Metagenomic 16S rRNA gene sequencing survey of  Borrelia  species in Irish samples of  Ixodes ricinus  ticks

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Abstract

The spirochetal bacterium Borrelia miyamotoi is a human pathogen and has been identified in many countries throughout the world. This study reports for the first time the presence of Borrelia miyamotoi in Ireland, and confirms prior work with the detection of B. garinii and B. valaisiana infected tick s. Questing Ixodes ricinus nymph samples were taken at six localities within Ireland. DNA extraction followed by Sanger sequencing was used to identify the species and strains present in each tick. The overall rate of borrelial infection in the Irish tick population was 5%, with a range from 2% to 12% depending on the locations of tick collection. The most prevalent species detected was B. garinii (70%) followed by B. valaisiana (20%) and B. miyamotoi (10%). Knowledge of Borrelia species prevalence is important and will guide appropriate selection of antigens for serology test kit manufacture, help define the risk of infection, and allow medical authorities to formulate appropriate strategies and guidelines for diagnosis and treatment of Borrelia diseases.

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Most cited references 15

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Genetic and phenotypic analysis of Borrelia miyamotoi sp. nov., isolated from the ixodid tick Ixodes persulcatus, the vector for Lyme disease in Japan.

M. Fukunaga, Y. Takahashi, Y Tsuruta … (1995)

The ixodid tick Ixodes persulcatus is the most important vector of Lyme disease in Japan. Most spirochete isolates obtained from I. persulcatus ticks have been classified as Borrelia burgdorferi sensu lato because of their genetic, biological, and immunological characteristics. However, we found that a small number of isolates obtained from I. persulcatus contained a smaller 38-kDa endoflagellar protein and single 23S-5S rRNA gene unit. Representative isolate HT31T (T = type strain) had the same 23S rRNA gene physical map as Borrelia turicatae. The DNA base composition of strain HT31T was 28.6 mol% G+C. DNA-DNA hybridization experiments revealed that strain HT31T exhibited moderate levels of DNA relatedness (24 to 51%) with Borrelia hermsii, B. turicatae, Borrelia parkeri, and Borrelia coriaceae. However, the levels of DNA reassociation with the previously described Lyme disease borreliae (B. burgdorferi, Borrelia garinii, and Borrelia afzelii) were only 8 to 13%. None of the previously described species examined exhibited a high level of DNA relatedness with strain HT31T. In addition, the 16S rRNA gene sequence (length, 1,368 nucleotides) of strain HT31T was determined and aligned with the 16S rRNA sequences of other Borrelia species. Distance matrix analyses were performed, and a phylogenetic tree was constructed. The results showed that isolate HT31T is only distantly related to both previously described Lyme disease borreliae and relapsing fever borreliae. Thus, the spirochetes isolated from I. persulcatus and closely related isolates should be classified as members of a new Borrelia species. We propose the name Borrelia miyamotoi sp. nov. for this spirochete; strain HT31 is the type strain.

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Genetic diversity of ospC in a local population of Borrelia burgdorferi sensu stricto.

I N Wang, D Dykhuizen, W Qiu … (1998)

The outer surface protein, OspC, is highly variable in Borrelia burgdorferi sensu stricto, the agent of Lyme disease. We have shown that even within a single population OspC is highly variable. The variation of ospA and ospC in the 40 infected deer ticks collected from a single site on Shelter Island, New York, was determined using PCR-SSCP. There is very strong apparent linkage disequilibrium between ospA and ospC alleles, even though they are located on separate plasmids. Thirteen discernible SSCP mobility classes for ospC were identified and the DNA sequence for each was determined. These sequences, combined with 40 GenBank sequences, allow us to define 19 major ospC groups. Sequences within a major ospC group are, on average, <1% different from each other, while sequences between major ospC groups are, on average, approximately 20% different. The tick sample contains 11 major ospC groups, GenBank contains 16 groups, with 8 groups found in both samples. Thus, the ospC variation within a local population is almost as great as the variation of a similar-sized sample of the entire species. The Ewens-Watterson-Slatkin test of allele frequency showed significant deviation from the neutral expectation, indicating balancing selection for these major ospC groups. The variation represented by major ospC groups needs to be considered if the OspC protein is to be used as a serodiagnostic antigen or a vaccine.

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Prevalence of Borrelia miyamotoi in Ixodes Ticks in Europe and the United States

Chris D Crowder, Heather E. Carolan, Megan A. Rounds … (2014)

Ixodes ticks can transmit a variety of pathogens, including viruses, bacteria, and protozoa ( 1 ). Borrelia spirochetes are one of the genera of bacteria transmitted by Ixodes ticks. Most Borrelia that infect ticks belong to the Borrelia burgdorferi senso lato group and include B. burgdorferi senso stricto, B. garinii, and B. afzelii, all of which cause Lyme disease in humans ( 1 ). Borrelia miyamotoi has been found in a variety of Ixodes ticks and is more closely related to the relapsing fever spirochetes that infect soft ticks than to the bacteria that cause Lyme disease ( 2 ). B. miyamotoi found in Europe and the United States also cause disease in humans ( 3 – 5 ). A study in Russia has shown that the spirochete B. miyamotoi has the ability to infect humans; infections with B. miyamotoi cause symptoms similar to those seen with relapsing fever, as well as erythema migrans-like skin lesions on rare occasions ( 6 ). B. miyamotoi has been found in ticks of the following species: Ixodes scapularis and I. pacificus in the United States, I. persulcatus in Japan, and I. ricinus and I. persulcatus in Europe and Asia ( 2 , 7 – 11 ). In North America, B. miyamotoi has been found as far north as the Canadian provinces of Ontario and Nova Scotia ( 12 ). In the United States, the geographic range of B. miyamotoi is from the Northeast to California and has been reported as far south as Tennessee ( 7 , 8 , 13 – 15 ). Previous studies have shown that B. miyamotoi can be placed into different genetic groups based upon its geographic location and has some variation within the genographic groups ( 6 , 9 ). To examine the prevalence distribution and diversity of B. miyamotoi in Ixodes ticks, we screened individual ticks by PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) to detect tickborne pathogens, including B. miyamotoi ( 16 ). This approach has been used to characterize tickborne microorganisms, including Ehrlichia and Borrelia, from clinical specimens, heartworms in canine blood, and naturally occurring tick endosymbionts ( 16 – 19 ). Ticks that tested positive for B. miyamotoi were further characterized by using a Borrelia genotyping assay to assess genetic diversity ( 20 ). Materials and Methods B. miyamotoi Culture Isolate The B. miyamotoi strain Fr74B was obtained by the Centers for Disease Control and Prevention (Fort Collins, CO, USA), as a culture isolate. This strain was originally isolated from an infected Apodemus argenteus field mouse from Japan. The DNA from this strain was isolated by diluting the culture 1:10 with phosphate-buffered saline and heating to 95°C for 10 min. The raw lysate was then used in the Borrelia PCR/ESI-MS genotyping assay (Abbott Laboratories, Des Plaines, IL, USA) at 1 μL per PCR well ( 20 ). Ixodes Tick Collection and Extractions Ticks were obtained from most locations by flagging during 2008–2012. In Germany, a subset of ticks were also obtained after they were removed from persons. The species of Ixodes tick was determined by an entomologist and confirmed by the detection of the species-specific endosymbionts ( 19 ). The numbers and locations of the collection sites are described in Table 1. Table 1 Prevelance of Borrelia miyamotoi in Ixodes ticks, Europe and the United States, 2008–2012* Region/subregion Species Total no. ticks tested (nymphs; adults) No. ticks positive for B. miyamotoi (% of total) Czech Republic Zavadilka I. ricinus 153 (153; 0) 4 (2.6) Blatna I. ricinus 100 (100; 0) 2 (2.0) Dacice I. ricinus 93 (93; 0) 3 (3.2) Netolice I. ricinus 89 (89; 0) 0 (0) Germany Constance I. ricinus 226 (0; 48)* 4 (1.8) United States Connecticut Fairfield County I. scapularis 322 (309; 13) 16 (5.0) Litchfield County I. scapularis 18 (18; 0) 0 New London County I. scapularis 29 (29; 0) 0 New York Dutchess County I. scapularis 357 (357; 0) 2 (0.56) Suffolk County I. scapularis 180 (24; 156) 2 (1.1) Westchester County I. scapularis 44 (0; 44) 3 (6.8) Pennsylvania Chester County I. scapularis 80 (79; 1) 2 (2.5) Indiana Pulaski County I. scapularis 81 (0; 81) 10 (12.3) California Alameda County I. pacificus 22 (0; 22) 1 (4.5) Del Norte County I. pacificus 33 (0; 33) 0 Glenn County I. pacificus 44 (0; 44) 0 Humbolt County I. pacificus 74 (0; 74) 0 Lake County I. pacificus 129 (0; 129) 0 Marin County I. pacificus 85 (0; 85) 1 (1.2) Mendocino County I. pacificus 57 (0; 57) 2 (3.5) Napa County I. pacificus 65 (0; 65) 10 (15.4) Orange County I. pacificus 15 (0; 15) 0 Placer County I. pacificus 250 (0; 250) 4 (1.6) San Bernardino County I. pacificus 18 (0; 18) 0 Santa Cruz County I. pacificus 64 (0; 64) 0 Sonoma County I. pacificus 126 (126; 0) 2 (1.6) *A total of 119 ticks were removed from humans, and the life stage of 178 of the 226 ticks tested was not recorded. Nucleic acids were extracted from ticks according to a published protocol by using bead-beating homogenization followed by isolation of RNA and DNA with DNeasy Blood and Tissue Kit columns (QIAGEN, Valencia, CA, USA) instead of the published QiaAmp Virus Elute Kits ( 21 ). A negative control consisting of a lysis buffer without a tick was with each set of extractions. Ticks from the United States were processed at Ibis Biosciences (Carlsbad, CA, USA). Ticks collected from the European countries were isolated at their respective sources. Nucleic acid samples from Germany and the Czech Republic were shipped to Ibis at ambient temperatures; those from Czech Republic were shipped after being stabilized by RNAstable (Biomatrica, San Diego, CA, USA) per the manufacturer’s instructions. Molecular Detection and Genotyping of B. miyamotoi from Nucleic Acid Extracts B. miyamotoi was detected and identified by using a previously described broad-range PCR/ESI-MS assay designed to detect tickborne pathogens ( 16 ). For each set of samples analyzed with the assay, an extraction negative control sample as well as a PCR plate negative-control sample of water was included. A PCR-positive control was already built into the plate for each well in the form of a calibrant ( 20 ). Amplicons were analyzed by using a research use only PLEX-ID system (Abbott Laboratories). Samples positive for B. miyamotoi were further characterized by using a Borrelia PCR/ESI-MS genotyping assay as described that is designed to differentiate between Borrelia species and genotypes ( 20 ). PCR/ESI-MS assay provides genetic information about the PCR amplicon in the form of A, G, C, and T basecounts, and B. miyamotoi detection was defined as positive when one or more primer pairs produced an amplicon basecount signature that was unique to B. miyamotoi. Although most researchers agree that the nymphal stage of Ixodes ticks is the most epidemiologically essential life stage for transmission of B. burgdorferi sensu lato, because little is known about the transmission of B. miyamotoi from Ixodes ticks to humans, the data for both nymphs and adults were combined. Sequence Confirmation of B. miyamotoi Detections Representative samples positive for B. miyamotoi were selected for 16S Sanger sequencing. Primers were designed to amplify a 676-bp region of the 16S rRNA gene for Borrelia. A M13 tag was added to each primer for sequencing. The M13 forward sequence tag was 5′-CCC AGT CAC GAC GTT GTA AAA CG-3′, and the reverse tag was 5′-AGC GGA TAA CAA TTT CAC ACA GG-3′. The forward primer used was 5′-M13-CGC TGG CAG TGC GTC TTA AG-3′, and the reverse primer was 5′-M13-GCG TCA GTC TTG ACC CAG AAG TTC-3′. The amplification of the 16S rRNA genes was performed in a 50 μL reaction containing 1 μL nucleic acid extract, 1 unit of Platinum Taq High Fidelity polymerase (Invitrogen, Carlsbad, CA, USA) or Immolase Taq (Bioline, Randolph, MA, USA), the manufacturer’s PCR buffer, 2.0 mmol/L MgSO4, 200 μmol/L dATP, 200 μmol/L dCTP, 200 μmol/L dTTP, 200 μmol/L dGTP (Bioline), and 250 nmol/L of each primer. The following PCR cycling conditions were used on an MJ Dyad 96-well thermocycler (Bio-Rad Inc., Hercules, CA, USA): 95°C for 2 min, followed by 8 cycles of 95°C for 15 s, 50°C for 45 s, and 68°C for 90 s, with the 50°C annealing temperature increasing 0.6°C for each cycle. PCR was continued for 37 additional cycles of 95°C for 15 s, 60°C for 15 s, and 68°C for 60 s. The PCR cycle ended with a final extension of 4 min at 72°C. Reactions were visualized by electrophoresis on 1% agarose gels to ensure the presence of appropriately-sized products before being sent to SeqWright (Houston, TX, USA) for purification and sequencing with M13 primers. Resulting sequences were trimmed of primer sequences and a consensus created. The consensus sequence was analyzed with NCBI BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) against the nucleotide database to determine the species. Results Multilocus PCR/ESI-MS Genotyping of B. miyamotoi The multilocus Borrelia PCR/ESI-MS genotyping assay differentiates strains and species of Borrelia by their unique combination of basecount signatures. To characterize the prevalence of B. miyamotoi in Ixodes ticks we examined the basecount signatures from ticks that were positive for B. miyamotoi. Positive specimens from each of the 3 regions (United States, Europe, and Japan) typically produced basecount signatures at 5 of the 8 loci evaluated in the Borrelia genotyping assay. Based upon these 5 signatures, B. miyamotoi from the United States, Europe, and Japan are distinct genotypes (Table 2). All the specimens from North America had the same basecount signatures for the 5 detecting primer pairs. A separate signature combination was found for all of the European isolates detected in ticks from Germany and the Czech Republic. A third signature was observed from the CDC culture isolate from the Japanese strain. Although all 3 genotypes shared the same basecount for the locus BCT3515, the European genotype did not have any other basecount signatures in common with the other 2 genotypes. The North American and Japanese genotypes had the same signatures for 2 of the 4 remaining loci, BCT 3519 and BCT3511. We detected B. miyamotoi with 3 or more primers in the Borrelia genotyping assay in all but 4 of the 68 positive specimens. Several factors may explain why all 5 primers did not detect the bacteria, including nucleic acid quality and quantity or differences in primer sensitivities. Table 2 Borrelia miyamotoi PCR/ESI-MS basecount signatures* Region Genotype BCT3515 (rplB) BCT3517 (flaB) BCT3519 (hbb) BCT3520 (hbb) BCT3511 (gyrB) Europe 1 A13G22C15T18 A41G30C23T27 A41G29C19T46 A52G29C13T47 A36G32C13T35 North America 2 A13G22C15T18 A43G28C23T27 A40G30C18T47 A52G30C13T46 A37G31C13T35 Japan 3 A13G22C15T18 A41G29C23T28 A40G30C18T47 A53G29C13T46 A37G31C13T35 *PCR/ESI-MS, PCR and electrospray ionization mass spectrometry. Prevalence of B. miyamotoi in Europe and the United States I. ricinus ticks from the Czech Republic and Germany in Europe and I. scapularis and I. pacificus ticks from 5 states in the United States were screened for B. miyamotoi by PCR/ESI-MS. B. miyamotoi was found in all regions examined in varying degrees (Table 1) and in all 3 Ixodes species examined. Germany had a low incidence rate; only 4 of the 226 ticks tested were infected (1.8%). Incidence of B. miyamotoi infection of ticks from the Czech Republic varied by region and ranged from 0% to 3.2% with an average infection rate of 2%. In North America, the infection rates of ticks varied from 0% to 15.4%. All negative controls were negative and all positive controls were positive. Sequence Confirmation of B. miyamotoi detections Representative samples were selected for 16S rRNA sequencing: 1 sample from Pennsylvania in the United States, 1 from Germany, and 1 from the Czech Republic. The samples from Germany and the Czech Republic were identical (KF740842 and KF740841, respectively) and matched 99.11% (669 bp out of 675 bp) of the B. miyamotoi LB-2001 sequence, a North American isolate from the East Coast (GenBank accession no. NC_022079). The sample from Pennsylvania (KF740843) was identical (675 bp of 675 bp) to the B. miyamotoi LB-2001 sequence. Discussion In this study, we identified 3 distinct B. miyamotoi genotypes in the United States, Europe, and Japan. Results show that B. miyamotoi is widely distributed across North America and Europe.We observed no genotypic differences using this PCR/ESI-MS assay between the B. miyamotoi detected in I. scapularis from the eastern US states and the midwest or between these bacteria and the B. miyamotoi detected in I. pacificus from California. In a study by Mun et al., a 766-bp region of the flagellin gene sequence were shown to have and a 0.9% difference between B. miyamotoi found in I. pacificus and those found in I. scapularis in the United States ( 8 ). However, our flagellin primers targeted a region of the flagellin gene that does not contain the differences identified by Mun et al., thus explaining why we found a single North American genotype. Previous studies that examined the sequence of the 16S rRNA gene from multiple B. miyamotoi strains indicated that strains from the United States and Europe were located in their own clusters ( 6 ). The Japanese strain FR64b grouped with isolates found in infected humans and I. persulcatus ticks in Russia, whereas the B. miyamotoi found in I. ricinus ticks from Russia grouped with those found in Europe ( 6 ). In our genetic analysis, the Japanese strain also differed from that found in I. ricinus in Europe. Our study demonstrates that the presence of B. miyamotoi in Ixodes ticks is widespread across the regions examined and was observed in all 3 species of field-collected Ixodes ticks. In Europe we observed B. miyamotoi in ≈2.0% of I. ricinus ticks tested, consistent with the detection rates in other studies examining I. ricinus prevalence at other locations in Europe ( 9 , 10 ). Our detection rates were also similar to those seen in an earlier study on ticks from Mendocino County, California ( 8 ). I. scapularis ticks from the East Coast region (New York, Connecticut, and Pennsylvania) were found to have infection rates ranging from 0% to 6.8% for ticks. In Indiana, however, a much higher percentage, ≈12%, of I. scapularis ticks examined were infected with B. miyamotoi. Other studies have also shown that local site-to-site prevalence of B. miyamotoi can vary greatly from the overall regional mean ( 13 ). Our study indicates that B. miyamotoi is likely present in any region where Ixodes ticks reside but that infection rates can vary greatly by region. Since the original description of B. miyamotoi as a human pathogen, studies have shown clinical infection in both healthy and immunocompromised patients in both Europe and the United States ( 3 – 6 , 22 ). If physicians know the regional infection rate in ticks, they will be alert for possible exposure risks for their patients. Standard Lyme borreliosis serologic tests offered by commercial laboratories cannot be relied on to detect B. miyamotoi infection in patients. B. miyamotoi has been shown to have transovarial transmission, suggesting that larval ticks may also pose a risk ( 7 ). Little is yet known about the transmission rates to humans, and further studies are required to better gauge the risk to humans in these B. miyamotoi-endemic regions.

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John S. Lambert:

ORCID: http://orcid.org/0000-0001-5404-2415

Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing

Michael John Cook:

ORCID: http://orcid.org/0000-0002-0678-1819

Role: Formal analysisRole: Writing – review & editing

John Eoin Healy: Role: ConceptualizationRole: Data curationRole: InvestigationRole: Writing – review & editing

Ross Murtagh: Role: VisualizationRole: Writing – review & editing

Gordana Avramovic:

ORCID: http://orcid.org/0000-0001-9610-6472

Role: Project administrationRole: Writing – review & editing

Sin Hang Lee: Role: InvestigationRole: MethodologyRole: ResourcesRole: Writing – review & editing

Yung-Fu Chang: Role: Editor

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Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

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Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, CA USA )

ISSN (Electronic): 1932-6203

Publication date (Electronic): 15 April 2019

Publication date Collection: 2019

Volume: 14

Issue: 4

Electronic Location Identifier: e0209881

Affiliations

[1 ] University College Dublin, Dublin, Ireland

[2 ] Mater Misericordiae University Hospital, Dublin, Ireland

[3 ] Vis a Vis Symposiums, Highcliffe, Dorset, United Kingdom

[4 ] University College Cork, Cork, Ireland

[5 ] Milford Molecular Diagnostics, Connecticut, United States of America

Cornell University, UNITED STATES

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Competing Interests: SHL is Director of Milford Molecular Diagnostics Laboratory. There are no patents, products in development or marketed products associated with this research to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

* E-mail: jlambert@ 123456mater.ie

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John S. Lambert http://orcid.org/0000-0001-5404-2415

Michael John Cook http://orcid.org/0000-0002-0678-1819

Gordana Avramovic http://orcid.org/0000-0001-9610-6472

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Publisher ID: PONE-D-18-34731

DOI: 10.1371/journal.pone.0209881

PMC ID: 6464168

PubMed ID: 30986208

SO-VID: a3104161-f626-4c89-98a0-8bf7389da1a9

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This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Date received : 4 December 2018

Date accepted : 7 March 2019

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Figures: 5, Tables: 1, Pages: 11

Funding

Milford Molecular Diagnostics Laboratory provided support in the form of salary for SHL. Milford Molecular Diagnostics is a CLIA-certified laboratory developing DNA sequencing-based diagnostic tests implementable in community hospital laboratories and providing commercial tests for Borrelia detection by core genome Sanger Sequencing. SHL contributed the laboratory investigations to this project. The specific roles of these authors are articulated in the ‘author contributions’ section. The funder had no additional role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks

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Tick microbiome

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Genetic and phenotypic analysis of Borrelia miyamotoi sp. nov., isolated from the ixodid tick Ixodes persulcatus, the vector for Lyme disease in Japan.

Genetic diversity of ospC in a local population of Borrelia burgdorferi sensu stricto.

Prevalence of Borrelia miyamotoi in Ixodes Ticks in Europe and the United States

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