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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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Phylogenetic evidence for intercontinental spread and hospital transmission of health‐care‐associated MRSA isolates, type ST239. Maximum‐likelihood phylogenetic tree based on core genome SNPs of ST239 isolates, annotated with the country and year of isolation. The continental origin of each isolate is indicated by the colour of the isolate name: blue, Asia; black, North America; green, South America; red, Europe; and yellow, Australasia. Bootstrap values are shown below each branch, with a star representing 100% bootstrap support. The scale bar represents substitutions per SNP site. A cladogram of the Thai clade is displayed for greater resolution with bootstrap values (above the branch), number of distinguishing SNPs (below the branch), and isolates labelled with date of isolation, where known. Reprinted from Harris et al. (2010), with permission from American Association for the Advancement of Science (AAAS).
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f1: Phylogenetic evidence for intercontinental spread and hospital transmission of health‐care‐associated MRSA isolates, type ST239. Maximum‐likelihood phylogenetic tree based on core genome SNPs of ST239 isolates, annotated with the country and year of isolation. The continental origin of each isolate is indicated by the colour of the isolate name: blue, Asia; black, North America; green, South America; red, Europe; and yellow, Australasia. Bootstrap values are shown below each branch, with a star representing 100% bootstrap support. The scale bar represents substitutions per SNP site. A cladogram of the Thai clade is displayed for greater resolution with bootstrap values (above the branch), number of distinguishing SNPs (below the branch), and isolates labelled with date of isolation, where known. Reprinted from Harris et al. (2010), with permission from American Association for the Advancement of Science (AAAS).

Mentions: Outbreaks of infections with health‐care‐associated pathogens, such as Clostridium difficile, Acinetobacter baumannii and methicillin‐resistant Staphylococcus aureus (MRSA) are prone to insufficient resolution with currently used typing techniques. Especially the precise relationships within spreading MRSA remain unclear because the multilocus‐sequence type ST239 accounts for at least 90% of health‐care‐associated MRSA in large parts of the world, including China (Xu et al., 2009), Thailand (Feil et al., 2008) and Turkey (Alp et al., 2009). Classical genotyping methods offer little discriminatory power to subtype ST239 isolates. Harris and colleagues (2010) therefore used a next‐generation sequencing platform to analyse 63 isolates of subtype ST239, consisting of a global collection (43 isolates) and a local collection from a hospital in Thailand within a 7‐month time frame (20 isolates). The phylogenetic tree (Fig. 1) established from core genes of these isolates was complemented with isolation date and geographical origin. The tree shows a high degree of consistency with the geographic source. Intercontinental transmission events were detected, such as the re‐introduction of MRSA in Portuguese hospitals that must have originated from a South American variant, or a Danish isolate that clustered with the Thai clade. Patient records indicated that this Danish patient in question was actually a Thai national.


Genomic tracing of epidemics and disease outbreaks.

Schürch AC, Siezen RJ - Microb Biotechnol (2010)

Phylogenetic evidence for intercontinental spread and hospital transmission of health‐care‐associated MRSA isolates, type ST239. Maximum‐likelihood phylogenetic tree based on core genome SNPs of ST239 isolates, annotated with the country and year of isolation. The continental origin of each isolate is indicated by the colour of the isolate name: blue, Asia; black, North America; green, South America; red, Europe; and yellow, Australasia. Bootstrap values are shown below each branch, with a star representing 100% bootstrap support. The scale bar represents substitutions per SNP site. A cladogram of the Thai clade is displayed for greater resolution with bootstrap values (above the branch), number of distinguishing SNPs (below the branch), and isolates labelled with date of isolation, where known. Reprinted from Harris et al. (2010), with permission from American Association for the Advancement of Science (AAAS).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3815338&req=5

f1: Phylogenetic evidence for intercontinental spread and hospital transmission of health‐care‐associated MRSA isolates, type ST239. Maximum‐likelihood phylogenetic tree based on core genome SNPs of ST239 isolates, annotated with the country and year of isolation. The continental origin of each isolate is indicated by the colour of the isolate name: blue, Asia; black, North America; green, South America; red, Europe; and yellow, Australasia. Bootstrap values are shown below each branch, with a star representing 100% bootstrap support. The scale bar represents substitutions per SNP site. A cladogram of the Thai clade is displayed for greater resolution with bootstrap values (above the branch), number of distinguishing SNPs (below the branch), and isolates labelled with date of isolation, where known. Reprinted from Harris et al. (2010), with permission from American Association for the Advancement of Science (AAAS).
Mentions: Outbreaks of infections with health‐care‐associated pathogens, such as Clostridium difficile, Acinetobacter baumannii and methicillin‐resistant Staphylococcus aureus (MRSA) are prone to insufficient resolution with currently used typing techniques. Especially the precise relationships within spreading MRSA remain unclear because the multilocus‐sequence type ST239 accounts for at least 90% of health‐care‐associated MRSA in large parts of the world, including China (Xu et al., 2009), Thailand (Feil et al., 2008) and Turkey (Alp et al., 2009). Classical genotyping methods offer little discriminatory power to subtype ST239 isolates. Harris and colleagues (2010) therefore used a next‐generation sequencing platform to analyse 63 isolates of subtype ST239, consisting of a global collection (43 isolates) and a local collection from a hospital in Thailand within a 7‐month time frame (20 isolates). The phylogenetic tree (Fig. 1) established from core genes of these isolates was complemented with isolation date and geographical origin. The tree shows a high degree of consistency with the geographic source. Intercontinental transmission events were detected, such as the re‐introduction of MRSA in Portuguese hospitals that must have originated from a South American variant, or a Danish isolate that clustered with the Thai clade. Patient records indicated that this Danish patient in question was actually a Thai national.

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