Molecular typing of micro-organisms: at the centre of diagnostics, genomics and pathogenesis of infectious diseases?

A, Van Belkum

doi:10.1099/0022-1317-51-1-7

Cited by 14 publications

(2 citation statements)

References 18 publications

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“…Microbial typing techniques are greatly enhancing our insights into microbial population epidemiology and microbial diversity and are widely used in diagnostics, genomics and pathogenesis related with microbiology research (Boers et al, 2012; Van Belkum, 2002). In fact, our ability to accurately distinguish among strains of infectious pathogens is crucial for efficient epidemiological and surveillance analysis, studying microbial population structure and dynamics and, ultimately, developing improved public health control strategies (Cooper and Feil, 2004).…”

Section: Introductionmentioning

confidence: 99%

Microbial sequence typing in the genomic era

Pérez‐Losada

Arenas

Castro-Nallar

2018

Infection, Genetics and Evolution

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Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.

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Section: Introductionmentioning

confidence: 99%

Microbial sequence typing in the genomic era

Pérez‐Losada

Arenas

Castro-Nallar

2018

Infection, Genetics and Evolution

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“…Microbial typing techniques are greatly enhancing our insights into microbial population epidemiology and microbial diversity, and are widely used in diagnostic, genomic and pathogenesis-related microbiology research [1]. For example, in the field of clinical microbiology, phenotypic methods such as biochemical typing of Enterobacteriaceae [2] and serological typing of streptococci [3] are performed to differentiate within microbial species.…”

Section: Introductionmentioning

confidence: 99%

High-Throughput Multilocus Sequence Typing: Bringing Molecular Typing to the Next Level

Boers¹,

Reijden²,

Jansen³

2012

PLoS ONE

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Multilocus sequence typing (MLST) is a widely used system for typing microorganisms by sequence analysis of housekeeping genes. The main advantage of MLST in comparison to other typing techniques is the unambiguity and transferability of sequence data. However, a main disadvantage is the high cost of DNA sequencing. Here we introduce a high-throughput MLST (HiMLST) method that employs next-generation sequencing (NGS) technology (Roche 454), to generate large quantities of high-quality MLST data at low costs. The HiMLST protocol consists of two steps. In the first step MLST target genes are amplified by PCR in multi-well plates. During this PCR the amplicons of each bacterial isolate are provided with a unique DNA barcode, the multiplex identifier (MID). In the second step all amplicons are pooled and sequenced in a single NGS-run. The MLST profile of each individual isolate can be retrieved easily using its unique MID. With HiMLST we have profiled 575 isolates of Legionella pneumophila , Staphylococcus aureus , Pseudomonas aeruginosa and Streptococcus pneumoniae in mixed species HiMLST experiments. In conclusion, the introduction of HiMLST paves the way for a broad employment of the MLST as a high-quality and cost-effective method for typing microbial species.

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Variants and Adaptations of the Standard PCR Protocol

2008

Principles and Technical Aspects of PCR Amplification

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Molecular typing of micro-organisms: at the centre of diagnostics, genomics and pathogenesis of infectious diseases?

Cited by 14 publications

References 18 publications

Microbial sequence typing in the genomic era

Microbial sequence typing in the genomic era

High-Throughput Multilocus Sequence Typing: Bringing Molecular Typing to the Next Level

Variants and Adaptations of the Standard PCR Protocol

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