Clotilde L. M., Salvador A., Bernard C. I. V., Lin A., Lauzon C., Muldoon M., et al. Hauser E., Tietze E., Helmuth R., Junker E., Prager R., Schroeter A., et al. (2004). Centers for Disease Control and Prevention [CDC] (1999). The data generated by MLVA can be readily analyzed and standardized for inter-laboratory comparisons (Torpdahl et al., 2007; Hopkins et al., 2011; Lindstedt et al., 2013; Wuyts et al., 2013). CRISPRs: molecular signatures used for pathogen subtyping. Comparison of typing methods with a new procedure based on sequence characterization for. As of November 2017, the number of legacy MLST sequence types for Salmonella has reached 3,929 (Alikhan et al., 2018). Comparison of multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and phage typing for subtype analysis of. (2011) describes many of these assays, most of which target the E. coli wzx and wzy genes. Eppinger M., Mammel M. K., Leclerc J. E., Ravel J., Cebula T. A. The results from these studies suggest that CRISPRMVLST has a higher discriminatory power than legacy MLST (Ferrari et al., 2017); however, discrimination is lower than PFGE in some cases (Almeida et al., 2015). (2015). Genomics of foodborne pathogens for microbial food safety. SeqSero uses a database of 473 alleles representing 56 fliC antigenic types and 190 alleles representing 18 fljB antigenic types in a combined H-antigen database (Zhang et al., 2015). (2011). This environmental difference will allow the chicken farm isolate to accumulate more mutations (per year or any other time unit) than the dry food processing environment isolate, because the chicken farm isolate will multiply more times during the same period than the dry food processing environment isolate. The cost of maintaining data analysis tools and bioinformatics personnel needs to be taken into consideration (Leekitcharoenphon et al., 2014; Ferrari et al., 2017; Nadon et al., 2017). Clooney A. G., Fouhy F., Sleator R. D., ODriscoll A., Stanton C., Cotter P. D., et al. The Neis diversity index for MLVA was 0.979 compared to 0.999 for PFGE (Kjeldsen et al., 2016). (2006). Multiple locus variable number of tandem repeats analysis is serovar specific, thus different Salmonella serovars usually require different MLVA schemes (Kruy et al., 2011). Eichhorn I., Heidemanns K., Semmler T., Kinnemann B., Mellmann A., Harmsen D., et al. The cgMLST method is very similar to the wgMLST method. Genetic-based approaches have been developed for in silico determination of serovars, because the phenotypic determination of Salmonella serovars is costly, time-consuming, and labor-intensive. Since subtype identification can be clinically relevant, we assessed the added value in HIV-1 subtyping using updated molecular phylogeny (Mphy) and the performance of routinely used automated tools. In this review, we focus on the most widely used Salmonella scheme targeting seven housekeeping genes [aroC, dnaN, hemD, hisD, thrA, sucA, and purE; hereafter denoted as legacy MLST to distinguish newer approaches (described below)] (Li et al., 2009; Yun et al., 2015). Moreno A. C. R., Guth B. E. C., Martinez M. B. One microarray method to identify E. coli serogroups involved spotting O-group-specific wzx or wzy gene oligonucleotides or PCR products onto the chip and hybridized with labeled PCR products of the entire O-AGCs (Liu and Fratamico, 2006). rskov F. I, rskov F., Bettelheim K. A., Chandler M. E. (1975). The authors declare that this study received funding from Mars Global Food Safety Center. Comparisons between the different stratification approaches used in these studies have not been possible due to the different cohorts, analytical methods, or sample sites used. Proof-of-concept study for successful inter-laboratory comparison of MLVA results. Very Interesting. Construction of such databases is also time-consuming and labor-intensive, with the difficulty increasing with the diversity of the organisms included in the same database (e.g., a database for S. enterica subspecies enterica serovar Agona will require less time and labor than a database for all S. enterica). While allele code schemes are used by some groups to summarize the differences observed among isolates subtyped by both cgMLST and wgMLST (Nadon et al., 2017), it generally is easier to define standard, stable, cgMLST allele codes. There is no current global recommendation for the application of molecular characterization methods for Salmonella, although the food industry has applied both banding pattern-based and sequence-based subtyping methods for incident investigations. Inns T., Lane C., Peters T., Dallman T., Chatt C., McFarland N. (2015). Moreover, the low discriminatory power of conventional serotyping may result in false-positive identification of relatedness between two unrelated isolates, as strains with the same serovar (such as the serovar Salmonella Enteritidis) may originate from multiple contamination sources. Escherichia coli O antigen typing using DNA microarrays. Poor typeability could be found in assays using a scheme that does not cover genetic variation in full; typeability may also be reduced if some isolates show high endogenous nuclease activity. Antimicrobial drug resistance and molecular characterization of. These two approaches can also be combined for more reliable serovar prediction. These cases highlight the need to reinforce Salmonella control measures in the food industry, including rapid and accurate tracking of pathogen contamination sources with appropriate subtyping tools. Therefore, there is a need to resolve these discrepancies, merge or eliminate serogroups and to revise the E. coli serotype nomenclature (DebRoy et al., 2016). Wiedmann M., Wang S., Post L., Nightingale K. (2014). Structure of the core and central channel of bacterial flagella. Later, the draft genome (i.e., assembly) is used to find matches against the database. Maciorowski K. G., Jones F. T., Pillaiand S. D., Ricke S. C. (2004). Dallman T., Inns T., Jombart T., Ashton P., Loman N., Chatt C. (2016). Ranieri et al. Comparison of multiplex immunochemical and molecular serotyping methods for Shiga toxinproducing. The major difference is the size and nature of the database. Epidemic profile of Shiga toxin-producing. Bioaerosols from municipal and animal wastes: background and contemporary issues. 1, one of the main milestones in the timeline of source attribution research is certainly the development of the Danish or Hald model, which was published in 2004 (Hald et al., 2004).This model put a spotlight on the microbial subtyping approach and it relies on the same type of data as the Dutch model, but it uses a Bayesian approach to attribute stochastically human cases . (1990). (2011) developed a CRISPRmulti-virulence-locus sequence typing (MVLST) approach using virulence genes sseL and fimH with CRISPR1 and CRISPR2 loci; this approach was used to compare 171 isolates representing nine serovars (Typhimurium, Enteritidis, Newport, Heidelberg, Javiana, I 4,[5],12:i:-, Montevideo, Muenchen, Saintpaul) and was reported to be able to subtype Salmonella with resolution at the outbreak level. As of May 2021, Bruker Daltonik GmbH is now Bruker Daltonics GmbH & Co. KG. Salmonellosis outbreaks in the United States due to fresh produce: sources and potential intervention measures. (2015). In food microbiology, molecular subtyping was initially primarily used to characterize foodborne pathogens, but these methods are also increasingly applied by the food industry to track sources of spoilage organisms with the goal to implement controls to increase product shelf life and decrease flavor defects (see Chapter 3 for a discussion of . Development of a multiplex PR assay for detection of Shiga toxin-producing, Low-density macroarray targeting non-locus of enterocyte effacement effectors (nle genes) and major virulence factors of Shiga toxin-producing. Multiplex PCR-based method for identification of common clinical serotypes of. Pinho A. J., Bastos C. A. C., Ferreira P. J. S. G., Garcia S. P., Afreixo V. (2009). Serology, chemistry, and genetics of O and K antigens of. Pearce M. E., Alikhan N. F., Dallman T. J., Zhou Z., Grant K., Maiden M. C. J., et al. In silico serotyping should be performed instead of traditional serotyping for determination of serovars once WGS is implemented as the subtyping method for Salmonella. This review will highlight key aspects of different subtyping methods for bacterial foodborne pathogens and provide examples of their applications in public health, food safety, epidemiology, and population genetics. Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic. The conventional serotyping method is based on agglutination reactions of the O-antigen with antisera that are generated in rabbits against each of the O-groups (rskov and rskov, 1984). Ability to accurately predict the serovar of a given strain. (2011). Hunter S. B., Vauterin P., Lambert-Fair M. A., Van Duyne M. S., Kubota K., Graves L., et al. Wyres K., Conway T., Garg S., Queiroz C., Reumann M., Holt K. (2014). The analysis consists of two main steps: (i) mapping the raw sequence reads against the reference genome and (ii) SNP calling using stringent criteria to prevent the misidentification of sequencing errors or misaligned regions as SNPs (Davis et al., 2015; Katz et al., 2017). (2016). (2018). The cost difference is more apparent when a small number of isolates are sequenced (as could be typical for the food industry). Phylogenetic or clustering analyses are thus better suited to an investigation, as these analyses group isolates by their similarities instead of their differences (Pightling et al., 2018). MLST multi-locus sequence typing . (2018). Its high discriminatory power allows for identification of thousands of different species, but there are some genera still difficult to differentiate. (2015) used the Luminex technology, both antibody- and multiplex PCR-based, and compared them to traditional E. coli serotyping. 92 and 95%, respectively (Zhang et al., 2015; Yoshida et al., 2016a, b; Robertson et al., 2018). Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. However, the system has been discontinued, making Rep-PCR unavailable as a commercial platform. Yoshida C., Lingohr E. J., Trognitz F., MacLaren N., Rosano A., Murphy S. A., et al. The prevalence of multidrug resistance is higher among bovine than human. Subtyping of foodborne and environmental isolates of. MLVA as a tool for public health surveillance of human. (2007). With its high discriminatory power, the fast and easy workflow of the IR Biotyper allows real-time monitoring and source-tracking. Minimum spanning trees are frequently applied to MLVA profiles, yielding maps of predicted relationships among isolates based on single-locus and dual-locus variants (Van Belkum et al., 2007). Bugarel M., Beutin L., Martin A., Gill A., Fach P. (2010b). Disclaimer, National Library of Medicine Historical Salmonella Typhimurium isolates from humans and foods involved in five outbreaks and consisting of five distinct MLVA subtypes were re-analyzed using hqSNP analysis by Octavia et al. Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing. Very Interesting. Low epidemiological concordance could be found in assays that either target low stability markers or an assay with limited discriminatory power, which will group together isolates that are epidemiologically unrelated. Poor ease of use is usually caused by the high level of expertise and experience required by a given assay, e.g., bioinformatics expertise to analyze data produced by the assay. Range, as the number of identifiable serovars, and accuracy (i.e., percentage of isolates with correct serovar identification) should be maximized. No use, distribution or reproduction is permitted which does not comply with these terms. On the other hand, PFGE may cluster epidemiologically unrelated isolates into identical PFGE types (Barco et al., 2013) and may even provide similar or identical PFGE types for isolates that represent different, but genetically very similar serovars that have a common ancestor (Barco et al., 2013; Shi et al., 2015), such as Typhimurium (antigenic formula: 1,4,[5],12:i:1,2) versus Typhimurium var. Only SNPs that have been vertically transferred from an ancestral isolate to the current isolates are subject to the hqSNP analysis, while SNPs that were supposedly horizontally transferred are filtered out from the results. Lindstedt B. The human gut is a reservoir for ExPEC that cause human illness. Based on O-AGC sequence data for all O-groups, Iguchi et al. While the relative discriminatory power of different subtyping methods depends on the strains and serovars tested, WGS methods were consistently found to be most discriminatory, followed by PFGE. R01GM63259/GM/NIGMS NIH HHS/United States. Genome analysis with inter-nucleotide distances. These studies show that public health agencies are increasingly relying on hqSNP analysis for outbreak investigation, including tracking the source of outbreaks. Analysis of the O-AGCs of all E. coli O-groups (Iguchi et al., 2015a; DebRoy et al., 2016) showed that the sizes of the O-AGCs and their gene content vary considerably, which results in the variability of O-antigens. 0 The given assay requires extremely high level of expertise and experience in specific techniques (PhD level scientist with >4 days of specialized training). Molecular subtyping of cancer is a critical step towards more individualized therapy and provides important biological insights into cancer heterogeneity. (2013). Jagadeesan B., Gerner-Smidt P., Allard M. W., Leuillet S., Winkler A., Xiao Y. Rapid Pulsed-Field Gel Electrophoresis Protocol for Subtyping of Campylobacter jejuni. The first step toward uniform standardization of the MLVA profiles was collectively taken by PulseNet International and ECDC in defining the standard protocols of MLVA for Salmonella Typhimurium and Salmonella Enteritidis (ECDC, 2011, 2016b; PulseNet, 2015c). Development of a mechanism for sharing data through anonymous hubs may allay concerns on confidentiality and encourage data sharing (FAO, 2016). (2001). CRISPR: new horizons in phage resistance and strain identification. Danin-Poleg Y, Cohen LA, Gancz H, Broza YY, Goldshmidt H, Malul E, Valinsky L, Lerner L, Broza M, Kashi Y. J Clin Microbiol. Due to the large variety of Salmonella serovars, a laboratory needs to maintain more than 250 different high-quality typing antisera and 350 different antigens for conventional serotyping of Salmonella (McQuiston et al., 2004; Fitzgerald et al., 2006). Fricke W. F., Mammel M. K., McDermott P. F., Tartera C., White D. G., Leclerc J. E., et al. Sequencing platforms that can be used currently for WGS include Illumina, Ion Torrent, Oxford Nanopore Technologies, and Pacific Biosciences (PacBio). Practical value of food pathogen traceability through building a whole-genome sequencing network and database. PhenotypeXpression (PhenoX) is a tool for rapid disease subtyping using publicly available gene expression data and literature. Validation should cover the end-to-end workflow for source tracking from isolate subculture to bioinformatic analysis, articulating the key quality requirements and criteria (Ferrari et al., 2017; Nadon et al., 2017; Portmann et al., 2018). Reduced handling time of pathogenic bacteria is beneficial for large-scale investigations. Nde C. W., Sherwood J. S., Doetkott C., Logue C. M. (2006). NCBI provides phylogenetic tree-based clustering of all publicly available sequence data at the NCBI pathogen detection site4. J Clin Microbiol. Soyer Y., Moreno Switt A., Davis M. A., Maurer J., McDonough P. L., Schoonmaker-Bopp D. J., et al. J3^yXd%:j:"p_`Al,Xd3X0\zw :@S6H@V2@" )G endstream endobj 80 0 obj <> endobj 81 0 obj <>/ExtGState<>/Font<>/ProcSet[/PDF/Text/ImageC]/XObject<>>>/Rotate 0/StructParents 0/TrimBox[30 30 597 804]/Type/Page>> endobj 82 0 obj <>stream ExPEC belong to specific phylogenetic groups (A, B1, B2, and D) determined based on multilocus enzyme electrophoresis, ribotyping, or by triplex PCR targeting the genes chuA and yjaA and a particular DNA fragment known as TSPE4.C2. Wattiau P., Boland C., Bertrand S. (2011). There are also many pathogenic groups of E. coli that cause disease in humans and animals, including diarrheagenic E. coli and the extra-intestinal pathogenic E. coli (ExPEC) that cause illness outside of the GI-tract. WGS (as well as other sequencing approaches that use the same next-generation sequencing technologies used for WGS) also have a number of additional applications in the food industry, which will further drive implementation of these tools. (2010). Nadon C., Van Walle I., Gerner-Smidt P., Campos J., Chinen I., Concepcion-Acevedo J., et al. Please contact your local representative for availability in your country. These PFGE patterns predominantly represent isolates collected since 1996 in North America and Europe (Zou et al., 2013). The results of any subtyping approach can be used to assess the relationship of isolates in an investigation. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers. Application of molecular techniques to the study of hospital infection. Unable to load your collection due to an error, Unable to load your delegates due to an error. Subtyping methods that allow for differentiation of E. coli beyond the species and subspecies level are critical for determining the source of outbreaks and establishing transmission pathways (Eppinger et al., 2011; Frank et al., 2011).Several phenotype-based and genotype-based methods for subtyping E. coli are listed in Table . These isolates had similar virulence gene profiles and did not cluster in separate polymorphism-derived genotypes, and thus human and cattle strains could not be distinguished within the phylogenetic clusters. Twenty years of bacterial genome sequencing. Alternative methods for Salmonella subtyping are commonly compared against PFGE (Call et al., 2008). Vibrio cholerae strain typing and phylogeny study based on simple sequence repeats. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes. Whole-genome mapping: a new paradigm in strain-typing technology. Liu Y., Fratamico P., Debroy C., Bumbaugh A. C., Allen J. W. (2008). Very Interesting. %PDF-1.5 % (2010). (1991). Theoretically, hqSNP analysis is the most discriminatory approach for molecular subtyping, as it investigates all possible SNPs between each pair of isolates in the dataset. Rapid mutations and recombination of the marker(s) during storage and subculture could lead to poor reproducibility. The large amount of data generated by WGS combined with a complex data analysis process generally requires expertise in bioinformatics to deploy and run (Wyres et al., 2014; Deurenberg et al., 2017). Whole genome-based population biology and epidemiological surveillance of. For more features follow our page Bruker Microbiology & Diagnostics.Bruker Microbiology However, in a study of 110 Salmonella isolates from 25 serovars (Torpdahl et al., 2005), MLST resulted in 43 sequence types, while PFGE was able to differentiate the isolates into 73 PFGE subtypes. A genomic overview of the population structure of. Food Microbiology; Medicine; Food Science; Nutrition and Dietetics; . The method is easy to carry out; however, it is laborious and error-prone, and thus, molecular methods are better alternatives for O-typing (Ballmer et al., 2007; Lacher et al., 2014). E. coli have traditionally been serotyped using antisera against the ca. Although various software platforms are available for PFGE pattern analysis, artifacts (e.g., brightly fluorescing spot) may lead to misidentification of bands. Currently, O-groups numbered O1-O188 have been defined, except for O31, O47, O67, O72, O94, and O122 that have not been designated (rskov and rskov, 1984; Scheutz et al., 2004), and four groups have been divided into subtypes O18ab/ac, O28ab/ac, O112ab/ac, and O125ab/ac, giving a total of 186 O-groups. The superb discriminatory power of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry allows for the accurate and fast identification of thousands of microorganism species, while powerful software automatically performs typing and result reporting. PFGE has relatively high concordance with epidemiological relatedness with two decades of data accumulation (CDC, 2018a). Amirkhanian V., Lui M., Guttman A., Szantai E. (2006). MLVA is less labor-intensive, time-consuming, and it is easier to perform than PFGE and MLST, as the protocol requires only a regular PCR step followed by capillary electrophoresis (Torpdahl et al., 2007; Lindstedt et al., 2013). Foley S. L., White D. G., McDermott P. F., Walker R. D., Rhodes B., Fedorka-Cray P. J., et al. Dr. Daniel Montano - CEO of Zhittya Genesis Medicine is giving a presentation entitled: "Parkinson's Disease and Other Brain Disorders: The 10 most common serovars in this S. enterica subspecies I dataset were serovars Enteritidis, Typhimurium, Infantis, Typhi, Newport, Virchow, Kentucky, Stanley, Paratyphi A, and Java. (2011). Unfortunately, it can also be imprecise (McQuiston et al., 2011). Public Health England (PHE) started adopting the seven-gene MLST (based on WGS data) approach as a replacement for traditional serotyping in 2015 (Ashton et al., 2016). However, with the advent of and transition into WGS, further development of MLVA may not occur. A cgMLST scheme is publicly available from EnteroBase (EnteroBase URL: https://enterobase.warwick.ac.uk/) and it is likely to be implemented within BioNumerics in the future. Tools used in incident investigations that can differentiate Salmonella beyond the species level (defined as Salmonella subtyping) are essential to improve control of this pathogen, as Salmonella contamination can occur from diverse sources at any stage of food production (Olaimat and Holley, 2012; Barco et al., 2013; Shi et al., 2015). An approach based on targeted amplicon sequencing for SNP genotyping was used to determine the relationship of stx-positive and stx-negative E. coli O26:H11 strains from cattle compared to the genomes of human clinical isolates (Ison et al., 2016). Krause U., Thomson-Carter F. M., Pennington T. H. (1996). Rapid whole-genome sequencing for surveillance of. Escherichia coli strains are commensal organisms that are part of the normal intestinal microflora of humans and other mammals. Kerouanton A., Marault M., Lailler R., Weill F. X., Feurer C., Espie E., et al. The raw sequence data generated by molecular-based subtyping methods, especially WGS, require both physical and virtual space for storage. The use of WGS for Salmonella subtyping in outbreak investigation and pathogen source tracking has proven effective by a rapidly increasing number of studies (den Bakker et al., 2011, 2014; Allard et al., 2012; Leekitcharoenphon et al., 2014; Deng et al., 2015; Taylor et al., 2015; Hoffmann et al., 2016; Inns et al., 2016). Poor reproducibility could be the results of (i) technically difficult assay (leading to technical errors by personnel, e.g., cross-contamination), (ii) reagents not standardized sufficiently, (iii) equipment not performing reproducibly, (iv) poorly optimized typing system, (v) sensitivity of equipment or assay system to environmental factors (e.g., humidity, temperature), (vi) bias in observing, recording, analysis, and interpretation of the results; (vii) or assays targeting biologically highly variable markers (e.g., some of the surface antigens targeted by classical serotyping). Wang W., Perepelov A. V., Feng L., Shevelev S. D., Wang Q., Senchenkova S. N., et al. Software with a more user-friendly interface, such as CLC Genomics Workbench5, BioNumerics, and Geneious (Biomatters, New Zealand), however, is available, including for industry users with limited bioinformatics expertise and an increasing number of user-friendly bioinformatics tools are being developed. Our literature-based assessment supports the superior discriminatory power of WGS and its advantages compared with other methods for Salmonella subtyping and source tracking for the food industry. Since SISTR can use genoserotyping and the cgMLST scheme to infer the serovar, higher confidence should be attributed to assignments where both genoserotyping and cgMLST agree on the serovar designation. PulseNet international is also making efforts to implement WGS within the PulseNet network as a routine tool to replace PFGE and MLVA (Nadon et al., 2017; Figure 1). B., Nutt J. D., Ricke S. C. (2009). Bioinformatics is a key capability required for WGS. A balance between efficiency/effectiveness and cost of a given assay is more important than pursuing low cost, because low cost may potentially lead to larger economic loss and extra investigation time caused by poor quality of typing result. $_GJk@ @ Kw endstream endobj startxref 0 %%EOF 129 0 obj <>stream Ison S. A., Delannoy S., Bugarel M., Nagaraja T. G., Renter D. G., Den Bakker H. C., et al. Kozyreva V. K., Crandall J., Sabol A., Poe A., Zhang P., Concepcion-Acevedo J., et al. Many of the characterization methods and technologies, as well as data analysis pipelines, are operated as research tools, and are under continuous development. It is important to mention that the serovars mentioned above (i.e., Enteritidis, Typhimurium, Newport, Mississippi, Saintpaul, and Kentucky) are ranked among the most common Salmonella serovars associated with human and animal salmonellosis globally (Galanis et al., 2006; CDC, 2009). Fast microorganism identification combined with instant and automated typing. (2017). SISTR is a platform for in silico analysis of Salmonella draft genome assemblies. 0 Extremely low repeatability (<90%; meaning for >10% of isolates results are not repeatable). In a study comparing different molecular methods to differentiate 52 Salmonella Enteritidis isolates, PFGE resulted in eight subtypes, while MLVA resulted in 18 subtypes and WGS resulted in 34 subtypes. Comparison of a semi-automated rep-PCR system and multilocus sequence typing for differentiation of. Investigations of community-acquired UTI and outbreaks of UTI suggested common point sources, such as contaminated food products (Nordstrom et al., 2013). A., Torpdahl M., Vergnaud G., Le Hello S., Weill F. X., Tietze E., et al. Shariat, N.; Sandt, C.H. Evaluation of molecular methods for identification of. Assembly free and assembly based wgMLST allele assignment should match for high confidence. These large fragments are separated in a flat agarose gel by constantly changing the direction of the electric current (pulsed field), which causes the DNA to separate by size, generating a specific fingerprint pattern for a given isolate (Foley et al., 2009).
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