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Masséglia S, René-Martellet M, Rates M, Hizo-Teufel C, Fingerle V, Margos G, Bailly X. Development and validation of a multi-target TaqMan qPCR method for detection of Borrelia burgdorferi sensu lato. J Microbiol Methods 2024; 222:106941. [PMID: 38714225 DOI: 10.1016/j.mimet.2024.106941] [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] [Received: 02/08/2024] [Revised: 04/05/2024] [Accepted: 04/30/2024] [Indexed: 05/09/2024]
Abstract
Reliable detection of bacteria belonging to the Borrelia burgdorferi sensu lato species complex in vertebrate reservoirs, tick vectors, and patients is key to answer questions regarding Lyme borreliosis epidemiology. Nevertheless, the description of characteristics of qPCRs for the detection of B. burgdorferi s. l. are often limited. This study covers the development and validation of two duplex taqman qPCR assays used to target four markers on the chromosome of genospecies of B. burgdorferi s. l. Analytical specificity was determined with a panel of spirochete strains. qPCR characteristics were specified using water or tick DNA spiked with controlled quantities of the targeted DNA sequences of B. afzelii, B. burgdorferi sensu stricto or B. bavariensis. The effectiveness of detection results was finally evaluated using DNA extracted from ticks and biopsies from mammals whose infectious status had been determined by other detection assays. The developed qPCR assays allow exclusive detection of B. burgdorferi s. l. with the exception of the M16 marker which also detect relapsing fever Borreliae. The limit of detection is between 10 and 40 copies per qPCR reaction depending on the sample type, the B. burgdorferi genospecies and the targeted marker. Detection tests performed on various kind of samples illustrated the accuracy and robustness of our qPCR assays. Within the defined limits, this multi-target qPCR method allows a versatile detection of B. burgdorferi s. l., regardless of the genospecies and the sample material analyzed, with a sensitivity that would be compatible with most applications and a reproducibility of 100% under measurement conditions of limits of detection, thereby limiting result ambiguities.
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Affiliation(s)
- Sébastien Masséglia
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France.
| | - Magalie René-Martellet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France; Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, F-69280 Marcy l'Etoile, France
| | - Maxime Rates
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France; Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, F-69280 Marcy l'Etoile, France
| | - Cecilia Hizo-Teufel
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany
| | - Gabriele Margos
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany
| | - Xavier Bailly
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France
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Mekata H, Yamada K, Umeki K, Yamamoto M, Ochi A, Umekita K, Kobayashi I, Hirai T, Okabayashi T. Nine-year seroepidemiological study of severe fever with thrombocytopenia syndrome virus infection in feral horses in Cape Toi, Japan. BMC Vet Res 2024; 20:190. [PMID: 38734647 PMCID: PMC11088034 DOI: 10.1186/s12917-024-04042-7] [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: 10/27/2023] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is a fatal zoonosis caused by ticks in East Asia. As SFTS virus (SFTSV) is maintained between wildlife and ticks, seroepidemiological studies in wildlife are important to understand the behavior of SFTSV in the environment. Miyazaki Prefecture, Japan, is an SFTS-endemic area, and approximately 100 feral horses, called Misaki horses (Equus caballus), inhabit Cape Toi in Miyazaki Prefecture. While these animals are managed in a wild-like manner, their ages are ascertainable due to individual identification. In the present study, we conducted a seroepidemiological survey of SFTSV in Misaki horses between 2015 and 2023. This study aimed to understand SFTSV infection in horses and its transmission to wildlife. A total of 707 samples from 180 feral horses were used to determine the seroprevalence of SFTSV using enzyme-linked immunosorbent assay (ELISA). Neutralization testing was performed on 118 samples. In addition, SFTS viral RNA was detected in ticks from Cape Toi and feral horses. The overall seroprevalence between 2015 and 2023 was 78.5% (555/707). The lowest seroprevalence was 55% (44/80) in 2016 and the highest was 92% (76/83) in 2018. Seroprevalence was significantly affected by age, with 11% (8/71) in those less than one year of age and 96.7% (435/450) in those four years of age and older (p < 0.0001). The concordance between ELISA and neutralization test results was 88.9% (105/118). SFTS viral RNA was not detected in ticks (n = 516) or feral horses. This study demonstrated that horses can be infected with SFTSV and that age is a significant factor in seroprevalence in wildlife. This study provides insights into SFTSV infection not only in horses but also in wildlife in SFTS-endemic areas.
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Affiliation(s)
- Hirohisa Mekata
- Division of Research & Inspection for Infectious Diseases, Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan.
| | - Kentaro Yamada
- Division of Research & Inspection for Infectious Diseases, Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
- Department of Microbiology, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita, 879-5593, Japan
| | - Kazumi Umeki
- Division of Respirology Rheumatology, Infectious Diseases and Neurology, Internal Medicine, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200-Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Mari Yamamoto
- Division of Research & Inspection for Infectious Diseases, Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
| | - Akihiro Ochi
- Equine Research Institute, Racing Association, 1400-4 Shiba, Shimotsuke, Tochigi, 329-0412, Japan
| | - Kunihiko Umekita
- Division of Research & Inspection for Infectious Diseases, Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
- Division of Respirology Rheumatology, Infectious Diseases and Neurology, Internal Medicine, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200-Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Ikuo Kobayashi
- Division of Research & Inspection for Infectious Diseases, Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
- Field Science Center, Faculty of Agriculture, University of Miyazaki, 10100-1 Shimanouchi, Miyazaki, 880-0121, Japan
| | - Takuya Hirai
- Division of Research & Inspection for Infectious Diseases, Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
| | - Tamaki Okabayashi
- Division of Research & Inspection for Infectious Diseases, Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai Nishi, Miyazaki, 889-2192, Japan
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Nienhold R, Mensah N, Frank A, Graber A, Koike J, Schwab N, Hernach C, Zsikla V, Willi N, Cathomas G, Hamelin B, Graf S, Junt T, Mertz KD. Unbiased screen for pathogens in human paraffin-embedded tissue samples by whole genome sequencing and metagenomics. Front Cell Infect Microbiol 2022; 12:968135. [PMID: 36204644 PMCID: PMC9530700 DOI: 10.3389/fcimb.2022.968135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022] Open
Abstract
Identification of bacterial pathogens in formalin fixed, paraffin embedded (FFPE) tissue samples is limited to targeted and resource-intensive methods such as sequential PCR analyses. To enable unbiased screening for pathogens in FFPE tissue samples, we established a whole genome sequencing (WGS) method that combines shotgun sequencing and metagenomics for taxonomic identification of bacterial pathogens after subtraction of human genomic reads. To validate the assay, we analyzed more than 100 samples of known composition as well as FFPE lung autopsy tissues with and without histological signs of infections. Metagenomics analysis confirmed the pathogenic species that were previously identified by species-specific PCR in 62% of samples, showing that metagenomics is less sensitive than species-specific PCR. On the other hand, metagenomics analysis identified pathogens in samples, which had been tested negative for multiple common microorganisms and showed histological signs of infection. This highlights the ability of this assay to screen for unknown pathogens and detect multi-microbial infections which is not possible by histomorphology and species-specific PCR alone.
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Affiliation(s)
- Ronny Nienhold
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Nadine Mensah
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Angela Frank
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Anne Graber
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Jacqueline Koike
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Nathalie Schwab
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Claudia Hernach
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Veronika Zsikla
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Niels Willi
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Gieri Cathomas
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Baptiste Hamelin
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Susanne Graf
- Central Laboratory, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Tobias Junt
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Kirsten D Mertz
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
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Co-infections with multiple pathogens in natural populations of Ixodes persulcatus ticks in Mongolia. Parasit Vectors 2022; 15:236. [PMID: 35765092 PMCID: PMC9238073 DOI: 10.1186/s13071-022-05356-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/10/2022] [Indexed: 12/11/2022] Open
Abstract
Background In Mongolia, the taiga tick Ixodes persulcatus is the major vector of tick-borne pathogens. Knowledge about co-infections of these pathogens in ticks is necessary both for understanding their persistence in nature and for diagnosing and treating tick-borne diseases. Methods The prevalence of seven tick-borne infections in 346 I. persulcatus collected from the Selenge and Bulgan provinces of Mongolia was evaluated using real-time PCR. Quantification of Borrelia spp. was performed using multiplex quantitative PCR targeting the 16S rRNA gene. Genetic analysis of Borrelia spp. in 11 ticks infected with Borrelia miyamotoi, including six ticks co-infected with Borrelia burgdorferi sensu lato (s.l.), was performed by high-throughput sequencing of the flaB gene fragment. Results Six ticks (1.7%) were infected with tick-borne encephalitis virus (TBEV); 171 (49.4%), with B. burgdorferi sensu lato; 17 (4.9%), with B. miyamotoi; 47 (13.6%), with Anaplasma phagocytophilum; and 56 (16.2%), with Ehrlichia sp. Neither Rickettsia sibirica nor R. heilongjiangensis were detected. Borrelia burgdorferi s.l. occurred as co-infection in 55 (32.2%) of all infected ticks. The other pathogens co-infected ticks in 58.8–70.2% of cases. No pairwise associations between co-infecting pathogens were observed, with the exception of a positive association between A. phagocytophilum and Ehrlichia sp. infections. The spirochete loads of B. miyamotoi were significantly higher than those of B. burgdorferi s.l. (mean: 5.2 vs 4.0 log10 genome copies/tick, respectively). Ten isolates of B. miyamotoi belonged to the Siberian lineage. Borrelia burgdorferi s.l was represented by nine isolates of B. afzelii, B. bavariensis and B. garinii. Conclusions In populations of I. persulcatus inhabiting the Selenge and Bulgan provinces of Mongolia, five vector-borne pathogens, i.e. TBEV, B. burgdorferi s.l., B. miyamotoi, A. phagocytophilum and Ehrlichia sp., persist independently from each other, with the exception of A. phagocytophilum and Ehrlichia sp. which seem to share the circulation mode. The discrepancies in B. burgdorferi s.l. and B. miyamotoi prevalence and spirochete load per tick suggest that different ecological niches are occupied by Lyme disease and relapsing fever agents. High-throughput sequencing allows genetic identification of borreliae species in co-infected ticks. Graphical Abstract ![]()
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Podbićanin-Ziburt A, Falk TM, Metze D, Böer-Auer A. Diagnosis of Lyme Borreliosis With a Novel, Seminested Real-Time Polymerase Chain Reaction Targeting the 5S-23S Intergenic Spacer Region: Clinical Features, Histopathology, and Immunophenotype in 44 Patients. Am J Dermatopathol 2022; 44:338-347. [PMID: 34966044 DOI: 10.1097/dad.0000000000002119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT Lyme borreliosis (LB) is the most common tick-borne infection in Europe and North America. Polymerase chain reaction (PCR) is an important tool to confirm the diagnosis, but not always successful, especially when organisms are sparse. We developed a novel, seminested real-time PCR assay [target: 5S-23S intergenic spacer region (IGS)] and compared it with 3 well-established conventional PCR assays (IGS/OspA/real-time IGS) on 596 formalin-fixed, paraffin-embedded routine skin biopsies. The seminested real-time assay identified 46 cases of borreliosis while 25, 27, and 38 were identified by the 3 other assays, respectively (P 0.01, P 0.02, and P 0.42; significance P < 0.05). Clinicopathologic and immunophenotypic analysis of PCR-positive cases revealed 38 erythema migrans (EM), 6 Borrelia lymphocytomas, and 2 acrodermatitis chronica atrophicans (ACA). In the 44 PCR-confirmed cases, plasma cells were present in only a third of EM cases. By contrast, CD123-positive plasmacytoid dendritic cells were common (74%) and therefore are unlikely to be helpful in the differential diagnosis between EM and tumid lupus erythematosus. A loss of CD34 in a third of all LB specimens limits its diagnostic value in the differential diagnosis with morphea. Interstitial macrophages were common in cutaneous LB (42/43) forming interstitial granulomas in a third of all cases, and 3/38 EM, 3/6 Borrelia lymphocytomas, and 1/2 ACA were only identified by the new seminested real-time assay, suggesting that it is especially helpful in confirming the diagnosis of Borrelia lymphocytoma.
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Affiliation(s)
| | | | - Dieter Metze
- Department of Dermatology, University of Münster, Münster, Germany
| | - Almut Böer-Auer
- Dermatologikum Hamburg, Hamburg, Germany ; and
- Department of Dermatology, University of Münster, Münster, Germany
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Simultaneous Detection and Differentiation of Clinically Relevant Relapsing Fever Borrelia with Semimultiplex Real-Time PCR. J Clin Microbiol 2021; 59:e0298120. [PMID: 33910966 DOI: 10.1128/jcm.02981-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial vector-borne diseases, including Borrelia species, present a significant diagnostic, clinical, and public health challenge due to their overlapping symptoms and the breadth of causative agents and arthropod vectors. The relapsing fever (RF) borreliae encompass both established and emerging pathogens and are transmitted to humans by soft ticks, hard ticks, or lice. We developed a real-time semimultiplex PCR assay that detects multiple RF borreliae causing human illness and classifies them into one of three groups. The groups are based on genetic similarity and include agents of soft-tick relapsing fever (Borrelia hermsii and others), the emerging hard-tick-transmitted pathogen B. miyamotoi, and the agent of louse-borne relapsing fever (B. recurrentis). The real-time PCR assay uses a single primer pair designed to amplify all known pathogenic RF borreliae and multiple TaqMan probes to allow the detection of and differentiation among the three groups. The assay detects all RF borreliae tested, with an analytical limit of detection below 15 genome equivalents per reaction. Thirty isolates of RF borreliae encompassing six species were accurately identified. Thirty-nine of 41 residual specimens (EDTA whole blood, serum, or plasma) from patients with RF were detected and correctly classified. None of 42 clinical samples from patients with other infections and 46 culture specimens from non-RF bacteria were detected. The development of a single-assay real-time PCR approach will help to improve the diagnosis of RF by simplifying the selection of tests to aid in the clinical management of acutely ill RF patients.
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Duplex TaqMan real-time PCR assay for simultaneous detection and quantification of Anaplasma capra and Anaplasma phagocytophilum infection. Mol Cell Probes 2019; 49:101487. [PMID: 31731011 DOI: 10.1016/j.mcp.2019.101487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/28/2019] [Accepted: 11/11/2019] [Indexed: 11/24/2022]
Abstract
Anaplasma capra and A. phagocytophilum, two species of the family Anaplasmataceae, are zoonotic tick-borne obligate intracellular bacteria affecting wild and domestic ruminants, dogs, cats, horses and humans. A. capra and A. phagocytophilum infections have been steadily increasing in both number and geographic distribution, and the accurate diagnosis of these infections is challenging. This study aimed to develop a rapid, sensitive and reliable duplex real-time PCR assay for the specific detection and differentiation of these Anaplasma species. We designed primers and probes against the conserved regions of A. capra groEL and A. phagocytophilum 16S rRNA genes. A range of PCR-related parameters were evaluated such as the dosage of primers and probes, and annealing temperature. The specificity, sensitivity and repeatability of this assay were evaluated. Assay performance was further evaluated using samples collected from 124 goats in four regions of Henan, China. This set of samples was also tested using conventional PCR under conditions previously described. The developed duplex real-time PCR assay allowed the simultaneous detection of A. capra and A. phagocytophilum in a reasonably short time at levels as small as 102 copies/μL, respectively, with optimal specificity and reproducibility. In addition, this duplex real-time PCR assay is the first DNA-based method designed to detect A. capra and A. phagocytophilum, and will be valuable for timely diagnosis and treatment of these infections.
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