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Huggins LG, Colella V, Young ND, Traub RJ. Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites. Mol Ecol Resour 2024; 24:e13878. [PMID: 37837372 DOI: 10.1111/1755-0998.13878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/07/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023]
Abstract
Apicomplexan haemoparasites generate significant morbidity and mortality in humans and other animals, particularly in many low-to-middle income countries. Malaria caused by Plasmodium remains responsible for some of the highest numbers of annual deaths of any human pathogen, whilst piroplasmids, such as Babesia and Theileria can have immense negative economic effects through livestock loss. Diagnosing haemoparasites via traditional methods like microscopy is challenging due to low-level and transient parasitaemia. PCR-based diagnostics overcome these limitations by being both highly sensitive and specific, but they may be unable to accurately detect coinfections or identify novel species. In contrast, next-generation sequencing (NGS)-based methods can characterize all pathogens from a group of interest concurrently, although, the short-read platforms previously used have been limited in the taxonomic resolution achievable. Here, we used Oxford Nanopore Technologies' (ONT) long-read MinION™ sequencer to conduct apicomplexan haemoparasite metabarcoding via sequencing the near full-length 18S ribosomal RNA gene, demonstrating its ability to detect Babesia, Hepatozoon, Neospora, Plasmodium, Theileria and Toxoplasma species. This method was tested on blood-extracted DNA from 100 dogs and the results benchmarked against qPCR and Illumina-based metabarcoding. For two common haemoparasites, nanopore sequencing performed as well as qPCR (kappa agreement statistics > 0.98), whilst also detecting one pathogen, Hepatozoon felis, missed by the other techniques. The long-reads obtained by nanopore sequencing provide an improved species-level taxonomic resolution whilst the method's broad applicability mean it can be used to explore apicomplexan communities from diverse mammalian hosts, on a portable sequencer that easily permits adaptation to field use.
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Affiliation(s)
- Lucas G Huggins
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J Traub
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
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2
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Kapo N, Zuber Bogdanović I, Gagović E, Žekić M, Veinović G, Sukara R, Mihaljica D, Adžić B, Kadriaj P, Cvetkovikj A, Djadjovski I, Potkonjak A, Velo E, Savić S, Tomanović S, Omeragić J, Beck R, Hodžić A. Ixodid ticks and zoonotic tick-borne pathogens of the Western Balkans. Parasit Vectors 2024; 17:45. [PMID: 38297327 PMCID: PMC10832161 DOI: 10.1186/s13071-023-06116-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024] Open
Abstract
Ixodid ticks are distributed across all countries of the Western Balkans, with a high diversity of species. Many of these species serve as vectors of pathogens of veterinary and medical importance. Given the scattered data from Western Balkan countries, we have conducted a comprehensive review of available literature, including some historical data, with the aim to compile information about all recorded tick species and associated zoonotic pathogens in this region. Based on the collected data, the tick fauna of the Western Balkans encompasses 32 tick species belonging to five genera: Ixodes, Haemaphysalis, Dermacentor, Rhipicephalus and Hyalomma. A range of pathogens responsible for human diseases has also been documented, including viruses, bacteria and parasites. In this review, we emphasize the necessity for integrated surveillance and reporting, urging authorities to foster research by providing financial support. Additionally, international and interdisciplinary collaborations should be encouraged that include the exchange of expertise, experiences and resources. The present collaborative effort can effectively address gaps in our knowledge of ticks and tick-borne diseases.
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Affiliation(s)
- Naida Kapo
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Ema Gagović
- Department for Bacteriology and Parasitology, Laboratory for Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Marina Žekić
- Scientific Veterinary Institute "Novi Sad", Novi Sad, Serbia
| | - Gorana Veinović
- Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ratko Sukara
- Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Darko Mihaljica
- Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Bojan Adžić
- Diagnostic Veterinary Laboratory, Podgorica, Montenegro
| | - Përparim Kadriaj
- Vector Control Unit, Department of Epidemiology and Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
| | - Aleksandar Cvetkovikj
- Veterinary Institute, Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, North Macedonia
| | - Igor Djadjovski
- Veterinary Institute, Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, North Macedonia
| | - Aleksandar Potkonjak
- Department of Veterinary Medicine, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Enkelejda Velo
- Vector Control Unit, Department of Epidemiology and Control of Infectious Diseases, Institute of Public Health, Tirana, Albania
| | - Sara Savić
- Scientific Veterinary Institute "Novi Sad", Novi Sad, Serbia
| | - Snežana Tomanović
- Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jasmin Omeragić
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Relja Beck
- Department for Bacteriology and Parasitology, Laboratory for Parasitology, Croatian Veterinary Institute, Zagreb, Croatia.
| | - Adnan Hodžić
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science (CMESS), University of Vienna, Vienna, Austria.
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Moutailler S, Galon C. Real-Time Microfluidic PCRs: A High-Throughput Method to Detect 48 or 96 Tick-borne Pathogens in 48 or 96 Samples. Methods Mol Biol 2024; 2742:1-17. [PMID: 38165611 DOI: 10.1007/978-1-0716-3561-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Tick-borne pathogens (TBPs) are often detected through classical molecular tools (PCR, nested PCR, real-time PCR), but these are limited in terms of the number of targeted pathogens due to the volume of DNA available for analysis. To solve this problem, in 2014 we developed a new high-throughput method based on real-time microfluidic PCRs that can detect 48 or 96 pathogens in 48 or 96 samples in a single run, such as ten species from the Borrelia burgdorferi sensu lato group. We then used this technique for large-scale epidemiological studies of TBPs in tick and animal samples on an international scale through numerous collaborative projects.
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Affiliation(s)
- Sara Moutailler
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France.
| | - Clemence Galon
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
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Corduneanu A, Zając Z, Kulisz J, Wozniak A, Foucault-Simonin A, Moutailler S, Wu-Chuang A, Peter Á, Sándor AD, Cabezas-Cruz A. Detection of bacterial and protozoan pathogens in individual bats and their ectoparasites using high-throughput microfluidic real-time PCR. Microbiol Spectr 2023; 11:e0153123. [PMID: 37606379 PMCID: PMC10581248 DOI: 10.1128/spectrum.01531-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/05/2023] [Indexed: 08/23/2023] Open
Abstract
Among the most studied mammals in terms of their role in the spread of various pathogens with possible zoonotic effects are bats. These are animals with a very complex lifestyle, diet, and behavior. They are able to fly long distances, thus maintaining and spreading the pathogens they may be carrying. These pathogens also include vector-borne parasites and bacteria that can be spread by ectoparasites such as ticks and bat flies. In the present study, high-throughput screening was performed and we detected three bacterial pathogens: Bartonella spp., Neoehrlichia mikurensis and Mycoplasma spp., and a protozoan parasite: Theileria spp. in paired samples from bats (blood and ectoparasites). In the samples from the bat-arthropod pairs, we were able to detect Bartonella spp. and Mycoplasma spp. which also showed a high phylogenetic diversity, demonstrating the importance of these mammals and the arthropods associated with them in maintaining the spread of pathogens. Previous studies have also reported the presence of these pathogens, with one exception, Neoehrlichia mikurensis, for which phylogenetic analysis revealed less genetic divergence. High-throughput screening can detect more bacteria and parasites at once, reduce screening costs, and improve knowledge of bats as reservoirs of vector-borne pathogens. IMPORTANCE The increasing number of zoonotic pathogens is evident through extensive studies and expanded animal research. Bats, known for their role as reservoirs for various viruses, continue to be significant. However, new findings highlight the emergence of Bartonella spp., such as the human-infecting B. mayotimonensis from bats. Other pathogens like N. mikurensis, Mycoplasma spp., and Theileria spp. found in bat blood and ectoparasites raise concerns, as their impact remains uncertain. These discoveries underscore the urgency for heightened vigilance and proactive measures to understand and monitor zoonotic pathogens. By deepening our knowledge and collaboration, we can mitigate these risks, safeguarding human and animal well-being.
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Affiliation(s)
- Alexandra Corduneanu
- Department of Animal Breeding and Animal Production, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Zbigniew Zając
- Department of Biology and Parasitology, Medical University of Lublin, Lublin, Poland
| | - Joanna Kulisz
- Department of Biology and Parasitology, Medical University of Lublin, Lublin, Poland
| | - Aneta Wozniak
- Department of Biology and Parasitology, Medical University of Lublin, Lublin, Poland
| | - Angélique Foucault-Simonin
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Sara Moutailler
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Áron Peter
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Attila D. Sándor
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
- ELKH-ÁTE Climate Change: New Blood-sucking Parasites and Vector-borne Pathogens Research Group, Budapest, Hungary
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
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Huggins LG, Baydoun Z, Mab R, Khouri Y, Schunack B, Traub RJ, Colella V. Transmission of haemotropic mycoplasma in the absence of arthropod vectors within a closed population of dogs on ectoparasiticides. Sci Rep 2023; 13:10143. [PMID: 37349533 PMCID: PMC10287653 DOI: 10.1038/s41598-023-37079-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Dog-infecting haemotropic mycoplasmas (haemoplasmas), such as Mycoplasma haemocanis and Candidatus Mycoplasma haematoparvum are common blood-borne pathogens of canines that can potentially inflict a substantial burden of disease, particularly in immunosuppressed individuals. Nonetheless, the transmission of these pathogens remains debated as more evidence emerges that they may not be transmitted by vectors, but instead use alternative methods such as aggressive interactions and vertical transmission. Here, we treated forty dogs with two different topically-acting ectoparasiticide products able to prevent vector-borne pathogen infections during an 8-month community trial in Cambodia. A total absence of ectoparasites were observed at all time points, and no new infections caused by pathogens confirmed as being vectorially-transmitted were detected, i.e., Babesia vogeli, Ehrlichia canis, Anaplasma platys, and Hepatozoon canis. Conversely, the number of haemoplasma infections in dogs on both ectoparasiticides rose significantly, with an incidence of 26 infections per 100 dogs at risk per year, providing strong evidence of non-vectorial transmission. Over the study period, dog aggression and fighting were frequently observed, highlighting a different potential mode of transmission. This study presents the first robust evidence that canine haemoplasmas may be transmitted without arthropod vectors drawing attention to the need for new methods to prevent their transmission.
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Affiliation(s)
- Lucas G Huggins
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia.
| | - Zahida Baydoun
- Animal Mama Veterinary Hospital, Phnom Penh, 12312, Cambodia
| | - Ron Mab
- Animal Mama Veterinary Hospital, Phnom Penh, 12312, Cambodia
| | - Yulia Khouri
- Animal Mama Veterinary Hospital, Phnom Penh, 12312, Cambodia
| | | | - Rebecca J Traub
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Vito Colella
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, VIC, 3050, Australia.
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Huggins LG, Colella V, Atapattu U, Koehler AV, Traub RJ. Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma. Microbiol Spectr 2022; 10:e0308822. [PMID: 36250862 PMCID: PMC9769565 DOI: 10.1128/spectrum.03088-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 01/09/2023] Open
Abstract
Dogs across the globe are afflicted by diverse blood- and vector-borne bacteria (VBB), many of which cause severe disease and can be fatal. Diagnosis of VBB infections can be challenging due to the low concentration of bacteria in the blood, the frequent occurrence of coinfections, and the wide range of known, emerging, and potentially novel VBB species encounterable. Therefore, there is a need for diagnostics that address these challenges by being both sensitive and capable of detecting all VBB simultaneously. We detail the first employment of a nanopore-based sequencing methodology conducted on the Oxford Nanopore Technologies (ONT) MinION device to accurately elucidate the "hemobacteriome" from canine blood through sequencing of the full-length 16S rRNA gene. We detected a diverse range of important canine VBB, including Ehrlichia canis, Anaplasma platys, Mycoplasma haemocanis, Bartonella clarridgeiae, "Candidatus Mycoplasma haematoparvum", a novel species of hemotropic mycoplasma, and Wolbachia endosymbionts of filarial worms, indicative of filariasis. Our nanopore-based protocol was equivalent in sensitivity to both quantitative PCR (qPCR) and Illumina sequencing when benchmarked against these methods, achieving high agreement as defined by the kappa statistics (k > 0.81) for three key VBB. Utilizing the ability of the ONT' MinION device to sequence long read lengths provides an excellent alternative diagnostic method by which the hemobacteriome can be accurately characterized to the species level in a way previously unachievable using short reads. We envision our method to be translatable to multiple contexts, such as the detection of VBB in other vertebrate hosts, including humans, while the small size of the MinION device is highly amenable to field use. IMPORTANCE Blood- and vector-borne bacteria (VBB) can cause severe pathology and even be lethal for dogs in many regions across the globe. Accurate characterization of all the bacterial pathogens infecting a canine host is critical, as coinfections are common and emerging and novel pathogens that may go undetected by traditional diagnostics frequently arise. Deep sequencing using devices from Oxford Nanopore Technologies (ONT) provides a solution, as the long read lengths achievable provide species-level taxonomic identification of pathogens that previous short-read technologies could not accomplish. We developed a protocol using ONT' MinION sequencer to accurately detect and classify a wide spectrum of VBB from canine blood at a sensitivity comparable to that of regularly used diagnostics, such as qPCR. This protocol demonstrates great potential for use in biosurveillance and biosecurity operations for the detection of VBB in a range of vertebrate hosts, while the MinION sequencer's portability allows this method to be used easily in the field.
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Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ushani Atapattu
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
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