A new genetic approach to distinguish strains of Anaplasma phagocytophilum that appear not to cause human disease

Geographic variation in the distribution of Anaplasma phagocytophilum variants in host-seeking Ixodes scapularis nymphs and adults in the eastern United States elucidated using next generation sequencing

Human anaplasmosis cases, caused by Anaplasma phagocytophilum, are increasing in the United States. This trend is explained, in part, by expansion in the geographic range of the primary vector, Ixodes scapularis. Multiple variants of A. phagocytophilum have been identified in field collected ticks, but only a single variant (human active, or "Ap-ha," variant) has been shown to be pathogenic in humans. Until recently, laboratory methods used to differentiate variants were cumbersome and seldomly used in large scale assessments of the pathogen's geographic distribution. As a result, many surveys reported A. phagocytophilum without segregating variants. Lack of discrimination among A. phagocytophilum variants could lead to overestimation of anaplasmosis risk to humans. Next Generation Sequencing (NGS) assays were recently developed to efficiently detect multiple Ixodes scapularis-borne human pathogens including Ap-ha. In this study, we utilized NGS to detect and differentiate A. phagocytophilum variants (Ap-ha vs. non ha) in host-seeking I. scapularis nymphs and adults collected across 23 states in the eastern United States from 2012 to 2023 as part of national tick surveillance efforts and research studies. Many of the included ticks were tested previously using a TaqMan PCR assay that could detect A. phagocytophilum but could not differentiate variants. We retested A. phagocytophilum infected ticks with NGS to differentiate variants. Anaplasma phagocytophilum (any variant) was identified in 165 (35 %) of 471 counties from which ticks were tested, whereas Ap-ha was detected in 70 (15 %) of 469 counties where variants were differentiated. Both variants were identified in 32 % (n = 40) of 126 counties with either variant detected. Among states where A. phagocytophilum (any variant) was detected, prevalence ranged from 2 % to 19 % in unfed adults and from 0.2 % to 7.8 % in unfed nymphs; prevalence of Ap-ha variant ranged from 0.0 % to 16 % in adults, and 0.0 % to 4.6 % in nymphs.

Prevalence of five human pathogens in host-seeking Ixodes scapularis and Ixodes pacificus by region, state, and county in the contiguous United States generated through national tick surveillance

The majority of vector-borne disease cases reported in the United States (U.S.) are caused by pathogens spread by the blacklegged tick, Ixodes scapularis. In recent decades, the geographic ranges of the tick and its associated human pathogens have expanded, putting an increasing number of communities at risk for tick-borne infections. In 2018, the U.S. Centers for Disease Control and Prevention (CDC) initiated a national tick surveillance program to monitor changes in the distribution and abundance of ticks and the presence and prevalence of human pathogens in them. We assessed the geographical representativeness of prevalence data submitted to CDC as part of the national tick surveillance effort. We describe county, state, and regional variation in the prevalence of five human pathogens (Borrelia burgdorferi sensu stricto (s.s.), Borrelia mayonii, Borrelia miyamotoi, Anaplasma phagocytophilum, and Babesia microti) in host-seeking I. scapularis and I. pacificus nymphs and adults. Although I. scapularis and I. pacificus are widely distributed in the eastern and western U.S., respectively, pathogen prevalence was estimated predominantly in ticks collected in the Northeast, Ohio Valley, and Upper Midwest regions, where human Lyme disease cases are most commonly reported. Within these regions, we found that state and regional estimates of pathogen prevalence generally reached predictable and stable levels, but variation in prevalence estimates at the sub-state level was considerable. Borrelia burgdorferi s.s. was the most prevalent and widespread pathogen detected. Borrelia miyamotoi and A. phagocytophilum shared a similarly broad geographic range, but were consistently detected at much lower prevalence compared with B. burgdorferi s.s. Babesia microti was detected at similar prevalence to A. phagocytophilum, where both pathogens co-occurred, but was reported over a much more limited geographic range compared with A. phagocytophilum or B. burgdorferi s.s. Borrelia mayonii was identified at very low prevalence with a focal distribution within the Upper Midwest. National assessments of risk for tick-borne diseases need to be improved through collection and testing of ticks in currently under-represented regions, including the West, South, Southeast, and eastern Plains states.

Distant genetic variants of Anaplasma phagocytophilum from Ixodes ricinus attached to people

BACKGROUND

Although the tick-borne pathogen Anaplasma phagocytophilum is currently described as a single species, studies using genetic markers can distinguish groups of variants associated with different hosts, pathogenicity, zoonotic potential and biotic and geographic niches. The objective of our study was to investigate the genetic diversity of A. phagocytophilum and Ixodes ricinus ticks attached to people.

METHODS

In collaboration with a commercial diagnostic company, a total of 52 DNA samples were obtained from ticks that tested positive for A. phagocytophilum by quantitative PCR. The genetic profile of each sample was determined using the groEL and ankA genes. Identification of the tick species was confirmed by partial sequencing of the COI subunit and a portion of the TROSPA gene.

RESULTS

All 52 ticks were identified as I. ricinus. Two protocols of nested PCR amplifying 1293- and 407-bp fragments of groEL of A. phagocytophilum yielded amplicons of the expected size for all 52 samples. Among all sequences, we identified 10 unique genetic variants of groEL belonging to ecotype I and ecotype II. The analysis targeting ankA was successful in 46 of 52 ticks. Among all sequences, we identified 21 unique genetic variants phylogenetically belonging to three clusters.

CONCLUSIONS

Our results indicate that ticks attached to people harbor distant genetic variants of A. phagocytophilum, some of which are not recognized as zoonotic. Further studies are needed to determine the risk of human infection by genetic variants other than those designated as zoonotic.

Using next generation sequencing for molecular detection and differentiation of Anaplasma phagocytophilum variants from host seeking Ixodes scapularis ticks in the United States

Anaplasmosis is increasingly common in the United States, with cases being reported over an expanding geographic area. To monitor for changes in risk of human infection, the U.S. Centers for Disease Control and Prevention monitors the distribution and abundance of host-seeking vector ticks (Ixodes scapularis and Ixodes pacificus) and their infection with Anaplasma phagocytophilum. While several variants of A. phagocytophilum circulate in I. scapularis, only the human-active variant (Ap-ha) appears to be pathogenic in humans. Failure to differentiate between human and non-human variants may artificially inflate estimates of the risk of human infection. Efforts to differentiate the Ap-ha variant from the deer variant (Ap-V1) in ticks typically rely on traditional PCR assays coupled with sequencing of PCR products. However, laboratories are increasingly turning to Next Generation Sequencing (NGS) to increase testing efficiency, retain high sensitivity, and increase specificity compared with traditional PCR assays. We describe a new NGS assay with novel targets that accurately segregate the Ap-ha variant from other non-human variants and further identify unique clades within the human and non-human variants. Recognizing that not all investigators have access to NGS technology, we also developed a PCR assay based on one of the novel targets so that variants can be visualized using agarose gel electrophoresis without the need for subsequent sequencing. Such an assay may be used to improve estimates of human risk of developing anaplasmosis in North America.

Comprehensive screening of tick-borne microorganisms indicates that a great variety of pathogens are circulating between hard ticks (Ixodoidea: Ixodidae) and domestic ruminants in natural foci of Anatolia

Grazing domestic ruminants serve as important reservoirs and/or amplificatory hosts in the ecology of tick-borne pathogens (TBPs) and tick vectors in the natural foci; however, many enzootic life cycles including ruminants and ticks are still unknown. This study investigated a wide range of TBPs circulating among ticks and grazing ruminants in the natural foci of Anatolia, Turkey. Tick specimens (n = 1815) were collected from cattle, sheep, and goats in three ecologically distinct areas (wooded, transitional, and semi-arid zones) of Anatolia and identified by species: Dermacentor marginatus, Dermacentor reticulatus, Hyalomma anatolicum, Hyalomma excavatum, Hyalomma marginatum, Hyalomma scupense, Haemaphysalis inermis, Haemaphysalis parva, Haemaphysalis punctata, Haemaphysalis sulcata, Ixodes ricinus, Rhipicephalus bursa, and Rhipicephalus turanicus. PCR-sequencing analyses revealed TBPs of great diversity, with 32 different agents identified in the ticks: six Babesia spp. (Babesia occultans, Babesia crassa, Babesia microti, Babesia rossi, Babesia sp. tavsan1, and Babesia sp. Ucbas); four Theileria spp., including one putative novel species (Theileria annulata, Theileria orientalis, Theileria ovis, and Theileria sp.); one Hepatozoon sp.; four Anaplasma spp., including one novel genotype (Anaplasma phagocytophilum, Anaplasma marginale, Anaplasma ovis, and Anaplasma sp.); six unnamed Ehrlichia spp. genotypes; Neoehrlichia mikurensis; nine spotted fever group rickettsiae, including one putative novel species (Rickettsia aeschlimannii, Rickettsia slovaca, Rickettsia hoogstraalii, Rickettsia monacensis with strain IRS3, Rickettsia mongolitimonae, Rickettsia raoultii, Candidatus Rickettsia goldwasserii, Candidatus Rickettsia barbariae, and Rickettsia sp.); and Borrelia valaisiana. Detailed phylogenetic analyses showed that some of the detected pathogens represent more than one haplotype, potentially relating to the tick species or the host. Additionally, the presence of Neoehrlichia mikurensis, an emerging pathogen for humans, was reported for the first time in Turkey, expanding its geographical distribution. Consequently, this study describes some previously unknown tick-borne protozoan and bacterial species/genotypes and provides informative epidemiological data on TBPs, which are related to animal and human health, serving the one health concept.