An overview of the genome sequencing in microbiology

Whole genome sequencing of bacterial genomes - tools and applications

Finally, NGS is a key technique to study the organization of the bacterial life-from complex communities to single cells. Conjugation, in particular, seems to play an important role in the transmission and spread of foodborne AMR of public health importance Madec and Haenni, Staphylococcus aureus and coagulase-negative staphylococci Genome characteristics Staphylococcus aureus has a genome size that ranges from 2. The worm Caenorhabditis elegans was the first animal to have its whole genome sequenced. Furthermore, important limitations with short-read technologies remain for plasmid assemblies due to the inability of assemblers to deal with repeats [ 11 ]. Serotypes O and H antigens , pathotypes and sequence types [like multi-locus sequence typing MLST based on 7—8 housekeeping genes] can be inferred from WGS data [ 12 , 19 , 20 , 21 ]. As an example, Mandal and Kwon recently identified 61 genes associated with Salmonella enterica serovar Typhimurium survival against desiccation stress; phenotypic evaluation confirmed that three out of 12 single gene knockout mutants had significantly reduced survival as compared to the wild type during desiccation Mandal and Kwon, Based on this detailed molecular profile, the expected AMR phenotype, including the potential for occurrence of multidrug resistance, can be predicted. Quantitative microbial risk assessment QMRA models are typically based on the Codex Alimentarius principles for the conduct of microbiological risk assessment and provide a transparent and science-based approach to identify and assess a chain of events that affect the frequency and amount of a microorganism to which humans are exposed through the consumption of food and to describe the magnitude and severity of the adverse health effects from that exposure Codex Alimentarius,

With the decreasing costs and increasing rapidity and reliability of sequencing technologies, the uptake of next-generation sequencing and especially whole-genome sequencing WGS by public health and food safety laboratories has ramped up in recent years, and these new methods are set to replace traditional phenotypic methods for routine surveillance of AMR and other food safety hazards in the near future Taboada et al.

The shift to more rapid, automated sequencing methods in the s finally allowed for sequencing of whole genomes.

Dna sequencing microbiology

Instead of considering all hazard strains as equally likely to cause disease, WGS data can improve hazard identification by focusing on those strains of highest public health relevance. The first multicellular eukaryote, and animal , to have its whole genome sequenced was the nematode worm: Caenorhabditis elegans in For example, GWAS studies have been successfully used to identify genetic markers of the ability of C. These sources also aggregate data at the species level, with no consideration to differences between strains of a given hazard. In such cases the normally necessary steps of isolation and growth of the organism in culture may be omitted, thus allowing the sequencing of a much greater spectrum of organism genomes. The major goal of next-generation sequencing for a microbiologist is not really resolving another circular genomic sequence. These data are currently not provided by WGS analyses, but can be generated through in vivo or in vitro experiments of horizontal transfer of AMR genes Poppe et al.

Virulence Robins-Browne et al. Solid arrows: direct connections between elements of the QMRA. However, further analysis must be performed to provide the biological or medical meaning of this sequence, such as how this knowledge can be used to help prevent disease.

An overview of the genome sequencing in microbiology

Coagulase-negative staphylococci CoNS have similar genome features to S. Serotypes O and H antigens , pathotypes and sequence types [like multi-locus sequence typing MLST based on 7—8 housekeeping genes] can be inferred from WGS data [ 12 , 19 , 20 , 21 ]. Newport human infections Carroll et al. Heidelberg and S. Hazard Characterization As part of the hazard characterization step of a foodborne AMR QMRA, risk assessors aim to translate levels of exposure to the hazard into a probability of one or more adverse health outcomes in humans Codex Alimentarius, The uncertainty around the probability estimate could be assessed using bootstrapping as proposed by Pightling et al. We argue that a similar framework could be developed for QMRA of foodborne AMR, with the objective of describing the probability of a hazard being transmitted from one step of the food chain to the next. However, this method of sequencing has been time-consuming, laborious and remains expensive even today. Further work is needed to explore other approaches and applications to other pathogens of public health interest. Using WGS of cephalosporin-susceptible and resistant S. They can be overcome using long-read sequencing to improve their detection [ 51 , 52 , 53 , 54 ] but the cost remains too high for most clinical laboratories. Indeed, particular resistance mechanisms, such as modification in the membrane permeability or up-regulation of efflux pumps, will be harder to predict, and further studies are required to improve accuracy among heterogeneous datasets [ 11 ]. The determination of plasmid sequences has remained a challenge due to the presence of repeated e.

Gene-by-gene analysis of isolate relatedness showed that poultry C. These attempts may have partly been hampered by the complexity of Campylobacter transmission in the food chain e. Since capillary sequencing has been progressively displaced by high-throughput formerly "next-generation" sequencing technologies such as Illumina dye sequencingpyrosequencingand SMRT sequencing.

They are largely based on human clinical experiments Teunis et al.

microbial whole genome sequencing

This can be done using comparative genomics of isolates collected at successive points or stages of the farm-to-fork continuum Figure 1. For example, comparative genomics of bacterial populations found in the abattoir environment with those found on carcasses in the abattoir could be used to inform the probability of cross-contamination occurring from the abattoir environment to the carcasses; this quantity is typically difficult to inform using phenotypic data Nauta et al.

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A crash course in sequencing for a microbiologist.