPR, while diversity in PVNP was the lowest of the three locations. Evenness was highest in SPR and lowest in CNP. The only community that presented dominance was PVNP. Beta diversity showed low similarity between the three locations with the lowest being CNP and SPR. For the three localities, estimates of the number of tick species based on presence/absence data was higher using flagging than CO2; and considering the stage of the ticks collected. More larvae were captured using CO2 traps than by flagging, while flagging was better for collecting adults. To our knowledge this is the first study in Costa Rica that compares these two sampling methods in three different environmental areas.

Fleas (Siphonaptera) Parasitizing Peridomestic and Indigenous Mammals in Panamá and Screening of Selected Fleas for Vector-Borne Bacterial Pathogens.

In total, 341 fleas belonging to 16 species were collected from 78 host mammals belonging to 10 species in Panamá from 2010 to 2016. The cat flea, Ctenocephalides felis (Bouché) predominated on domestic dogs and was also recorded from domestic cats, the raccoon, Procyon lotor (Linnaeus) and the common opossum, Didelphis marsupialis Linnaeus. The largest number of flea species (7) was recorded from D. marsupialis and the most common flea on that host was the ctenophthalmid, Adoratopsylla intermedia copha Jordan. One Oriental rat flea, Xenopsylla cheopis (Rothschild), was collected from D. marsupialis. Native rodents were parasitized by indigenous ceratophyllid, rhopalopsyllid, and stephanocircid fleas. The Mexican deermouse, Peromyscus mexicanus (Saussure), was parasitized by six species of ceratophyllids belonging to the mostly Central American genera, Baculomeris, Jellisonia, Kohlsia and Plusaetis. The long-tailed singing mouse, Scotinomys xerampelinus (Bangs), was parasitized by Plocopsylla scotinomi Tipton and Méndez, the only species of stephanocircid flea known from Central America. Twenty-six pools of extracted flea DNA representing 5 flea species (C. felis, Pulex echidnophagoides (Wagner), Pulex simulans Baker, A. intermedia copha, and P. scotinomi) and 79 individual fleas were all real-time polymerase chain reaction negative for Rickettsia felis, Rickettsia typhi, and Bartonella henselae.

Diversity of Rickettsia in ticks collected from wild animals in Panama.

This paper presents new data about Rickettsia species detected in ticks collected from wild animals, using 16S rRNA, gltA and ompA. Rickettsia DNA was found in 66 of 101 ticks. Using EZ BioCloud libraries were produced reads that identified Rickettsia aeschlimannii, and Illumina BaseSpace produced reads of Rickettsia rickettsii group, Rickettsia bellii group, and unclassified Rickettsia. Using gltA and ompA gene-specific primers, R. aeschlimannii could not be confirmed, but detection of Rickettsia amblyommatis was achieved in Amblyomma auricularium, Amblyomma geayi, Amblyomma mixtum, and Amblyomma pacae; R. bellii from Amblyomma dissimile, "Candidatus Rickettsia colombianensi" from A. dissimile, Rickettsia spp. closely related to R. raoultii from A. geayi, Rickettsia tamurae from A. dissimile, and Rickettsia endosymbionts of Ixodes from Ixodes affinis. There were no databases available specifically for 16S rRNA of Neotropical Rickettsia, highlighting the need to use species primers over only 16S rRNA primers to achieve more accurate interpretations and identifications. These findings increase the number of Rickettsia species detected in Panama and highlight the need to establish isolates to further characterize the nature of Rickettsia in the area.

Isolation and genetic characterization of a relapsing fever spirochete isolated from Ornithodoros puertoricensis collected in central Panama.

Tick-borne relapsing fever (TBRF) spirochetes are likely an overlooked cause of disease in Latin America. In Panama, the pathogens were first reported to cause human disease in the early 1900s. Recent collections of Ornithodoros puertoricensis from human dwellings in Panama prompted our interest to determine whether spirochetes still circulate in the country. Ornithodoros puertoricensis ticks were collected at field sites around the City of Panama. In the laboratory, the ticks were determined to be infected with TBRF spirochetes by transmission to mice, and we report the laboratory isolation and genetic characterization of a species of TBRF spirochete from Panama. Since this was the first isolation of a species of TBRF spirochete from Central America, we propose to designate the bacteria as Borrelia puertoricensis sp. nov. This is consistent with TBRF spirochete species nomenclature from North America that are designated after their tick vector. These findings warrant further investigations to assess the threat B. puertoricensis sp. nov. may impose on human health.