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2.
Elife ; 122023 07 04.
Article in English | MEDLINE | ID: mdl-37401629

ABSTRACT

The bloodstream represents a hostile environment that bacteria must overcome to cause bacteraemia. To understand how the major human pathogen Staphylococcus aureus manages this we have utilised a functional genomics approach to identify a number of new loci that affect the ability of the bacteria to survive exposure to serum, the critical first step in the development of bacteraemia. The expression of one of these genes, tcaA, was found to be induced upon exposure to serum, and we show that it is involved in the elaboration of a critical virulence factor, the wall teichoic acids (WTA), within the cell envelope. The activity of the TcaA protein alters the sensitivity of the bacteria to cell wall attacking agents, including antimicrobial peptides, human defence fatty acids, and several antibiotics. This protein also affects the autolytic activity and lysostaphin sensitivity of the bacteria, suggesting that in addition to changing WTA abundance in the cell envelope, it also plays a role in peptidoglycan crosslinking. With TcaA rendering the bacteria more susceptible to serum killing, while simultaneously increasing the abundance of WTA in the cell envelope, it was unclear what effect this protein may have during infection. To explore this, we examined human data and performed murine experimental infections. Collectively, our data suggests that whilst mutations in tcaA are selected for during bacteraemia, this protein positively contributes to the virulence of S. aureus through its involvement in altering the cell wall architecture of the bacteria, a process that appears to play a key role in the development of bacteraemia.


Subject(s)
Bacteremia , Staphylococcal Infections , Animals , Humans , Mice , Staphylococcal Infections/microbiology , Staphylococcus aureus/metabolism , Cell Wall/metabolism , Anti-Bacterial Agents/pharmacology , Teichoic Acids/metabolism
3.
Elife ; 122023 Jun 08.
Article in English | MEDLINE | ID: mdl-37289634

ABSTRACT

Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.


Subject(s)
Bacteremia , Staphylococcal Infections , Humans , Staphylococcus aureus/metabolism , Staphylococcal Infections/microbiology , Bacteremia/microbiology , Mutation , Cell Line , Bacterial Proteins/genetics , Bacterial Proteins/metabolism
4.
bioRxiv ; 2023 Apr 24.
Article in English | MEDLINE | ID: mdl-36865143

ABSTRACT

The bloodstream represents a hostile environment that bacteria must overcome to cause bacteraemia. To understand how the major human pathogen Staphylococcus aureus manages this we have utilised a functional genomics approach to identify a number of new loci that affect the ability of the bacteria to survive exposure to serum, the critical first step in the development of bacteraemia. The expression of one of these genes, tcaA, was found to be induced upon exposure to serum, and we show that it is involved in the elaboration of a critical virulence factor, the wall teichoic acids (WTA), within the cell envelope. The activity of the TcaA protein alters the sensitivity of the bacteria to cell wall attacking agents, including antimicrobial peptides, human defence fatty acids, and several antibiotics. This protein also affects the autolytic activity and lysostaphin sensitivity of the bacteria, suggesting that in addition to changing WTA abundance in the cell envelope, it also plays a role in peptidoglycan crosslinking. With TcaA rendering the bacteria more susceptible to serum killing, while simultaneously increasing the abundance of WTA in the cell envelope, it was unclear what effect this protein may have during infection. To explore this, we examined human data and performed murine experimental infections. Collectively, our data suggests that whilst mutations in tcaA are selected for during bacteraemia, this protein positively contributes to the virulence of S. aureus through its involvement in altering the cell wall architecture of the bacteria, a process that appears to play a key role in the development of bacteraemia.

5.
Microbiology (Reading) ; 169(1)2023 01.
Article in English | MEDLINE | ID: mdl-36748621

ABSTRACT

In recent work we identified genes that confer the slow-growing and antibiotic-resistant small-colony variant (SCV) form of Staphylococcus aureus, as associated with the amount of capsule the bacteria produce. In this study we isolated a triclosan-resistant SCV (tr-SCV) and demonstrated that it produces significantly less capsule, an effect that appears to be mediated at the transcriptional stage. As with other SCVs, we found that the tr-SCV produces less toxins, and when compared to both a capsule and an Agr mutant we found the tr-SCV to be significantly attenuated in an insect model of infection.


Subject(s)
Staphylococcal Infections , Triclosan , Humans , Triclosan/pharmacology , Staphylococcus aureus/genetics , Microbial Sensitivity Tests , Anti-Bacterial Agents/pharmacology , Staphylococcal Infections/microbiology
6.
Nature ; 613(7945): 639-649, 2023 01.
Article in English | MEDLINE | ID: mdl-36697862

ABSTRACT

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.


Subject(s)
Biomass , DNA Contamination , Fetus , Microbiota , Animals , Female , Humans , Pregnancy , Amniotic Fluid/immunology , Amniotic Fluid/microbiology , Mammals , Microbiota/genetics , Placenta/immunology , Placenta/microbiology , Fetus/immunology , Fetus/microbiology , Reproducibility of Results
7.
Microbiology (Reading) ; 168(8)2022 08.
Article in English | MEDLINE | ID: mdl-35997594

ABSTRACT

Staphylococcus aureus bacteraemia (SAB) is a major cause of blood-stream infection (BSI) in both healthcare and community settings. While the underlying comorbidities of a patient significantly contributes to their susceptibility to and outcome following SAB, recent studies show the importance of the level of cytolytic toxin production by the infecting bacterium. In this study we demonstrate that this cytotoxicity can be determined directly from the diagnostic MALDI-TOF mass spectrum generated in a routine diagnostic laboratory. With further development this information could be used to guide the management and improve the outcomes for SAB patients.


Subject(s)
Bacteremia , Staphylococcal Infections , Bacteremia/diagnosis , Bacteremia/microbiology , Humans , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Staphylococcal Infections/diagnosis , Staphylococcal Infections/microbiology , Staphylococcus aureus
8.
Microbiol Spectr ; 10(4): e0101122, 2022 08 31.
Article in English | MEDLINE | ID: mdl-35863033

ABSTRACT

A major feature of the pathogenicity of Staphylococcus aureus is its ability to secrete cytolytic toxins. This process involves the translocation of the toxins from the cytoplasm through the bacterial membrane and the cell wall to the external environment. The process of their movement through the membrane is relatively well defined, involving both general and toxin-specific secretory systems. Movement of the toxins through the cell wall was considered to involve the passive diffusion of the proteins through the porous cell wall structures; however, recent work suggests that this is more complex, and here we demonstrate a role for the wall teichoic acids (WTA) in this process. Utilizing a genome-wide association approach, we identified a polymorphism in the locus encoding the WTA biosynthetic machinery as associated with the cytolytic activity of the bacteria. We verified this association using an isogenic mutant set and found that WTA are required for the release of several cytolytic toxins from the bacterial cells. We show that this effect is mediated by a change in the electrostatic charge across the cell envelope that results from the loss of WTA. As a major target for the development of novel therapeutics, it is important that we fully understand the entire process of cytolytic toxin production and release. These findings open up a new aspect to the process of toxin release by a major human pathogen while also demonstrating that clinical isolates can utilize WTA production to vary their cytotoxicity, thereby altering their pathogenic capabilities. IMPORTANCE The production and release of cytolytic toxins is a critical aspect for the pathogenicity of many bacterial pathogens. In this study, we demonstrate a role for wall teichoic acids, molecules that are anchored to the peptidoglycan of the bacterial cell wall, in the release of toxins from S. aureus cells into the extracellular environment. Our findings suggest that this effect is mediated by a gradient of electrostatic charge which the presence of the negatively charged WTA molecules create across the cell envelope. This work brings an entirely new aspect to our understanding of the cytotoxicity of S. aureus and demonstrates a further means by which this major human pathogen can adapt its pathogenic capabilities.


Subject(s)
Staphylococcus aureus , Teichoic Acids , Cell Wall/metabolism , Genome-Wide Association Study , Staphylococcus aureus/genetics , Staphylococcus aureus/metabolism , Teichoic Acids/metabolism
9.
Microb Genom ; 8(4)2022 04.
Article in English | MEDLINE | ID: mdl-35416147

ABSTRACT

Streptococcus pneumoniae is a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia and meningitis. Young children are at a particularly high risk, with an estimated 3-4 million cases of severe disease and between 300 000 and 500 000 deaths attributable to pneumococcal disease each year. The haemolytic toxin pneumolysin (Ply) is a primary virulence factor for this bacterium, yet despite its key role in pathogenesis, immune evasion and transmission, the regulation of Ply production is not well defined. Using a genome-wide association approach, we identified a large number of potential affectors of Ply activity, including a gene acquired horizontally on the antibiotic resistance-conferring Integrative and Conjugative Element (ICE) ICESp23FST81. This gene encodes a novel modular protein, ZomB, which has an N-terminal UvrD-like helicase domain followed by two Cas4-like domains with potent ATP-dependent nuclease activity. We found the regulatory effect of ZomB to be specific for the ply operon, potentially mediated by its high affinity for the BOX repeats encoded therein. Using a murine model of pneumococcal colonization, we further demonstrate that a ZomB mutant strain colonizes both the upper respiratory tract and lungs at higher levels when compared to the wild-type strain. While the antibiotic resistance-conferring aspects of ICESp23FST81 are often credited with contributing to the success of the S. pneumoniae lineages that acquire it, its ability to control the expression of a major virulence factor implicated in bacterial transmission is also likely to have played an important role.


Subject(s)
Genome-Wide Association Study , Streptococcus pneumoniae , Animals , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Interspersed Repetitive Sequences/genetics , Mice , Streptococcus pneumoniae/genetics , Streptolysins , Virulence Factors/genetics , Virulence Factors/metabolism
10.
Microbiology (Reading) ; 167(12)2021 12.
Article in English | MEDLINE | ID: mdl-34928202

ABSTRACT

Staphylococcus aureus is a major human pathogen where the emergence of antibiotic resistant lineages, such as methicillin-resistant S. aureus (MRSA), is a major health concern. While some MRSA lineages are restricted to the healthcare setting, the epidemiology of MRSA is changing globally, with the rise of specific lineages causing disease in healthy people in the community. In the past two decades, community-associated MRSA (CA-MRSA) has emerged as a clinically important and virulent pathogen associated with serious skin and soft-tissue infections (SSTI). These infections are primarily cytotoxin driven, leading to the suggestion that hypervirulent lineages/multi-locus sequence types (STs) exist. To examine this, we compared the cytotoxicity of 475 MRSA isolates representing five major MRSA STs (ST22, ST93, ST8, ST239 and ST36) by employing a monocyte-macrophage THP-1 cell line as a surrogate for measuring gross cytotoxicity. We demonstrate that while certain MRSA STs contain highly toxic isolates, there is such variability within lineages to suggest that this aspect of virulence should not be inferred from the genotype of any given isolate. Furthermore, by interrogating the accessory gene regulator (Agr) sequences in this collection we identified several Agr mutations that were associated with reduced cytotoxicity. Interestingly, the majority of isolates that were attenuated in cytotoxin production contained no mutations in the agr locus, indicating a role of other undefined genes in S. aureus toxin regulation.


Subject(s)
Methicillin-Resistant Staphylococcus aureus , Staphylococcal Infections , Anti-Bacterial Agents/pharmacology , Genotype , Humans , Methicillin-Resistant Staphylococcus aureus/genetics , Microbial Sensitivity Tests , Staphylococcal Infections/epidemiology , Staphylococcus aureus/genetics
11.
Microbiology (Reading) ; 167(11)2021 11.
Article in English | MEDLINE | ID: mdl-34825882

ABSTRACT

Staphylococcus aureus is a major human pathogen that utilises a wide array of pathogenic and immune evasion strategies to cause disease. One immune evasion strategy, common to many bacterial pathogens, is the ability of S. aureus to produce a capsule that protects the bacteria from several aspects of the human immune system. To identify novel regulators of capsule production by S. aureus, we applied a genome wide association study (GWAS) to a collection of 300 bacteraemia isolates that represent the two major MRSA clones in UK and Irish hospitals: CC22 and CC30. One of the loci associated with capsule production, the menD gene, encodes an enzyme critical to the biosynthesis of menadione. Mutations in this gene that result in menadione auxotrophy induce the slow growing small-colony variant (SCV) form of S. aureus often associated with chronic infections due to their increased resistance to antibiotics and ability to survive inside phagocytes. Utilising such an SCV, we functionally verified this association between menD and capsule production. Although the clinical isolates with polymorphisms in the menD gene in our collections had no apparent growth defects, they were more resistant to gentamicin when compared to those with the wild-type menD gene. Our work suggests that menadione is involved in the production of the S. aureus capsule, and that amongst clinical isolates polymorphisms exist in the menD gene that confer the characteristic increased gentamicin resistance, but not the major growth defect associated with SCV phenotype.


Subject(s)
Staphylococcal Infections , Staphylococcus aureus , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Genome-Wide Association Study , Humans , Microbial Sensitivity Tests , Staphylococcal Infections/microbiology , Staphylococcus aureus/metabolism , Vitamin K 3/metabolism , Vitamin K 3/pharmacology
12.
Microbiology (Reading) ; 167(10)2021 10.
Article in English | MEDLINE | ID: mdl-34618666

ABSTRACT

Understanding the role specific bacterial factors play in the development of severe disease in humans is critical if new approaches to tackle such infections are to be developed. In this study we focus on genes we have found to be associated with patient outcome following bacteraemia caused by the major human pathogen Staphylococcus aureus. By examining the contribution these genes make to the ability of the bacteria to survive exposure to the antibacterial factors found in serum, we identify three novel serum resistance-associated genes, mdeA, mpsB and yycH. Detailed analysis of an MpsB mutant supports its previous association with the slow growing small colony variant (SCV) phenotype of S. aureus, and we demonstrate that the effect this mutation has on membrane potential prevents the activation of the Agr quorum sensing system, and as a consequence the mutant bacteria do not produce cytolytic toxins. Given the importance of both toxin production and immune evasion for the ability of S. aureus to cause disease, we believe that these findings explain the role of the mpsB gene as a mortality-associated locus during human disease.


Subject(s)
Bacterial Proteins/metabolism , Immune Evasion , Staphylococcus aureus/pathogenicity , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Bacteremia/microbiology , Bacterial Proteins/genetics , Bacterial Toxins/metabolism , Drug Resistance, Bacterial , Humans , Membrane Potentials , Mutation , Quorum Sensing , Staphylococcal Infections/microbiology , Staphylococcus aureus/drug effects , Staphylococcus aureus/physiology
13.
Elife ; 92020 12 17.
Article in English | MEDLINE | ID: mdl-33331820

ABSTRACT

Here, we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massive and escalating levels of T-cell activation. These were both SARS-CoV-2 and P. aeruginosa specific, and bystander activated, which may have contributed to this patient's persistent symptoms and radiological changes.


Subject(s)
Anti-Bacterial Agents/therapeutic use , COVID-19/complications , Lymphocyte Activation , Pneumonia, Ventilator-Associated/drug therapy , Pseudomonas Infections/drug therapy , SARS-CoV-2 , T-Lymphocytes/immunology , Anti-Bacterial Agents/pharmacology , COVID-19/immunology , COVID-19/therapy , Drug Resistance, Multiple, Bacterial , Humans , Lung/microbiology , Male , Meropenem/pharmacology , Meropenem/therapeutic use , Metagenomics , Middle Aged , Piperacillin, Tazobactam Drug Combination/pharmacology , Piperacillin, Tazobactam Drug Combination/therapeutic use , Pneumonia, Ventilator-Associated/diagnostic imaging , Pneumonia, Ventilator-Associated/etiology , Pseudomonas Infections/diagnostic imaging , Pseudomonas Infections/etiology , Pseudomonas aeruginosa/isolation & purification , Recurrence , Respiration, Artificial
14.
Infect Immun ; 88(9)2020 08 19.
Article in English | MEDLINE | ID: mdl-32571989

ABSTRACT

Staphylococcus aureus is a major human pathogen, and the emergence of antibiotic-resistant strains is making all types of S. aureus infections more challenging to treat. With a pressing need to develop alternative control strategies to use alongside or in place of conventional antibiotics, one approach is the targeting of established virulence factors. However, attempts at this have had little success to date, suggesting that we need to better understand how this pathogen causes disease if effective targets are to be identified. To address this, using a functional genomics approach, we have identified a small membrane-bound protein that we have called MspA. Inactivation of this protein results in the loss of the ability of S. aureus to secrete cytolytic toxins, protect itself from several aspects of the human innate immune system, and control its iron homeostasis. These changes appear to be mediated through a change in the stability of the bacterial membrane as a consequence of iron toxicity. These pleiotropic effects on the ability of the pathogen to interact with its host result in significant impairment in the ability of S. aureus to cause infection in both a subcutaneous and sepsis model of infection. Given the scale of the effect the inactivation of MspA causes, it represents a unique and promising target for the development of a novel therapeutic approach.


Subject(s)
Bacteremia/microbiology , Immune Evasion , Staphylococcal Infections/microbiology , Staphylococcal Skin Infections/microbiology , Staphylococcus aureus/pathogenicity , Virulence Factors/genetics , A549 Cells , Animals , Bacteremia/immunology , Bacteremia/pathology , Bacterial Toxins/genetics , Bacterial Toxins/immunology , Erythrocytes/drug effects , Gene Expression Profiling , Gene Expression Regulation , Heme/immunology , Heme/metabolism , Hemolysin Proteins/genetics , Hemolysin Proteins/immunology , Homeostasis/immunology , Humans , Iron/immunology , Iron/metabolism , Mice, Inbred BALB C , Mice, Inbred C57BL , Mutation , Phagocytosis , Proteomics/methods , Staphylococcal Infections/immunology , Staphylococcal Infections/pathology , Staphylococcal Skin Infections/immunology , Staphylococcal Skin Infections/pathology , Staphylococcal Toxoid/genetics , Staphylococcal Toxoid/immunology , Staphylococcus aureus/genetics , Staphylococcus aureus/immunology , THP-1 Cells , Virulence , Virulence Factors/immunology , Virulence Factors/toxicity , alpha-Defensins/genetics , alpha-Defensins/immunology
15.
BJPsych Bull ; 44(6): 239-243, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32081110

ABSTRACT

AIMS AND METHOD: A series of eleven patients prescribed intramuscular clozapine at five UK sites is presented. Using routinely collected clinical data, we describe the use, efficacy and safety of this treatment modality. RESULTS: We administered 188 doses of intramuscular clozapine to eight patients. The remaining three patients accepted oral medication. With the exception of minor injection site pain and nodules, side-effects were as expected with oral clozapine, and there were no serious untoward events. Nine patients were successfully established on oral clozapine with significant improvement in their clinical presentations. CLINICAL IMPLICATIONS: Although a novel formulation in the UK, we have shown that intramuscular clozapine can be used safely and effectively when the oral route is initially refused.

16.
mBio ; 10(6)2019 11 26.
Article in English | MEDLINE | ID: mdl-31772058

ABSTRACT

The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood. In this study, we traced the recent origins and global spread of a multidrug-resistant, community-associated Staphylococcus aureus lineage from the Indian subcontinent, the Bengal Bay clone (ST772). We generated whole-genome sequence data of 340 isolates from 14 countries, including the first isolates from Bangladesh and India, to reconstruct the evolutionary history and genomic epidemiology of the lineage. Our data show that the clone emerged on the Indian subcontinent in the early 1960s and disseminated rapidly in the 1990s. Short-term outbreaks in community and health care settings occurred following intercontinental transmission, typically associated with travel and family contacts on the subcontinent, but ongoing endemic transmission was uncommon. Acquisition of a multidrug resistance integrated plasmid was instrumental in the emergence of a single dominant and globally disseminated clade in the early 1990s. Phenotypic data on biofilm, growth, and toxicity point to antimicrobial resistance as the driving force in the evolution of ST772. The Bengal Bay clone therefore combines the multidrug resistance of traditional health care-associated clones with the epidemiological transmission of community-associated methicillin-resistant S. aureus (MRSA). Our study demonstrates the importance of whole-genome sequencing for tracking the evolution of emerging and resistant pathogens. It provides a critical framework for ongoing surveillance of the clone on the Indian subcontinent and elsewhere.IMPORTANCE The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in the region. ST772 progressively acquired specific resistance elements at limited cost to its fitness and continues to be exported globally, resulting in small-scale community and health care outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug resistance of health care-associated S. aureus lineages. This study demonstrates the importance of whole-genome sequencing for the surveillance of highly antibiotic-resistant pathogens, which may emerge in the community setting of regions with poor antibiotic stewardship and rapidly spread into hospitals and communities across the world.


Subject(s)
Community-Acquired Infections/microbiology , Drug Resistance, Multiple, Bacterial , Methicillin-Resistant Staphylococcus aureus/genetics , Staphylococcal Infections/microbiology , Staphylococcus aureus/isolation & purification , Anti-Bacterial Agents/pharmacology , Asia/epidemiology , Community-Acquired Infections/epidemiology , Community-Acquired Infections/transmission , Evolution, Molecular , Genome, Bacterial , Humans , India , Methicillin-Resistant Staphylococcus aureus/classification , Methicillin-Resistant Staphylococcus aureus/drug effects , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Phylogeny , Staphylococcal Infections/epidemiology , Staphylococcal Infections/transmission , Staphylococcus aureus/classification , Staphylococcus aureus/drug effects , Staphylococcus aureus/genetics
17.
J Bacteriol ; 201(20)2019 10 15.
Article in English | MEDLINE | ID: mdl-31358609

ABSTRACT

Mutations in the polymorphic Staphylococcus aureusagr locus responsible for quorum sensing (QS)-dependent virulence gene regulation occur frequently during host adaptation. In two genomically closely related S. aureus clinical isolates exhibiting marked differences in Panton-Valentine leukocidin production, a mutation conferring an N267I substitution was identified in the cytoplasmic domain of the QS sensor kinase, AgrC. This natural mutation delayed the onset and accumulation of autoinducing peptide (AIP) and showed reduced responsiveness to exogenous AIPs. Other S. aureus strains harboring naturally occurring AgrC cytoplasmic domain mutations were identified, including T247I, I311T, A343T, L245S, and F264C. These mutations were associated with reduced cytotoxicity, delayed/reduced AIP production, and impaired sensitivity to exogenous AIP. Molecular dynamics simulations were used to model the AgrC cytoplasmic domain conformational changes arising. Although mutations were localized in different parts of the C-terminal domain, their impact on molecular structure was manifested by twisting of the leading helical hairpin α1-α2, accompanied by repositioning of the H-box and G-box, along with closure of the flexible loop connecting the two and occlusion of the ATP-binding site. Such conformational rearrangements of key functional subdomains in these mutants highlight the cooperative response of molecular structure involving dimerization and ATP binding and phosphorylation, as well as the binding site for the downstream response element AgrA. These appear to increase the threshold for agr activation via AIP-dependent autoinduction, thus reducing virulence and maintaining S. aureus in an agr-downregulated "colonization" mode.IMPORTANCE Virulence factor expression in Staphylococcus aureus is regulated via autoinducing peptide (AIP)-dependent activation of the sensor kinase AgrC, which forms an integral part of the agr quorum sensing system. In response to bound AIP, the cytoplasmic domain of AgrC (AgrC-cyt) undergoes conformational changes resulting in dimerization, autophosphorylation, and phosphotransfer to the response regulator AgrA. Naturally occurring mutations in AgrC-cyt are consistent with repositioning of key functional domains, impairing dimerization and restricting access to the ATP-binding pocket. Strains harboring specific AgrC-cyt mutations exhibit reduced AIP autoinduction efficiency and a timing-dependent attenuation of cytotoxicity which may confer a survival advantage during established infection by promoting colonization while restricting unnecessary overproduction of exotoxins.


Subject(s)
Amino Acid Substitution , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Peptides, Cyclic/metabolism , Protein Kinases/chemistry , Protein Kinases/genetics , Staphylococcus aureus/metabolism , Adenosine Triphosphate/metabolism , Binding Sites , Cytoplasm/metabolism , Models, Molecular , Molecular Dynamics Simulation , Phosphorylation , Protein Binding , Protein Domains , Protein Kinases/metabolism , Protein Multimerization , Protein Structure, Secondary , Quorum Sensing , Staphylococcus aureus/genetics , Staphylococcus aureus/pathogenicity , Time Factors , Trans-Activators/metabolism
18.
Nat Microbiol ; 4(10): 1680-1691, 2019 10.
Article in English | MEDLINE | ID: mdl-31235959

ABSTRACT

Antibiotic resistance in bacterial pathogens threatens the future of modern medicine. One such resistant pathogen is methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to nearly all ß-lactam antibiotics, limiting treatment options. Here, we show that a significant proportion of MRSA isolates from different lineages, including the epidemic USA300 lineage, are susceptible to penicillins when used in combination with ß-lactamase inhibitors such as clavulanic acid. Susceptibility is mediated by a combination of two different mutations in the mecA promoter region that lowers mecA-encoded penicillin-binding protein 2a (PBP2a) expression, and in the majority of isolates by either one of two substitutions in PBP2a (E246G or M122I) that increase the affinity of PBP2a for penicillin in the presence of clavulanic acid. Treatment of S. aureus infections in wax moth and mouse models shows that penicillin/ß-lactamase inhibitor susceptibility can be exploited as an effective therapeutic choice for 'susceptible' MRSA infection. Finally, we show that isolates with the PBP2a E246G substitution have a growth advantage in the presence of penicillin but the absence of clavulanic acid, which suggests that penicillin/ß-lactamase susceptibility is an example of collateral sensitivity (resistance to one antibiotic increases sensitivity to another). Our findings suggest that widely available and currently disregarded antibiotics could be effective in a significant proportion of MRSA infections.


Subject(s)
Bacterial Proteins/genetics , Clavulanic Acid/pharmacology , Methicillin-Resistant Staphylococcus aureus/drug effects , Methicillin-Resistant Staphylococcus aureus/genetics , Penicillin-Binding Proteins/genetics , Penicillins/pharmacology , beta-Lactamase Inhibitors/pharmacology , Amino Acid Substitution , Animals , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Bacterial Proteins/metabolism , Clavulanic Acid/therapeutic use , Drug Therapy, Combination , Methicillin-Resistant Staphylococcus aureus/growth & development , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Mice , Microbial Sensitivity Tests , Moths , Mutation , Penicillin-Binding Proteins/metabolism , Penicillins/metabolism , Penicillins/therapeutic use , Promoter Regions, Genetic , Staphylococcal Infections/drug therapy , Staphylococcal Infections/microbiology , beta-Lactam Resistance/drug effects , beta-Lactamase Inhibitors/therapeutic use
19.
Nat Commun ; 9(1): 5034, 2018 11 28.
Article in English | MEDLINE | ID: mdl-30487573

ABSTRACT

Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.


Subject(s)
Skin Diseases/microbiology , Staphylococcal Infections/microbiology , Staphylococcus epidermidis/genetics , Staphylococcus epidermidis/pathogenicity , Genome, Bacterial/genetics , Genome-Wide Association Study , Genotype , Humans , Interleukin-8/metabolism
20.
Genome Med ; 10(1): 65, 2018 08 23.
Article in English | MEDLINE | ID: mdl-30103826

ABSTRACT

BACKGROUND: Large-scale genomic studies of within-host diversity in Staphylococcus aureus bacteraemia (SAB) are needed to understanding bacterial adaptation underlying persistence and thus refining the role of genomics in management of SAB. However, available comparative genomic studies of sequential SAB isolates have tended to focus on selected cases of unusually prolonged bacteraemia, where secondary antimicrobial resistance has developed. METHODS: To understand bacterial genetic diversity during SAB more broadly, we applied whole genome sequencing to a large collection of sequential isolates obtained from patients with persistent or relapsing bacteraemia. After excluding genetically unrelated isolates, we performed an in-depth genomic analysis of point mutations and chromosome structural variants arising within individual SAB episodes. RESULTS: We show that, while adaptation pathways are heterogenous and episode-specific, isolates from persistent bacteraemia have a distinctive molecular signature, characterised by a low mutation frequency and high proportion of non-silent mutations. Analysis of structural genomic variants revealed that these often overlooked genetic events are commonly acquired during SAB. We discovered that IS256 insertion may represent the most effective driver of within-host microevolution in selected lineages, with up to three new insertion events per isolate even in the absence of other mutations. Genetic mechanisms resulting in significant phenotypic changes, such as increases in vancomycin resistance, development of small colony phenotypes, and decreases in cytotoxicity, included mutations in key genes (rpoB, stp, agrA) and an IS256 insertion upstream of the walKR operon. CONCLUSIONS: This study provides for the first time a large-scale analysis of within-host genomic changes during invasive S. aureus infection and describes specific patterns of adaptation that will be informative for both understanding S. aureus pathoadaptation and utilising genomics for management of complicated S. aureus infections.


Subject(s)
Bacteremia/microbiology , Genes, Bacterial , Polymorphism, Genetic , Staphylococcus aureus/genetics , Point Mutation , Staphylococcus aureus/isolation & purification , Staphylococcus aureus/pathogenicity
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