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Tomaiuolo S, Boarbi S, Fancello T, Michel P, Desqueper D, Grégoire F, Callens J, Fretin D, Devriendt B, Cox E, Mori M. Phylogeography of Human and Animal Coxiella burnetii Strains: Genetic Fingerprinting of Q Fever in Belgium. Front Cell Infect Microbiol 2021; 10:625576. [PMID: 33718257 PMCID: PMC7952626 DOI: 10.3389/fcimb.2020.625576] [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: 11/03/2020] [Accepted: 12/31/2020] [Indexed: 12/24/2022] Open
Abstract
Q fever is a zoonotic disease caused by the bacteria Coxiella burnetii. Domestic ruminants are the primary source for human infection, and the identification of likely contamination routes from the reservoir animals the critical point to implement control programs. This study shows that Q fever is detected in Belgium in abortion of cattle, goat and sheep at a different degree of apparent prevalence (1.93%, 9.19%, and 5.50%, respectively). In addition, and for the first time, it is detected in abortion of alpaca (Vicugna pacos), raising questions on the role of these animals as reservoirs. To determine the relationship between animal and human strains, Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) (n=146), Single-Nucleotide Polymorphism (SNP) (n=92) and Whole Genome Sequencing (WGS) (n=4) methods were used to characterize samples/strains during 2009-2019. Three MLVA clusters (A, B, C) subdivided in 23 subclusters (A1-A12, B1-B8, C1-C3) and 3 SNP types (SNP1, SNP2, SNP6) were identified. The SNP2 type/MLVA cluster A was the most abundant and dispersed genotype over the entire territory, but it seemed not responsible for human cases, as it was only present in animal samples. The SNP1/MLVA B and SNP6/MLVA C clusters were mostly found in small ruminant and human samples, with the rare possibility of spillovers in cattle. SNP1/MLVA B cluster was present in all Belgian areas, while the SNP6/MLVA C cluster appeared more concentrated in the Western provinces. A broad analysis of European MLVA profiles confirmed the host-species distribution described for Belgian samples. In silico genotyping (WGS) further identified the spacer types and the genomic groups of C. burnetii Belgian strains: cattle and goat SNP2/MLVA A isolates belonged to ST61 and genomic group III, while the goat SNP1/MLVA B strain was classified as ST33 and genomic group II. In conclusion, Q fever is widespread in all Belgian domestic ruminants and in alpaca. We determined that the public health risk in Belgium is likely linked to specific genomic groups (SNP1/MLVA B and SNP6/MLVA C) mostly found in small ruminant strains. Considering the concordance between Belgian and European results, these considerations could be extended to other European countries.
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Affiliation(s)
- Sara Tomaiuolo
- Zoonoses of Animals Unit, Veterinary Bacteriology, Infectious Diseases in Animals Scientific Directorate, Sciensano, Brussels, Belgium.,Belgian Reference Centrum for Coxiella burnetii and Bartonella, Brussels, Belgium.,Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Samira Boarbi
- Zoonoses of Animals Unit, Veterinary Bacteriology, Infectious Diseases in Animals Scientific Directorate, Sciensano, Brussels, Belgium.,Belgian Reference Centrum for Coxiella burnetii and Bartonella, Brussels, Belgium
| | - Tiziano Fancello
- Zoonoses of Animals Unit, Veterinary Bacteriology, Infectious Diseases in Animals Scientific Directorate, Sciensano, Brussels, Belgium.,Belgian Reference Centrum for Coxiella burnetii and Bartonella, Brussels, Belgium
| | - Patrick Michel
- Zoonoses of Animals Unit, Veterinary Bacteriology, Infectious Diseases in Animals Scientific Directorate, Sciensano, Brussels, Belgium.,Belgian Reference Centrum for Coxiella burnetii and Bartonella, Brussels, Belgium
| | - Damien Desqueper
- Zoonoses of Animals Unit, Veterinary Bacteriology, Infectious Diseases in Animals Scientific Directorate, Sciensano, Brussels, Belgium.,Belgian Reference Centrum for Coxiella burnetii and Bartonella, Brussels, Belgium
| | - Fabien Grégoire
- Serology and Molecular Biology Unit, Association Régionale de Santé et d'Identification Animales (Arsia), Ciney, Belgium
| | - Jozefien Callens
- Small Ruminant Section, Dierengezondheidszorg (DGZ), Torhout, Belgium
| | - David Fretin
- Zoonoses of Animals Unit, Veterinary Bacteriology, Infectious Diseases in Animals Scientific Directorate, Sciensano, Brussels, Belgium.,Belgian Reference Centrum for Coxiella burnetii and Bartonella, Brussels, Belgium
| | - Bert Devriendt
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Eric Cox
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Marcella Mori
- Zoonoses of Animals Unit, Veterinary Bacteriology, Infectious Diseases in Animals Scientific Directorate, Sciensano, Brussels, Belgium.,Belgian Reference Centrum for Coxiella burnetii and Bartonella, Brussels, Belgium
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Furstenau TN, Cocking JH, Sahl JW, Fofanov VY. Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites. BMC Bioinformatics 2018; 19:222. [PMID: 29890941 PMCID: PMC5996513 DOI: 10.1186/s12859-018-2225-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/30/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaST was developed to address this challenge by finding the minimum number of targets that, in combination, achieve maximum strain-level resolution for any strain complex. The final combination of target regions identified by the algorithm produce a unique haplotype for each strain which can be used as a fingerprint for identifying unknown samples in a TAS assay. VaST ensures that the targets have conserved primer regions so that the targets can be amplified in all of the known strains and it also favors the inclusion of targets with basal variants which makes the set more robust when identifying previously unseen strains. RESULTS We analyzed VaST's performance using a number of different pathogenic species that are relevant to human disease outbreaks and biodefense. The number of targets required to achieve full resolution ranged from 20 to 88% fewer sites than what would be required in the worst case and most of the resolution is achieved within the first 20 targets. We computationally and experimentally validated one of the VaST panels and found that the targets led to accurate phylogenetic placement of strains, even when the strains were not a part of the original panel design. CONCLUSIONS VaST is an open source software that, when provided a set of variant sites, can find the minimum number of sites that will provide maximum resolution of a strain complex, and it has many different run-time options that can accommodate a wide range of applications. VaST can be an effective tool in the design of strain identification panels that, when combined with TAS technologies, offer an efficient and inexpensive strain typing protocol.
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Affiliation(s)
- Tara N Furstenau
- The School of Informatics, Computing, and Cyber Systems, Northern Arizona University, 1295 S Knoles Dr., Flagstaff, Arizona, 86001, USA
| | - Jill H Cocking
- The School of Informatics, Computing, and Cyber Systems, Northern Arizona University, 1295 S Knoles Dr., Flagstaff, Arizona, 86001, USA
- Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Flagstaff, Arizona, 86001, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Flagstaff, Arizona, 86001, USA
| | - Viacheslav Y Fofanov
- The School of Informatics, Computing, and Cyber Systems, Northern Arizona University, 1295 S Knoles Dr., Flagstaff, Arizona, 86001, USA.
- Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr., Flagstaff, Arizona, 86001, USA.
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3
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Mori M, Mertens K, Cutler SJ, Santos AS. Critical Aspects for Detection of Coxiella burnetii. Vector Borne Zoonotic Dis 2017; 17:33-41. [PMID: 28055578 DOI: 10.1089/vbz.2016.1958] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coxiella burnetii is a globally distributed zoonotic γ-proteobacterium with an obligatory intracellular lifestyle. It is the causative agent of Q fever in humans and of coxiellosis among ruminants, although the agent is also detected in ticks, birds, and various other mammalian species. Requirements for intracellular multiplication together with the necessity for biosafety level 3 facilities restrict the cultivation of C. burnetii to specialized laboratories. Development of a novel medium formulation enabling axenic growth of C. burnetii has facilitated fundamental genetic studies. This review provides critical insights into direct diagnostic methods currently available for C. burnetii. It encompasses molecular detection methods, isolation, and propagation of the bacteria and its genetic characterization. Differentiation of C. burnetii from Coxiella-like organisms is an essential diagnostic prerequisite, particularly when handling and analyzing ticks.
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Affiliation(s)
- Marcella Mori
- 1 Bacterial Zoonoses of Livestock, Operational Directorate Bacterial Diseases, Veterinary and Agrochemical Research Centre, CODA-CERVA , Brussels, Belgium .,2 Belgian Reference Centre for Coxiella burnetii and Bartonella , Brussels, Belgium
| | - Katja Mertens
- 3 Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Bacterial Infections and Zoonoses , Jena, Germany
| | | | - Ana Sofia Santos
- 5 Centre for Vector and Infectious Diseases Research, National Institute of Health Doutor Ricardo Jorge , Águas de Moura, Portugal
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Eldin C, Mélenotte C, Mediannikov O, Ghigo E, Million M, Edouard S, Mege JL, Maurin M, Raoult D. From Q Fever to Coxiella burnetii Infection: a Paradigm Change. Clin Microbiol Rev 2017; 30:115-190. [PMID: 27856520 PMCID: PMC5217791 DOI: 10.1128/cmr.00045-16] [Citation(s) in RCA: 550] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Coxiella burnetii is the agent of Q fever, or "query fever," a zoonosis first described in Australia in 1937. Since this first description, knowledge about this pathogen and its associated infections has increased dramatically. We review here all the progress made over the last 20 years on this topic. C. burnetii is classically a strict intracellular, Gram-negative bacterium. However, a major step in the characterization of this pathogen was achieved by the establishment of its axenic culture. C. burnetii infects a wide range of animals, from arthropods to humans. The genetic determinants of virulence are now better known, thanks to the achievement of determining the genome sequences of several strains of this species and comparative genomic analyses. Q fever can be found worldwide, but the epidemiological features of this disease vary according to the geographic area considered, including situations where it is endemic or hyperendemic, and the occurrence of large epidemic outbreaks. In recent years, a major breakthrough in the understanding of the natural history of human infection with C. burnetii was the breaking of the old dichotomy between "acute" and "chronic" Q fever. The clinical presentation of C. burnetii infection depends on both the virulence of the infecting C. burnetii strain and specific risks factors in the infected patient. Moreover, no persistent infection can exist without a focus of infection. This paradigm change should allow better diagnosis and management of primary infection and long-term complications in patients with C. burnetii infection.
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Affiliation(s)
- Carole Eldin
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - Cléa Mélenotte
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - Oleg Mediannikov
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - Eric Ghigo
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - Matthieu Million
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - Sophie Edouard
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - Jean-Louis Mege
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
| | - Max Maurin
- Institut de Biologie et de Pathologie, CHU de Grenoble, Grenoble, France
| | - Didier Raoult
- URMITE, UMR CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, Marseille, France
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Joulié A, Sidi-Boumedine K, Bailly X, Gasqui P, Barry S, Jaffrelo L, Poncet C, Abrial D, Yang E, Leblond A, Rousset E, Jourdain E. Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability. INFECTION GENETICS AND EVOLUTION 2016; 48:142-149. [PMID: 28007602 DOI: 10.1016/j.meegid.2016.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/14/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
Abstract
Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need to be investigated to adapt control measures in livestock farms.
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Affiliation(s)
- Aurelien Joulié
- EPIA, INRA, 63122 Saint-Genès Champanelle, France; Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile, France; Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France
| | - Karim Sidi-Boumedine
- Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France
| | | | | | | | | | | | - David Abrial
- EPIA, INRA, 63122 Saint-Genès Champanelle, France
| | - Elise Yang
- Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France
| | | | - Agnès Leblond
- EPIA, INRA, 63122 Saint-Genès Champanelle, France; Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile, France
| | - Elodie Rousset
- Anses (French Agency for Food, Environmental, and Occupational Health and Safety), Laboratory of Sophia Antipolis, Animal Q Fever Unit, Sophia Antipolis, France
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Myrtennäs K, Marinov K, Johansson A, Niemcewicz M, Karlsson E, Byström M, Forsman M. Introduction and persistence of tularemia in Bulgaria. Infect Ecol Epidemiol 2016; 6:32838. [PMID: 27790972 PMCID: PMC5084392 DOI: 10.3402/iee.v6.32838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/14/2016] [Accepted: 09/20/2016] [Indexed: 12/23/2022] Open
Abstract
Introduction Outbreaks of the zoonotic disease tularemia occurred in north-east Bulgaria in the 1960s. Then came 30 years of epidemiological silence until new outbreaks occurred in west Bulgaria in the 1990s. To investigate how bacterial strains of Francisella tularensis causing tularemia in wildlife and humans in the 1960s and the 1990s were related, we explored their genetic diversity. Material and methods Ten F. tularensis genomes from the 1960s (n=3) and the 1990s (n=7) were sequenced, assigned to canonical single-nucleotide polymorphism (canSNP) clades, and compared to reference genomes. We developed four new canSNP polymerase chain reaction (PCR) assays based on the genome sequence information. Results and discussion The genetic analysis showed that the outbreaks in the 1960s as well as in the 1990s involved multiple clones and new genetic diversity. The smallest genetic difference found between any of the Bulgarian strains was five SNPs between the strains L2 and 81 isolated 43 years apart, indicating that F. tularensis may persist locally over long time periods without causing outbreaks. The existence of genetically highly similar strain-pairs isolated the same year in the same area from different hosts supports a hypothesis of local expansion of clones during outbreaks. Close relationship (two SNPs) was found between one strain isolated 1961 in northeast Bulgaria and one strain isolated 5 years before in USSR. Historical data coinciding with the actual time point describe the introduction of water rats from USSR into the Bulgarian outbreak area, which may explain the close genetic relationship and the origin of the outbreak. Conclusion Genome analysis of strains from two outbreaks in the 1960s and the 1990s provided valuable information on the genetic diversity and persistence of F. tularensis in Bulgaria.
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Affiliation(s)
- Kerstin Myrtennäs
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden;
| | - Krustyu Marinov
- Department of Microbiology, Military Medical Academy (MMA), Sofia, Bulgaria
| | - Anders Johansson
- Departments of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Marcin Niemcewicz
- Biological Threat Identification Center, Military Institute of Hygiene and Epidemiology (MIHE), Pulawy, Poland
| | - Edvin Karlsson
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mona Byström
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mats Forsman
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
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Tu Q, Li J, Shi Z, Chen Y, Lin L, Li J, Wang H, Yan J, Zhou Q, Li X, Li L, Zhou J, He Z. HuMiChip2 for strain level identification and functional profiling of human microbiomes. Appl Microbiol Biotechnol 2016; 101:423-435. [PMID: 27734124 DOI: 10.1007/s00253-016-7910-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/18/2016] [Accepted: 09/27/2016] [Indexed: 01/20/2023]
Abstract
With the massive data generated by the Human Microbiome Project, how to transform such data into useful information and knowledge remains challenging. Here, with currently available sequencing information (reference genomes and metagenomes), we have developed a comprehensive microarray, HuMiChip2, for strain-level identification and functional characterization of human microbiomes. HuMiChip2 was composed of 29,467 strain-specific probes targeting 2063 microbial strains/species and 133,924 sequence- and group-specific probes targeting 157 key functional gene families involved in various metabolic pathways and host-microbiome interaction processes. Computational evaluation of strain-specific probes suggested that they were not only specific to mock communities of sequenced microorganisms and metagenomes from different human body sites but also to non-sequenced microbial strains. Experimental evaluation of strain-specific probes using single strains/species and mock communities suggested a high specificity of these probes with their corresponding targets. Application of HuMiChip2 to human gut microbiome samples showed the patient microbiomes of alcoholic liver cirrhosis significantly (p < 0.05) shifted their functional structure from the healthy individuals, and the relative abundance of 21 gene families significantly (p < 0.1) differed between the liver cirrhosis patients and healthy individuals. At the strain level, five Bacteroides strains were significantly (p < 0.1) and more frequently detected in liver cirrhosis patients. These results suggest that the developed HuMiChip2 is a useful microbial ecological microarray for both strain-level identification and functional profiling of human microbiomes.
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Affiliation(s)
- Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, China.,Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China.,Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Jiabao Li
- Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu, Sichuan, China
| | - Zhou Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yanfei Chen
- The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lu Lin
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, China
| | - Juan Li
- College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Hongling Wang
- Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China
| | - Jianbo Yan
- Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China
| | - Qingming Zhou
- College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiangzhen Li
- Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu, Sichuan, China
| | - Lanjuan Li
- The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
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Vincent G, Stenos J, Latham J, Fenwick S, Graves S. Novel genotypes of Coxiella burnetii identified in isolates from Australian Q fever patients. Int J Med Microbiol 2016; 306:463-70. [DOI: 10.1016/j.ijmm.2016.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 11/24/2022] Open
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Abstract
Q fever is a zoonosis of worldwide distribution with the exception of New Zealand. It is caused by an intracellular bacterium, Coxiella burnetii. The disease often goes underdiagnosed because the main manifestation of its acute form is a general self-limiting flu-like syndrome. The Dutch epidemics renewed attention to this disease, which was less considered before. This review summarizes the description of C. burnetii (taxonomy, intracellular cycle, and genome) and Q fever disease (description, diagnosis, epidemiology, and pathogenesis). Finally, vaccination in humans and animals is also considered.
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Affiliation(s)
- Samira Boarbi
- Centre d'étude et de recherches vétérinaires et agrochimiques (CERVA), Direction opérationnelle des maladies bactériennes, Zoonoses bactériennes des animaux de rente, Groeselenberg 99, 1180 Bruxelles, Belgique.,Centre d'étude et de recherches vétérinaires et agrochimiques (CERVA), Direction opérationnelle des maladies bactériennes, Zoonoses bactériennes des animaux de rente, Groeselenberg 99, 1180 Bruxelles, Belgique
| | - David Fretin
- Centre d'étude et de recherches vétérinaires et agrochimiques (CERVA), Direction opérationnelle des maladies bactériennes, Zoonoses bactériennes des animaux de rente, Groeselenberg 99, 1180 Bruxelles, Belgique.,Centre d'étude et de recherches vétérinaires et agrochimiques (CERVA), Direction opérationnelle des maladies bactériennes, Zoonoses bactériennes des animaux de rente, Groeselenberg 99, 1180 Bruxelles, Belgique
| | - Marcella Mori
- Centre d'étude et de recherches vétérinaires et agrochimiques (CERVA), Direction opérationnelle des maladies bactériennes, Zoonoses bactériennes des animaux de rente, Groeselenberg 99, 1180 Bruxelles, Belgique.,Centre d'étude et de recherches vétérinaires et agrochimiques (CERVA), Direction opérationnelle des maladies bactériennes, Zoonoses bactériennes des animaux de rente, Groeselenberg 99, 1180 Bruxelles, Belgique
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ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol 2015; 33:1045-52. [PMID: 26344404 PMCID: PMC4676274 DOI: 10.1038/nbt.3319] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 07/16/2015] [Indexed: 01/21/2023]
Abstract
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.
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11
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Walter MC, Öhrman C, Myrtennäs K, Sjödin A, Byström M, Larsson P, Macellaro A, Forsman M, Frangoulidis D. Genome sequence of Coxiella burnetii strain Namibia. Stand Genomic Sci 2014; 9:22. [PMID: 25593636 PMCID: PMC4286197 DOI: 10.1186/1944-3277-9-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022] Open
Abstract
We present the whole genome sequence and annotation of the Coxiella burnetii strain Namibia. This strain was isolated from an aborting goat in 1991 in Windhoek, Namibia. The plasmid type QpRS was confirmed in our work. Further genomic typing placed the strain into a unique genomic group. The genome sequence is 2,101,438 bp long and contains 1,979 protein-coding and 51 RNA genes, including one rRNA operon. To overcome the poor yield from cell culture systems, an additional DNA enrichment with whole genome amplification (WGA) methods was applied. We describe a bioinformatics pipeline for improved genome assembly including several filters with a special focus on WGA characteristics.
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Affiliation(s)
- Mathias C Walter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Department of Genome-Oriented Bioinformatics, Center of Life and Food Science Weihenstephan, Technische Universität München, Freising, Germany
| | - Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Kerstin Myrtennäs
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Andreas Sjödin
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mona Byström
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Pär Larsson
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Anna Macellaro
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
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12
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Genome Sequence of Coxiella burnetii Strain AuQ01 (Arandale) from an Australian Patient with Acute Q Fever. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00964-14. [PMID: 25278528 PMCID: PMC4183872 DOI: 10.1128/genomea.00964-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Coxiella burnetii strain AuQ01 was isolated from the serum of an Australian acute Q fever patient and represents the first whole genome from this historical Q fever country. This new genome shows distinct differences from existing genomic data and will enhance the understanding of this query pathogen.
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13
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Thierry S, Tourterel C, Le Flèche P, Derzelle S, Dekhil N, Mendy C, Colaneri C, Vergnaud G, Madani N. Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database. PLoS One 2014; 9:e95131. [PMID: 24901417 PMCID: PMC4046976 DOI: 10.1371/journal.pone.0095131] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 03/24/2014] [Indexed: 12/28/2022] Open
Abstract
Background Bacillus anthracis is known to have low genetic variability. In spite of this lack of diversity, multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) and single nucleotide polymorphisms (SNPs) including the canonical SNPs assay (canSNP) have proved to be highly effective to differentiate strains. Five different MLVA schemes based on a collection of 31 VNTR loci (MLVA8, MLVA15, MLVA20, MLVA25 and MLVA31) with increased resolving power have been described. Results MLVA31 was applied to characterize the French National Reference Laboratory collection. The total collection of 130 strains is resolved in 35 genotypes. The 119 veterinary and environmental strains collection in France were resolved into 26 genotypes belonging to three canSNP lineages and four MLVA clonal complexes (CCs) with particular geographical clustering. A subset of seven loci (MLVA7) is proposed to constitute a first line assay. The loci are compatible with moderate resolution equipment such as agarose gel electrophoresis and show a good congruence value with MLVA31. The associated MLVA and SNP data was imported together with published genotyping data by taking advantage of major enhancements to the MLVAbank software and web site. Conclusions The present report provides a wide coverage of the genetic diversity of naturally occurring B. anthracis strains in France as can be revealed by MLVA. The data obtained suggests that once such coverage is achieved, it becomes possible to devise optimized first-line MLVA assays comprising a sufficiently low number of loci to be typed either in one multiplex PCR or on agarose gels. Such a selection of seven loci is proposed here, and future similar investigations in additional countries will indicate to which extend the same selection can be used worldwide as a common minimum set. It is hoped that this approach will contribute to an efficient and low-cost routine surveillance of important pathogens for biosecurity such as B. anthracis.
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Affiliation(s)
- Simon Thierry
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Christophe Tourterel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Philippe Le Flèche
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Division of Analytical Microbiology, DGA CBRN Defence, Vert le Petit, France
| | - Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Neira Dekhil
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Christiane Mendy
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Cécile Colaneri
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
| | - Gilles Vergnaud
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France
| | - Nora Madani
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonosis Unit, Maisons-Alfort, France
- * E-mail:
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14
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Draft Genome Sequences of Six Ruminant Coxiella burnetii Isolates of European Origin. GENOME ANNOUNCEMENTS 2014; 2:genomeA.00285-14. [PMID: 24831135 PMCID: PMC4022799 DOI: 10.1128/genomea.00285-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Coxiella burnetii is responsible for Q fever, a worldwide zoonosis attributed to the inhalation of aerosols contaminated by livestock birth products. Six draft genome sequences of European C. burnetii isolates from ruminants are presented here. The availability of these genomes will help in understanding the potential host specificity and pathogenicity and in identifying pertinent markers for surveillance and tracing.
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15
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Lärkeryd A, Myrtennäs K, Karlsson E, Dwibedi CK, Forsman M, Larsson P, Johansson A, Sjödin A. CanSNPer: a hierarchical genotype classifier of clonal pathogens. Bioinformatics 2014; 30:1762-4. [PMID: 24574113 DOI: 10.1093/bioinformatics/btu113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SUMMARY Advances in typing methodologies have recently reformed the field of molecular epidemiology of pathogens. The falling cost of sequencing technologies is creating a deluge of whole genome sequencing data that burdens bioinformatics resources and tool development. In particular, single nucleotide polymorphisms in core genomes of pathogens are recognized as the most important markers for inferring genetic relationships because they are evolutionarily stable and amenable to high-throughput detection methods. Sequence data will provide an excellent opportunity to extend our understanding of infectious disease when the challenge of extracting knowledge from available sequence resources is met. Here, we present an efficient and user-friendly genotype classification pipeline, CanSNPer, based on an easily expandable database of predefined canonical single nucleotide polymorphisms. AVAILABILITY AND IMPLEMENTATION All documentation and Python-based source code for the CanSNPer are freely available at http://github.com/adrlar/CanSNPer.
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Affiliation(s)
- Adrian Lärkeryd
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Kerstin Myrtennäs
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Edvin Karlsson
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Chinmay Kumar Dwibedi
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, SwedenDepartment of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Mats Forsman
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Pär Larsson
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Andreas Sjödin
- Department of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, SwedenDepartment of Clinical Microbiology, Umeå University, Division of CBRN Security and Defence, FOI, Swedish Defence Research Agency, Department of Clinical Microbiology, The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Chemistry, Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
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