subtyping microbiology

Timeline of the development of selected molecular subtyping and characterization methods for Salmonella (Salmonella Subcommittee of the Nomenclature Committee of the International Society for, Microbiology, 1934; Gilson et al., 1990; Threlfall and Frost, 1990; Hulton et al., 1991; Martin et al., 1992; Lindstedt et al., 2003, 2013; Healy et al., 2005; Grimont and Weill, 2007; Zou et al., 2010; Wattiau et al., 2011; PulseNet, 2014; CDC, 2016a, 2019; Nadon et al., 2017). 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). Zou W., Lin W. J., Foley S. L., Chen C. H., Nayak R., Chen J. J., et al. Larsson J. T., Torpdahl M. Copenhagen (antigenic formula: 1,4,12:i:1,2) (Heisig et al., 1995; Hauser et al., 2011), and Typhimurium versus 4,5,12:i:- (Guerra et al., 2000; Soyer et al., 2009; Wiedmann and Nightingale, 2009; Hoelzer et al., 2010; Ranieri et al., 2013). Pinho A. J., Bastos C. A. C., Ferreira P. J. S. G., Garcia S. P., Afreixo V. (2009). Brukers MALDI Biotyperhas revolutionized microorganism identification over the past decade. This process uses fragmented DNA templates to detect single bases as they are incorporated during a DNA replication reaction on a solid surface flow cell (Illumina (2019)). Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. The hqSNP analysis can easily be kept private as the analysis can be run within a closed dataset of genomes. The commercial introduction of next-generation sequencing technologies has made it possible to perform routine WGS of E. coli and other bacteria relatively rapidly and at affordable costs (Franz et al., 2014). Comparison of whole genome sequences from human and non-human. Indeed, high genetic similarity, including antibiotic resistance and virulence gene patterns, between APEC and ExPEC strains causing disease in poultry and humans, respectively, has been observed (Smith et al., 2007; Manges and Johnson, 2012). (2018). 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. The MBT Subtyping Module combines the identification of important pathogens with automated subsequent detection of specific marker peaks, all in one workflow. McQuiston J. R., Waters R. J., Dinsmore B. Multilocus sequence typing supports the hypothesis that cow- and human-associated. The food industry may choose to invest in in-house capability that can interface with outside resources (e.g., academic partners, industry partners, government agencies), however, there are also opportunities to outsource data analyses to commercial or academic partner labs. The MBT Subtyping Module enables the automated detection of specific marker peaks, and provides confidence in microbial identification. 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. Bacterial identification methods in our microbiology laboratory. den Bakker H. C., Cummings C. A., Ferreira V., Vatta P., Orsi R. H., Degoricija L., et al. Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012. Bethesda, MD 20894, Web Policies (2016). This section briefly provides some examples of comparative studies of subtyping methods. Centers for Disease Control and Prevention [CDC] (1999). The authors declare that this study received funding from Mars Global Food Safety Center. Assessment and Comparison of Molecular Subtyping and Characterization Methods for, Edited by: Learn-Han Lee, Monash University Malaysia, Malaysia, Reviewed by: Min Yue, Zhejiang University, China; Dapeng Wang, Shanghai Jiao Tong University, China; Soohyoun Ahn, University of Florida, United States, This article was submitted to Food Microbiology, a section of the journal Frontiers in Microbiology. Food safety hazards associated with ready-to-bake cookie dough and its ingredients. Good subtyping discrimination for most serovars. The MBT Lipid Xtract Kit facilitates efficient sample preparation for analysis of microbial lipids, enabling fast resistance detection based on MALDI-TOF analysis of Lipid A modifications, on the MALDI Biotyper sirius, using negative ion mode. 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). Examples of serovars incorrectly predicted by PFGE. about navigating our updated article layout. At least 27 MLVA schemes have been developed to subtype different Salmonella serovars, whereas only Salmonella Typhimurium and Salmonella Enteritidis MLVA assays have been standardized in Europe and in the PulseNet network (PulseNet, 2015c; Kjeldsen et al., 2016). (2015). (2015). already built in. One-step identification of five prominent chicken. Simultaneous analysis of multiple enzymes increases accuracy of pulsed-field gel electrophoresis in assigning genetic relationships among homogeneous. Brenner F. W., Villar R. G., Angulo F. J., Tauxe R., Swaminathan B. (2014). You may notice problems with PFGE is currently still the gold standard and most widely used Salmonella DNA fingerprinting method used by public health authorities and food regulators to characterize and track this pathogen in outbreaks, although it is being replaced by WGS. The application of DNA-based methods for characterization of pathogens such as Salmonella has become common practice. Twenty years of bacterial genome sequencing. With its high discriminatory power, the fast and easy workflow of the IR Biotyper allows real-time monitoring and source-tracking. (2018). Campos L. C., Whittam T. S., Gomes T. A. T., Andrade J. R. C., Trabulsi L. R. (1994). HHS Vulnerability Disclosure, Help (2011). Sequenced Salmonella genomes can be deposited and made publicly available on the National Center for Biotechnology Information site1, the European Bioinformatics Institute site2, or the DNA Data Bank of Japan site3 with data shared between all three (Kodama et al., 2012; Jagadeesan et al., 2019). Kotewicz M. L., Jackson S. A., LeClerc J. E., Cebula T. A. MLVA is the second major genotyping tool (after PFGE) used in the PulseNet network (PulseNet, 2015c); prior to WGS, MLVA was one of the most popular subtyping methods used in public health surveillance and outbreak investigation of Salmonella, particularly in Europe (Torpdahl et al., 2007; Hopkins et al., 2011; Barco et al., 2013; Bauer et al., 2013; Lindstedt et al., 2013; Mughini-Gras et al., 2018). B., Andrysiak A. K., Tracz D. M., Guard-Bouldin J., Demczuk W., Ng L. K., et al. Based on O-AGC sequence data for all O-groups, Iguchi et al. In order to reproduce the results obtained from hqSNP analysis, one needs to use the same reference and parameters that were used in the original analysis (Nadon et al., 2017). Comparison of subtyping methods for differentiating. A high-throughput PCR method based on the GeneDisc array targeted virulence genes and O- and H-type-specific genes for identification of STEC associated with severe illness (Bugarel et al., 2010b). Persing D. H., Tenover F. C., Versalovic J., Tang Y. W., Unger E. R., Relman D. A. The genes that encode for O-antigens are located on the chromosome in a cluster designated as the O-antigen gene cluster (O-AGC). Pearce M. E., Alikhan N. F., Dallman T. J., Zhou Z., Grant K., Maiden M. C. J., et al. It is costly, labor-intensive and time consuming, cross reactivity of the antisera with different serogroups occurs, antisera are available only in specialized laboratories, batch-to-batch variations in antibodies can occur, and many E. coli strains isolated from various sources are non-typeable (Lacher et al., 2014). Some PFGE patterns are very common within some serovars (e.g., Pattern 4 for, Has been the gold standard subtyping method for, Multiple locus variable number of tandem repeats (VNTR) analysis (MLVA). Ability to accurately predict the serovar of a given strain. 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. In contrast to traditional serotyping, Luminex-based suspension assays allow for simultaneous testing for multiple serogroups in a single assay. PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Recent developments and future prospects in subtyping of foodborne bacterial pathogens. Structure of the core and central channel of bacterial flagella. Genomics of foodborne pathogens for microbial food safety. (2013) showed that Rep-PCR accurately predicted the serovar of 30 out of 46 isolates representing the top 40 Salmonella serovars isolated from human and non-human sources, with an accuracy of 65%. Nevertheless, standardization of WGS operation and data analysis, in particularly source tracking analysis, is required at a global level. Reference genomes that are not closely related to the set of isolates under investigation may result in underestimation of the number of SNPs, due to specific regions of the genome that may be present in the dataset under investigation, but that are missing in the reference genome (Pightling et al., 2014). Wang L., Rothemund D., Curd H., Reeves P. R. (2003). (2015). Development of a mechanism for sharing data through anonymous hubs may allay concerns on confidentiality and encourage data sharing (FAO, 2016). Poor repeatability could be the result 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. (2002). Sukhnanand S, Alcaine S, Warnick LD, Su WL, Hof J, Craver MP, McDonough P, Boor KJ, Wiedmann M. J Clin Microbiol. (2018). Both wgMLST and cgMLST are reference-independent which makes the results more reproducible and transferable than hqSNP analysis (Nadon et al., 2017). 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). The traditional method for identifying E. coli uses antibodies to test for surface antigens: the O- polysaccharide antigens, flagellar H-antigens, and capsular K-antigens (described below). The advantages of WGS approaches are being recognized by academic, government, industry, and the private sector for addressing regulatory and public health needs. Hyyti-Trees EK, Cooper K, Ribot EM, Gerner-Smidt P. Future Microbiol. Comparison of a semi-automated rep-PCR system and multilocus sequence typing for differentiation of. Park S. Y., Woodward C. L., Kubena L. F., Nisbet D. J., Birkhold S. G., Ricke S. C., et al. 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). An investigation into a multi-state outbreak caused by Salmonella Poona was carried out in 2015 using PFGE and hqSNP analysis. Because this approach deals directly with the raw sequence reads, it allows filtering low-quality reads or specific nucleotides with low quality within a good-quality read. A. However, for specific serovars (e.g., Salmonella Enteritidis) MLVA has been reported to provide improved discriminatory power over PFGE (Boxrud et al., 2007; Beranek et al., 2009; De Cesare et al., 2015). Comparison of multiplex immunochemical and molecular serotyping methods for Shiga toxinproducing. More than 2,500 serovars of Salmonella enterica, the Salmonella species responsible for virtually all salmonellosis cases have been identified by conventional serotyping (Hadjinicolaou et al., 2009; Ferrari et al., 2017), but less than 100 serovars account for the vast majority of human infections (CDC, 2015). Clustered regularly interspaced short palindromic repeats (CRISPR) are short, highly conserved DNA repeats separated by unique sequences of similar length, and they have been used for subtyping, identification, and detection of bacteria (Shariat and Dudley, 2014). The metadata should include information such as the geographic and temporal background of the isolates, the sample type, and sample source (e.g., raw ingredients, finished products, environment), etc. Thus, molecular serotyping offers alternative methods for E. coli serotyping, and furthermore, they can be coupled with assays for specific virulence gene enabling the determination of O- and H-group, pathotype, and the strains pathogenic potential simultaneously. 2005 Aug;43(8):3688-98. doi: 10.1128/JCM.43.8.3688-3698.2005. Singh A., Goering R. V., Simjee S., Foley S. L., Zervos M. J. No genetic information such as virulence potential or presence of antimicrobial resistance genes can be provided by PFGE, as the DNA fragments are separated by size rather than sequence (Ferrari et al., 2017). Allard M. W., Luo Y., Strain E., Li C., Keys C. E., Son I., et al. CRISPR typing and subtyping for improved laboratory surveillance of. SNP or allelic differences show objectively the genetic distance between two isolates. Has been used as a secondary subtyping method to compensate the low discriminatory power of serotyping and PFGE for some, Legacy multilocus sequence typing (legacy MLST). Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. (2015) identified unique STEC O26 genotypes in human and cattle strains. Molecular beacon-based real-time PCR detection of primary isolates of. 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). Zhang S., Yin Y., Jones M. B., Zhang Z., Kaiser D. B. L., Dinsmore B. Please contact your local representative for availability in your country. Classical serotyping is likely to be replaced rapidly by WGS-based serovar prediction. The sensitivity of cytology was 17%, the specificity was 100%, and the accuracy was 74.7%. Smith J. L., Fratamico P. M., Gunther N. (2007). However, the discriminatory power of Rep-PCR in subtyping Salmonella is reportedly lower than that of PFGE (Tiong et al., 2010; Thong and Ang, 2011; Elemfareji and Thong, 2013; Ngoi et al., 2015). 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. (2011) describes many of these assays, most of which target the E. coli wzx and wzy genes. Tandem repeat analysis for surveillance of human. (2016). The ability to differentiate commensal E. coli from ExPEC and other pathotypes is important for risk assessment and epidemiological and ecological studies. An official website of the United States government. Hadjinicolaou A. V., Demetriou V. L., Emmanuel M. A., Kakoyiannis C. K., Kostrikis L. G. (2009). Wise M. G., Siragusa G. R., Plumblee J., Healy M., Cray P. J., Seal B. S. (2009). Results should be highly reproducible (>99%). Funding. Kruy S. L., van Cuyck H., Koeck J. L. (2011). Would you like email updates of new search results? Geue L., Monecke S., Engelmann I., Braun S., Slickers P., Ehricht R. (2014). Sequence analysis of the rfb loci, encoding proteins involved in the biosynthesis of the. 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). Main value for industry is as a rapid confirmation and subtype screen if access exists to lab that can provide rapid turnaround time. Wang W., Perepelov A. V., Feng L., Shevelev S. D., Wang Q., Senchenkova S. N., et al. These databases are creating a vast resource of microbial genome information for WGS-based surveillance of microbial pathogens. Use of Subtyping to Support Salmonellosis Attribution Estimates. The reference can be a closely related genome outside the dataset, or a genome within the dataset. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic. This was developed by the US FDA and NCBI as the first distributed network of laboratories to utilize WGS, with both genomic and geographic data, for foodborne pathogen characterization. 2001 May-Jun;7(3):382-9. doi: 10.3201/eid0703.010303. B., Luo Y., Payne J., Shpuntoff A., Rand H., et al. Octavia S., Wang Q., Tanaka M. M., Kaur S., Sintchenko V., Lan R., et al. De Cesare A., Krishnamani K., Parisi A., Ricci A., Luzzi I., Barco L., et al. The choice of a closely related reference has been shown to be a key step in the analysis. PulseNet Centrals database managers then analyze the uploaded pattern to see if a new outbreak has emerged or whether the isolate is part of an ongoing outbreak (CDC, 2018a). The last 5 years have seen tremendous advancement in the development of sensitive, rapid, automated, and increasingly easy-to-use molecular subtyping methods for a variety of different bacterial foodborne pathogens. Total cost encompasses cost of equipment reagent/consumables, data analysis platform, and staffing. Application of next generation sequencing in clinical microbiology and infection prevention. Van Cuyck H., Farbos-Granger A., Leroy P., Yith V., Guillard B., Sarthou J. L., et al. When the bacterium has been identified, the software automatically performs the typing and result reporting, ensuring efficient laboratory practice and rapid time-to-result. Lacher et al. Liu Y., Fratamico P., Debroy C., Bumbaugh A. C., Allen J. W. (2008). Avian colibacillosis caused by APEC is a major cause of morbidity and mortality associated with economic losses in the poultry industry throughout the world. Siragusa GR, Danyluk MD, Hiett KL, Wise MG, Craven SE. Selander R. K., Caugant K. A., Ochman H., Musser J. M., Gilmour M. N., Whittam T. S. (1986). Compared to phenotypic methods, genetic subtyping methods that are based on bacterial DNA, generally have better discriminatory ability. ST, RO, and HL collected the data, conducted data analysis, and interpreted it. However, current typing methods are limited in both speed and precision. B., Nataro J. P., Mobley H. L. (2004). In one study, PFGE was compared to MLVA to subtype 163 non-typhoidal Salmonella isolates representing 15 serovars; MLVA differentiated the isolates into 79 MLVA subtypes while PFGE differentiated the same isolates into 87 subtypes. These studies show that public health agencies are increasingly relying on hqSNP analysis for outbreak investigation, including tracking the source of outbreaks. (1995). (2005). MW serves as a compensated scientific advisor for BioMrieux, Mrieux NutriSciences, Mars, and Neogen and has served as a paid speaker for 3M and IBM. Before The CRISPR approach has been shown to be feasible for subtyping of Salmonella (Liu et al., 2011; Fabre et al., 2012; DiMarzio et al., 2013; Shariat et al., 2013a, b, c; Almeida et al., 2017). (2012). Its relatively low reproducibility (which can at least be partially addressed by automation, such as in the DiversiLab system), and low accuracy of serovar prediction (Weigel et al., 2004; Wise et al., 2009) have limited its application in Salmonella subtyping. Comparison of molecular characterization methods for prediction of Salmonella1 serovars. When neither the genoserotyping nor cgMLST can identify the serovar, SeqSero may be used and may allow for serovar prediction. The combination of profiles generated by using additional restriction enzymes can enhance the value of this method for differentiating highly homogeneous Salmonella strains (Zheng et al., 2011); however, the cost increases as additional enzymes are used. Hence, this approach does not require de novo assembly of the genome prior to its utilization. Pulsed-field gel electrophoresis was first described in 1984 and developed as a subtyping method for Salmonella in the 1990s (Threlfall and Frost, 1990; Figure 1). Evaluation of a multiplex PCR real-time PCR method for detecting Shiga toxin-producing. Wzx proteins translocates the O-units across the inner membrane, and Wzy polymerizes the O-antigen (Samuel and Reeves, 2003). Give examples of the applications of Whole Genome Sequencing to Surveillance of bacterial pathogens and antimicrobial resistance 3. High-quality SNP analyses rely on identification of SNP differences across a set of closely related isolates using raw sequence data, which are mapped to a closed or draft genome assembly (also referred to as the reference genome). Larsson J. T., Torpdahl M., Petersen R. F., Sorensen G., Lindstedt B. When serovar determination using genoserotyping is not possible or is incomplete, SISTR also has the option to use the core genome MLST (cgMLST) scheme to infer the serovar based on phylogenetic context. Unfortunately, it can also be imprecise (McQuiston et al., 2011). Foley S. L., Lynne A. M., Nayak R. (2009). Manges A. R., Harel J., Masson L., Edens T. J., Portt A., Reid-Smith R. J., et al. . Describe the general Principles in typing of Bacteria 2. Molecular subtyping and characterization methods may also facilitate the development of a novel framework for tracking, preventing, and regulating foodborne bacterial diseases, which is based on evolutionary relationships and genetic characteristics rather than traditional species definitions. Environmental conditions or mutations in the DNA repair system may influence the rate of genetic change accumulated in a genome; e.g., a Salmonella isolate persisting in a humid, nutritious environment such as in a chicken farm may multiply much faster than an isolate persisting in a dry food processing environment. (2014). Commercial clouds can provide a storage solution, provided that special attention is paid to data security. Molecular subtyping is an instrumental tool for foodborne illness surveillance and outbreak investigation. CRISPRMVLST using different schemes of virulence genes has also been applied by others for subtyping Salmonella (DiMarzio et al., 2013; Shariat et al., 2013a; Almeida et al., 2017). Rapid mutations and recombination of the marker(s) during storage and subculture could lead to poor reproducibility. The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters. When more than one genome is analyzed, the list of alleles from each genome can be compared and the number of allele differences can be computed. The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of. Hence, similarly to the wgMLST approach, polymorphisms present in intergenic regions and in genes not included in the cgMLST scheme will not be assessed (Chen et al., 2017). Another high-throughput method, known as the BioMarkTM real-time PCR system (Fluidigm), used a panel of virulence genes as discriminative markers to differentiate EHEC O26 strains, EHEC-like O26 pathogenic strains, and avirulent O26 strains (Bugarel et al., 2011a). Petersen A., Aarestrup F. M., Angulo F. J., Wong S., Sthr K., Wegener H. C., et al. Phylogenetic analysis using WGS data showed that the distinct PFGE types did not necessarily correlate with increased genetic distance between isolates. Bioinformatics is a key capability required for WGS. A., Torpdahl M., Vergnaud G., Le Hello S., Weill F. X., Tietze E., et al. In some cases, it can take much longer (>12 days) as multiple antibody/agglutination reactions may be needed in a step-wise fashion to assign a final classification for complex serovars (Kim et al., 2006; Boxrud, 2010). (2015). Comparative analysis of core genome MLST and SNP typing within a European. Therefore, pathogenic E. coli constitutes a genetically heterogeneous family of bacteria, and they continue to evolve. (1990). Methods that can be used by the food industry must be thoroughly validated before implementation to ensure reliability and consistency of the method when it is used across different laboratories. Approximately 45% of serovar Enteritidis isolates reported to PulseNet display the same PFGE XbaI pattern (JEGX01.0004), although many of these isolates are not epidemiologically related (Zheng et al., 2007). Commercially available software, which can run cgMLST and wgMLST (e.g., BioNumerics) tends to be more user-friendly. MLST has the advantage of being highly reproducible and easily transferable among laboratories. This is because hqSNP analysis, as compared to cgMLST or wgMLST analyses, requires more parameter settings, which must be communicated for better interpretation. In addition to these methods, single-plex or multiplex PCR assays that can detect and identify specific Salmonella serotypes have been described (Kim et al., 2006; Akiba et al., 2011; Zhu et al., 2015; Xiong et al., 2018; Xu L. et al., 2018; Xu Y. et al., 2018); these tools provide an alternative approach for detection and identification of specific Salmonella serovars. The pathways for biosynthesis of the O-AGCs and assembly of O-antigens have been studied extensively (Samuel and Reeves, 2003). Moura A., Criscuolo A., Pouseele H., Maury M. M., Leclercq A., Tarr C., et al. High-quality SNP analysis clearly improves subtype accuracy and outbreak investigations by not only allowing for increased discriminatory power, but also reducing instances where closely related isolates are being classified as different.. Improved traceability of Shiga-toxin-producing, Use of clustered regularly interspaced short palindromic repeat sequence polymorphism for specific detection of enterohemorrhagic. Results are often shown as a distance matrix of allele differences and a dendrogram constructed from this distance matrix. 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. 73 . Multiple locus variable number of tandem repeats analysis assesses the variation in the number of tandem repeated DNA sequences referred to as variable-number tandem repeats (VNTRs) in multiple regions of the bacterial genome to characterize bacterial isolates. The wgMLST methods allow for comparison of non-closely related isolates from different groups since all genomes are compared against the same database, which is a great advantage of this method over hqSNP (Maiden et al., 2013; Nadon et al., 2017). 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). (2015a). Discriminatory power should be as high as possible. We consider that WGS is the most suitable method to characterize Salmonella for incident investigation at production facilities in the food industry. We are experimenting with display styles that make it easier to read articles in PMC. Molecular subtyping of cancer is a critical step towards more individualized therapy and provides important biological insights into cancer heterogeneity. The DiversiLab system (bioMrieux, Marcy-lEtoile, France) automated the whole process of the Rep-PCR subtyping approach after 2000 and has been used for subtyping pathogens in hospitals worldwide (Healy et al., 2005; Chenu et al., 2012; Sabat et al., 2013; Figure 1). Wyres K., Conway T., Garg S., Queiroz C., Reumann M., Holt K. (2014). The cost of WGS is also comparable to that of the conventional subtyping tools, considering the high quality and volume of information provided by WGS within one experimental procedure. (2010). Standardization of pulsed-field gel electrophoresis protocols for the subtyping of, Medical and economic impact of extraintestinal infections due to. (2009). To facilitate . For companies with high demand of isolates to be subtyped, WGS is probably the most affordable and fastest method that provides the best discrimination. Boxrud D., Pederson-Gulrud K., Wotton J., Medus C., Lyszkowicz E., Besser J., et al. It is also more universal to all Salmonella serovars than MLVA which usually requires a specific scheme for each serovar. Infect Genet Evol. . Whole genome-based population biology and epidemiological surveillance of. MLST multi-locus sequence typing . (2014). Wright A. V., Liu J. J., Knott G. J., Doxzen K. W., Nogales E., Doudna J. A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common. Based on spacer content or sequencing of CRISPR loci, CRISPR-based typing analyses can be used to differentiate strains for epidemiological investigations or for detection. Shariat N., Sandt C. H., DiMarzio M. J., Barrangou R., Dudley E. G. (2013b). The ECID chip was designed based on >250 E. coli genomes and incorporates over 40,000 E. coli genes, including O- and H-group-specific genes, and approximately 9800 single nucleotide polymorphisms (SNPs). $_GJk@ @ Kw endstream endobj startxref 0 %%EOF 129 0 obj <>stream

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