Self-reported tick exposure as an indicator of Lyme disease risk in an endemic region of Quebec, Canada.

BACKGROUND: Lyme disease (LD) and other tick-borne diseases are emerging across Canada. Spatial and temporal LD risk is typically estimated using acarological surveillance and reported human cases, the former not considering human behavior leading to tick exposure and the latter occurring after infection. OBJECTIVES: The primary objective was to explore, at the census subdivision level (CSD), the associations of self-reported tick exposure, alternative risk indicators (predicted tick density, eTick submissions, public health risk level), and ecological variables (Ixodes scapularis habitat suitability index and cumulative degree days > 0 °C) with incidence proportion of LD. A secondary objective was to explore which of these predictor variables were associated with self-reported tick exposure at the CSD level. METHODS: Self-reported tick exposure was measured in a cross-sectional populational health survey conducted in 2018, among 10,790 respondents living in 116 CSDs of the Estrie region, Quebec, Canada. The number of reported LD cases per CSD in 2018 was obtained from the public health department. Generalized linear mixed-effets models accounting for spatial autocorrelation were built to fulfill the objectives. RESULTS: Self-reported tick exposure ranged from 0.0 % to 61.5 % (median 8.9 %) and reported LD incidence rates ranged from 0 to 324 cases per 100,000 person-years, per CSD. A positive association was found between self-reported tick exposure and LD incidence proportion (ß = 0.08, CI = 0.04,0.11, p < 0.0001). The best-fit model included public health risk level (AIC: 144.2), followed by predicted tick density, ecological variables, self-reported tick exposure and eTick submissions (AIC: 158.4, 158.4, 160.4 and 170.1 respectively). Predicted tick density was the only significant predictor of self-reported tick exposure (ß = 0.83, CI = 0.16,1.50, p = 0.02). DISCUSSION: This proof-of-concept study explores self-reported tick exposure as a potential indicator of LD risk using populational survey data. This approach may offer a low-cost and simple tool for evaluating LD risk and deserves further evaluation.

Surveillance for Ixodes scapularis and Ixodes pacificus ticks and their associated pathogens in Canada, 2020.

Background: Ixodes scapularis and Ixodes pacificus ticks are the principal vectors of the agent of Lyme disease and several other tick-borne diseases in Canada. Tick surveillance data can be used to identify local tick-borne disease risk areas and direct public health interventions. The objective of this article is to describe the seasonal and spatial characteristics of the main Lyme disease vectors in Canada, and the tick-borne pathogens they carry, using passive and active surveillance data from 2020. Methods: Passive and active surveillance data were compiled from the National Microbiology Laboratory Branch (Public Health Agency of Canada), provincial and local public health authorities, and eTick (an online, image-based platform). Seasonal and spatial analyses of ticks and their associated pathogens are presented, including infection prevalence estimates. Results: In passive surveillance, I. scapularis (n=7,534) were submitted from all provinces except Manitoba and British Columbia, while I. pacificus (n=718) were submitted only from British Columbia. No ticks were submitted from the Territories. The seasonal distribution of I. scapularis submissions was bimodal, but unimodal for I. pacificus. Four tick-borne pathogens were identified in I. scapularis (Borrelia burgdorferi, Anaplasma phagocytophilum, Babesia microti and Borrelia miyamotoi) and one in I. pacificus (B. miyamotoi). In active surveillance, I. scapularis (n=688) were collected in Ontario, Québec and New Brunswick. Five tick-borne pathogens were identified: B. burgdorferi, A. phagocytophilum, B. microti, B. miyamotoi and Powassan virus. Conclusion: This article provides a snapshot of the distribution of I. scapularis and I. pacificus and their associated human pathogens in Canada in 2020, which can help assess the risk of exposure to tick-borne pathogens in different provinces.

DNA barcoding of the leaf-miner flies (Diptera, Agromyzidae) of Mitaraka, French Guiana.

Species level identification of Agromyzidae based on morphology is often challenging due to their small size and morphological homogeneity. DNA barcoding has been used regularly to assist with the identification of economically important species of Agromyzidae, but rarely as a tool for species delineation or identification in biodiversity surveys. The main objective of this study was to investigate whether DNA barcoding and the BIN (Barcoding Index) system could assist with species identification, species delineation, male/ female association, and diversity assessment of Agromyzidae material previously determined to morphospecies from Mitaraka, French Guiana. Amplification success was low, with sequences over 400 bp recovered for only 24 (48%) of the selected specimens. Sequences assigned to 17 morphospecies formed 16 distinct branches or clusters separated by very high (minimum of 10%) sequence divergence. Following the reassessment and subsequent reassignment of one specimen, congruence between morphology and DNA barcodes was high with a single instance of two morphospecies sharing identical sequences. While DNA barcoding did not assist with identification (none of our sequences matched those of named taxa in BOLD or GenBank), it did provide support for most of our morphospecies concepts, including male/female associations. The BIN system also provided access to information about the distribution and habitat preferences of several taxa. We conclude that DNA barcoding was a useful approach to study the species diversity of our samples but that much work remains to be done before it can be used as an identification tool for the Agromyzidae fauna of Mitaraka and the rest of the Neotropical region.

Review of the North American fauna of Drymeia Meigen (Diptera, Muscidae) and evaluation of DNA barcodes for species-level identification in the genus.

The North American fauna of Drymeia Meigen was studied. Four new species are described (Drymeia hucketti sp. nov., Drymeia ponti sp. nov., Drymeia vockerothi sp. nov., Drymeia woodorum sp. nov.), and three new synonymies are proposed: Drymeia amnicola (Huckett, 1966) (= Drymeia rivalis (Huckett, 1966), syn. nov.); Drymeia glacialis (Rondani, 1866) (= Drymeia alpicola (Rondani, 1871), syn. nov.); and Drymeia spinitarsis (Aldrich, 1918) (= Drymeia longiseta Sorokina & Pont, 2015, syn. nov.). An annotated checklist, DNA barcodes (when available), and keys for each sex of the 24 named species of North American Drymeia are provided. The utility of DNA barcodes for the identification of Drymeia species across a wide geographical range was explored using sequences from five countries. A match between morphology and DNA barcodes was found for 71% (22/31) of species studied (including three unnamed taxa). The remaining nine species clustered into two groups of taxa with very little interspecific variation within clusters (groups of two and seven species). Caution is advised against using DNA barcoding as the only determination tool for Drymeia material without prior knowledge of its limitations for certain species groups.

A HRM Assay for Rapid Identification of Members of the Seedcorn Maggot Complex (Delia florilega and D. platura) (Diptera: Anthomyiidae) and Evidence of Variation in Temporal Patterns of Larval Occurrence.

The seedcorn maggot Delia platura (Meigen), and the bean seed maggot Delia florilega (Zetterstedt) can cause considerable feeding damage to a wide range of cultivated crops. The recent discovery of two distinct genetic lines of D. platura, each with a unique distribution pattern overlapping only in eastern Canada, suggests the presence of a new cryptic species for the group. The reliable identification of the three species/lines in the seedcorn maggot complex is crucial to our understanding of their distribution, phenology, and respective contribution to crop damage as well as to the development of specific integrated pest management approaches. As these taxa are morphologically indistinguishable in the immature stages, we developed a high-resolution melting PCR (HRM) assay using primers amplifying a variable 96-bp PCR product in the CO1 mitochondrial gene for rapid and economical identification of specimens. The three species/lines exhibited distinguishable melting profiles based on their different Tm values (between 0.4 and 0.9°C) and identification results based on HRM and DNA sequencing were congruent for all specimens in the validation data set (n = 100). We then used the new, highly sensitive HRM assay to identify survey specimens from the seedcorn maggot complex collected in Quebec, Canada, between 2017 and 2019. Progress curves developed to document the temporal occurrence patterns of each species/lines indicate differences between taxa, with the N-line (BOLD:AAA3453) of D. platura appearing approximately 17 d before D. florilega (BOLD:ACR4394) and the H-line (BOLD:AAG2511) of D. platura.

Identification of Delia spp. (Robineau-Desvoidy) (Diptera, Anthomyiidae) and its cruciferous hosts in Mexico.

Soil pests of cruciferous crops in Mexico have been gaining importance in recent years; such is the case of Delia spp. (Robineau-Desvoidy) (Diptera, Anthomyiidae), of which, to date, there are no studies on the correct identification of associated species, as well as the range of hosts. In an integrated pest management program, it is essential to know this information to design and implement adequate phytosanitary measures. Plants infested by Delia spp. were collected in the states of Guanajuato, Puebla, and Mexico from June to November 2017 and March to December 2018 in commercial plantations of cruciferous crops (Brassica oleracea L. var. italica, botrytis and capitata), B. napus L., and Raphanus sativus L.) as well as some cruciferous weeds (R. raphanistrum L., Sisymbrium irio L., B. campestris L., Capsella bursa-pastoris L., and Lepidium virginicum L.) in the edges of these crops. The two species found in this study, Delia planipalpis (Stein) and Delia platura (Meigen), identified using male genitalia was corroborated by molecular techniques. Both species emerged from all the sampled hosts, except for C. bursa-pastoris and L. virginicum. The association of the two species in cruciferous crops and weeds, provides valuable information for the management of these insects not only in cruciferous crops but other ones that are strongly attacked by D. platura.

Individual and environmental determinants of Cuterebra bot fly parasitism in the eastern chipmunk (Tamias striatus).

Understanding the interactions between parasites, hosts, and their shared environment is central to ecology. Variation in infestation prevalence may be the result of varying environmental and population characteristics; however, variations in parasitism may also depend on individual characteristics that influence both the exposure and susceptibility to parasites. Using 12 years of data from a population of wild eastern chipmunks relying on pulsed food resources, we investigated the determinants of bot fly parasitism at both the population and individual level. We assessed the relationship between infestation prevalence and weather conditions, population size and food abundance. Then, we assessed the relationship between infestation intensity and chipmunk behavior, sex, age, body mass and food abundance. Precipitation, temperature and population size were positively related to infestation prevalence, while beech masts were negatively related to infestation prevalence, highlighting the importance of local environmental conditions on hosts and parasites. We also found that the influence of activity and exploration on infestation intensity varied according to sex in adults. More active and faster exploring males had more parasites compared to females, suggesting that reproductive behaviors may influence parasite exposure. For juveniles, infestation intensity was greater when juveniles emerged in the spring as opposed to fall, possibly because spring emergence is synchronized with the peak of bot fly eggs in the environment, low food availability and longer activity period. Our results suggest that the environmental, population and host characteristics that are advantageous for reproduction and resource acquisition may come at the cost of increasing parasitism.

Diptera of Canada.

The Canadian Diptera fauna is updated. Numbers of species currently known from Canada, total Barcode Index Numbers (BINs), and estimated numbers of undescribed or unrecorded species are provided for each family. An overview of recent changes in the systematics and Canadian faunistics of major groups is provided as well as some general information on biology and life history. A total of 116 families and 9620 described species of Canadian Diptera are reported, representing more than a 36% increase in species numbers since the last comparable assessment by JF McAlpine et al. (1979). Almost 30,000 BINs have so far been obtained from flies in Canada. Estimates of additional number of species remaining to be documented in the country range from 5200 to 20,400.

Comprehensive inventory of true flies (Diptera) at a tropical site.

Estimations of tropical insect diversity generally suffer from lack of known groups or faunas against which extrapolations can be made, and have seriously underestimated the diversity of some taxa. Here we report the intensive inventory of a four-hectare tropical cloud forest in Costa Rica for one year, which yielded 4332 species of Diptera, providing the first verifiable basis for diversity of a major group of insects at a single site in the tropics. In total 73 families were present, all of which were studied to the species level, providing potentially complete coverage of all families of the order likely to be present at the site. Even so, extrapolations based on our data indicate that with further sampling, the actual total for the site could be closer to 8000 species. Efforts to completely sample a site, although resource-intensive and time-consuming, are needed to better ground estimations of world biodiversity based on limited sampling.

Remarkable fly (Diptera) diversity in a patch of Costa Rican cloud forest: Why inventory is a vital science.

Study of all flies (Diptera) collected for one year from a four-hectare (150 x 266 meter) patch of cloud forest at 1,600 meters above sea level at Zurquí de Moravia, San José Province, Costa Rica (hereafter referred to as Zurquí), revealed an astounding 4,332 species. This amounts to more than half the number of named species of flies for all of Central America. Specimens were collected with two Malaise traps running continuously and with a wide array of supplementary collecting methods for three days of each month. All morphospecies from all 73 families recorded were fully curated by technicians before submission to an international team of 59 taxonomic experts for identification.        Overall, a Malaise trap on the forest edge captured 1,988 species or 51% of all collected dipteran taxa (other than of Phoridae, subsampled only from this and one other Malaise trap). A Malaise trap in the forest sampled 906 species. Of other sampling methods, the combination of four other Malaise traps and an intercept trap, aerial/hand collecting, 10 emergence traps, and four CDC light traps added the greatest number of species to our inventory. This complement of sampling methods was an effective combination for retrieving substantial numbers of species of Diptera. Comparison of select sampling methods (considering 3,487 species of non-phorid Diptera) provided further details regarding how many species were sampled by various methods.        Comparison of species numbers from each of two permanent Malaise traps from Zurquí with those of single Malaise traps at each of Tapantí and Las Alturas, 40 and 180 km distant from Zurquí respectively, suggested significant species turnover. Comparison of the greater number of species collected in all traps from Zurquí did not markedly change the degree of similarity between the three sites, although the actual number of species shared did increase.        Comparisons of the total number of named and unnamed species of Diptera from four hectares at Zurquí is equivalent to 51% of all flies named from Central America, greater than all the named fly fauna of Colombia, equivalent to 14% of named Neotropical species and equal to about 2.7% of all named Diptera worldwide. Clearly the number of species of Diptera in tropical regions has been severely underestimated and the actual number may surpass the number of species of Coleoptera.        Various published extrapolations from limited data to estimate total numbers of species of larger taxonomic categories (e.g., Hexapoda, Arthropoda, Eukaryota, etc.) are highly questionable, and certainly will remain uncertain until we have more exhaustive surveys of all and diverse taxa (like Diptera) from multiple tropical sites.        Morphological characterization of species in inventories provides identifications placed in the context of taxonomy, phylogeny, form, and ecology. DNA barcoding species is a valuable tool to estimate species numbers but used alone fails to provide a broader context for the species identified.

DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits.

BACKGROUND: Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. RESULTS: Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. CONCLUSIONS: Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.