Page 306 - The Veterinary Laboratory and Field Manual 3rd Edition

Microbiology 275

dIGItaLIzEd ISoLatE InForMatIon,
bIoInForMatIcS and EPIdEMIoLoGy
The use of digitalized data for the identification
of isolates, as described in the preceding sec-
tions, combined with computer-based modelling
that draws on mathematics, statistical principles
(bioinformatics) and geographic information
systems, has enabled the development of pow-
erful tools for use in the field of epidemiology.
Strain type information can be used along with
such programmes to identify the likely infection
source, overall risk assessment from various Figure 4.37 Next-generation sequencing equip-
sources as well as monitoring disease outbreaks ment used for rapid sequencing of whole genomes
and the change in population composition and or metagenomes. Photo: Paul Gajda, University of
distribution over time (Figure 4.36), and can be Calgary, Canada.
used to inform public health policies and disease
management strategies (French, 2009).
with portable units that can be used in the field
nExt-GEnEratIon SEquEncInG and (for example, MinIon® from Oxford Nanopore
MEtaGEnoMIcS Technologies). Such technology has been used
In recent years, different platforms have been to randomly sequence DNA from a specific envi-
developed that enable the rapid sequencing of ronment (metagenomics), for example, soil or
whole genomes or metagenomes very quickly from the gut, and by matching sequencing data
and have the advantage of being highly auto- against large databanks of DNA sequences, can
mated (Figure 4.37). There are a number of be utilized to determine what organisms are
different sequencing techniques used, but the present. As the technology matures, the pos-
chain termination process (Sanger sequencing) sibilities for different uses in the molecular
and pyrosequencing (sequencing by synthesis) bacteriology field will expand accordingly.
are common formats. Of the two techniques,
pyrosequencing is a better method for sequenc- MaLdI-toF
ing a short stretch of DNA (up to 30 bases) due Matrix-assisted laser desorption/ionization
to (1) cost effectiveness, (2) less time consuming – time-of-flight (MALDI-TOF) is a form of
and (3) real-time monitoring of data whereas the mass spectrometry that is emerging as a useful
Sanger method of sequencing is more optimized technology for the identification of microbial
for sequencing long stretches of DNA (up to identification and disease diagnosis. Briefly, the
600 bases). High throughput formats (formerly bacterium or fungus of interest (the analyte in
referred to as ‘next-generation sequencing’) is a this case) is dried onto the surface of a metal
quickly evolving area. Where once the struggle plate (a chip), and over-laid with a matrix mate-
lay with the acquiring sequence data, the chal- rial. A pulsed laser is then fired at the sample.
lenge now is how to store and manage the vast The energy from the laser causes vaporization
quantities of sequence information that are and ionization of proteins from the prepared
generated and the interpretation of these data. sample. A time-of-flight mass spectrometer
Sequencing equipment is developing rapidly and measures the mass-to-charge ratio of these ion-
will soon be within reach of many laboratories ized proteins by determining the length of time

Vet Lab.indb 275 26/03/2019 10:25