Development of a comparative genomic fingerprinting assay for rapid and high resolution genotyping of Arcobacter butzleri

BMC Microbiology

Eduardo N Taboada¹  G Douglas Inglis³  L Brent Selinger²  Peter Kruczkiewicz¹  Andrew L Webb² 

[1] Public Health Agency of Canada, Township Rd. 9-1, Lethbridge, AB, Canada;Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada;Agriculture and Agri-Food Canada, 5403 – 1st Avenue S, Lethbridge, AB, Canada

关键词: Genome sequencing;    Arcobacter butzleri;    Comparative genomics;    Subtyping;    Molecular epidemiology;   

Others  :  1212049
DOI  :  10.1186/s12866-015-0426-4

 received in 2014-10-22, accepted in 2015-04-15,  发布年份 2015

【 摘 要 】

Background

Molecular typing methods are critical for epidemiological investigations, facilitating disease outbreak detection and source identification. Study of the epidemiology of the emerging human pathogen Arcobacter butzleri is currently hampered by the lack of a subtyping method that is easily deployable in the context of routine epidemiological surveillance. In this study we describe a comparative genomic fingerprinting (CGF) method for high-resolution and high-throughput subtyping of A. butzleri. Comparative analysis of the genome sequences of eleven A. butzleri strains, including eight strains newly sequenced as part of this project, was employed to identify accessory genes suitable for generating unique genetic fingerprints for high-resolution subtyping based on gene presence or absence within a strain.

Results

A set of eighty-three accessory genes was used to examine the population structure of a dataset comprised of isolates from various sources, including human and non-human animals, sewage, and river water (n=156). A streamlined assay (CGF₄₀) based on a subset of 40 genes was subsequently developed through marker optimization. High levels of profile diversity (121 distinct profiles) were observed among the 156 isolates in the dataset, and a high Simpson’s Index of Diversity (ID) observed (ID > 0.969) indicate that the CGF₄₀ assay possesses high discriminatory power. At the same time, our observation that 115 isolates in this dataset could be assigned to 29 clades with a profile similarity of 90% or greater indicates that the method can be used to identify clades comprised of genetically similar isolates.

Conclusions

The CGF₄₀ assay described herein combines high resolution and repeatability with high throughput for the rapid characterization of A. butzleri strains. This assay will facilitate the study of the population structure and epidemiology of A. butzleri.

【 授权许可】

   
2015 Webb et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Vandamme P. Taxonomy of the family Campylobacteraceae . 2nd ed. ASM Press, Washington DC, USA; 2000.
• [2]Merga JY, Williams NJ, Miller WG, Leatherbarrow AJH, Bennett M, Hall N et al.. Exploring the diversity of Arcobacter butzleri from cattle in the UK using MLST and whole genome sequencing. PLoS Biol. 2013; 8(2):12.
• [3]Nieva-Echevarria B, Martinez-Malaxetxebarria I, Girbau C, Alonso R, Fernández-Astorga A. Prevalence and genetic diversity of Arcobacter in food products in the north of Spain. J Food Prot. 2013; 76(8):1447-50.
• [4]Revez J, Huuskonen M, Ruusunen M, Lindström M, Hänninen M-L. Arcobacter species and their pulsed-field gel electrophoresis genotypes in Finnish raw milk during summer 2011. J Food Prot. 2013; 76(9):1630-2.
• [5]Rasmussen LH, Kjeldgaard J, Christensen JP, Ingmer H. Multilocus sequence typing and biocide tolerance of Arcobacter butzleri from Danish broiler carcasses. BMC Res Notes. 2013; 6(322):7.
• [6]Miller WG, Wesley IV, On SLW, Houf K, Megraud F, Wang G et al.. First multi-locus sequence typing scheme for Arcobacter spp. BMC Microbiol. 2009; 9(1):196. BioMed Central Full Text
• [7]de Boer RF, Ott A, Güren P, van Zanten E, van Belkum A, Kooistra-Smid AMD. Detection of Campylobacter species and Arcobacter butzleri in stool samples by use of real-time multiplex PCR. J Clin Microbiol. 2013; 51(1):253-9.
• [8]Miller WG, Parker CT, Rubenfield M, Mendz GL, Wösten MMSM, Ussery DW et al.. The complete genome sequence and analysis of the Epsilonproteobacterium Arcobacter butzleri. PLoS Biol. 2007; 2(12):e1358.
• [9]Douidah L, De Zutter L, Vandamme P, Houf K. Identification of five human and mammal associated Arcobacter species by a novel multiplex-PCR assay. J Microbiol Methods. 2010; 80(3):281-6.
• [10]Samie A, Obi CL, Barrett LJ, Powell SM, Guerrant RL. Prevalence of Campylobacter species, Helicobacter pylori and Arcobacter species in stool samples from the Venda region, Limpopo, South Africa: Studies using molecular diagnostic methods. J Infection. 2007; 54(6):558-66.
• [11]Houf K, Stephan R. Isolation and characterization of the emerging foodborne pathogen Arcobacter from human stool. J Microbiol Methods. 2007; 68(2):408-13.
• [12]Collado L, Gutiérrez M, González M, Fernández H. Assessment of the prevalence and diversity of emergent Campylobacteria in human stool samples using a combination of traditional and molecular methods. Diagn Microbiol Infect Dis. 2013; 75(4):3.
• [13]Fitzgerald C, Helsel LO, Nicholson MA, Olsen SJ, Swerdlow DL, Flahart R et al.. Evaluation of methods for subtyping Campylobacter jejuni during an outbreak involving a food handler. J Clin Microbiol. 2001; 39(7):2386-90.
• [14]Van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK et al.. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infect. 2007; 13:46.
• [15]Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R et al.. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A. 1998; 95(6):3140-5.
• [16]Korczak BM, Zurfluh M, Emler S, Kuhn-Oertli J, Kuhnert P. Multiplex strategy for multilocus sequence typing, fla typing, and genetic determination of antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolates collected in Switzerland. J Clin Microbiol. 2009; 47(7):1996-2007.
• [17]Lévesque S, Michaud S, Arbeit RD, Frost EH. High-resolution melting system to perform multilocus sequence typing of Campylobacter jejuni. PLoS ONE. 2011; 6(1):e16167.
• [18]Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010; 95(6):315-27.
• [19]Cody AJ, McCarthy ND, Jansen Van Rensburg M, Isinkaye T, Bentley SD, Parkhill J et al.. Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol. 2013; 51(8):2526-34.
• [20]Struelens M, Brisse S. From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases. Euro Surveill. 2013; 18(4):e20386.
• [21]Taboada EN, Ross SL, Mutschall SK, MacKinnon JM, Roberts MJ, Buchanan CJ et al.. Development and validation of a comparative genomic fingerprinting method for high-resolution genotyping of Campylobacter jejuni. J Clin Microbiol. 2012; 50(3):788-97.
• [22]Clark CG, Taboada E, Grant CCR, Blakeston C, Pollari F, Marshall B et al.. Comparison of molecular typing methods useful for detecting clusters of Campylobacter jejuni and C. coli isolates through routine surveillance. J Clin Microbiol. 2011; 50(3):47.
• [23]Taylor DN, Perlman DM, Echeverria PD, Lexomboon U, Blaser MJ. Campylobacter immunity and quantitative excretion rates in Thai children. J Infect Dis. 1993; 168:754-8.
• [24]Kokotovic B, On SLW. High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms. FEMS Microbiol Lett. 1999; 173(1):77-84.
• [25]Kruczkiewicz P. A comparative genomic framework for the in silico design and assessment of molecular typing methods using whole-genome sequence data with application to Listeria monocytogenes. M.Sc . University of Lethbridge, Lethbridge, AB; 2013.
• [26]Elliot EJ. Acute gastroenteritis in children. Brit Med J. 2007; 334(7583):35-40.
• [27]Notifiable Diseases On-Line. Public Health Agency of Canada, Ottawa ON. [http://dsol-smed.phac-aspc.gc.ca/dsol-smed/ndis/index-eng.php]
• [28]Inglis GD, McAllister TA, Larney FJ, Topp E. Prolonged survival of Campylobacter species in bovine manure compost. Appl Environ Microbiol. 2010; 76(4):1110-9.
• [29]Hannon SJ, Taboada EN, Russell ML, Allan B, Waldner C, Wilson HL et al.. Genomics-based molecular epidemiology of Campylobacter jejuni isolates from feedlot cattle and from people in Alberta Canada. J Clin Microbiol. 2009; 47(2):410-20.
• [30]Collado L, Figueras MJ. Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter. Clin Microbiol Rev. 2011; 24(1):174-92.
• [31]Douidah L, de Zutter L, Baré J, De Vos P, Vandamme P, Vandenberg O et al.. Occurrence of putative virulence genes in Arcobacter species isolated from humans and animals. J Clin Microbiol. 2012; 50(3):735-41.
• [32]Douidah L, De Zutter L, Baré J, Houf K. Towards a typing strategy for Arcobacter species isolated from humans and animals and assessment of the in vitro genomic stability. Foodborne Pathog Dis. 2014; 11(4):272-80.
• [33]Jolley KA, Maiden MCJ. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010; 11:595. BioMed Central Full Text
• [34]Taboada EN, MacKinnon JM, Luebbert CC, Gannon VPJ, Nash JHE, Rahn K. Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni. BMC Evol Biol. 2008; 8(1):229. BioMed Central Full Text
• [35]Dagerhamn J, Blomberg C, Browall S, Sjostrom K, Morfeldt E, Henriques-Normark B. Determination of accessory gene patterns predicts the same relatedness among strains of Streptococcus pneumoniae as sequencing of housekeeping genes does and represents a novel approach in molecular epidemiology. J Clin Microbiol. 2008; 46(3):863-8.
• [36]Deng X, Phillippy A, Li Z, Salzberg S, Zhang W. Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics. 2010; 11(1):500. BioMed Central Full Text
• [37]Carrillo CD, Kruczkiewicz P, Mutschall S, Tudor A, Clark C, Taboada EN. A framework for assessing the concordance of molecular typing methods and the true strain phylogeny of Campylobacter jejuni and C. coli using draft genome sequence data. Front Cell Infect Microbiol. 2012; 2(57):12.
• [38]Taboada EN, Clark CG, Sproston EL, Carrillo CD. Current methods for molecular typing of Campylobacter species. J Microbiol Methods. 2013; 95(1):24-31.
• [39]On SLW, Atabay HI, Amisu KO, Coker AO, Harrington CS. Genotyping and genetic diversity of Arcobacter butzleri by amplified fragment length polymorphism (AFLP) analysis. Lett Appl Microbiol. 2004; 39(4):347-52.
• [40]Merga JY, Leatherbarrow AJH, Winstanley C, Bennett M, Hart CA, Miller WG et al.. Comparison of Arcobacter isolation methods, and diversity of Arcobacter spp. in Cheshire, United Kingdom. Appl Environ Microbiol. 2011; 77(5):1646-50.
• [41]Hume ME, Harvey RB, Stanker LH, Droleskey RE, Poole TL, Zhang H-B. Genotypic variation among Arcobacter isolates from a farrow-to-finish swine facility. J Food Prot. 2001; 64(5):645-51.
• [42]Inglis GD, Boras VF, Houde A. Enteric campylobacteria and RNA viruses associated with healthy and diarrheic humans in the Chinook health region of southwestern Alberta Canada. J Clin Microbiol. 2011; 49(1):209-19.
• [43]Blaser MJ. Epidemiologic and clinical features of Campylobacter jejuni infections. J Infect Dis. 1997; 176(2):S103-5.
• [44]On SLW, Harrington CS, Atabay HI. Differentiation of Arcobacter species by numerical analysis of AFLP profiles and description of a novel Arcobacter from pig abortions and turkey faeces. J Appl Microbiol. 2003; 95(5):1096-105.
• [45]Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S et al.. The NCBI BioSystems database. Nucleic Acids Res. 2010; 38(suppl 1):D492-6.
• [46]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10.
• [47]Ewing B, Green P. Base-calling of automated sequencer traces using Phred II Error probabilities. Genome Res. 1998; 8(3):186-94.
• [48]Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Biral I. ABySS: A parallel assembler for short read sequence data. Genome Res. 2009; 19:1117-23.
• [49]Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA et al.. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9(75):15.
• [50]Kruczkiewicz P, Mutschall S, Barker D, Thomas J, Van Domselaar G, Gannon VPJ, et al. MIST: a tool for rapid in silico generation of molecular data from bacterial genome sequences. https://bitbucket.org/peterk87/microbialinsilicotyper/wiki/Home#markdown-header-paper.
• [51]R: A language and environment for statistical computing [http://www.R-project.org]
• [52]Carriço JA, Costa-Silva C, Melo-Cristino J, Pinto FR, de Lencastre H, Almeida JS et al.. Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. J Clin Microbiol. 2006; 44(7):2524-32.
• [53]Robinson DF, Foulds LR. Comparison of phylogenetic trees. Math Biosci. 1981; 53(1–2):131-47.
• [54]Severiano A, Pinto FR, Ramirez M, Carriço JA. Adjusted Wallace Coefficient as a measure of congruence between typing methods. J Clin Microbiol. 2011; 49(11):3997-4000.
• [55]Rodrigo AG, Kelly-Borges M, Bergquist PR, Bergquist PL. A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N Z J Bot. 1993; 31(3):257-68.
• [56]Rozen S, Skaletsky HJ. Primer3 on the WWW for general users and for biologist programmers. Humana Press Inc, Totowa, NJ; 2000.
• [57]Kaplinski L, Andreson R, Puurand T, Remm M. MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics. 2005; 21(8):1701-2.
• [58]Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson’s index of diversity. J Clin Microbiol. 1988; 26(11):2465-6.