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Genomic tracing of epidemics and disease outbreaks.

Schürch AC, Siezen RJ - Microb Biotechnol (2010)

View Article: PubMed Central - PubMed

Affiliation: RIVM, National Institute for Public Health and the Environment, 3730BA Bilthoven, the Netherlands.

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Tracing the source of an infectious human disease can save lives... Although the mode of transmission for many human pathogens is known, it often remains difficult to trace the exact source of an outbreak of a disease with laboratory methods... In the UK, military patients returning from Iraq or Afghanistan are often colonized with multidrug‐resistant A. baumannii (MDR‐Aci)... During an outbreak in 2008, four military patients were diagnosed with MDR‐Aci infections, and subsequently two civilian patients were found to be colonized as well... The application of next‐generation sequencing shed light on transmission events within the outbreak, while standard typing techniques were unable to differentiate between alternative epidemiological hypotheses... To track the sources of an outbreak, typing of the bacterial isolates of diseased patients and of potential sources is necessary... Two L. monocytogenes isolates of a large Canadian outbreak of listeriosis that was associated with ready‐to‐eat meat products were subjected to next‐generation sequencing and the sequences compared... The identified SNPs, three indels and a prophage were then used to type other isolates of the same outbreak... The resulting evolutionary model is illustrated in Fig.  3, where isolates with an identical type cluster at the same nodes... This analysis indicated that three distinct strains were involved in the outbreak, and it was possible to study the strain‐specific features of these outbreak strains... Most infections of tuberculosis in humans result in asymptomatic, latent infections, and only about one in 10 infections progress to active disease... Next‐generation whole‐genome sequencing of bacterial isolates aids in identification of a source of an outbreak, determination of transmission events or description of the dynamics of an outbreak... Therefore, whole‐genome sequencing should eventually replace or amend other bacterial typing methods in (clinical) microbiological laboratories... However, although the future application of whole‐genome sequencing is highly desirable, in order to achieve this in routine laboratory settings, the sequencing techniques and data analysis and storage need to be more efficient and come at lower costs, especially if used for thousands and thousands of strains... The quality and per‐sample costs of the next wave of DNA sequencers that is expected in coming years will show us if this inevitable development will be accomplished in the near future.

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Most likely transmission scheme suggested by SNP typing, temporal and contact tracing data. Black arrow: the most likely transmission events based on the SNP type clustering and integration of temporal data and supported by contact tracing information. Arrows with dashed lines: transmission events suspected based only on contact tracing information. Stickmen with the same colour had Mycobacterium tuberculosis isolates that belonged to the same SNP cluster. Reprinted from Schürch and colleagues (2010a) with permission from the American Society for Microbiology.
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f4: Most likely transmission scheme suggested by SNP typing, temporal and contact tracing data. Black arrow: the most likely transmission events based on the SNP type clustering and integration of temporal data and supported by contact tracing information. Arrows with dashed lines: transmission events suspected based only on contact tracing information. Stickmen with the same colour had Mycobacterium tuberculosis isolates that belonged to the same SNP cluster. Reprinted from Schürch and colleagues (2010a) with permission from the American Society for Microbiology.

Mentions: Most infections of tuberculosis in humans result in asymptomatic, latent infections, and only about one in 10 infections progress to active disease. This can happen at any time in a patient's life, which makes it often impossible to track the source of infection that might have been a contact of decennia ago. However, patient interviews can give some indications and this information was used when selecting three bacterial isolates for next‐generation sequencing that were part of well‐characterized transmission chains of a tuberculosis outbreak in the Netherlands (Schürch et al., 2010a,b). All other Mycobacterium tuberculosis isolates of the same outbreak were typed with the identified SNPs. By integration of SNP types, isolation dates and contact information, a detailed scheme of the outbreak was established (Fig. 4), and new transmission chains were identified. The study results comprised a surprising amount of information detail, such as the example of a married couple that both were infected with M. tuberculosis by a third source. Later, after the isolate underwent a single‐nucleotide change, the couple infected each other. Furthermore, the genomic variability within populations of the same patient was addressed in this study, which can be considerable in M. tuberculosis isolates of the same patients (Al‐Hajoj et al., 2010).


Genomic tracing of epidemics and disease outbreaks.

Schürch AC, Siezen RJ - Microb Biotechnol (2010)

Most likely transmission scheme suggested by SNP typing, temporal and contact tracing data. Black arrow: the most likely transmission events based on the SNP type clustering and integration of temporal data and supported by contact tracing information. Arrows with dashed lines: transmission events suspected based only on contact tracing information. Stickmen with the same colour had Mycobacterium tuberculosis isolates that belonged to the same SNP cluster. Reprinted from Schürch and colleagues (2010a) with permission from the American Society for Microbiology.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815338&req=5

f4: Most likely transmission scheme suggested by SNP typing, temporal and contact tracing data. Black arrow: the most likely transmission events based on the SNP type clustering and integration of temporal data and supported by contact tracing information. Arrows with dashed lines: transmission events suspected based only on contact tracing information. Stickmen with the same colour had Mycobacterium tuberculosis isolates that belonged to the same SNP cluster. Reprinted from Schürch and colleagues (2010a) with permission from the American Society for Microbiology.
Mentions: Most infections of tuberculosis in humans result in asymptomatic, latent infections, and only about one in 10 infections progress to active disease. This can happen at any time in a patient's life, which makes it often impossible to track the source of infection that might have been a contact of decennia ago. However, patient interviews can give some indications and this information was used when selecting three bacterial isolates for next‐generation sequencing that were part of well‐characterized transmission chains of a tuberculosis outbreak in the Netherlands (Schürch et al., 2010a,b). All other Mycobacterium tuberculosis isolates of the same outbreak were typed with the identified SNPs. By integration of SNP types, isolation dates and contact information, a detailed scheme of the outbreak was established (Fig. 4), and new transmission chains were identified. The study results comprised a surprising amount of information detail, such as the example of a married couple that both were infected with M. tuberculosis by a third source. Later, after the isolate underwent a single‐nucleotide change, the couple infected each other. Furthermore, the genomic variability within populations of the same patient was addressed in this study, which can be considerable in M. tuberculosis isolates of the same patients (Al‐Hajoj et al., 2010).

View Article: PubMed Central - PubMed

Affiliation: RIVM, National Institute for Public Health and the Environment, 3730BA Bilthoven, the Netherlands.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Tracing the source of an infectious human disease can save lives... Although the mode of transmission for many human pathogens is known, it often remains difficult to trace the exact source of an outbreak of a disease with laboratory methods... In the UK, military patients returning from Iraq or Afghanistan are often colonized with multidrug‐resistant A. baumannii (MDR‐Aci)... During an outbreak in 2008, four military patients were diagnosed with MDR‐Aci infections, and subsequently two civilian patients were found to be colonized as well... The application of next‐generation sequencing shed light on transmission events within the outbreak, while standard typing techniques were unable to differentiate between alternative epidemiological hypotheses... To track the sources of an outbreak, typing of the bacterial isolates of diseased patients and of potential sources is necessary... Two L. monocytogenes isolates of a large Canadian outbreak of listeriosis that was associated with ready‐to‐eat meat products were subjected to next‐generation sequencing and the sequences compared... The identified SNPs, three indels and a prophage were then used to type other isolates of the same outbreak... The resulting evolutionary model is illustrated in Fig.  3, where isolates with an identical type cluster at the same nodes... This analysis indicated that three distinct strains were involved in the outbreak, and it was possible to study the strain‐specific features of these outbreak strains... Most infections of tuberculosis in humans result in asymptomatic, latent infections, and only about one in 10 infections progress to active disease... Next‐generation whole‐genome sequencing of bacterial isolates aids in identification of a source of an outbreak, determination of transmission events or description of the dynamics of an outbreak... Therefore, whole‐genome sequencing should eventually replace or amend other bacterial typing methods in (clinical) microbiological laboratories... However, although the future application of whole‐genome sequencing is highly desirable, in order to achieve this in routine laboratory settings, the sequencing techniques and data analysis and storage need to be more efficient and come at lower costs, especially if used for thousands and thousands of strains... The quality and per‐sample costs of the next wave of DNA sequencers that is expected in coming years will show us if this inevitable development will be accomplished in the near future.

Show MeSH
Related in: MedlinePlus