From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence?

Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes

Multidrug-resistant nosocomial pathogens present a major burden for hospitals. Rapid cluster identification and pathogen profiling, i.e., of antibiotic resistance and virulence genes, are crucial for effective infection control. Methicillin-resistant Staphylococcus aureus (MRSA), in particular, is now one of the leading causes of nosocomial infections. In this study, whole-genome sequencing (WGS) was applied retrospectively to an unusual spike in MRSA cases in two intensive care units (ICUs) over the course of 4 weeks. While the epidemiological investigation concluded that there were two separate clusters, each associated with one ICU, S. aureus protein A gene (spa) typing data suggested that they belonged to single clonal cluster (all cases shared spa type t001). Standardized gene sets were used to extract an allele-based profile for typing and an antibiotic resistance and toxin gene profile. The WGS results produced high-resolution allelic profiles, which were used to discriminate the MRSA clusters, corroborating the epidemiological investigation and identifying previously unsuspected transmission events. The antibiotic resistance profile was in agreement with the original clinical laboratory susceptibility profile, and the toxin profile provided additional, previously unknown information. WGS coupled with allelic profiling provided a high-resolution method that can be implemented as regular screening for effective infection control.

Predicting the virulence of MRSA from its genome sequence

Microbial virulence is a complex and often multifactorial phenotype, intricately linked to a pathogen’s evolutionary trajectory. Toxicity, the ability to destroy host cell membranes, and adhesion, the ability to adhere to human tissues, are the major virulence factors of many bacterial pathogens, including Staphylococcus aureus. Here, we assayed the toxicity and adhesiveness of 90 MRSA (methicillin resistant S. aureus) isolates and found that while there was remarkably little variation in adhesion, toxicity varied by over an order of magnitude between isolates, suggesting different evolutionary selection pressures acting on these two traits. We performed a genome-wide association study (GWAS) and identified a large number of loci, as well as a putative network of epistatically interacting loci, that significantly associated with toxicity. Despite this apparent complexity in toxicity regulation, a predictive model based on a set of significant single nucleotide polymorphisms (SNPs) and insertion and deletions events (indels) showed a high degree of accuracy in predicting an isolate’s toxicity solely from the genetic signature at these sites. Our results thus highlight the potential of using sequence data to determine clinically relevant parameters and have further implications for understanding the microbial virulence of this opportunistic pathogen.

A non-coding RNA promotes bacterial persistence and decreases virulence by regulating a regulator in Staphylococcus aureus

Staphylococcus aureus produces a high number of RNAs for which the functions are poorly understood. Several non-coding RNAs carry a C-rich sequence suggesting that they regulate mRNAs at the post-transcriptional level. We demonstrate that the Sigma B-dependent RsaA RNA represses the synthesis of the global transcriptional regulator MgrA by forming an imperfect duplex with the Shine and Dalgarno sequence and a loop-loop interaction within the coding region of the target mRNA. These two recognition sites are required for translation repression. Consequently, RsaA causes enhanced production of biofilm and a decreased synthesis of capsule formation in several strain backgrounds. These phenotypes led to a decreased protection of S. aureus against opsonophagocytic killing by polymorphonuclear leukocytes compared to the mutant strains lacking RsaA. Mice animal models showed that RsaA attenuates the severity of acute systemic infections and enhances chronic catheter infection. RsaA takes part in a regulatory network that contributes to the complex interactions of S. aureus with the host immune system to moderate invasiveness and favour chronic infections. It is the first example of a conserved small RNA in S. aureus functioning as a virulence suppressor of acute infections. Because S. aureus is essentially a human commensal, we propose that RsaA has been positively selected through evolution to support commensalism and saprophytic interactions with the host.

Staphylococcus aureus is a commensal and an opportunistic pathogen that causes a large range of community and hospital-acquired infections. The bacteria produce an array of virulence factors, the expression of which is regulated by a set of regulators including proteins and RNAs. In recent years, a large number of small non-coding RNAs encoded by the S. aureus genome have been identified but determination of their function is still lagging behind. This study shows that RsaA, a staphylococcal conserved non-coding RNA, operates at the post-transcriptional level by repressing the translation of the master regulatory protein MgrA. The repression is based on a direct interaction of RsaA with the ribosome binding site of mgrA mRNA. Through MgrA regulation, RsaA activates biofilm formation and inhibits capsule synthesis. Using appropriate animal models, we showed that RsaA acts as a suppressor of virulence because the deletion of its gene increases the invasiveness of S. aureus in the mice sepsis model. RsaA is thus part of complex regulatory network that modify the interactions of S. aureus with the eukaryotic immune system. These findings illustrate how small RNAs can have a major impact in bacterial biology.

Emerging functions for the Staphylococcus aureus RNome

Staphylococcus aureus is a leading pathogen for animals and humans, not only being one of the most frequently isolated bacteria in hospital-associated infections but also causing diseases in the community. To coordinate the expression of its numerous virulence genes for growth and survival, S. aureus uses various signalling pathways that include two-component regulatory systems, transcription factors, and also around 250 regulatory RNAs. Biological roles have only been determined for a handful of these sRNAs, including cis, trans, and cis-trans acting RNAs, some internally encoding small, functional peptides and others possessing dual or multiple functions. Here we put forward an inventory of these fascinating sRNAs; the proteins involved in their activities; and those involved in stress response, metabolisms, and virulence.

Microarray-based genotyping and clinical outcomes of Staphylococcus aureus bloodstream infection: an exploratory study

The clinical course of Staphylococcus aureus bacteremia varies extensively. We sought to determine the relationship between genetic characteristics of the infecting pathogen and clinical outcomes in an exploratory study. In two study centers, 317 blood culture isolates were analyzed by DNA microarray and spa genotyping. By uni- and multivariate regression analyses associations of genotype data with 30-day all-cause mortality, severe sepsis/septic shock, disseminated disease, endocarditis, and osteoarticular infection were investigated. Univariate analysis showed significant association between S. aureus genes/gene-clusters or clonal complexes and clinical endpoints. For example CC15 was associated with 30-day mortality and CC22 with osteoarticular infection. In multivariate analysis methicillin resistance (mecA, OR 4.8 [1.43–16.06]) and the beta-lactamase-gene (bla, OR 3.12 [1.17–8.30]) remained independently associated with 30-day mortality. The presence of genes for enterotoxins (sed/sej/ser) was associated with endocarditis (OR 5.11 [1.14–18.62]). Host factors such as McCabe classification (OR 4.52 [2.09–9.79] for mortality), age (OR 1.06 [1.03–1.10] per year), and community-acquisition (OR 3.40 [1.31–8.81]) had a major influence on disease severity, dissemination and mortality. Individual genotypes and clonal complexes of S. aureus can only partially explain clinical features and outcomes of S. aureus bacteremia. Genotype-phenotype association studies need to include adjustments for host factors like age, comorbidity and community-acquisition.

Functional genomics of Staphylococcus aureus

Staphylococcus aureus remains a major opportunistic human pathogen, and while in many individuals it is associated with asymptomatic colonization, it is also capable of causing a range of clinical syndromes from minor skin infections to life-threatening septicemia. Staphylococcus aureus has also demonstrated a remarkable capacity to acquire antimicrobial resistance. Recent technological advances in genomics have led to an avalanche of studies providing deep insights into how S. aureus is evolving globally and within the human host. However, there are still significant experimental barriers in using these insights to try and better understand the biology of S. aureus. Here, we summarize recent advances in the understanding of S. aureus through the use of genomic approaches, and contemplate what the near future holds for truly functional genomics that will allow us to better understand the biology of this pathogen.