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RNA sequencing-based transcriptional overview of Xerotolerance in Cronobacter sakazakii SP291


Srikumar, Shabarinath; Cao, Yu; Yan, Qiongqiong; Van Hoorde, Koenraad; Nguyen, Scott; Cooney, Shane; Gopinath, Gopal R; Tall, Ben D; Sivasankaran, Sathesh K; Lehner, Angelika; Stephan, Roger; Fanning, Séamus (2018). RNA sequencing-based transcriptional overview of Xerotolerance in Cronobacter sakazakii SP291. Applied and Environmental Microbiology, 85(3):pii: e01993-18.

Abstract

<jats:named-content content-type="genus-species">Cronobacter sakazakii</jats:named-content> is a xerotolerant neonatal pathogen epidemiologically linked to powdered infant food formula, often resulting in high mortality rates. Here, we used transcriptome sequencing (RNA-seq) to provide transcriptional insights into the survival of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> in desiccated conditions. Our RNA-seq data show that about 22% of the total <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> genes were significantly upregulated and 9% were downregulated during desiccation survival. When reverse transcription-quantitative PCR (qRT-PCR) was used to validate the RNA-seq data, we found that the primary desiccation response was gradually downregulated during the tested 4 hours of desiccation, while the secondary response remained constitutively upregulated. The 4-hour desiccation tolerance of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> was dependent on the immediate microenvironment surrounding the bacterial cell. The removal of Trypticase soy broth (TSB) salts and the introduction of sterile infant formula residues in the microenvironment enhanced the desiccation survival of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> SP291. The trehalose biosynthetic pathway encoded by <jats:italic>otsA</jats:italic> and <jats:italic>otsB</jats:italic>, a prominent secondary bacterial desiccation response, was highly upregulated in desiccated <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content>. <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> SP291 Δ<jats:italic>otsAB</jats:italic> was significantly inhibited compared with the isogenic wild type in an 8-hour desiccation survival assay, confirming the physiological importance of trehalose in desiccation survival. Overall, we provide a comprehensive RNA-seq-based transcriptional overview along with confirmation of the phenotypic importance of trehalose metabolism in <jats:named-content content-type="genus-species">Cronobacter sakazakii</jats:named-content> during desiccation.
<jats:bold>IMPORTANCE</jats:bold> <jats:named-content content-type="genus-species">Cronobacter sakazakii</jats:named-content> is a pathogen of importance to neonatal health and is known to persist in dry food matrices, such as powdered infant formula (PIF) and its associated production environment. When infections are reported in neonates, mortality rates can be high. The success of this bacterium in surviving these low-moisture environments suggests that <jats:named-content content-type="genus-species">Cronobacter</jats:named-content> species can respond to a variety of environmental signals. Therefore, understanding those signals that aid the persistence of this pathogen in these ecological niches is an important step toward the development of strategies to reduce the risk of contamination of PIF. This research led to the identification of candidate genes that play a role in the persistence of this pathogen in desiccated conditions and, thereby, serve as a model target to design future strategies to mitigate PIF-associated survival of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content>.

Abstract

<jats:named-content content-type="genus-species">Cronobacter sakazakii</jats:named-content> is a xerotolerant neonatal pathogen epidemiologically linked to powdered infant food formula, often resulting in high mortality rates. Here, we used transcriptome sequencing (RNA-seq) to provide transcriptional insights into the survival of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> in desiccated conditions. Our RNA-seq data show that about 22% of the total <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> genes were significantly upregulated and 9% were downregulated during desiccation survival. When reverse transcription-quantitative PCR (qRT-PCR) was used to validate the RNA-seq data, we found that the primary desiccation response was gradually downregulated during the tested 4 hours of desiccation, while the secondary response remained constitutively upregulated. The 4-hour desiccation tolerance of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> was dependent on the immediate microenvironment surrounding the bacterial cell. The removal of Trypticase soy broth (TSB) salts and the introduction of sterile infant formula residues in the microenvironment enhanced the desiccation survival of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> SP291. The trehalose biosynthetic pathway encoded by <jats:italic>otsA</jats:italic> and <jats:italic>otsB</jats:italic>, a prominent secondary bacterial desiccation response, was highly upregulated in desiccated <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content>. <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content> SP291 Δ<jats:italic>otsAB</jats:italic> was significantly inhibited compared with the isogenic wild type in an 8-hour desiccation survival assay, confirming the physiological importance of trehalose in desiccation survival. Overall, we provide a comprehensive RNA-seq-based transcriptional overview along with confirmation of the phenotypic importance of trehalose metabolism in <jats:named-content content-type="genus-species">Cronobacter sakazakii</jats:named-content> during desiccation.
<jats:bold>IMPORTANCE</jats:bold> <jats:named-content content-type="genus-species">Cronobacter sakazakii</jats:named-content> is a pathogen of importance to neonatal health and is known to persist in dry food matrices, such as powdered infant formula (PIF) and its associated production environment. When infections are reported in neonates, mortality rates can be high. The success of this bacterium in surviving these low-moisture environments suggests that <jats:named-content content-type="genus-species">Cronobacter</jats:named-content> species can respond to a variety of environmental signals. Therefore, understanding those signals that aid the persistence of this pathogen in these ecological niches is an important step toward the development of strategies to reduce the risk of contamination of PIF. This research led to the identification of candidate genes that play a role in the persistence of this pathogen in desiccated conditions and, thereby, serve as a model target to design future strategies to mitigate PIF-associated survival of <jats:named-content content-type="genus-species">C. sakazakii</jats:named-content>.

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Item Type:Journal Article, refereed, original work
Communities & Collections:05 Vetsuisse Faculty > Institute of Food Safety and Hygiene
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Scopus Subject Areas:Life Sciences > Biotechnology
Life Sciences > Food Science
Life Sciences > Applied Microbiology and Biotechnology
Physical Sciences > Ecology
Uncontrolled Keywords:Biotechnology, Food Science, Ecology, Applied Microbiology and Biotechnology, Cronobacter sakazakii ; RNA-seq; desiccation; transcriptome; xerotolerance
Language:English
Date:16 November 2018
Deposited On:24 Feb 2020 15:17
Last Modified:29 Jul 2020 14:29
Publisher:American Society for Microbiology
ISSN:0099-2240
OA Status:Closed
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1128/aem.01993-18
PubMed ID:30446557

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