Biology subjects

Shanks, R. M.

Publications and source records attributed to Shanks, R. M..

9 recordsLinked to original sources

bioRxiv2025

Methicillin-Resistant Staphylococcus aureus has Phenotypic Variation in mecA Expression that Alters Antibiotic Sensitivity

Methicillin resistant Staphylococcus aureus (MRSA) sepsis has a high rate of morbidity and mortality. Multiple clinical studies have demonstrated improved outcomes when MRSA sepsis is treated with dual antibiotic therapy that includes a {beta}-lactam antibiotic such as cefazolin. This is a paradox as MRSA should be inherently resistant to this class of antibiotics. We report a serendipitous observation revealed a phenotype where MRSA became sensitive to cefazolin when cultured in a physiologic relevant media of fetal bovine serum as well as in synovial fluid. This could be observed across multiple clinical isolates. Expected resistance was maintained when cultured in Muller Hinton Broth (MHB). MRSA {beta}-lactam antibiotic resistance is mediated by PBP2a, a penicillin-binding protein encoded by mecA. We hypothesized that this phenotype of antibiotic sensitivity in physiologic medium was based, in part, on levels of PBP2a expression and post-translational modifications of peptidoglycan wall teichoic acid (WTA). We therefore conducted quantitative RT-PCR analysis and Western blotting which demonstrated limited mecA expression in the mRNA level and limited PBP2a protein level when cultured in FBS or synovial fluid as compared to the clinical microbiology standard MHB, respectively. Whole genome sequencing of loss of function mutants generated through serial passaging in FBS revealed that the clp family of proteins and rpo genes were involved in {beta}-lactam resistance. Cell wall peptidoglycan analysis suggested that WTA glycosylation was altered between {beta}-lactam resistant and sensitive MRSA phenotypes. Together, this suggests pathways for clpP, rpoB, and WTA glycosylation can be new potential targets for MRSA treatment. IMPORTANCEThis study demonstrates that MRSA has phenotypic variation in mecA expression, PBP2a protein levels, and patterns of wall teichoic acid glycosylation based on environmental conditions which can result in a phenotype of {beta}-lactam antibiotic sensitivity. The presence of an antibiotic resistance gene does not necessarily result in antibiotic resistance. This provides a possible explanation for the clinical observations of potential therapeutic benefit of {beta}-lactam antibiotics in dual therapy treatment of MRSA sepsis and suggests new therapeutic strategies to combat multidrug resistant bacteria. More importantly, identifying genes potentially responsible for this phenotype offers new potential therapeutic targets for the treatment of multidrug resistant infection.

microbiology↗

bioRxiv2023

In vivo evolution of a Klebsiella pneumoniae capsule defect promotes complement-mediated opsono-phagocytosis and persistence during recurrent infection

Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) bloodstream infections rarely overwhelm the host but are associated with high mortality. The complement system is a key host defense against bloodstream infection. However, there are varying reports of serum resistance among KPC-Kp isolates. We assessed growth of 59 KPC-Kp clinical isolates in human serum and found increased resistance in 16/59 (27%). We identified five genetically-related bloodstream isolates with varying serum resistance profiles collected from a single patient during an extended hospitalization marked by recurrent KPC-Kp bloodstream infections. We noted a loss-of-function mutation in the capsule biosynthesis gene, wcaJ, that emerged during infection was associated with decreased polysaccharide capsule content, and resistance to complement-mediated killing. Surprisingly, disruption of wcaJ increased deposition of complement proteins on the microbial surface compared to the wild-type strain and led to increased complement-mediated opsono-phagocytosis in human whole blood. Disabling opsono-phagocytosis in the airspaces of mice impaired in vivo control of the wcaJ loss-of-function mutant in an acute lung infection model. These findings describe the rise of a capsular mutation that promotes KPC-Kp persistence within the host by enabling co-existence of increased bloodstream fitness and reduced tissue virulence. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/542722v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@155736eorg.highwire.dtl.DTLVardef@10d47c0org.highwire.dtl.DTLVardef@e1ab83org.highwire.dtl.DTLVardef@1c33131_HPS_FORMAT_FIGEXP M_FIG Graphical abstract Created with BioRender.com C_FIG

microbiology↗

bioRxiv2022

The short chain fatty acid propionic acid activates the Rcs stress response system partially through inhibition of D-alanine racemase

The Enterobacterial Rcs stress response system reacts to envelope stresses through a complex two-component phosphorelay system to regulate a variety of environmental response genes such as capsular polysaccharide and flagella biosynthesis. However, beyond Escherichia coli, the stresses that activate Rcs are not well understood. In this study, we used a Rcs system dependent luminescent transcriptional reporter to screen a library of over 240 antimicrobial compounds for those that activated the Rcs system in Serratia marcescens, a Yersiniaceae family bacterium. Using an isogenic rcsB mutant to establish specificity, both new and expected activators were identified including the short chain fatty acid propionic acid found at millimolar levels in the human gut. Propionic acid did not reduce bacterial intracellular pH as hypothesized for its antibacterial mechanism. Rather than reduction of intracellular pH, data suggests that the Rcs-activating mechanism of propionic acid is, in part, due to inactivation of the enzyme alanine racemase. This enzyme is responsible for D-alanine biosynthesis, an amino-acid required for generating bacterial cell walls. These results suggest host gut short chain fatty acids can influence bacterial behavior through activation of the Rcs stress response system.

microbiology↗

bioRxiv2022

IgaA protein, GumB, has a global impact on the transcriptome and surface proteome of Serratia marcescens

Bacterial stress response signaling systems, like the Rcs system, can be triggered by membrane and cell wall damaging compounds including antibiotics and innate immune system factors. These regulatory systems help bacteria survive envelope stress by altering the transcriptome resulting in protective phenotypic changes that may also the influence the virulence of the bacterium. This study investigated the role of the Rcs stress response system using a clinical keratitis isolate of S. marcescens with a mutation in the gumB gene. GumB, an IgaA ortholog, inhibits activation of the Rcs system, such that mutants have overactive Rcs signaling. Transcriptomic analysis indicated that approximately 15% of all S. marcescens genes were significantly altered with two-fold or greater changes in expression in the {Delta}gumB mutant compared to the wild type indicating a global transcriptional regulatory role for GumB. We further investigated the phenotypic consequences of two classes of genes with altered expression in the {Delta}gumB mutant expected to contribute to infections: serralysin metalloproteases PrtS, SlpB and SlpE, and type I pili coded by fimABCD. Secreted fractions from the {Delta}gumB mutant had reduced cytotoxicity to a corneal cell line, and could be complemented by induced expression of prtS, but not cytolysin shlBA, phospholipase phlAB, or flagellar master regulator flhDC operons. Proteomic analysis, qRT-PCR, and type I pili dependent yeast agglutination indicated an inhibitory role for the Rcs system in adhesin production. Together these data demonstrate that GumB and the Rcs stress response system control S. marcescens virulence factors beyond the ShlA cytolysin. IMPORTANCEPrevious studies indicate that the bacterial Rcs system is a key regulator of envelope stress. This study demonstrated that activation of the Rcs system had a global impact on the transcriptome of a clinical isolate of S. marcescens including decreased expression of cytotoxic serralysin metalloproteases and biofilm promoting type I pili. These results give mechanistic insight into how the Rcs system contributes to pathogenesis.

microbiology↗

bioRxiv2021

Bacterial keratitis: similar bacterial and clinical outcomes in female versus male New Zealand White rabbits infected with Serratia marcescens

Females and males respond differently to a number of systemic viral infections. Differences between females and males with respect to the severity of keratitis caused by Gram-negative bacteria such as Serratia marcescens are less well established. In this study we injected female and male New Zealand White rabbit corneas with a keratitis isolate of S. marcescens and evaluated the eyes after 48 hours for a number of clinical and microbiological parameters. No statistical differences in bacterial burden and corneal scores were recorded between female and male rabbits although there was a non-significant trend toward a higher frequency of female rabbits demonstrating hypopyons. This data suggests that for experimental bacterial keratitis studies involving Gram-negative rods, a single sex or mixed group of rabbit is sufficient for evaluating pathology and bacterial burdens. This will reduce the number of animals used for subsequent studies.

microbiology↗

bioRxiv2020

The Rcs stress response system modulates Serratia marcescens induced inflammation and bacterial proliferation in a rabbit keratitis model

In this study, we tested the hypothesis that the conserved bacterial Rcs stress response system mediates corneal pathogenesis associated with Serratia marcescens ocular infections. This was accomplished by modifying Rcs activity using mutant strains. These include a mutant that has a hyper-active Rcs system due to deletion of the IgaA family gene, gumB, and a gumB rcsC double mutant that is defective for Rcs signaling. The role of the Rcs system and bacterial stress response systems for microbial keratitis is not known. Here we observed that the Rcs-activated gumB mutant had a >50-fold reduction in proliferation compared to the wild type within rabbit corneas at 48 h, and demonstrated a notable reduction in inflammation based on inflammatory signs and proinflammatory markers measured at the RNA and protein levels. The gumB mutant phenotypes could be complemented by wild-type gumB on a plasmid and partially complemented by restoration of shlA cytolysin expression and elimination of capsular polysaccharide production. We observed that inactivation of the Rcs stress response system completely restored corneal virulence to the gumB mutant. NanoString transcriptional analysis of bacterial genes expressed during microbial keratitis demonstrated expression of gumB, rcsB, shlA, and three metalloprotease genes. Data suggest that the bacterial capsular polysaccharide is not necessary for infection, but capsule overexpression reduces inflammation. Together, these data indicate that GumB regulates virulence factor production through the Rcs system and this overall stress response system is a key mediator of a bacteriums ability to induce vision-threatening keratitis.

microbiology↗

bioRxiv2020

Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis

Enterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics of E. faecalis isolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected with E. faecalis of diverse multi-locus sequence types (STs) previously associated with clinical, commensal, and environmental sources. We identified known E. faecalis virulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable, as were biofilm formation and cytolysin production. In addition, we found evidence of E. faecalis adaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight-months from the same patient. We identified a mutation in the DNA mismatch repair gene mutS that was associated with a hypermutator phenotype in the final isolate from the patient, which was also more resistant to ceftazidime. Overall this study documents the genomic and phenotypic variability among E. faecalis causing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection. IMPORTANCEBacterial endophthalmitis is a sight-threatening infection of the inside of the eye. Enterococcus faecalis cause endophthalmitis occasionally, but when they do the infections are often severe. Here we investigated the genomes, antibiotic susceptibilities, and virulence-associated traits among E. faecalis collected from 13 patients with post-operative endophthalmitis. We wondered whether there were common bacterial factors that might explain why enterococcal endophthalmitis is so destructive to ocular tissues. Instead we found that E. feacalis isolated from endophthalmitis were genetically and phenotypically diverse; isolates belonged to a variety of genetic lineages and showed varying levels of antibiotic resistance and biofilm formation. We also undertook further characterization of three closely related E. faecalis isolates from a patient with recurrent endophthalmitis, and found that a hypermutator strain emerged during persistent infection. Hypermutators have been found in a variety of other infection contexts; here we describe what we believe is the first case of a hypermutator arising during ocular infection.

microbiology↗

bioRxiv2020

Generation of Xylose-inducible promoter tools for Pseudomonas species and their use in implicating a role for the Type II secretion system protein XcpQ in inhibition of corneal epithelial wound closure

Tunable control of gene expression is an invaluable tool for biological experiments. In this study, we describe a new xylose-inducible promoter system and evaluate it in both Pseudomonas aeruginosa and P. fluorescens. The Pxut promoter derived from the P. flurorescens xut operon was incorporated into a broad host-range pBBR1-based plasmid and compared to the Escherichia coli-derived PBAD promoter using gfp as a reporter. GFP-fluorescence from the Pxut promoter was inducible in both Pseudomonas species, but not in E. coli, which may facilitate cloning of toxic genes using E. coli to generate plasmids. The Pxut promoter was expressed at a lower inducer concentration than PBAD in P. fluorescens and higher gfp levels were achieved using Pxut. Flow cytometry analysis indicated that Pxut was more leaky than PBAD in the tested Pseudomonas species, but was expressed in a higher proportion of cells when induced. D-xylose did not support growth of P. aeruginosa or P. fluorescens as a sole carbon source and is less expensive than many other commonly used inducers which could facilitate large scale applications. The efficacy of this system aided in demonstrating a role for the P. aeruginosa type II secretion system gene from xcpQ in bacterial inhibition of corneal epithelial cell wound closure. This study introduces a new inducible promoter system for gene expression for use in Pseudomonas species. ImportancePseudomonas species are enormously important in human infections, biotechnology, and as a model system for interrogating basic science questions. In this study we have developed a xylose-inducible promoter system and evaluated it in P. aeruginosa and P. fluorescens and found it to be suitable for the strong induction of gene expression. Furthermore, we have demonstrated its efficacy in controlled gene expression to show that a type 2 secretion system protein from P. aeruginosa, XcpQ, is important for host-pathogen interactions in a corneal wound closure model.

microbiology↗

bioRxiv2019

The Toxin Antitoxin MazEF Drives Staphylococcus aureus Chronic Infection

Staphylococcus aureus is the major organism responsible for surgical implant infections. Antimicrobial treatment of these infections often fails leading to expensive surgical intervention and increased risk of mortality to the patient. The challenge in treating these infections is associated with the high tolerance of S. aureus biofilm to antibiotics. MazEF, a toxin-antitoxin system, is thought to be an important regulator of this phenotype, but its physiological function in S. aureus is controversial. Here, we examined the role of MazEF in developing chronic infections by comparing growth and antibiotic tolerance phenotypes in three S. aureus strains to their corresponding strains with disruption of mazF expression. Strains lacking mazF production showed increased biofilm growth, and decreased biofilm antibiotic tolerance. Deletion of icaADBC in the mazF::tn background suppressed the growth phenotype observed with mazF-disrupted strains, suggesting the phenotype was ica-dependent. We confirmed these phenotypes in our murine animal model. Loss of mazF resulted in increased bacterial burden and decreased survival rate compared to its wild-type strain demonstrating that loss of the mazF gene caused an increase in S. aureus virulence. Although lack of mazF gene expression increased S. aureus virulence, it was more susceptible to antibiotics in vivo. Combined, the ability of mazF to inhibit biofilm formation and promote biofilm antibiotic tolerance plays a critical role in transitioning from an acute to chronic infection that is difficult to eradicate with antibiotics alone.\n\nImportanceSurgical infections are one of the most common types of infections obtained in a hospital. Staphylococcus aureus is the most common pathogen associated with this infection. These infections are resilient and difficult to eradicate as the bacteria form a biofilm, a community of bacteria held together by an extracellular matrix. Compared to bacteria floating in liquid, bacteria in a biofilm are more resistant to antibiotics. The mechanism behind how bacteria develop this resistance and establish a chronic infection is unknown. We demonstrate that mazEF, a toxin-antitoxin gene, inhibits biofilm formation and promotes biofilm antibiotic tolerance which allows S. aureus to transition from an acute to chronic infection that cannot be eradicated with antibiotics but is less virulent. This gene not only makes the bacteria more tolerant to antibiotics but makes the bacteria more tolerant to the host.

microbiology↗