1
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Hölzer M. POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae175. [PMID: 38561180 DOI: 10.1093/bioinformatics/btae175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/15/2024] [Accepted: 03/28/2024] [Indexed: 04/04/2024]
Abstract
SUMMARY Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies. AVAILABILITY AND IMPLEMENTATION The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.
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Affiliation(s)
- Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, 13353 Berlin, Germany
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2
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Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024; 14:1273665. [PMID: 38249459 PMCID: PMC10797017 DOI: 10.3389/fmicb.2023.1273665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024] Open
Abstract
Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.
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Affiliation(s)
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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3
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Lynch MJ, Deshpande M, Kurniyati K, Zhang K, James M, Miller M, Zhang S, Passalia FJ, Wunder EA, Charon NW, Li C, Crane BR. Lysinoalanine cross-linking is a conserved post-translational modification in the spirochete flagellar hook. PNAS NEXUS 2023; 2:pgad349. [PMID: 38047041 PMCID: PMC10691653 DOI: 10.1093/pnasnexus/pgad349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023]
Abstract
Spirochetes cause Lyme disease, leptospirosis, syphilis, and several other human illnesses. Unlike other bacteria, spirochete flagella are enclosed within the periplasmic space where the filaments distort and push the cell body by the action of the flagellar motors. We previously demonstrated that the oral pathogen Treponema denticola (Td) and Lyme disease pathogen Borreliella burgdorferi (Bb) form covalent lysinoalanine (Lal) cross-links between conserved cysteine and lysine residues of the FlgE protein that composes the flagellar hook. In Td, Lal is unnecessary for hook assembly but is required for motility, presumably due to the stabilizing effect of the cross-link. Herein, we extend these findings to other, representative spirochete species across the phylum. We confirm the presence of Lal cross-linked peptides in recombinant and in vivo-derived samples from Treponema spp., Borreliella spp., Brachyspira spp., and Leptospira spp. As was observed with Td, a mutant strain of Bb unable to form the cross-link has greatly impaired motility. FlgE from Leptospira spp. does not conserve the Lal-forming cysteine residue which is instead substituted by serine. Nevertheless, Leptospira interrogans FlgE also forms Lal, with several different Lal isoforms being detected between Ser-179 and Lys-145, Lys-148, and Lys-166, thereby highlighting species or order-specific differences within the phylum. Our data reveal that the Lal cross-link is a conserved and necessary posttranslational modification across the spirochete phylum and may thus represent an effective target for the development of spirochete-specific antimicrobials.
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Affiliation(s)
- Michael J Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Maithili Deshpande
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kurni Kurniyati
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, VA 23298, USA
| | - Kai Zhang
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, VA 23298, USA
| | - Milinda James
- Department of Microbiology, Immunology, and Cell Biology, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26505, USA
| | - Michael Miller
- Department of Biochemistry, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26505, USA
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Felipe J Passalia
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT 06269, USA
| | - Nyles W Charon
- Department of Microbiology, Immunology, and Cell Biology, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV 26505, USA
| | - Chunhao Li
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, VA 23298, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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4
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Khan M, Almutairi MM, Alouffi A, Tanaka T, Chang SC, Chen CC, Ali A. Molecular evidence of Borrelia theileri and closely related Borrelia spp. in hard ticks infesting domestic animals. Front Vet Sci 2023; 10:1297928. [PMID: 38089703 PMCID: PMC10715414 DOI: 10.3389/fvets.2023.1297928] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/01/2023] [Indexed: 06/09/2024] Open
Abstract
Ticks pose significant threats to hosts by transmitting Borrelia spp., which are grouped into Lyme borreliae, relapsing fever borreliae (RF), and reptiles- and monotremes-associated borreliae. The RF borreliae encompass a group of Borrelia species predominantly transmitted by soft ticks, but some of its members can also be transmitted by hard ticks. Information on the detection and genetic characterization of tick-borne RF borreliae, including Borrelia theileri, is notably rare in Asia, particularly in Pakistan. Herein, we employed molecular techniques to detect borreliae in hard ticks collected from domestic animals in Khyber Pakhtunkhwa, Pakistan. Ticks were subjected to morphological analysis, followed by DNA extraction and PCR amplification of partial fragments of borrelial 16S rRNA and flaB genes. A total of 729 ticks were collected from 264 hosts, with Haemaphysalis cornupunctata (12.9%; 94/729) being the most prevalent, followed by Hyalomma anatolicum (11.7%; 85/729), Rhipicephalus microplus (10.0%; 73/729), Haemaphysalis kashmirensis (9.1%; 66/729), Haemaphysalis bispinosa (8.5%; 62/729), Rhipicephalus sanguineus (8%; 58/729), Haemaphysalis montgomeryi (6.2%; 45/729), Rhipicephalus turanicus (5.5%; 40/729), Hyalomma dromedarii and Ixodes kashmirensis (4.4%; 32/729 each), Rhipicephalus haemaphysaloides (4.1%; 30/729), Haemaphysalis sulcata and Hyalomma scupense (3.8%; 28/729 each), Haemaphysalis danieli (2.9%; 21/729), Hyalomma kumari (2.6%; 19/729), and Hyalomma isaaci (2.2%; 16/729). Based on 16S rRNA detection of Borrelia spp., only R. turanicus yielded positive results, resulting in an overall infection rate of 0.3% (2/160), while using flaB-based detection, four tick species including R. microplus, R. turanicus, Ha. sulcata, and Ha. cornupunctata showed positive results, yielding an overall infection rate of 6.9% (11/160). The amplified DNA fragments of borrelial 16S rRNA and flaB in R. turanicus from goats shared maximum identities of 100 and 99.40% with Borrelia theileri, respectively. Amplified borrelial flaB fragments in R. microplus from cows and sheep displayed 100% identity with B. theileri, while flaB fragments in Ha. cornupunctata and Ha. sulcata from goats revealed identities of 99.32 and 99.75% with undetermined RF Borrelia spp., respectively. Phylogenetic analysis revealed clustering of B. theileri from R. microplus and R. turanicus with the same species, while Borrelia spp. from Ha. cornupunctata and Ha. sulcata with undetermined RF Borrelia spp. Notably, this research marks the first documentation of B. theileri in R. turanicus and the identification of RF Borrelia spp. in Ha. cornupunctata and Ha. sulcata.
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Affiliation(s)
- Mehran Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Shun-Chung Chang
- Department of Emergency Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
- Ph.D. Program in Translational Medicine, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
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Val-Calvo J, Vázquez-Boland JA. Mycobacteriales taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation. mBio 2023; 14:e0220723. [PMID: 37796005 PMCID: PMC10653829 DOI: 10.1128/mbio.02207-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order Mycobacteriales. Formal descriptions of proposed taxonomic changes based on our study are included.
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Affiliation(s)
- Jorge Val-Calvo
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - José A. Vázquez-Boland
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
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Wu-Chuang A, Mateos-Hernandez L, Maitre A, Rego ROM, Šíma R, Porcelli S, Rakotobe S, Foucault-Simonin A, Moutailler S, Palinauskas V, Aželytė J, Sǐmo L, Obregon D, Cabezas-Cruz A. Microbiota perturbation by anti-microbiota vaccine reduces the colonization of Borrelia afzelii in Ixodes ricinus. MICROBIOME 2023; 11:151. [PMID: 37482606 PMCID: PMC10364381 DOI: 10.1186/s40168-023-01599-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Ticks can transmit a broad variety of pathogens of medical importance, including Borrelia afzelii, the causative agent of Lyme borreliosis in Europe. Tick microbiota is an important factor modulating, not only vector physiology, but also the vector competence. Anti-microbiota vaccines targeting keystone taxa of tick microbiota can alter tick feeding and modulate the taxonomic and functional profiles of bacterial communities in the vector. However, the impact of anti-microbiota vaccine on tick-borne pathogen development within the vector has not been tested. RESULTS Here, we characterized the Ixodes ricinus microbiota modulation in response to B. afzelii infection and found that the pathogen induces changes in the microbiota composition, its beta diversity and structure of bacterial community assembly. Tick microbiota perturbation by anti-microbiota antibodies or addition of novel commensal bacteria into tick midguts causes departures from the B. afzelii-induced modulation of tick microbiota which resulted in a lower load of the pathogen in I. ricinus. Co-occurrence networks allowed the identification of emergent properties of the bacterial communities which better defined the Borrelia infection-refractory states of the tick microbiota. CONCLUSIONS These findings suggest that Borrelia is highly sensitive to tick microbiota perturbations and that departure from the modulation induced by the pathogen in the vector microbiota pose a high cost to the spirochete. Network analysis emerges as a suitable tool to identify emergent properties of the vector microbiota associated with infection-refractory states. Anti-microbiota vaccines can be used as a tool for microbiota perturbation and control of important vector-borne pathogens. Video Abstract.
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Affiliation(s)
- Alejandra Wu-Chuang
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Lourdes Mateos-Hernandez
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Apolline Maitre
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Ryan O M Rego
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Radek Šíma
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Biopticka Laborator S.R.O, Plzen, Czech Republic
| | - Stefania Porcelli
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Sabine Rakotobe
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Angélique Foucault-Simonin
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Sara Moutailler
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | | | - Justė Aželytė
- Nature Research Centre, Akademijos 2, 09412, Vilnius, Lithuania
| | - Ladislav Sǐmo
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Dasiel Obregon
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France.
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Lynch MJ, Deshpande M, Kyrniyati K, Zhang K, James M, Miller M, Zhang S, Passalia FJ, Wunder EA, Charon NW, Li C, Crane BR. Lysinoalanine crosslinking is a conserved post-translational modification in the spirochete flagellar hook. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544825. [PMID: 37398457 PMCID: PMC10312707 DOI: 10.1101/2023.06.13.544825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Spirochete bacteria cause Lyme disease, leptospirosis, syphilis and several other human illnesses. Unlike other bacteria, spirochete flagella are enclosed within the periplasmic space where the filaments distort and push the cell body by action of the flagellar motors. We previously demonstrated that the oral pathogen Treponema denticola (Td) catalyzes the formation of covalent lysinoalanine (Lal) crosslinks between conserved cysteine and lysine residues of the FlgE protein that composes the flagellar hook. Although not necessary for hook assembly, Lal is required for motility of Td, presumably due to the stabilizing effect of the crosslink. Herein, we extend these findings to other, representative spirochete species across the phylum. We confirm the presence of Lal crosslinked peptides in recombinant and in vivo -derived samples from Treponema spp., Borreliella spp., Brachyspira spp., and Leptospira spp.. Like with Td, a mutant strain of the Lyme disease pathogen Borreliella burgdorferi unable to form the crosslink has impaired motility. FlgE from Leptospira spp. does not conserve the Lal-forming cysteine residue which is instead substituted by serine. Nevertheless, Leptospira interrogans also forms Lal, with several different Lal isoforms being detected between Ser-179 and Lys-145, Lys-148, and Lys-166, thereby highlighting species or order-specific differences within the phylum. Our data reveals that the Lal crosslink is a conserved and necessary post-translational modification across the spirochete phylum and may thus represent an effective target for spirochete-specific antimicrobials. Significance Statement The phylum Spirochaetota contains bacterial pathogens responsible for a variety of diseases, including Lyme disease, syphilis, periodontal disease, and leptospirosis. Motility of these pathogens is a major virulence factor that contributes to infectivity and host colonization. The oral pathogen Treponema denticola produces a post-translational modification (PTM) in the form of a lysinoalanine (Lal) crosslink between neighboring subunits of the flagellar hook protein FlgE. Herein, we demonstrate that representative spirochetes species across the phylum all form Lal in their flagellar hooks. T. denticola and B. burgdorferi cells incapable of forming the crosslink are non-motile, thereby establishing the general role of the Lal PTM in the unusual type of flagellar motility evolved by spirochetes.
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Gupta RS, Kanter-Eivin DA. AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159410 DOI: 10.1099/ijsem.0.005844] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
| | - David A Kanter-Eivin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
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9
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Che Lah EF, Ahamad M, Dmitry A, Md Zain BM, Yaakop S. Metagenomic profile of the bacterial communities associated with Ixodes granulatus (Acari: Ixodidae): a potential vector of tick-borne diseases. JOURNAL OF MEDICAL ENTOMOLOGY 2023:7131392. [PMID: 37075471 DOI: 10.1093/jme/tjad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
Ixodes granulatus Supino, 1897 (Acari: Ixodida) is one of Malaysia's most common hard ticks and is a potential vector for tick-borne diseases (TBDs). Despite its great public health importance, research on I. granulatus microbial communities remains largely unexplored. Therefore, this study aimed to investigate the bacterial communities of on-host I. granulatus collected from three different recreational areas on the East Coast of Peninsular Malaysia using high throughput Next Generation Sequencing (NGS). A total of 9 females on-host I. granulatus were subjected to metabarcoding analysis targeting V3-V4 regions of 16S ribosomal RNA (rRNA) using the Illumina MiSeq platform. This study identified 15 bacterial phyla corresponding to 19 classes, 54 orders, and 90 families from 435 amplicon sequence variants (ASVs), revealing a diverse bacterial community profile. Together with 130 genera assigned, local I. granulatus harbored 4 genera of pathogens, i.e., Rickettsia da Rocha Lima, 1916 (Rickettsiales: Rickettsiaceae) (58.6%), Borrelia Swellengrebel 1907 (Spirochaetales: Borreliaceae) (31.6%), Borreliella Adeolu and Gupta 2015 (Spirochaetales: Borreliaceae) (0.6%), and Ehrlichia Cowdria Moshkovski 1947 (Rickettsiales: Ehrlichiaceae) (39.9%). Some endosymbiont bacteria, such as Coxiella (Philip, 1943) (Legionellales: Coxiellaceae), Wolbachia Hertig 1936 (Rickettsiales: Ehrlichiaceae), and Rickettsiella Philip, 1956 (Legionellales: Coxiellaceae), were also detected at very low abundance. Interestingly, this study reported the co-infection of Borrelia and Ehrlichia for the first time, instilling potential health concerns in the context of co-transmission to humans, especially in areas with a high population of I. granulatus. This study successfully characterized the tick microbiome and provided the first baseline data of I. granulatus bacterial communities in Malaysia. These results support the need for way-forward research on tick-associated bacteria using NGS, focusing on medically important species toward TBD prevention.
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Affiliation(s)
- Ernieenor Faraliana Che Lah
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, Shah Alam, Selangor 40170, Malaysia
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
| | - Mariana Ahamad
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, Shah Alam, Selangor 40170, Malaysia
| | - Apanaskevich Dmitry
- United States National Tick Collection, The James H. Oliver, Jr. Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA 30460-8042, USA
| | - Badrul Munir Md Zain
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
| | - Salmah Yaakop
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
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Stevenson B, Brissette CA. Erp and Rev Adhesins of the Lyme Disease Spirochete's Ubiquitous cp32 Prophages Assist the Bacterium during Vertebrate Infection. Infect Immun 2023; 91:e0025022. [PMID: 36853019 PMCID: PMC10016077 DOI: 10.1128/iai.00250-22] [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] [Indexed: 03/01/2023] Open
Abstract
Almost all spirochetes in the genus Borrelia (sensu lato) naturally contain multiple variants of closely related prophages. In the Lyme disease borreliae, these prophages are maintained as circular episomes that are called circular plasmid 32 kb (cp32s). The cp32s of Lyme agents are particularly unique in that they encode two distinct families of lipoproteins, namely, Erp and Rev, that are expressed on the bacterial outer surface during infection of vertebrate hosts. All identified functions of those outer surface proteins involve interactions between the spirochetes and host molecules, as follows: Erp proteins bind plasmin(ogen), laminin, glycosaminoglycans, and/or components of complement and Rev proteins bind fibronectin. Thus, cp32 prophages provide their bacterial hosts with surface proteins that can enhance infection processes, thereby facilitating their own survival. Horizontal transfer via bacteriophage particles increases the spread of beneficial alleles and creates diversity among Erp and Rev proteins.
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Affiliation(s)
- Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Catherine A. Brissette
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, USA
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11
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Čorak N, Anniko S, Daschkin-Steinborn C, Krey V, Koska S, Futo M, Široki T, Woichansky I, Opašić L, Kifer D, Tušar A, Maxeiner HG, Domazet-Lošo M, Nicolaus C, Domazet-Lošo T. Pleomorphic Variants of Borreliella (syn. Borrelia) burgdorferi Express Evolutionary Distinct Transcriptomes. Int J Mol Sci 2023; 24:ijms24065594. [PMID: 36982667 PMCID: PMC10057712 DOI: 10.3390/ijms24065594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Borreliella (syn. Borrelia) burgdorferi is a spirochete bacterium that causes tick-borne Lyme disease. Along its lifecycle B. burgdorferi develops several pleomorphic forms with unclear biological and medical relevance. Surprisingly, these morphotypes have never been compared at the global transcriptome level. To fill this void, we grew B. burgdorferi spirochete, round body, bleb, and biofilm-dominated cultures and recovered their transcriptomes by RNAseq profiling. We found that round bodies share similar expression profiles with spirochetes, despite their morphological differences. This sharply contrasts to blebs and biofilms that showed unique transcriptomes, profoundly distinct from spirochetes and round bodies. To better characterize differentially expressed genes in non-spirochete morphotypes, we performed functional, positional, and evolutionary enrichment analyses. Our results suggest that spirochete to round body transition relies on the delicate regulation of a relatively small number of highly conserved genes, which are located on the main chromosome and involved in translation. In contrast, spirochete to bleb or biofilm transition includes substantial reshaping of transcription profiles towards plasmids-residing and evolutionary young genes, which originated in the ancestor of Borreliaceae. Despite their abundance the function of these Borreliaceae-specific genes is largely unknown. However, many known Lyme disease virulence genes implicated in immune evasion and tissue adhesion originated in this evolutionary period. Taken together, these regularities point to the possibility that bleb and biofilm morphotypes might be important in the dissemination and persistence of B. burgdorferi inside the mammalian host. On the other hand, they prioritize the large pool of unstudied Borreliaceae-specific genes for functional characterization because this subset likely contains undiscovered Lyme disease pathogenesis genes.
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Affiliation(s)
- Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Sirli Anniko
- BCA-Research, BCA-Clinic Betriebs GmbH & Co. KG, D-86159 Augsburg, Germany
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | | | - Viktoria Krey
- BCA-Research, BCA-Clinic Betriebs GmbH & Co. KG, D-86159 Augsburg, Germany
- Physics of Synthetic Biological Systems-E14, Physics Department and ZNN, Technische Universität München, D-85748 Garching, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
- Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000 Zagreb, Croatia
- School of Medicine, Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000 Zagreb, Croatia
| | | | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, HR-10000 Zagreb, Croatia
| | - Anja Tušar
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
| | - Horst-Günter Maxeiner
- BCA-Research, BCA-Clinic Betriebs GmbH & Co. KG, D-86159 Augsburg, Germany
- Comlamed, Friedrich-Bergius Ring 15, D-97076 Würzburg, Germany
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000 Zagreb, Croatia
| | - Carsten Nicolaus
- BCA-Research, BCA-Clinic Betriebs GmbH & Co. KG, D-86159 Augsburg, Germany
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia
- School of Medicine, Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
- Correspondence:
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12
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Lyme Borreliosis in Dogs: Background, Epidemiology, Diagnostics, Treatment and Prevention. FOLIA VETERINARIA 2023. [DOI: 10.2478/fv-2023-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023] Open
Abstract
Abstract
Lyme borreliosis (LB) is a multisystemic tick-borne disease that can affect many organs and have various clinical manifestations in dogs. We attempted to summarise various aspects of Lyme disease: i. e., pathogenesis, epidemiology, benefits and risks of diagnostic approaches, treatment options, and prevention in dogs. Several diagnostic bottlenecks for LB in dogs and humans are compared. Because the occurrence of LB in both humans and dogs is closely related, monitoring its prevalence in dogs as sentinel animals is an excellent aid in assessing the risk of Lyme disease in a given geographic area. Although clinical symptoms in humans help clinicians diagnose LB, they are ineffective in dogs because canines rarely exhibit LB symptoms. Despite significant differences in sensitivity and specificity, sero-logical two-step detection of antibodies against Borrelia spp. (ELISA and Western blot) is the most commonly used method in humans and dogs. The limitations of the assay highlight the need for further research to develop new clinical markers and more accurate diagnostic tests. Due to the lack of a specific all-encompassing LB test, a definitive diagnosis of LB remains a difficult and time-consuming process in human and veterinary medicine. Understanding the disease prevalence and diagnostics, as well as preventing its spread with effective and timely treatment, are fundamental principles of good disease management.
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13
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Pietruszka K, Reagan F, Stążka J, Kozioł MM. Serologic Status of Borrelia burgdorferi sensu lato in Patients with Cardiovascular Changes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2239. [PMID: 36767604 PMCID: PMC9915009 DOI: 10.3390/ijerph20032239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Cardiovascular diseases, particularly coronary heart disease (CHD) caused by atherosclerosis, have the highest worldwide incidence and mortality rate of any type of disease. Aside from risk factors associated with lifestyle and comorbidities, infectious agents such as Borrelia burgdorferi sensu lato spirochetes, which cause Lyme disease, may also play a role in the development of cardiovascular disease. A growing number of scientific papers have mentioned Lyme carditis. The aim of this study was to find the level of anti-Borrelia IgG antibodies in the blood serum of patients with advanced coronary heart disease. Materials and methods: The study group included 70 patients undergoing coronary artery bypass grafting (CABG) and off-pump coronary artery bypass (OPCAB) surgery aged 50 to 82 (average 68.26). The ELISA test was used to detect anti-Borrelia/IgG antibodies in the blood serum. Serological testing revealed seropositivity in 34.29% of patients and 'borderline results' in 17.14% of patients. We found a link between antibody levels and tick bites but not with other risk factors for the development of CHD. Conclusions: These findings support the idea that, as one of many factors, the contact with spirochetal antigens may indicate a potential positive correlation with the formation of cardiovascular changes. More research, not only at the diagnostic level but also at the advanced research level, is needed.
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Affiliation(s)
- Katarzyna Pietruszka
- Students Scientific Association at the Chair and Department of Medical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Farbod Reagan
- Chair and Department of Medical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Janusz Stążka
- Department of Cardiac Surgery, Medical University of Lublin, 20-093 Lublin, Poland
| | - Małgorzata M. Kozioł
- Chair and Department of Medical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland
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14
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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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15
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Dong C, Wei L, Wang J, Lai Q, Huang Z, Shao Z. Genome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus. Front Microbiol 2022; 13:1051202. [PMID: 36605514 PMCID: PMC9807766 DOI: 10.3389/fmicb.2022.1051202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus. Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1 T and 59MF3M-4 T , for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.
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Affiliation(s)
- Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Lin Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China,*Correspondence: Zongze Shao,
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16
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Zawada SG, von Fricken ME, Weppelmann TA, Sikaroodi M, Gillevet PM. Genetic variation of Borreliella burgdorferi in Fairfax County, Virginia, targeting the OspC gene in white-footed mice. Front Microbiol 2022; 13:998365. [DOI: 10.3389/fmicb.2022.998365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/20/2022] [Indexed: 11/20/2022] Open
Abstract
Outer surface protein C (OspC) is a commonly used marker in population studies of Borreliella to differentiate types and establish evolution over time. Investigating the ospC genetic types of Borreliella burgdorferi across multiple organ tissues of white-footed mice has the potential to contribute to our understanding of Lyme disease and the wide spectrum of clinical presentation associated with infection. In this study, five unique tissue types were sampled from 90 mice and screened for B. burgdorferi infections. This initial screening revealed a 63% overall B. burgdorferi infection rate in the mice collected (57/90). A total of 163 tissues (30.4%) tested positive for B. burgdorferi infections and when mapped to Borreliella types, 143,894 of the initial 322,480 reads mapped to 10 of the reference sequences in the ospC strain library constructed for this study at a 97% MOI. Two tissue types, the ear and the tongue, each accounted for 90% of the observed Borreliella sequence diversity in the tissue samples surveyed. The largest amount of variation was observed in an individual ear tissue sample with six ospC sequence types, which is equivalent to 60% of the observed variation seen across all tested specimens, with statistically significant associations observed between tissue type and detected Borreliella. There is strong evidence for genetic variability in B. burgdorferi within local white-footed mouse populations and even within individual hosts by tissue type. These findings may shed light on drivers of infection sequalae in specific tissues in humans and highlights the need for expanded surveillance on the epigenetics of B. burgdorferi across reservoirs, ticks, and infected patients.
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17
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Goff NK, Dou T, Higgins S, Horn EJ, Morey R, McClellan K, Kurouski D, Rogovskyy AS. Testing Raman spectroscopy as a diagnostic approach for Lyme disease patients. Front Cell Infect Microbiol 2022; 12:1006134. [PMID: 36389168 PMCID: PMC9647194 DOI: 10.3389/fcimb.2022.1006134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Lyme disease (LD), the leading tick-borne disease in the Northern hemisphere, is caused by spirochetes of several genospecies of the Borreliella burgdorferi sensu lato complex. LD is a multi-systemic and highly debilitating illness that is notoriously challenging to diagnose. The main drawbacks of the two-tiered serology, the only approved diagnostic test in the United States, include poor sensitivity, background seropositivity, and cross-reactivity. Recently, Raman spectroscopy (RS) was examined for its LD diagnostic utility by our earlier proof-of-concept study. The previous investigation analyzed the blood from mice that were infected with 297 and B31 strains of Borreliella burgdorferi sensu stricto (s.s.). The selected strains represented two out of the three major clades of B. burgdorferi s.s. isolates found in the United States. The obtained results were encouraging and prompted us to further investigate the RS diagnostic capacity for LD in this study. The present investigation has analyzed blood of mice infected with European genospecies, Borreliella afzelii or Borreliella garinii, or B. burgdorferi N40, a strain of the third major class of B. burgdorferi s.s. in the United States. Moreover, 90 human serum samples that originated from LD-confirmed, LD-negative, and LD-probable human patients were also analyzed by RS. The overall results demonstrated that blood samples from Borreliella-infected mice were identified with 96% accuracy, 94% sensitivity, and 100% specificity. Furthermore, human blood samples were analyzed with 88% accuracy, 85% sensitivity, and 90% specificity. Together, the current data indicate that RS should be further explored as a potential diagnostic test for LD patients.
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Affiliation(s)
- Nicolas K. Goff
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Tianyi Dou
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Samantha Higgins
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | | | - Rohini Morey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Kyle McClellan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- *Correspondence: Dmitry Kurouski, ; Artem S. Rogovskyy,
| | - Artem S. Rogovskyy
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Dmitry Kurouski, ; Artem S. Rogovskyy,
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18
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Sangal V, Goodfellow M, Jones AL, Sutcliffe IC. A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named
Rhodococcus equi
, ‘Prescottella equi’ and
Rhodococcus hoagii
. As a consequence, we present here the genus name
Prescottella
and that of its nomenclatural type species,
Prescottella equi
comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus
Prescottella
. Nearly a century after the original description of the type strain of the type species as
Corynebacterium equi
, we provide a stable home for
Prescottella equi
and its relatives.
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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Amanda L. Jones
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Iain C. Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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19
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Margos G, Wormser GP, Schwartz I, Markowicz M, Henningsson AJ, Lienhard R, Stevenson B, Estrada-Peña A, Sing A, Fingerle V, Göker M. Evidence of taxonomic bias in public databases: the example of the genus Borrelia. Ticks Tick Borne Dis 2022; 13:101994. [DOI: 10.1016/j.ttbdis.2022.101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
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20
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Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov. Microorganisms 2022; 10:microorganisms10071312. [PMID: 35889031 PMCID: PMC9318685 DOI: 10.3390/microorganisms10071312] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023] Open
Abstract
Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB, and Chlorobium sp. 445, is now proposed as a new family (Chloroherpetonaceae fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class Chlorobia or its two families, providing reliable means for identification. Two known Ignavibacteria species in our phylogenomic tree are found to group within a larger clade containing several Candidatus species and uncultured Chlorobi strains. A CSI in the SecY protein is uniquely shared by the species/strains from this “larger Ignavibacteria clade”. Two additional CSIs, which are commonly shared by Chlorobia species and the “larger Ignavibacteria clade”, support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms.
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21
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Octaviana S, Lorenczyk S, Ackert F, Fenske L, Wink J. Four new members of the family Cytophagaceae: Chryseosolibacter histidini gen. nov., sp. nov., Chryseosolibacter indicus gen. nov., sp. nov., Dawidia cretensis, gen. nov., sp. nov., and Dawidia soli, gen. nov., sp. nov. isolated from diverse habitat. Antonie Van Leeuwenhoek 2022; 115:1059-1072. [PMID: 35732971 PMCID: PMC9296434 DOI: 10.1007/s10482-022-01756-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/28/2022] [Indexed: 11/29/2022]
Abstract
Four novel strains were isolated: PWU4T and PWU20T were both from soil in Germany, PWU5T was isolated from soil in India and PWU37T was obtained from sheep faeces collected on the Island of Crete. Cells of each were observed to be Gram-negative, strictly aerobic, rod shaped, and to grow optimally between 28 and 34 °C, between pH 7.0 and 8.0 and without the addition of NaCl. The strains were found to be catalase and oxidase-negative and able to grow on most mono- and disaccharides, a few polysaccharides and organic acids. Their predominant menaquinone was identified as MK-7. Their major fatty acids were identified as C16:1ω7c (PWU4T and PWU20T) and C16:1ω5c (PWU5T and PWU37T). The DNA G + C contents of strains PWU4T, PWU20T, PWU5T and PWU37T were determined to be 50.2 mol%, 51.6 mol %, 39.8 mol% and 53.8 mol%, respectively. The 16S rRNA gene sequence analysis revealed that the close relatives Ohtaekwangia koreensis 3B-2T and Ohtaekwangia kribbensis 10AOT share less than 93.8% sequence similarity. The strains were classified in two groups, where PWU4T and PWU20T share 93.0% sequence similarity, and PWU5T and PWU37T share 97.5% sequence similarity. However, the members of each group were concluded to represent different species based on the low average nucleotide identity (ANI) of their genomes, 69.7% and 83.8%, respectively. We propose that the four strains represent four novel species of two new genera in the family Cytophagaceae. The type species of the novel genus Chryseosolibacter is Chryseosolibacter histidini gen. nov., sp. nov. with the type strain PWU4T (= DSM 111594T = NCCB 100798T), whilst strain PWU20T (= DSM 111597T = NCCB 100800T) is the type strain of a second species, Chryseosolibacter indicus sp. nov. The type species of the novel genus Dawidia is Dawidia cretensis gen. nov., sp. nov. with the type strain PWU5T (= DSM 111596T = NCCB 100799T), whilst strain PWU37T (= DSM 111595T = NCCB 100801T) is the type stain of a second species, Dawidia soli sp. nov.
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Affiliation(s)
- Senlie Octaviana
- Microbial Strain Collection, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Stefan Lorenczyk
- Faculty of Mechanical Engineering, Technical University of Braunschweig, Schleinitzstraße 20, 38106, Brunswick, Germany
| | - Frederike Ackert
- Microbial Strain Collection, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany
| | - Linda Fenske
- Bioinformatic and Systems Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 58, 35390, Gießen, Germany
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.
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22
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Kneubehl AR, Krishnavajhala A, Leal SM, Replogle AJ, Kingry LC, Bermúdez SE, Labruna MB, Lopez JE. Comparative genomics of the Western Hemisphere soft tick-borne relapsing fever borreliae highlights extensive plasmid diversity. BMC Genomics 2022; 23:410. [PMID: 35641918 PMCID: PMC9158201 DOI: 10.1186/s12864-022-08523-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/30/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tick-borne relapsing fever (TBRF) is a globally prevalent, yet under-studied vector-borne disease transmitted by soft and hard bodied ticks. While soft TBRF (sTBRF) spirochetes have been described for over a century, our understanding of the molecular mechanisms facilitating vector and host adaptation is poorly understood. This is due to the complexity of their small (~ 1.5 Mb) but fragmented genomes that typically consist of a linear chromosome and both linear and circular plasmids. A majority of sTBRF spirochete genomes' plasmid sequences are either missing or are deposited as unassembled sequences. Consequently, our goal was to generate complete, plasmid-resolved genomes for a comparative analysis of sTBRF species of the Western Hemisphere. RESULTS Utilizing a Borrelia specific pipeline, genomes of sTBRF spirochetes from the Western Hemisphere were sequenced and assembled using a combination of short- and long-read sequencing technologies. Included in the analysis were the two recently isolated species from Central and South America, Borrelia puertoricensis n. sp. and Borrelia venezuelensis, respectively. Plasmid analyses identified diverse sequences that clustered plasmids into 30 families; however, only three families were conserved and syntenic across all species. We also compared two species, B. venezuelensis and Borrelia turicatae, which were isolated ~ 6,800 km apart and from different tick vector species but were previously reported to be genetically similar. CONCLUSIONS To truly understand the biological differences observed between species of TBRF spirochetes, complete chromosome and plasmid sequences are needed. This comparative genomic analysis highlights high chromosomal synteny across the species yet diverse plasmid composition. This was particularly true for B. turicatae and B. venezuelensis, which had high average nucleotide identity yet extensive plasmid diversity. These findings are foundational for future endeavors to evaluate the role of plasmids in vector and host adaptation.
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Affiliation(s)
- Alexander R Kneubehl
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | - Sebastián Muñoz Leal
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad de Concepción, Concepción, Chile
| | - Adam J Replogle
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Luke C Kingry
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Sergio E Bermúdez
- Medical Entomology Department, Gorgas Memorial Institute for Health Research, Panamá City, Panamá
| | - Marcelo B Labruna
- Departamento de Medicina Veterinária Preventiva E Saúde Animal, Faculdade de Medicina Veterinária E Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Job E Lopez
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA.
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23
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Genome-based reclassification of the genus Meiothermus along with the proposal of a new genus Allomeiothermus gen. nov. Antonie van Leeuwenhoek 2022; 115:645-659. [PMID: 35348967 DOI: 10.1007/s10482-022-01723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
Phylogenomic analyses were performed on the nine species of the genus Meiothermus and four species of the genus Calidithermus. Phylogenetic analysis, low values of genomic relatedness indices and functional diversity analysis indicated that Meiothermus silvanus should not be classified within the clades for Meiothermus and Calidithermus but instead be reclassified as a new genus, for which we propose the name Allomeiothermus gen. nov., with Allomeiothermus silvanus comb. nov. as type species. In addition, the species Meiothermus cateniformans Zhang et al. (Int J Syst Evol Microbial 60:840-844, 2010) should also be reclassified as a later heterotypic synonym of Meiothermus taiwanensis Chen et al. (Int J Syst Evol Microbiol 52:1647-1654, 2002) emend. Raposo et al. (2019). This reclassification is based on the high genomic relatedness indices (98.8% ANI; 90.2% dDDH; 99% AAI) that are above the threshold values necessary for defining a new species, as well as on the observation of overlapping functions on Principal Coordinate Analysis plot generated from Clusters of Orthologous Genes.
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24
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Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov. Mol Genet Genomics 2022; 297:213-225. [PMID: 34988605 DOI: 10.1007/s00438-021-01829-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.
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25
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Ali A, Ahmad S, de Albuquerque PMM, Kamil A, Alshammari FA, Alouffi A, da Silva Vaz I. Prediction of Novel Drug Targets and Vaccine Candidates against Human Lice (Insecta), Acari (Arachnida), and Their Associated Pathogens. Vaccines (Basel) 2021; 10:vaccines10010008. [PMID: 35062669 PMCID: PMC8778234 DOI: 10.3390/vaccines10010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/12/2023] Open
Abstract
The emergence of drug-resistant lice, acari, and their associated pathogens (APs) is associated with economic losses; thus, it is essential to find new appropriate therapeutic approaches. In the present study, a subtractive proteomics approach was used to predict suitable therapeutics against these vectors and their infectious agents. We found 9701 proteins in the lice (Pediculus humanus var. corporis) and acari (Ixodes scapularis, Leptotrombidium deliense), and 4822 proteins in the proteomes of their APs (Babesia microti, Borreliella mayonii, Borrelia miyamotoi, Borrelia recurrentis, Rickettsia prowazekii, Orientia tsutsugamushi str. Boryong) that were non-homologous to host proteins. Among these non-homologous proteins, 365 proteins of lice and acari, and 630 proteins of APs, were predicted as essential proteins. Twelve unique essential proteins were predicted to be involved in four unique metabolic pathways of lice and acari, and 103 unique proteins were found to be involved in 75 unique metabolic pathways of APs. The sub cellular localization analysis of 115 unique essential proteins of lice and acari and their APs revealed that 61 proteins were cytoplasmic, 42 as membrane-bound proteins and 12 proteins with multiple localization. The druggability analysis of the identified 73 cytoplasmic and multiple localization essential proteins revealed 22 druggable targets and 51 novel drug targets that participate in unique pathways of lice and acari and their APs. Further, the predicted 42 membrane bound proteins could be potential vaccine candidates. Screening of useful inhibitors against these novel targets may result in finding novel compounds efficient for the control of these parasites.
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Affiliation(s)
- Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
| | - Shabir Ahmad
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
| | | | - Atif Kamil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
| | - Fahdah Ayed Alshammari
- College of Sciences and Literature Microbiology, Nothern Border University, Rafha 76413, Saudi Arabia;
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia;
- Vaccines Research for Infectious Diseases, King Saud University, Riyadh 11495, Saudi Arabia
- Veterinary Laboratories and Vaccines Center, Ministry of Environment Water & Agriculture, Riyadh 11195, Saudi Arabia
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
- Correspondence: ; Tel.: +55-(51)-33086078; Fax: +55-(51)-33087309
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26
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Barbour AG, Gupta RS. The Family Borreliaceae (Spirochaetales), a Diverse Group in Two Genera of Tick-Borne Spirochetes of Mammals, Birds, and Reptiles. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1513-1524. [PMID: 33903910 DOI: 10.1093/jme/tjab055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Spirochetes of the family Borreliaceae are, with one exception, tick-borne pathogens of a variety of vertebrates. The family at present comprises two genera: Borrelia (Swellengrebel), which includes the agents of relapsing fever, avian spirochetosis, and bovine borreliosis, and Borreliella (Gupta et al.), which includes the agents of Lyme disease and was formerly known as 'Borrelia burgdorferi sensulato complex'. The two genera are distinguished not only by their disease associations but also biological features in the tick vector, including tissue location in unfed ticks and transovarial transmission. Borrelia species transmitted by argasid (soft) ticks tend to have more exclusive relationships with their tick vectors than do other Borrelia species and all Borreliella species that have ixodid (hard) ticks as vectors. The division of genera is supported by phylogenomic evidence from whole genomes and by several specific molecular markers. These distinguishing phylogenetic criteria also applied to three new species or isolates of Borrelia that were discovered in ixodid ticks of reptiles, a monotreme, and birds. Although the deep branching of the family from other spirochetes has been a challenge for inferences about evolution of the family, the discovery of related microorganisms in the gut microbiota of other arachnids suggests an ancestral origin for the family as symbionts of ticks and other arachnids.
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Affiliation(s)
- Alan G Barbour
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA
- Department of Medicine, University of California, Irvine, CA, USA
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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27
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The Diadenylate Cyclase CdaA Is Critical for Borrelia turicatae Virulence and Physiology. Infect Immun 2021; 89:IAI.00787-20. [PMID: 33846120 PMCID: PMC8316131 DOI: 10.1128/iai.00787-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Relapsing fever (RF), caused by spirochetes of the genus Borrelia, is a globally distributed, vector-borne disease with high prevalence in developing countries. To date, signaling pathways required for infection and virulence of RF Borrelia spirochetes are unknown. Cyclic di-AMP (c-di-AMP), synthesized by diadenylate cyclases (DACs), is a second messenger predominantly found in Gram-positive organisms that is linked to virulence and essential physiological processes. Although Borrelia is Gram-negative, it encodes one DAC (CdaA), and its importance remains undefined. To investigate the contribution of c-di-AMP signaling in the RF bacterium Borrelia turicatae, a cdaA mutant was generated. The mutant was significantly attenuated during murine infection, and genetic complementation reversed this phenotype. Because c-di-AMP is essential for viability in many bacteria, whole-genome sequencing was performed on cdaA mutants, and single-nucleotide polymorphisms identified potential suppressor mutations. Additionally, conditional mutation of cdaA confirmed that CdaA is important for normal growth and physiology. Interestingly, mutation of cdaA did not affect expression of homologs of virulence regulators whose levels are impacted by c-di-AMP signaling in the Lyme disease bacterium Borrelia burgdorferi Finally, the cdaA mutant had a significant growth defect when grown with salts, at decreased osmolarity, and without pyruvate. While the salt treatment phenotype was not reversed by genetic complementation, possibly due to suppressor mutations, growth defects at decreased osmolarity and in media lacking pyruvate could be attributed directly to cdaA inactivation. Overall, these results indicate CdaA is critical for B. turicatae pathogenesis and link c-di-AMP to osmoregulation and central metabolism in RF spirochetes.
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28
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Abstract
With one exception (epidemic relapsing fever), borreliae are obligately maintained in nature by ticks. Although some Borrelia spp. may be vertically transmitted to subsequent generations of ticks, most require amplification by a vertebrate host because inheritance is not stable. Enzootic cycles of borreliae have been found globally; those receiving the most attention from researchers are those whose vectors have some degree of anthropophily and, thus, cause zoonoses such as Lyme disease or relapsing fever. To some extent, our views on the synecology of the borreliae has been dominated by an applied focus, viz., analyses that seek to understand the elements of human risk for borreliosis. But, the elements of borrelial perpetuation do not necessarily bear upon risk, nor do our concepts of risk provide the best structure for analyzing perpetuation. We identify the major global themes for the perpetuation of borreliae, and summarize local variations on those themes, focusing on key literature to outline the factors that serve as the basis for the distribution and abundance of borreliae.
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Affiliation(s)
- Sam R. Telford
- Dept of Infectious Disease and Global Health, Tufts University, Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA 01536, USA
| | - Heidi K. Goethert
- Dept of Infectious Disease and Global Health, Tufts University, Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA 01536, USA
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29
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Muñoz-Leal S, Ramirez DG, Luz HR, Faccini JLH, Labruna MB. "Candidatus Borrelia ibitipoquensis," a Borrelia valaisiana-Related Genospecies Characterized from Ixodes paranaensis in Brazil. MICROBIAL ECOLOGY 2020; 80:682-689. [PMID: 32367214 DOI: 10.1007/s00248-020-01512-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Borrelia burgdorferi sensu lato (Bbsl) spirochetes include the agents of Lyme borreliosis in temperate regions of the Northern Hemisphere, and merge their transmission cycles mainly with ticks of the Ixodes ricinus complex. Twenty genospecies compose Bbsl currently, and with the exception of Borrelia chilensis, and Borrelia garinii, all have been described only for North America, Europe, North Africa, and Asia. Here, we collected specimens of Ixodes paranaensis, a tick associated with swifts in a Brazilian natural park from the state of Minas Gerais, and performed a molecular characterization of 11 borrelial genes. Based on comparisons of inter and intraspecific genetic divergences, and Bayesian phylogenetic trees inferred for 16S rRNA, flaB, p66, and concatenated clpA, clpX, pepX, pyrG, recG, nifS rlpB, and uvrA genes, we demonstrate the occurrence of a new genospecies of Bbsl. "Candidatus Borrelia ibitipoquensis" Ip37 is closely related to Borrelia sp. Am501, and Borrelia valaisiana, a spirochete transmitted by ticks of the I. ricinus complex in Eurasia that uses birds as reservoirs. In a similar ecological scenario involving ticks and avian hosts, the migratory swift Streptoprocne biscutata is the sole-documented bird associated with I. paranaensis, and, although not assessed in this study, could correspond to the vertebrate reservoir of this newly described genospecies in Brazil. Pathogenic roles of "Ca. B. ibitipoquensis" are still unknown. However, its possible vector I. paranaensis is not an anthropophilic tick, so human infections would be unlikely to occur. Our finding enhances the knowledge on Bbsl in South America, highlights the occurrence of ecologically and genetically related genospecies with vastly separated geographical distributions, and calls for the attention to explore a barely known diversity of spirochetes of this group in the region.
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Affiliation(s)
- Sebastián Muñoz-Leal
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Diego G Ramirez
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
- Departamento de Parasitologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Hermes R Luz
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
- Departamento de Patologia, Programa de Pós Graduação em Biotecnologia do RENORBIO, Ponto Focal Maranhão, Universidade Federal do Maranhão, São Luis, MA, Brazil
| | - João L H Faccini
- Departamento de Parasitologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Marcelo B Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
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30
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Colunga-Salas P, Sánchez-Montes S, Volkow P, Ruíz-Remigio A, Becker I. Lyme disease and relapsing fever in Mexico: An overview of human and wildlife infections. PLoS One 2020; 15:e0238496. [PMID: 32941463 PMCID: PMC7497999 DOI: 10.1371/journal.pone.0238496] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/15/2020] [Indexed: 01/16/2023] Open
Abstract
Lyme borreliosis and Relapsing fever are considered emerging and re-emerging diseases that cause major public health problems in endemic countries. Epidemiology and geographical distribution of these diseases are documented in the US and in Europe, yet in Mexico, studies are scarce and scattered. The aims of this study were (1) to present the first confirmatory evidence of an endemic case of Lyme disease in Mexico and (2) to analyze the epidemiological trend of these both diseases by compiling all the information published on Borrelia in Mexico. Two databases were compiled, one of human cases and another of wild and domestic animals in the country. The analysis included the evaluation of risk factors for the human population, the diversity of Borrelia species and their geographic distribution. Six Borrelia species were reported in a total of 1,347 reports, of which 398 were of humans. Women and children from rural communities were shown to be more susceptible for both Lyme borreliosis and Relapsing fever. The remaining reports were made in diverse mammalian species and ticks. A total of 17 mammalian species and 14 tick species were recorded as hosts for this bacterial genus. It is noteworthy that records of Borrelia were only made in 18 of the 32 states, mainly in northern and central Mexico. These results highlight the importance of performing further studies in areas where animal cases have been reported, yet no human studies have been done, in order to complete the epidemiological panorama for Lyme borreliosis and Relapsing fever. Finally, the search for Borrelia infections in other vertebrates, such as reptiles and amphibians is recommended to gain a more accurate view of Borrelia species and their distribution. The geographical approach presented herein justifies an intense sampling effort to improve epidemiological knowledge of these diseases to aid vector control and prevention programs.
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Affiliation(s)
- Pablo Colunga-Salas
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biomédicas, Unidad de Posgrado, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sokani Sánchez-Montes
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Patricia Volkow
- Departamento de Infectología, Instituto Nacional de Cancerologia, Ciudad de México, México
| | - Adriana Ruíz-Remigio
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ingeborg Becker
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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31
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Margos G, Castillo-Ramirez S, Cutler S, Dessau RB, Eikeland R, Estrada-Peña A, Gofton A, Graña-Miraglia L, Hunfeld KP, Krause A, Lienhard R, Lindgren PE, Oskam C, Rudolf I, Schwartz I, Sing A, Stevenson B, Wormser GP, Fingerle V. Rejection of the name Borreliella and all proposed species comb. nov. placed therein. Int J Syst Evol Microbiol 2020; 70:3577-3581. [PMID: 32320380 DOI: 10.1099/ijsem.0.004149] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Rejection (nomen rejiciendum) of the name Borreliella and all new combinations therein is being requested on grounds of risk to human health and patient safety (Principle 1, subprinciple 2 and Rule 56a) and violation to aim for stability of names, to avoid useless creation of names (Principle 1, subprinciple 1 and 3) and that names should not be changed without sufficient reason (Principle 9 of the International Code of Nomenclature of Prokaryotes).
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Affiliation(s)
- Gabriele Margos
- Bavarian Health and Food Safety Authority, National Reference Center for Borrelia, Oberschleissheim, Germany.,Members of the ESCMID Study Group for Lyme Borreliosis (ESGBOR, www.escmid.org/esgbor)
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónomade México, CP 62210, Cuernavaca, Morelos, México
| | - Sally Cutler
- School of Health, Sport and Bioscience, University of East London, London E15 4LZ, UK.,Members of the ESCMID Study Group for Lyme Borreliosis (ESGBOR, www.escmid.org/esgbor)
| | - Ram B Dessau
- Department of Clinical Microbiology, Slagelse Hospital, Denmark.,Members of the ESCMID Study Group for Lyme Borreliosis (ESGBOR, www.escmid.org/esgbor)
| | - Randi Eikeland
- Norwegian Advisory Unit for Tick Borne Diseases, Sørlandet Hospital, Norway.,Members of the ESCMID Study Group for Lyme Borreliosis (ESGBOR, www.escmid.org/esgbor)
| | - Agustin Estrada-Peña
- Department of Animal Pathology, Faculty of Veterinary Medicine, 50013 Zaragoza, Spain
| | - Alexander Gofton
- Australian National Insect Collection CSIRO, Black Mountain, Acton, ACT, 2901, Australia
| | - Lucía Graña-Miraglia
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónomade México, CP 62210, Cuernavaca, Morelos, México
| | - Klaus-Peter Hunfeld
- Zentralinstitut für Labormedizin, Mikrobiologie & Krankenhaushygiene, Krankenhaus Nordwest, Akademisches Lehrkrankenhaus der Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany.,Members of the ESCMID Study Group for Lyme Borreliosis (ESGBOR, www.escmid.org/esgbor)
| | - Andreas Krause
- Abteilung Rheumatologie und Klinische Immunologie, Immanuel Krankenhaus Berlin, Berlin, Germany
| | - Reto Lienhard
- Microbiologiste FAMH, Laboratoire Borrelia (CNRT/ NRZK Spiez), La Chaux-de-Fonds, Switzerland
| | - Per-Eric Lindgren
- Department of Biomedical and Clinical Sciences (BKV), Division of Inflammation and Infection (II), Linköping University, Sweden.,Members of the ESCMID Study Group for Lyme Borreliosis (ESGBOR, www.escmid.org/esgbor)
| | - Charlotte Oskam
- Vector & Waterborne Pathogens Research Group, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150, Australia
| | - Ivo Rudolf
- Institute of Vertebrate Biology, v.v.i., Academy of Sciences of the Czech Republic, CZ-691 42 Valtice, Czech Republic
| | - Ira Schwartz
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - Andreas Sing
- Bavarian Health and Food Safety Authority, National Reference Center for Borrelia, Oberschleissheim, Germany
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics and Department of Entomology, University of Kentucky, Lexington, Kentucky, 40502, USA
| | - Gary P Wormser
- Division of Infectious Diseases, New York Medical College, Valhalla, NY, USA
| | - Volker Fingerle
- Members of the ESCMID Study Group for Lyme Borreliosis (ESGBOR, www.escmid.org/esgbor).,Bavarian Health and Food Safety Authority, National Reference Center for Borrelia, Oberschleissheim, Germany
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32
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Abstract
Lyme borreliosis is the most common vectorborne disease in the northern hemisphere. It usually begins with erythema migrans; early disseminated infection particularly causes multiple erythema migrans or neurologic disease, and late manifestations predominantly include arthritis in North America, and acrodermatitis chronica atrophicans (ACA) in Europe. Diagnosis of Lyme borreliosis is based on characteristic clinical signs and symptoms, complemented by serological confirmation of infection once an antibody response has been mounted. Manifestations usually respond to appropriate antibiotic regimens, but the disease can be followed by sequelae, such as immune arthritis or residual damage to affected tissues. A subset of individuals reports persistent symptoms, including fatigue, pain, arthralgia, and neurocognitive symptoms, which in some people are severe enough to fulfil the criteria for post-treatment Lyme disease syndrome. The reported prevalence of such persistent symptoms following antimicrobial treatment varies considerably, and its pathophysiology is unclear. Persistent active infection in humans has not been identified as a cause of this syndrome, and randomized treatment trials have invariably failed to show any benefit of prolonged antibiotic treatment. For prevention of Lyme borreliosis, post-exposure prophylaxis may be indicated in specific cases, and novel vaccine strategies are under development.
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Affiliation(s)
- Bart Jan Kullberg
- Department of Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hedwig D Vrijmoeth
- Department of Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Freek van de Schoor
- Department of Medicine and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Joppe W Hovius
- Amsterdam University Medical Centers, location AMC, Department of Medicine, Division of Infectious Diseases, and Amsterdam Multidisciplinary Lyme borreliosis Center, Amsterdam, Netherlands
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33
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Gupta RS, Patel S. Robust Demarcation of the Family Caryophanaceae ( Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures. Front Microbiol 2020; 10:2821. [PMID: 32010063 PMCID: PMC6971209 DOI: 10.3389/fmicb.2019.02821] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
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34
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2020; 70:1-5. [DOI: 10.1099/ijsem.0.003881] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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35
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Margos G, Fingerle V, Cutler S, Gofton A, Stevenson B, Estrada-Peña A. Controversies in bacterial taxonomy: The example of the genus Borrelia. Ticks Tick Borne Dis 2019; 11:101335. [PMID: 31836459 DOI: 10.1016/j.ttbdis.2019.101335] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 01/30/2023]
Abstract
In this paper we survey key issues in bacterial taxonomy and review the literature regarding the recent genus separation proposed for the genus Borrelia. We discuss how information on members of the genus Borrelia is increasing but detailed knowledge on the relevant features is available only for a small subset of species. The data accumulated here show that there is considerable overlap in ecology, clinical aspects and molecular features between clades that argue against splitting of the genus Borrelia.
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Affiliation(s)
- Gabriele Margos
- Bavarian Health and Food Safety Authority, German National Reference Center for Borrelia, Veterinärstr. 2, Oberschleissheim, Germany.
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority, German National Reference Center for Borrelia, Veterinärstr. 2, Oberschleissheim, Germany
| | - Sally Cutler
- School of Health, Sport and Bioscience, University of East London, London E15 4LZ, UK
| | - Alexander Gofton
- Australian National Insect Collection, CSIRO, Black Mountain, Clunies Ross St, Acton, ACT, 2901, Australia
| | - Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, and Department of Entomology, University of Kentucky, Lexington, Kentucky, 40502, USA
| | - Agustín Estrada-Peña
- Department of Animal Pathology, Faculty of Veterinary Medicine, Miguel Servet, 177, 50013 Zaragoza, Spain
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36
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Margos G, Fingerle V, Oskam C, Stevenson B, Gofton A. Comment on: Gupta, 2019, distinction between Borrelia and Borreliella is more robustly supported by molecular and phenotypic characteristics than all other neighbouring prokaryotic genera: Response to Margos' et al. "The genus Borrelia reloaded" (PLoS One 13(12): e0208432). PLoS One 14(8):e0221397. Ticks Tick Borne Dis 2019; 11:101320. [PMID: 31722850 DOI: 10.1016/j.ttbdis.2019.101320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 01/11/2023]
Affiliation(s)
- Gabriele Margos
- Bavarian Health and Food Safety Authority, National Reference Center for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany.
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority, National Reference Center for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany
| | - Charlotte Oskam
- Vector & Waterborne Pathogens Research Group, College of Science, Health, Engineering and Education, Murdoch University, Murdoch 6150, Australia
| | - Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, and Department of Entomology, University of Kentucky, Lexington, KY 40502, USA
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