Identification of Key Determinants of Staphylococcus aureus Vaginal Colonization

Deng, Liwen; Schilcher, Katrin; Burcham, Lindsey R.; Kwieciński, Jakub; Johnson, Paige; Head, Steven R.; Heinrichs, David E.; Horswill, Alexander R.; Doran, Kelly S.

doi:10.1128/mbio.02321-19

Cited by 36 publications

(21 citation statements)

References 117 publications

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“…Recently, two studies have utilized RNA-Seq to examine the transcriptional response of S. aureus in vivo. Work by Ibberson and Whiteley examined the S. aureus transcriptome in the lung of patients with cystic fibrosis (CF) (14), while Deng et al examined the S. aureus transcriptome during vaginal colonization (15). The RNA-Seq data sets for these two studies were not yet available at the time that we performed the original search of the GEO database (for our global sRNA expression analysis described above).…”

Section: Resultsmentioning

confidence: 99%

“…Analysis of in vivo data sets. In vivo RNA-Seq data sets were acquired from GEO under accession number SRP222773 for CF data and accession number SRP229518 for vaginal data (14,15). For the CF lung data, sRNA expression values (in RPKM) from nine clinical isolate samples were averaged and compared to the averaged sRNA expression values from nine S. aureus cultures grown in chemically defined media (CDM) as well as to those from nine samples from synthetic cystic fibrosis media (SCFM).…”

Section: Methodsmentioning

confidence: 99%

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Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in Staphylococcus aureus

Sorensen

Keogh

Wittekind

et al. 2020

mSphere

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Regulatory small RNAs (sRNAs) are known to play important roles in the Gram-positive bacterial pathogen Staphylococcus aureus; however, their existence is often overlooked, primarily because sRNA genes are absent from genome annotation files. Consequently, transcriptome sequencing (RNA-Seq)-based experimental approaches, performed using standard genome annotation files as a reference, have likely overlooked data for sRNAs. Previously, we created an updated S. aureus genome annotation file, which included annotations for 303 known sRNAs in USA300. Here, we utilized this updated reference file to reexamine publicly available RNA-Seq data sets in an attempt to recover lost information on sRNA expression, stability, and potential to encode peptides. First, we used transcriptomic data from 22 studies to identify how the expression of 303 sRNAs changed under 64 different experimental conditions. Next, we used RNA-Seq data from an RNA stability assay to identify highly stable/unstable sRNAs. We went on to reanalyze a ribosome profiling (Ribo-seq) data set to identify sRNAs that have the potential to encode peptides and to experimentally confirm the presence of three of these peptides in the USA300 background. Interestingly, one of these sRNAs/peptides, encoded at the tsr37 locus, influences the ability of S. aureus cells to autoaggregate. Finally, we reexamined two recently published in vivo RNA-Seq data sets, from the cystic fibrosis (CF) lung and a murine vaginal colonization study, and identified 29 sRNAs that may play a role in vivo. Collectively, these results can help inform future studies of these important regulatory elements in S. aureus and highlight the need for ongoing curating and updating of genome annotation files. IMPORTANCE Regulatory small RNAs (sRNAs) are a class of RNA molecules that are produced in bacterial cells but that typically do not encode proteins. Instead, they perform a variety of critical functions within the cell as RNA. Most bacterial genomes do not include annotations for sRNA genes, and any type of analysis that is performed using a bacterial genome as a reference will therefore overlook data for sRNAs. In this study, we reexamined hundreds of previously generated S. aureus RNA-Seq data sets and reanalyzed them to generate data for sRNAs. To do so, we utilized an updated S. aureus genome annotation file, previously generated by our group, which contains annotations for 303 sRNAs. The data generated (which were previously discarded) shed new light on sRNAs in S. aureus, most of which are unstudied, and highlight certain sRNAs that are likely to play important roles in the cell.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in Staphylococcus aureus

Sorensen

Keogh

Wittekind

et al. 2020

mSphere

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“…However, we showed that increasing rnaIII expression actually promotes mortality, with efficient larval necrosis. Furthermore, we found low rnaIII expression levels in the infected larvae, just as low amounts were detected in a mouse model of osteomyelitis, in human abscesses, during murine vaginal colonization, and in the lungs of cystic fibrosis patients (Song et al, 2012;Szafranska et al, 2014;Deng et al, 2019;Ibberson et al, 2019). Nevertheless, this sRNA is still involved in virulence since disruption of the agr QS system inhibits the upregulation of many toxins and proteases and a DagrB strain protects mice from mortality (Date et al, 2014).…”

Section: Discussionmentioning

confidence: 75%

“…Only a few studies have monitored in situ expression of sRNAs (Song et al, 2012;Szafranska et al, 2014), which differ from the levels encountered in growth media. Recent publications on S. aureus transcriptional adaptation in vitro and during infection or colonization (Chaffin et al, 2012;Szafranska et al, 2014;Jenkins et al, 2015;Chaves-Moreno et al, 2016;Deng et al, 2019;Ibberson and Whiteley, 2019) have highlighted major differences between in vitro and in vivo transcriptional gene regulation. This suggests that in situ exploration of the regulatory networks involving sRNAs in human pathogens is essential for understanding their roles.…”

Section: Introductionmentioning

confidence: 99%

Galleria mellonella Larvae as an Infection Model to Investigate sRNA-Mediated Pathogenesis in Staphylococcus aureus

Ménard

Rouillon

Ghukasyan

et al. 2021

Front. Cell. Infect. Microbiol.

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Small regulatory RNAs (sRNAs) are key players in bacterial regulatory networks. Monitoring their expression inside living colonized or infected organisms is essential for identifying sRNA functions, but few studies have looked at sRNA expression during host infection with bacterial pathogens. Insufficient in vivo studies monitoring sRNA expression attest to the difficulties in collecting such data, we therefore developed a non-mammalian infection model using larval Galleria mellonella to analyze the roles of Staphylococcus aureus sRNAs during larval infection and to quickly determine possible sRNA involvement in staphylococcal virulence before proceeding to more complicated animal testing. We began by using the model to test infected larvae for immunohistochemical evidence of infection as well as host inflammatory responses over time. To monitor sRNA expression during infection, total RNAs were extracted from the larvae and invading bacteria at different time points. The expression profiles of the tested sRNAs were distinct and they fluctuated over time, with expression of both sprD and sprC increased during infection and associated with mortality, while rnaIII expression remained barely detectable over time. A strong correlation was observed between sprD expression and the mortality. To confirm these results, we used sRNA-knockout mutants to investigate sRNA involvement in Staphylococcus aureus pathogenesis, finding that the decrease in death rates is delayed when either sprD or sprC was lacking. These results demonstrate the relevance of this G. mellonella model for investigating the role of sRNAs as transcriptional regulators involved in staphylococcal virulence. This insect model provides a fast and easy method for monitoring sRNA (and mRNA) participation in S. aureus pathogenesis, and can also be used for other human bacterial pathogens.

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“…Deng et al [46] identified fibrinogen binding adhesins as key factors for S. aureus persistence within the mouse vagina; following the introduction of several S. aureus strain into mice vagina, they recovered S. aureus from the vagina and counted CFU that were significantly lower in mice that were infected with adhesins-deficient strain compared to the Wild-type [46]. Thus, it seems that the biofilm forming ability may affect vaginal colonization.…”

Section: Biofilm Formation In Transmitted Mrsa Isolates Compared To Non-transmitted Isolatesmentioning

confidence: 99%

Mother-to-Neonate Transmission of Antibiotic-Resistant Bacteria: A Cross-Sectional Study

et al. 2021

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We evaluated carriage rates of extended spectrum β-lactam-producing Enterobacterales (ESBL-E), Carbapeneme-resistant Enterobacterales (CRE), vancomycin-resistant Enterococci (VRE), and methicillin-resistant Staphylococcus aureus (MRSA) among pregnant women and determined the maternal-to-neonate transmission rates of these antibiotic-resistant bacteria (ARB). Pregnant women provided rectal and vaginal samples, proximal to delivery. Stool samples were collected from newborns within 48 h of birth. All samples were cultured on selective media for ARB identification. Clinical and demographic data were collected from the participants’ medical files. We performed molecular and phenotypic characterization of the different resistance mechanisms, and determined the isolates’ antibiotic susceptibility and biofilm-forming ability. The prevalence of ESBL-E, MRSA and VRE among pregnant women were 16%, 6% and 1%, respectively. The prevalence of ESBL-E and MRSA among neonates were 7.6% and 1.6%, respectively. Maternal-to-neonate transmission rates of ESBL-E and MRSA were 48% and 27.8%, respectively. Maternal and neonatal isolates shared similar characteristics. Maternal-to-neonate transmission of ARB plays an important role in bacterial colonization in newborns. Future studies should investigate the outcomes of the high ESBL-E transmission rate. The biofilm-forming ability of ARB was found to affect transmission. Additional factors should be investigated in order to understand the differences between transmitted and non-transmitted bacteria.

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Identification of Key Determinants of Staphylococcus aureus Vaginal Colonization

Cited by 36 publications

References 117 publications

Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in Staphylococcus aureus

Reading between the Lines: Utilizing RNA-Seq Data for Global Analysis of sRNAs in Staphylococcus aureus

Galleria mellonella Larvae as an Infection Model to Investigate sRNA-Mediated Pathogenesis in Staphylococcus aureus

Mother-to-Neonate Transmission of Antibiotic-Resistant Bacteria: A Cross-Sectional Study

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