Anthony R. Flores

Group A Streptococcus (GAS) is a human-restricted pathogen whose global incidence has surged in the post-COVID era. The ability of GAS to shift from a colonizing to invasive phenotype depends on coordinated virulence gene regulation in response to host-derived signals. However, the mechanisms by which individual stress-sensing systems interact to reshape the virulence gene regulatory landscape remain incompletely understood. Here, we define the regulatory programs of two conserved transcriptional regulator paralogs, SpxA1 and SpxA2, using an integrated multi-omic approach combining RNA-seq, data-independent acquisition proteomics, NanoString-based transcriptional profiling across multiple host-relevant stress conditions, and chromatin immunoprecipitation with exonuclease treatment (ChIP-exo). RNA-seq revealed functionally distinct regulons with SpxA1 governing oxidative stress defense and SpxA2 coordinating virulence-associated gene expression linked to the CovRS two-component regulatory system. Proteomic analysis established SpxA2 as a ClpXP protease substrate in GAS and identified reciprocal paralog accumulation upon loss of either SpxA1 or SpxA2, consistent with compensatory transcriptional upregulation. NanoString profiling under bacitracin and human neutrophil peptide-1 challenge identified four gene modules with distinct stoichiometry-dependent and condition-dependent regulatory logic, revealing that the SpxA1/SpxA2 ratio rather than the activity of either paralog alone determines which transcriptional programs are engaged. ChIP-exo demonstrated that SpxA2 directly modulates CovR-DNA binding occupancy in a CovR-binding motif-dependent manner, simultaneously antagonizing CovR dimer binding at an extended (25 bp) CovR motif and facilitating CovR monomer binding at the canonical ATTARA motif. These findings establish the LiaFSR-SpxA2-CovRS axis as a cross-regulatory circuit through which GAS cell envelope stress sensing is directly transduced into coordinated virulence gene regulatory changes. IMPORTANCE: Group A Streptococcus (GAS) causes millions of infections annually, including a recent global surge in invasive disease. To survive in the human host, GAS must rapidly reprogram virulence gene expression in response to host-derived stresses. This study characterizes two conserved transcriptional regulators, SpxA1 and SpxA2, that govern this response through interaction with RNA polymerase to indirectly influence the DNA-binding activity of downstream transcription factors. We show that SpxA2, activated by a cell envelope stress-sensing system responding to human antimicrobial peptides, reshapes the binding of the master virulence regulator CovR in a promoter-specific manner, coupling cell envelope stress sensing to virulence gene regulation. The stoichiometric balance between SpxA1 and SpxA2 functions as a regulatory rheostat calibrating overall virulence gene regulatory tone, providing a framework for understanding how RNA polymerase-interacting regulators coordinate stress responses and virulence gene control across Gram-positive bacterial pathogens.

Group A Streptococcus (GAS) is a human-restricted pathogen whose global incidence has surged in the post-COVID era. The ability of GAS to shift from a colonizing to invasive phenotype depends on coordinated virulence gene regulation in response to host-derived signals. However, the mechanisms by which individual stress-sensing systems interact to reshape the virulence gene regulatory landscape remain incompletely understood. Here we define the regulatory programs of two conserved transcriptional regulator paralogs, SpxA1 and SpxA2, using an integrated multi-omic approach combining RNA-seq, data-independent acquisition proteomics, NanoString-based transcriptional profiling across multiple host-relevant stress conditions, and chromatin immunoprecipitation with exonuclease treatment (ChIP-exo). RNA-seq revealed functionally distinct regulons with SpxA1 governing oxidative stress defense and SpxA2 coordinating virulence-associated gene expression linked to the CovRS two-component regulatory system. Proteomic analysis established SpxA2 as a ClpXP protease substrate in GAS and identified reciprocal paralog accumulation upon loss of either SpxA1 or SpxA2, consistent with compensatory transcriptional upregulation. NanoString profiling under bacitracin and human neutrophil peptide-1 challenge identified four gene modules with distinct stoichiometry-dependent and condition-dependent regulatory logic, revealing that the SpxA1/SpxA2 ratio rather than the activity of either paralog alone determines which transcriptional programs are engaged. ChIP-exo demonstrated that SpxA2 directly modulates CovR-DNA binding occupancy in a CovR binding motif-dependent manner, simultaneously antagonizing CovR dimer binding at an extended (25-bp) CovR motif and facilitating CovR monomer binding at the canonical ATTARA motif. These findings establish the LiaFSR-SpxA2-CovRS axis as a cross-regulatory circuit through which GAS cell envelope stress sensing is directly transduced into coordinated virulence gene regulatory changes. Importance: Group A Streptococcus (GAS) causes millions of infections annually, including a recent global surge in invasive disease. To survive in the human host, GAS must rapidly reprogram virulence gene expression in response to host-derived stresses. This study characterizes two conserved transcriptional regulators, SpxA1 and SpxA2, that govern this response through interaction with RNA polymerase to indirectly influence the DNA-binding activity of downstream transcription factors. We show that SpxA2, activated by a cell envelope stress-sensing system responding to human antimicrobial peptides, reshapes the binding of the master virulence regulator CovR in a promoter-specific manner, coupling cell envelope stress sensing to virulence gene regulation. The stoichiometric balance between SpxA1 and SpxA2 functions as a regulatory rheostat calibrating overall virulence gene regulatory tone, providing a framework for understanding how RNA polymerase-interacting regulators coordinate stress responses and virulence gene control across Gram-positive bacterial pathogens.

Toward the end of the COVID-19 pandemic, many reports described increasing group A streptococcal (GAS) infections. We sought to describe pandemic-associated changes in GAS clinical and molecular epidemiology. GAS isolates were collected from Texas Children’s Hospital laboratory from 01 January 2013 to 31 December 2023 and grouped into pre-pandemic (2013–2019) and pandemic (2020–2023) periods. Invasive (INV), skin and soft tissue infection (SSTI), and pharyngeal (PHG) disease types were determined by medical record review. All isolates were emm typed, and nonsusceptibility (NS) to tetracycline, erythromycin, and clindamycin was determined using standard methods. We analyzed 2,717 isolates (pre-pandemic, n = 1,640; pandemic, n = 1,077). Year-to-year variation was observed, but the highest GAS disease burden occurred in 2022 and 2023. Comparing disease types, we observed a subtle but significant increase in the frequency of GAS strains derived from INV infections. Relative to pre-pandemic, emm 12 and emm3 GAS showed significant increases in frequency, while emm89 , emm4 , and emm6 showed concomitant decreases. Second-line antimicrobial NS increased during the pandemic period but was transient with a rapid return to pre-pandemic rates in 2023. The pandemic-related surge in GAS disease in the Houston, TX, pediatric population was associated with changes in the frequency of GAS emm types and a small shift toward invasive disease. NS to second-line antimicrobials fluctuated during the pandemic and differed substantially from GAS derived from adult infections. Continued surveillance will be paramount to monitor ongoing changes in GAS epidemiology in pediatric populations. IMPORTANCE: Group A Streptococcus (GAS) causes common childhood infections such as strep throat but can also lead to severe, life-threatening disease. During and after the COVID-19 pandemic, many regions reported sharp increases in GAS infections, yet the reasons for these changes were unclear. Using long-term surveillance of children in a large US city, this study shows that the post-pandemic rise in GAS was accompanied by meaningful changes in both the types of infections and the strains causing them. We found a small but significant increase in invasive disease, shifts in the most common GAS strain types, and temporary increases in resistance to certain antibiotics. These changes likely reflect how pandemic-related disruptions altered bacterial spread. By examining both mild and severe infections over more than a decade, this work demonstrates how large-scale changes in human behavior can reshape bacterial disease patterns and highlights the importance of continued monitoring to protect child health.

Dermal fibrosis is a cardinal feature of systemic sclerosis (SSc) for which there are limited effective disease-modifying therapies. SSc is characterized by dermal fibrosis accompanied by loss of dermal white adipose tissue (DWAT), yet the mechanisms linking adipocyte depletion to fibroblast activation remain unclear. Here we identify the transcription factor SIX1 as a central regulator coupling adipogenic repression with profibrotic signaling. SIX1 expression was increased in skin biopsies from 2 independent SSc cohorts and localized to fibroblast and perivascular stromal cells. In mice, ubiquitous or adipocyte-specific deletion of Six1 preserved DWAT, reduced collagen accumulation, and selectively decreased profibrotic mediators. In cultured fibroblasts, CRISPR/Cas9-mediated Six1 loss enhanced adipogenic markers while reducing profibrotic mediators and directly suppressed PAI-1 ( SERPINE1 ) promoter activity. Together, these data position SIX1 as a transcriptional switch that promotes adipocyte reprogramming and fibrotic progression, and they highlight SIX1 inhibition as a potential therapeutic strategy to preserve adipocyte identity and limit dermal fibrosis.

Adverse pregnancy outcomes represent a global health burden. Bacterial infection and subsequent inflammation in gestational membranes lead to immunological and physiological changes that contribute to adverse pregnancy outcomes. Although animal models of infection during pregnancy are useful to interrogate tissue and cellular level changes in host responses, these models also have numerous drawbacks, including cost, complexity, and ethical considerations. The advent of organ-on-a-chip models provides cutting-edge new approaches to model host-pathogen interactions in multicellular organ and tissue environments. In this work, we employ an organ-on-a-chip model of the maternal-fetal interface as a tool to study immunological responses to infection with the perinatal pathogen, Group B Streptococcus (GBS). Furthermore, we validate the organ-on-a-chip assays using an ex vivo culture model of primary human gestational membranes. GBS infection leads to enhanced production of EGF, FGF-2, G-CSF, GRO-α, IL-6, IL-8, MCP-1, MIP-1α, TNF-β, IL-10, IL-17F in gestational membranes and both the maternal and fetal chambers of the organ-on-a-chip model. Additionally, GBS infection is associated with enhanced TNF-α, RANTES, IL-12p70, IP-10, MIG, FLT3L, GM-CSF, IL-1β, IL-2, PDGF-AB/BB, and IL-17E/IL-25 cytokine production in gestational membranes and the maternal compartment of the organ-on-a-chip model. Gestational membranes challenged with GBS produce IL-15, IL-27, M-CSF, MCP-3, MDC, and MIP-1β, a result that was not seen in the organ-on-a-chip model. GBS infection leads to enhanced production of eotaxin, IFN-γ, IL-1α, IL-4, IL-12p40, IL-13, and SCD40L in the maternal and fetal chambers of the organ-on-a-chip model, but not the gestational membranes ex vivo . Together, these results indicate that GBS infection induces comparable production of a repertoire of cytokines and chemokines in both models, with some salient differences, underscoring the utility of these complementary approaches to study immunological responses to infection at the maternal-fetal interface.

Objective: In Staphylococcus aureus the qacA/B and smr genes have been associated with elevated MICs to antiseptics with such organisms often termed antiseptic tolerant S. aureus (ATSA). The impact of repeated healthcare or antiseptic exposure on colonization with ATSA is uncertain. Design: Prospective longitudinal cohort study. Setting/Participants: The high-risk cohort included children with a new diagnosis of malignancy recruited from a pediatric oncology clinic. The low-risk cohort were otherwise healthy children enrolled from general pediatrics clinics. Methods: Subjects had anterior nares and axillary cultures collected at 3-month intervals for one year. Identified S. aureus isolates underwent PCR for qacA/B and smr . The primary outcome was colonization with ATSA at least once during study follow-up. Logistic regression models were utilized to adjust for confounding across cohorts. Results: 226 subjects were evaluable for the primary outcome. It was noted that 93.5% of high-risk subjects reported regularly using chlorhexidine gluconate (CHG) antiseptic products. Colonization with ATSA was found in 15.5% of subjects. In univariable analyses, subjects in the low-risk cohort more frequently had ATSA colonization; following adjustment for confounders, the rates of overall ATSA colonization were similar in the high- and low-risk cohorts. Only 2 subjects had colonization with an ATSA strain at more than one encounter. Conclusions: Pediatric oncology patients do not experience higher rates of ATSA colonization than healthy children. In addition, ATSA colonization is transient relative to strains negative for smr / qacA/B . These findings suggest that repeated use of infection prevention strategies including CHG do not predispose to colonization with ATSA in the ambulatory setting.

The ability to sense and respond to host defenses is essential for pathogen survival. Some mechanisms involve two-component systems (TCSs) that respond to host molecules, such as antimicrobial peptides (AMPs), and activate specific gene regulatory pathways to aid in survival. Alongside TCSs, bacteria coordinate cell division proteins, chaperones, cell wall sortases, and secretory translocons at discrete locations within the cytoplasmic membrane, referred to as functional membrane microdomains (FMMs). In group A Streptococcus (GAS), the FMM or “ExPortal” coordinates protein secretion, cell wall synthesis, and sensing of AMP-mediated cell envelope stress via the LiaFSR three-component system. Previously, we showed that GAS exposure to a subset of AMPs (α-defensins) activates the LiaFSR system by disrupting LiaF and LiaS co-localization in the ExPortal, leading to increased LiaR phosphorylation, expression of the transcriptional regulator SpxA2, and altered GAS virulence gene expression. The mechanisms by which LiaFSR integrates cell envelope stress with responses to AMP activity and virulence are not fully elucidated. Here, we show the LiaFSR regulon is comprised of genes encoding SpxA2 and three membrane-associated proteins: a PspC domain-containing protein (PCP), the lipoteichoic acid-modifying protein LafB, and the membrane protein insertase YidC2. Our data support that phosphorylated LiaR induces transcription of these genes via a conserved operator, whose disruption attenuates GAS virulence and increases susceptibility to AMPs in a manner primarily dependent on differential expression of SpxA2. Our work expands our understanding of the LiaFSR regulatory network in GAS and identifies targets for further investigation of mechanisms of cell envelope stress tolerance contributing to GAS pathogenesis.

The major gram-positive pathogen group A Streptococcus (GAS) is a model organism for studying microbial epidemics as it causes waves of infections. Since 1980, several GAS epidemics have been ascribed to the emergence of clones producing increased amounts of key virulence factors such as streptolysin O (SLO). Herein, we sought to identify mechanisms underlying our recently identified temporal clonal emergence among emm4 GAS, given that emergent strains did not produce augmented levels of virulence factors relative to historic isolates. By creating and analyzing isoallelic strains, we determined that a conserved mutation in a previously undescribed gene encoding a putative carbonic anhydrase was responsible for the defective in vitro growth observed in the emergent strains. We also identified that the emergent strains survived better inside macrophages and killed macrophages at lower rates than the historic strains. Via the creation of isogenic mutant strains, we linked the emergent strain “survival” phenotype to the downregulation of the SLO encoding gene and upregulation of the msrAB operon which encodes proteins involved in defense against extracellular oxidative stress. Our findings are in accord with recent surveillance studies which found a high ratio of mucosal (i.e., pharyngeal) relative to invasive infections among emm4 GAS. Since ever-increasing virulence is unlikely to be evolutionarily advantageous for a microbial pathogen, our data further understanding of the well-described oscillating patterns of virulent GAS infections by demonstrating mechanisms by which emergent strains adapt a “survival” strategy to outcompete previously circulating isolates.