WGS analysis of colonising and infecting EBSL Klebsiella pneumoniae paired samples to set the SNV cut-off value for determining bacterial clonality

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F19%3A00070630" target="_blank" >RIV/65269705:_____/19:00070630 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.escmid.org/escmid_publications/escmid_elibrary/?q=P2666&id=2173&L=0&tx_solr%5Bfilter%5D%5B0%5D=main_filter_eccmid%253Atrue&x=0&y=0" target="_blank" >https://www.escmid.org/escmid_publications/escmid_elibrary/?q=P2666&id=2173&L=0&tx_solr%5Bfilter%5D%5B0%5D=main_filter_eccmid%253Atrue&x=0&y=0</a>

DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

WGS analysis of colonising and infecting EBSL Klebsiella pneumoniae paired samples to set the SNV cut-off value for determining bacterial clonality

Popis výsledku v původním jazyce

Background: ESBL Klebsiella pneumoniae is a gram-negative opportunistic pathogen and leading cause of hospital-associated infections in haematology patients. Commonly, K. pneumoniae colonize human mucosal surfaces and is part of the healthy human gastrointestinal microbiome. In our study, we used the general assumption that the colonization strain is the cause of the subsequent infection in most cases to set the SNV cut off value for determining clonality in ESBL K. pneumoniae. Materials/methods: In the monitored period, 27 ESBL K. pneumoniae positive blood cultures were recorded in the haematological department of the University hospital Brno (Czech Republic). Of these, 41% (11 from 27) patients had a positive rectal swab. In total, we collected 11 pairs (each included a rectal swab and a blood culture) of ESBL K. pneumoniae isolates. For all 22 isolates, we performed whole genome sequencing using Illumina Miseq platform.The MLST, cgMLSTand SNV analysis were done for both the core genome and accessory genome. Results: We identified 6 distinct ST profiles in 22 ESBL K. pneumoniae isolates: ST405 (n=6), ST433 (n=6), ST323 (n=4), ST1271 (n=2),ST458 (n=2) and ST23 (n=2).The isolates from each patient share the same ST within the pair. In 10/11 pairs, the core genome SNVs number within each pair varies in range from 0 to 3 SNVs, while together with the accessory genome SNVs number varies in range from 0 to 5 SNVs. The last pair differed by 11 SNVs in the core genome and 40 SNVs in the core and accessory genome, which we concluded to be different strains. Conclusions: Currently, there is a lack of data under which a cut-off determining bacterial strain clonality can be clearly established. Based on the general assumption that colonization strains are directly related to the subsequent infection, pair samples do appear to be the ideal group to determine clonality cut-offs values. Based on our analysis, weset cut-off to 3 SNVs in the core genome, and 5 SNVs in the core with accessory genome.

Název v anglickém jazyce

WGS analysis of colonising and infecting EBSL Klebsiella pneumoniae paired samples to set the SNV cut-off value for determining bacterial clonality

Popis výsledku anglicky

Background: ESBL Klebsiella pneumoniae is a gram-negative opportunistic pathogen and leading cause of hospital-associated infections in haematology patients. Commonly, K. pneumoniae colonize human mucosal surfaces and is part of the healthy human gastrointestinal microbiome. In our study, we used the general assumption that the colonization strain is the cause of the subsequent infection in most cases to set the SNV cut off value for determining clonality in ESBL K. pneumoniae. Materials/methods: In the monitored period, 27 ESBL K. pneumoniae positive blood cultures were recorded in the haematological department of the University hospital Brno (Czech Republic). Of these, 41% (11 from 27) patients had a positive rectal swab. In total, we collected 11 pairs (each included a rectal swab and a blood culture) of ESBL K. pneumoniae isolates. For all 22 isolates, we performed whole genome sequencing using Illumina Miseq platform.The MLST, cgMLSTand SNV analysis were done for both the core genome and accessory genome. Results: We identified 6 distinct ST profiles in 22 ESBL K. pneumoniae isolates: ST405 (n=6), ST433 (n=6), ST323 (n=4), ST1271 (n=2),ST458 (n=2) and ST23 (n=2).The isolates from each patient share the same ST within the pair. In 10/11 pairs, the core genome SNVs number within each pair varies in range from 0 to 3 SNVs, while together with the accessory genome SNVs number varies in range from 0 to 5 SNVs. The last pair differed by 11 SNVs in the core genome and 40 SNVs in the core and accessory genome, which we concluded to be different strains. Conclusions: Currently, there is a lack of data under which a cut-off determining bacterial strain clonality can be clearly established. Based on the general assumption that colonization strains are directly related to the subsequent infection, pair samples do appear to be the ideal group to determine clonality cut-offs values. Based on our analysis, weset cut-off to 3 SNVs in the core genome, and 5 SNVs in the core with accessory genome.

Druh

O - Ostatní výsledky

CEP obor

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OECD FORD obor

10606 - Microbiology

Projekt

<a href="/cs/project/GA17-01821S" target="_blank" >GA17-01821S: Výkonnostní techniky pro sestavování a anotaci bakteriálního genomu využívající číslicové zpracování genomických signálů</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů