Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M.; Barrangou, Rodolphe; Gerner‐Smidt, Peter; Ribot, Efrain M.; Knabel, Stephen J.; Dudley, Edward G.

doi:10.1128/aem.00468-11

Cited by 92 publications

(77 citation statements)

References 41 publications

(62 reference statements)

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“…Moreover, attempts have been undertaken to develop MLST schemes that are entirely based on virulence genes. Such approaches, termed multivirulence-locus sequence typing (MVLST), have been applied for the subtyping of pathogens like Listeria monocytogenes, V. cholerae, S. enterica and S. aureus [69][70][71][72]. Altogether, the currently available data suggest that MVLST is endowed with a higher discriminatory power than that of the 'classical' MLST.…”

Section: Multilocus Sequence Typingmentioning

confidence: 94%

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

et al. 2013

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Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages.

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Section: Multilocus Sequence Typingmentioning

confidence: 94%

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

et al. 2013

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“…In Salmonella, established techniques such as combining MLST with virulence gene polymorphisms were not able to distinguish between individual outbreak strains, rendering subtyping of Salmonella isolates causing food-related infections during outbreaks impossible (39). The use of Salmonella CRISPR genotypes, either alone (39) or in combination with gene polymorphisms present in virulence-associated genes (35,40), has strongly improved the ability to separate Salmonella strain collections into individual outbreak isolates.…”

Section: Figmentioning

confidence: 99%

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

Louwen

Staals

Endtz

et al. 2014

Microbiol Mol Biol Rev

216

178

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SUMMARY Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.

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“…Experimentally, it can be estimated either by the size of the amplicons [12,13], or, more precisely, by direct sequencing [14]. Repetitive extragenic palindromes [15], mobile elements [16], CRISPR-Cas cassettes [17], and other genomic features are also used. It is important, however, that for the genomes of each species, the optimal method for typing over variable regions must be selected individually.…”

Section: Introductionmentioning

confidence: 99%

Короткие Уникальные Последовательности В Бактериальных Геномах Как Штамм- И Видоспецифические Маркеры

Панюков¹,

Panyukov²

2017

Math.Biol.Bioinf.

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Abstract. The paper presents a new approach for phylotyping that can be potentially used for pure cultures and for mixed bacterial populations. It is based on the use of short unique nucleotide sequences (k-mers) that are present in the genomes of all strains of the same species and are absent in bacterial genomes of other taxonomic groups. We show that the number N of such sequences depends on the percentage bias towards A/T or G/C base pairs, increasing for genomes with approximately equal composition. We found that the largest contribution to the set of primarily unique sequences is given by 16-17-mers, while sigmoidal curves reflecting the dependence of N on the length of k-mers showed the maximum slope increment (ΔN/Δk) for k = 17, 18. Unique sequences of the length 16-18 bases can therefore be offered as potential markers. Comparing the sets of unique k-mers in the genomes of four Enterobacter strains, we estimated the level of their intraspecies stability and interspecies plasticity. As a result, we suggest discriminatory subsets as stencils for phylotyping, thereby increasing the list of genotyping markers with signatures of the new type.

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Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

Cited by 92 publications

References 41 publications

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

Короткие Уникальные Последовательности В Бактериальных Геномах Как Штамм- И Видоспецифические Маркеры

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