Nucleotide sequence‐based typing of bacteria and the impact of automation

Clarke, Stuart C.

doi:10.1002/bies.10142

Cited by 45 publications

(24 citation statements)

References 37 publications

(56 reference statements)

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“…Crude DNA extraction proved to be sufficient for the assessment of variants from the 60 colonies. All colonies from a specific strain showed amplification of the expected alleles [23 and 24 repeats at VCA0283-(6) 14 and 10 repeats at VC0147-(6) 9 for O1 In-1 (ϩ) and O1 Og ET-109 (Ϫ), respectively (see Table SA2 in the supplemental material)], supporting the appropriate consistency of L-SSR loci.…”

Section: Resultsmentioning

confidence: 68%

“…The same alleles were observed in both multiplex and separate amplifications, supporting the use of the multiplex assay for high-throughput typing. The consistency of L-SSR markers was verified in a stability experiment of 4-day colony transfers ("generations") of two representative V. cholerae strains, O1 In-1 (ϩ) and O1 Og ET-109 (Ϫ), each tested for the stability of two loci, VCA0283-(6) 14 and VC0147-(6) 9 . In order to examine the stability of these markers each day, two single colonies were picked from an overnight grown plate and streaked onto a fresh LB plate.…”

Section: Resultsmentioning

confidence: 98%

“…MLST utilizing differences mainly in housekeeping genes is a rising DNA sequence-based method for bacterial strain typing (14,44,51). DNA sequencing uncovers far more variation per locus than any other method currently used for bacterial strain typing, and it provides a uniform platform for strain comparison analyzed in different laboratories and for database storage.…”

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confidence: 99%

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Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

et al. 2007

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Vibrio cholerae is the etiological agent of cholera. Its natural reservoir is the aquatic environment. To date, practical typing of V. cholerae is mainly serological and requires about 200 antisera. Simple sequence repeats (SSR), also termed VNTR (for variable number of tandem repeats), provide a source of high genomic polymorphism used in bacterial typing. Here we describe an SSR-based typing method that combines the variation in highly mutable SSR loci, with that of shorter, relatively more stable mononucleotide repeat (MNR) loci, for accurate and rapid typing of V. cholerae. Vibrio cholerae, a gram-negative bacterium, is the causal agent of the severe diarrheal disease cholera. Its natural reservoir is the aquatic environment (49, 84). Cholera pandemics are caused by specific serogroups of V. cholerae that are pathogenic only to humans (35,84). Since 1817, V. cholerae has caused a number of pandemics. The first seven were presumed to be caused by O1 serogroup of V. cholerae (68). In October 1992, a new serogroup, defined O139, caused a severe outbreak of cholera in southeast India. Within 10 months, the O139 serogroup was disseminated all over the Indian subcontinent and soon thereafter spread to 11 neighboring countries, temporarily displacing the O1 serogroups (64). Since then both serogroups coexist and are responsible for large outbreaks. Genomic studies indicated that O139 epidemic strain arose by horizontal acquisition of unique DNA (15, 47).Traditionally, V. cholerae classification is serological and requires about 200 antisera based on the somatic O antigen (72). Isolates of V. cholerae are divided into three major subgroups: O1, O139, and non-O1/non-O139, of which only the O1 and O139 serogroups are associated with cholera pandemics and epidemics. Non-O1, non-O139 serogroups are recognized as causative agents of sporadic and localized outbreaks (73). Pathogenic V. cholerae isolates carry virulence genes, such as the toxins genes ctxAB (25,65,68). The environmental V. cholerae strains from non-O1, non-O139 serogroups are a possible natural reservoir of potentially new emerging epidemic strains (67,73). This assumption is supported by the finding that some of these environmental strains harbor virulence genes (23) and thus are likely to evolve into novel pathogenic strains by horizontal gene transfer (24,25). The emergence of new pathogenic V. cholerae strains requires not only an efficient, rapid, and accurate identification tool but also a means for determining genetic relationships among environmental and clinical isolates.Genome-based bacterial identification and typing is essential for several disciplines, including taxonomy, epidemiology, determining phylogenetic relationships, and the study of evolutionary mechanisms. It allows distinguishing among strains within a species to monitor epidemics and routes of contamination. Recent advances in biotechnology have resulted in the development of numerous methods for microorganism typing that differ in their sensitivity, rapidity, complexity, discrimin...

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Section: Resultsmentioning

confidence: 68%

Section: Resultsmentioning

confidence: 98%

mentioning

confidence: 99%

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Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

et al. 2007

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“…Applications are often high-throughput in nature, and appropriate typing methods require accuracy, reproducibility, and laboratory automation (1).…”

mentioning

confidence: 99%

Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing

Honisch

Chen

Mortimer³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…In the nucleocapsid, there is an incomplete dsDNA and a DNA polymerase (Seeger & Zoulim, 2007). Real-time and traditional PCR methods are useful for the detection and quantification of infectious agents in clinical specimens (Olive & Bean, 1999;Clarke, 2002;Metwally et al, 2008). These methods can be employed to decide if establishment of HBV treatment is necessary and to monitor the efficacy of that treatment (Dai et al, 2004;Lu et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

A comparison of molecular methods for hepatitis B virus (HBV) DNA detection from oral fluid samples

Portilho

Martins

Lampe

et al. 2012

Journal of Medical Microbiology

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The objective of the present study was to evaluate four commercial DNA extraction methods and three PCR protocols for hepatitis B virus (HBV) detection in artificially contaminated oral fluid samples. The extraction protocols were selected based on ease of use and cost, and were also compared with respect to sensitivity and cost. Prior PCR optimization was conducted, in which the sample volume for DNA extraction and the concentrations of DNA and Taq DNA polymerase in the PCR were adjusted. One-round PCR, used to amplify the core region of the HBV genome, achieved high levels of sensitivity in comparison with nested and semi-nested PCR experiments that were designed for the amplification of HBV surface protein genes. Of the four extraction protocols evaluated, the RTP DNA/RNA Virus Mini kit and the QIAamp DNA Mini kit gave the highest recovery rates, presenting 20 copies of HBV DNA ml "1 as the limit of detection. These results suggest that HBV DNA can be detected from oral fluid samples but that the optimization of the PCR assays and the choice of extraction methods must be determined by laboratories before the implementation of this method in routine diagnostics.

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Nucleotide sequence‐based typing of bacteria and the impact of automation

Cited by 45 publications

References 37 publications

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

Vibrio cholerae Strain Typing and Phylogeny Study Based on Simple Sequence Repeats

Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing

A comparison of molecular methods for hepatitis B virus (HBV) DNA detection from oral fluid samples

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