Dataset Information

Metagenomic profiles of Dermacentor tick pathogens from across Mongolia, using next generation sequencing.

ABSTRACT: Tick-borne diseases are a major public health concern in Mongolia. Nomadic pastoralists, which make up ~ 26% of Mongolia's population, are at an increased risk of both tick bite exposure and economic loss associated with clinical disease in herds. This study sought to further characterize tick-borne pathogens present in Dermacentor ticks (n = 1,773) sampled in 2019 from 15 of Mongolia's 21 aimags (provinces). The ticks were morphologically identified and sorted into 377 pools which were then screened using Next-Generation Sequencing paired with confirmatory PCR and DNA sequence analysis. Rickettsia spp. were detected in 88.33% of pools, while Anaplasma spp. and Bartonella spp. were detected in 3.18 and 0.79% of pools, respectively. Khentii had the highest infection rate for Rickettsia spp. (76.61%; CI: 34.65-94.79%), while Arkhangai had the highest infection rate for Anaplasma spp. (7.79%; CI:4.04-13.72%). The exclusive detection of Anaplasma spp. in tick pools collected from livestock supports previous work in this area that suggests livestock play a significant role in disease maintenance. The detection of Anaplasma, Bartonella, and Rickettsia demonstrates a heightened risk for infection throughout Mongolia, with this study, to our knowledge, documenting the first detection of Bartonella melophagi in ticks collected in Mongolia. Further research deploying NGS methods is needed to characterize tick-borne pathogens in other endemic tick species found in Mongolia, including Hyalomma asiaticum and Ixodes persulcatus.

SUBMITTER: Altantogtokh D

PROVIDER: S-EPMC9399792 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Metagenomic profiles of Dermacentor tick pathogens from across Mongolia, using next generation sequencing.

Altantogtokh Doniddemberel D Lilak Abigail A AA Takhampunya Ratree R Sakolvaree Jira J Chanarat Nitima N Matulis Graham G Poole-Smith Betty Katherine BK Boldbaatar Bazartseren B Davidson Silas S Hertz Jeffrey J Bolorchimeg Buyandelger B Tsogbadrakh Nyamdorj N Fiorenzano Jodi M JM Lindroth Erica J EJ von Fricken Michael E ME

Frontiers in microbiology 20220810

Tick-borne diseases are a major public health concern in Mongolia. Nomadic pastoralists, which make up ~ 26% of Mongolia's population, are at an increased risk of both tick bite exposure and economic loss associated with clinical disease in herds. This study sought to further characterize tick-borne pathogens present in Dermacentor ticks (n = 1,773) sampled in 2019 from 15 of Mongolia's 21 aimags (provinces). The ticks were morphologically identified and sorted into 377 pools which ...[more]

PMID: 36033893

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Project description:BackgroundHard ticks act as arthropod vectors in the transmission of human and animal pathogens and are widely distributed in northern China. The aim of this study is to screen the important tick-borne pathogens (TBPs) carried by hard ticks in Inner Mongolia using metagenomic next-generation sequencing (mNGS) and to estimate the risk of human infection imposed by tick bites.MethodsThe adult Dermacentor nuttalli (n = 203) and Ixodes persulcatus (n = 36) ticks feeding on cattle were collected. The pooled DNA samples prepared from these ticks were sequenced as the templates for mNGS to survey the presence of TBPs at the genus level. Individual tick DNA samples were detected by genus--specific or group-specific nested polymerase chain reaction (PCR) of these TBPs and combined with DNA sequencing assay to confirm the results of mNGS.ResultsR. raoultii (45.32%, 92/203), Candidatus R. tarasevichiae (5.42%, 11/203), Anaplasma sp. Mongolia (26.60%, 54/203), Coxiella-like endosymbiont (CLE) (53.69%, 109/203), and Babesia venatorum (7.88%, 16/203) were detected in D. nuttalli, while R. raoultii (30.56%, 11/36), Anaplasma sp. Mongolia (27.80%, 10/36), and CLE (27.80%, 10/36) were detected in I. persulcatus. The double- and triple-pathogen/endosymbiont co-infections were detected in 40.39% of D. nuttalli and 13.89% of I. persulcatus, respectively. The dual co-infection with R. raoultii and CLE (14.29%, 29/203) and triple co-infection with R. raoultii, Anaplasma sp. Mongolia, and CLE (13.79%, 28/203) were most frequent in D. nuttalli.ConclusionsThis study provides insight into the microbial diversity of D. nuttalli and I. persulcatus in Inner Mongolia, China, reporting for the first time that Candidatus R. tarasevichiae had been found in D. nuttalli in China, and for the first time in the world that Anaplasma sp. Mongolia has been detected in I. persulcatus. This study proves that various vertically transmitted pathogens co-inhabit D. nuttalli and I. persulcatus, and indicates that cattle in Inner Mongolia are exposed to several TBPs.

Project description:BackgroundThis study aimed to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) technology for identifying pathogens associated with spinal infection (SI).MethodsA retrospective analysis was conducted on clinical data from 193 patients with suspected SI between August 2020 and September 2024. Based on histopathological results, the patients were divided into the SI group (n=162) and the non-SI group (n=31). The diagnostic performance of mNGS technology was compared with that of laboratory examination, imaging examination, and microbial culture.ResultsAmong SI group, mNGS detected 135 pathogens in 77.78% (126/162) of the cases, including nine cases of multiple infections. One or more pathogens were detected using mNGS in 86 patients with SI and negative microbial cultures. Staphylococcus aureus (22.22%, n=30) and Mycobacterium tuberculosis (22.22%, n=30) were the major pathogens, while various rare pathogens such as anaerobes, Brucella, and Coxiella burnetii were also detected. For the 40 cases with positive results for both culture- and mNGS-based identification, high consistency (77.50%) was observed. Antibiotic use did not significantly affect the mNGS detection rate (P = 0.45). There was no significant difference in the positivity rate of mNGS between CT-guided needle biopsy (80.00%) and surgical sampling (77.17%) (P = 0.72). The sensitivity of mNGS (77.78%) was significantly higher than that of traditional microbial culture (27.16%), and the specificity was similar (90.32% vs. 96.77%). Although the sensitivities of erythrocyte sedimentation rate-based assay (91.36%), magnetic resonance imaging (88.27%), and C-reactive protein-based assay (87.65%) were better than those of mNGS, their specificities were generally low (20%-40%).ConclusionThe pathogens responsible for SI are complex and diverse. As a novel diagnostic method, mNGS exhibits a high sensitivity and extensive pathogen coverage for SI diagnosis. When combined with imaging and laboratory indicators, mNGS can significantly improve the accuracy of SI diagnosis and provide strong support for clinical treatment.

Project description:BACKGROUND: The introduction of benchtop sequencers has made adoption of whole genome sequencing possible for a broader community of researchers than ever before. Concurrently, metagenomic sequencing (MGS) is rapidly emerging as a tool for interrogating complex samples that defy conventional analyses. In addition, next-generation sequencers are increasingly being used in clinical or related settings, for instance to track outbreaks. However, information regarding the analytical sensitivity or limit of detection (LoD) of benchtop sequencers is currently lacking. Furthermore, the specificity of sequence information at or near the LoD is unknown. RESULTS: In the present study, we assess the ability of three next-generation sequencing platforms to identify a pathogen (viral or bacterial) present in low titers in a clinically relevant sample (blood). Our results indicate that the Roche-454 Titanium platform is capable of detecting Dengue virus at titers as low as 1X102.5 pfu/mL, corresponding to an estimated 5.4X104 genome copies/ml maximum. The increased throughput of the benchtop sequencers, the Ion Torrent PGM and Illumina MiSeq platforms, enabled detection of viral genomes at concentrations as low as 1X104 genome copies/mL. Platform-specific biases were evident in sequence read distributions as well as viral genome coverage. For bacterial samples, only the MiSeq platform was able to provide sequencing reads that could be unambiguously classified as originating from Bacillus anthracis. CONCLUSION: The analytical sensitivity of all three platforms approaches that of standard qPCR assays. Although all platforms were able to detect pathogens at the levels tested, there were several noteworthy differences. The Roche-454 Titanium platform produced consistently longer reads, even when compared with the latest chemistry updates for the PGM platform. The MiSeq platform produced consistently greater depth and breadth of coverage, while the Ion Torrent was unequaled for speed of sequencing. None of the platforms were able to verify a single nucleotide polymorphism responsible for antiviral resistance in an Influenza A strain isolated from the 2009 H1N1 pandemic. Overall, the benchtop platforms perform well for identification of pathogens from a representative clinical sample. However, unlike identification, characterization of pathogens is likely to require higher titers, multiple libraries and/or multiple sequencing runs.

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Metagenomic profiles of Dermacentor tick pathogens from across Mongolia, using next generation sequencing.

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Metagenomic profiles of <i>Dermacentor</i> tick pathogens from across Mongolia, using next generation sequencing.

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