Emily Woods

All Publications

• Likelihood of COVID-19 Outbreaks in US Immigration and Customs Enforcement (ICE) Detention Centers, 2020‒2021. American journal of public health Woods, E. C., Andrews, J. R., Goldhaber-Fiebert, J. D. 2024: e1-e4

  Abstract

  Objectives. To determine facility-level factors associated with COVID-19 outbreaks in US Immigration and Customs Enforcement (ICE) detention centers. Methods. We obtained COVID-19 case counts at 88 ICE detention facilities from May 6, 2020, through June 21, 2021, from the COVID Prison Project. We obtained information about facility population size, facility type (dedicated to immigrants or mixed with other incarcerated populations), and facility operator (public vs private contractor) from third-party sources. We defined the threshold for a COVID-19 outbreak as a cumulative 3-week incidence of 10% or more of the detained population. Results. Sixty-three facilities (72%) had at least 1 outbreak. Facilities with any outbreak were significantly more likely to be privately operated (P < .001), to have larger populations (113 vs 37; P = .002), and to have greater changes in their population size over the study period (‒56% vs -26%; P < .001). Conclusions. Several facility-level factors were associated with the occurrence of COVID-19 outbreaks in ICE facilities. Public Health Implications. Structural and organizational factors that promote respiratory infection spread in ICE facilities must be addressed to protect detainee health. (Am J Public Health. Published online ahead of print June 20, 2024:e1-e4. https://doi.org/10.2105/AJPH.2024.307704).

  View details for DOI 10.2105/AJPH.2024.307704

  View details for PubMedID 38900981

• Polymer-tethered quenched fluorescent probes for enhanced imaging of tumor associated proteases. bioRxiv : the preprint server for biology Hadzima, M., Faucher, F., Blažková, K., Yim, J. J., Guerra, M., Chen, S., Woods, E. C., Park, K. W., Šácha, P., Šubr, V., Kostka, L., Etrych, T., Majer, P., Konvalinka, J., Bogyo, M. 2024

  Abstract

  Fluorescence-based contrast agents enable real-time detection of solid tumors and their neovasculature, making them ideal for use in image-guided surgery. Several agents have entered late-stage clinical trials or secured FDA approval, suggesting they are likely to become standard of care in cancer surgeries. One of the key parameters to optimize in contrast agent is molecular size, which dictates much of the pharmacokinetic and pharmacodynamic properties of the agent. Here, we describe the development of a class of protease-activated quenched fluorescent probes in which a N-(2-hydroxypropyl)methacrylamide copolymer is used as the primary scaffold. This copolymer core provides a high degree of probe modularity to generate structures that cannot be achieved with small molecules and peptide probes. We used a previously validated cathepsin substrate and evaluated the effects of length and type of linker as well as positioning of the fluorophore/quencher pair on the polymer core. We found that the polymeric probes could be optimized to achieve increased over-all signal and tumor-to-background ratios compared to the reference small molecule probe. Our results also revealed multiple structure-activity relationship trends that can be used to design and optimize future optical imaging probes. Furthermore, they confirm that a hydrophilic polymer is an ideal scaffold for use in optical imaging contrast probes, allowing a highly modular design that enables efficient optimization to maximize probe accumulation and overall biodistribution properties.

  View details for DOI 10.1101/2024.05.06.592849

  View details for PubMedID 38766164

  View details for PubMedCentralID PMC11100723

• Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections. Journal of the American Chemical Society Jo, J., Upadhyay, T., Woods, E. C., Park, K. W., Pedowitz, N. J., Jaworek-Korjakowska, J., Wang, S., Valdez, T. A., Fellner, M., Bogyo, M. 2024

  Abstract

  Staphylococcus aureus (S. aureus) is a major human pathogen that is responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here, we describe the development of oxadiazolone-based activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologues in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling, and mouse models of infection, we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes and validate FphE as a target for the development of imaging contrast agents for the rapid detection of S. aureus infections.

  View details for DOI 10.1021/jacs.3c13974

  View details for PubMedID 38411555

• Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of S. aureus Infections. bioRxiv : the preprint server for biology Jo, J., Upadhyay, T., Woods, E. C., Park, K. W., Pedowitz, N. J., Jaworek-Korjakowska, J., Wang, S., Valdez, T. A., Fellner, M., Bogyo, M. 2023

  Abstract

  Staphylococcus aureus is a major human pathogen responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here we describe the development of oxadiazolonebased activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologs in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling and mouse models of infection we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes (ABPs) and validate FphE as a target for development of imaging contrast agents for the rapid detection of S. aureus infections.

  View details for DOI 10.1101/2023.12.11.571116

  View details for PubMedID 38168396

  View details for PubMedCentralID PMC10760020

• Clinical reasoning for performance of transesophageal echocardiography in veterans with Staphylococcus aureus bacteremia. Antimicrobial stewardship & healthcare epidemiology : ASHE Woods, E. C., Nakasone, T. S., Renault, C. A. 2023; 3 (1): e221

  Abstract

  This study examined physicians' reasoning about obtaining transesophageal echocardiography (TEE) in cases of Staphylococcus aureus bacteremia (SAB). In 221 cases of SAB over 5 years, the most common reasons for not performing TEE were clinical response to antibiotics, negative TTE results, and the expectation that TEE would not change management.

  View details for DOI 10.1017/ash.2023.493

  View details for PubMedID 38156239

  View details for PubMedCentralID PMC10753505

• Comparison of Antibody Class-Specific SARS-CoV-2 Serologies for the Diagnosis of Acute COVID-19. Journal of clinical microbiology Verkerke, H., Horwath, M., Saeedi, B., Boyer, D., Allen, J. W., Owens, J., Arthur, C. M., Nakahara, H., Rha, J., Patel, K., Wu, S. C., Paul, A., Yasin, N., Wang, J., Shin, S., Brown, D., Normile, K., Cole, L., Meyers, M., Lin, H., Woods, E., Isaac, J., Broder, K., Wade, J., Kauffman, R. C., Patel, R., Josephson, C. D., Reynolds, S., Sherman, M., Wrammert, J., Alter, D., Guarner, J., Roback, J. D., Neish, A., Stowell, S. R. 2021; 59 (4)

  Abstract

  Accurate diagnosis of acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is critical for appropriate management of patients with this disease. We examined the possible complementary role of laboratory-developed class-specific clinical serology in assessing SARS-CoV-2 infection in hospitalized patients. Serological tests for immunoglobulin G (IgG), IgA, and IgM antibodies against the receptor binding domain (RBD) of SARS-CoV-2 were evaluated using samples from real-time reverse transcription-quantitative PCR (qRT-PCR)-confirmed inpatient coronavirus disease 2019 (COVID-19) cases. We analyzed the influence of timing and clinical severity on the diagnostic value of class-specific COVID-19 serology testing. Cross-sectional analysis revealed higher sensitivity and specificity at lower optical density cutoffs for IgA in hospitalized patients than for IgG and IgM serology (IgG area under the curve [AUC] of 0.91 [95% confidence interval {CI}, 0.89 to 0.93] versus IgA AUC of 0.97 [95% CI, 0.96 to 0.98] versus IgM AUC of 0.95 [95% CI, 0.92 to 0.97]). The enhanced performance of IgA serology was apparent in the first 2 weeks after symptom onset and the first week after PCR testing. In patients requiring intubation, all three tests exhibit enhanced sensitivity. Among PCR-negative patients under investigation for SARS-CoV-2 infection, 2 out of 61 showed clear evidence of seroconversion IgG, IgA, and IgM. Suspected false-positive results in the latter population were most frequently observed in IgG and IgM serology tests. Our findings suggest the potential utility of IgA serology in the acute setting and explore the benefits and limitations of class-specific serology as a complementary diagnostic tool to PCR for COVID-19 in the acute setting.

  View details for DOI 10.1128/JCM.02026-20

  View details for PubMedID 33468605

  View details for PubMedCentralID PMC8092741

• Cationic Homopolymers Inhibit Spore and Vegetative Cell Growth of Clostridioides difficile. ACS infectious diseases Jones, J. B., Liu, L., Rank, L. A., Wetzel, D., Woods, E. C., Biok, N., Anderson, S. E., Lee, M., Liu, R., Huth, S., Sandhu, B. K., Gellman, S. H., McBride, S. M. 2021

  Abstract

  A wide range of synthetic polymers have been explored for antimicrobial activity. These materials usually contain both cationic and hydrophobic subunits because these two characteristics are prominent among host-defense peptides. Here, we describe a series of nylon-3 polymers containing only cationic subunits and their evaluation against the gastrointestinal, spore-forming pathogen Clostridioides difficile. Despite their highly hydrophilic nature, these homopolymers showed efficacy against both the vegetative and spore forms of the bacterium, including an impact on C.difficile spore germination. The polymer designated P34 demonstrated the greatest efficacy against C.difficile strains, along with low propensities to lyse human red blood cells or intestinal epithelial cells. To gain insight into the mechanism of P34 action, we evaluated several cell-surface mutant strains of C.difficile to determine the impacts on growth, viability, and cell morphology. The results suggest that P34 interacts with the cell wall, resulting in severe cell bending and death in a concentration-dependent manner. The unexpected finding that nylon-3 polymers composed entirely of cationic subunits display significant activities toward C.difficile should expand the range of other polymers considered for antibacterial applications.

  View details for DOI 10.1021/acsinfecdis.0c00843

  View details for PubMedID 33739823

• Regulation and Anaerobic Function of the Clostridioides difficile beta-Lactamase ANTIMICROBIAL AGENTS AND CHEMOTHERAPY Sandhu, B. K., Edwards, A. N., Anderson, S. E., Woods, E. C., McBride, S. M. 2020; 64 (1)

  Abstract

  Clostridioides difficile causes severe antibiotic-associated diarrhea and colitis. C. difficile is an anaerobic, Gram-positive sporeformer that is highly resistant to β-lactams, the most commonly prescribed antibiotics. The resistance of C. difficile to β-lactam antibiotics allows the pathogen to replicate and cause disease in antibiotic-treated patients. However, the mechanisms of β-lactam resistance in C. difficile are not fully understood. Our data reinforce prior evidence that C. difficile produces a β-lactamase, which is a common β-lactam resistance mechanism found in other bacterial species. Here, we characterize the C. difficilebla operon that encodes a lipoprotein of unknown function and a β-lactamase that was greatly induced in response to several classes of β-lactam antibiotics. An in-frame deletion of the operon abolished β-lactamase activity in C. difficile strain 630Δerm and resulted in decreased resistance to the β-lactam ampicillin. We found that the activity of this β-lactamase, BlaCDD, is dependent upon the redox state of the enzyme. In addition, we observed that transport of BlaCDD out of the cytosol and to the cell surface is facilitated by an N-terminal signal sequence. Our data demonstrate that a cotranscribed lipoprotein, BlaX, aids in BlaCDD activity. Further, we identified a conserved BlaRI regulatory system and demonstrated via insertional disruption that BlaRI controls transcription of the blaXCDD genes in response to β-lactams. These results provide support for the function of a β-lactamase in C. difficile antibiotic resistance and reveal the unique roles of a coregulated lipoprotein and reducing environment in C. difficile β-lactamase activity.

  View details for DOI 10.1128/AAC.01496-19

  View details for Web of Science ID 000503839600047

  View details for PubMedID 31611350

  View details for PubMedCentralID PMC7187622

• Examination of the Clostridioides (Clostridium) difficile VanZ ortholog, CD1240 Woods, E. C., Wetzel, D., Mukerjee, M., McBride, S. M. ELSEVIER SCI LTD. 2018: 108–15

  Abstract

  Clostridioides (Clostridium) difficile causes severe diarrheal disease that is directly associated with antibiotic use and resistance. Although C. difficile demonstrates intrinsic resistance to many antimicrobials, few genetic mechanisms of resistance have been characterized in this pathogen. In this study, we investigated the putative resistance factor, CD1240 (VanZ1), an ortholog of the teicoplanin resistance factor, VanZ, of Enterococcus faecium. In C. difficile, the vanZ1 gene is located within the skin element of the sporulation factor σK, which is excised from the mother cell compartment during sporulation. This unique localization enabled us to create a vanZ1 deletion mutant by inducing excision of the skin element. The Δskin mutant exhibited moderately decreased resistance to teicoplanin and had small effects on growth in some other cell-surface antimicrobials tested. Examination of vanZ1 expression revealed induction of vanZ1 transcription by the antimicrobial peptide LL-37; however, LL-37 resistance was not impacted by VanZ1, and none of the other tested antimicrobials induced vanZ1 expression. Further, expression of vanZ1 via an inducible promoter in the Δskin mutant restored growth in teicoplanin. These results demonstrate that like the E. faecium VanZ, C. difficile VanZ1 contributes to low-level teicoplanin resistance through an undefined mechanism.

  View details for DOI 10.1016/j.anaerobe.2018.06.013

  View details for Web of Science ID 000449900000016

  View details for PubMedID 29940245

  View details for PubMedCentralID PMC6309587

• The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37 PLOS PATHOGENS Woods, E. C., Edwards, A. N., Childress, K. O., Jones, J. B., McBride, S. M. 2018; 14 (8): e1007153

  Abstract

  To cause disease, Clostridioides (Clostridium) difficile must resist killing by innate immune effectors in the intestine, including the host antimicrobial peptide, cathelicidin (LL-37). The mechanisms that enable C. difficile to adapt to the intestine in the presence of antimicrobial peptides are unknown. Expression analyses revealed an operon, CD630_16170-CD630_16190 (clnRAB), which is highly induced by LL-37 and is not expressed in response to other cell-surface active antimicrobials. This operon encodes a predicted transcriptional regulator (ClnR) and an ABC transporter system (ClnAB), all of which are required for function. Analyses of a clnR mutant indicate that ClnR is a pleiotropic regulator that directly binds to LL-37 and controls expression of numerous genes, including many involved in metabolism, cellular transport, signaling, gene regulation, and pathogenesis. The data suggest that ClnRAB is a novel regulatory mechanism that senses LL-37 as a host signal and regulates gene expression to adapt to the host intestinal environment during infection.

  View details for DOI 10.1371/journal.ppat.1007153

  View details for Web of Science ID 000443296800008

  View details for PubMedID 30125334

  View details for PubMedCentralID PMC6117091

• Ethanolamine is a valuable nutrient source that impacts Clostridium difficile pathogenesis ENVIRONMENTAL MICROBIOLOGY Nawrocki, K. L., Wetzel, D., Jones, J. B., Woods, E. C., McBride, S. M. 2018; 20 (4): 1419–35

  Abstract

  Clostridium (Clostridioides) difficile is a gastrointestinal pathogen that colonizes the intestinal tract of mammals and can cause severe diarrheal disease. Although C. difficile growth is confined to the intestinal tract, our understanding of the specific metabolites and host factors that are important for the growth of the bacterium is limited. In other enteric pathogens, the membrane-derived metabolite, ethanolamine (EA), is utilized as a nutrient source and can function as a signal to initiate the production of virulence factors. In this study, we investigated the effects of ethanolamine and the role of the predicted ethanolamine gene cluster (CD1907-CD1925) on C. difficile growth. Using targeted mutagenesis, we disrupted genes within the eut cluster and assessed their roles in ethanolamine utilization, and the impact of eut disruption on the outcome of infection in a hamster model of disease. Our results indicate that the eut gene cluster is required for the growth of C. difficile on ethanolamine as a primary nutrient source. Further, the inability to utilize ethanolamine resulted in greater virulence and a shorter time to morbidity in the animal model. Overall, these data suggest that ethanolamine is an important nutrient source within the host and that, in contrast to other intestinal pathogens, the metabolism of ethanolamine by C. difficile can delay the onset of disease.

  View details for DOI 10.1111/1462-2920.14048

  View details for Web of Science ID 000430171900009

  View details for PubMedID 29349925

  View details for PubMedCentralID PMC5903940

• Regulation of antimicrobial resistance by extracytoplasmic function (ECF) sigma factors. Microbes and infection Woods, E. C., McBride, S. M. 2017; 19 (4-5): 238-248

  Abstract

  Extracytoplasmic function (ECF) sigma factors are a subfamily of σ70 sigma factors that activate genes involved in stress-response functions. In many bacteria, ECF sigma factors regulate resistance to antimicrobial compounds. This review will summarize the ECF sigma factors that regulate antimicrobial resistance in model organisms and clinically relevant pathogens.

  View details for DOI 10.1016/j.micinf.2017.01.007

  View details for PubMedID 28153747

  View details for PubMedCentralID PMC5403605

• The Phosphotransfer Protein CD1492 Represses Sporulation Initiation in Clostridium difficile INFECTION AND IMMUNITY Childress, K. O., Edwards, A. N., Nawrocki, K. L., Anderson, S. E., Woods, E. C., McBride, S. M. 2016; 84 (12): 3434–44

  Abstract

  The formation of spores is critical for the survival of Clostridium difficile outside the host gastrointestinal tract. Persistence of C. difficile spores greatly contributes to the spread of C. difficile infection (CDI), and the resistance of spores to antimicrobials facilitates the relapse of infection. Despite the importance of sporulation to C. difficile pathogenesis, the molecular mechanisms controlling spore formation are not well understood. The initiation of sporulation is known to be regulated through activation of the conserved transcription factor Spo0A. Multiple regulators influence Spo0A activation in other species; however, many of these factors are not conserved in C. difficile and few novel factors have been identified. Here, we investigated the function of a protein, CD1492, that is annotated as a kinase and was originally proposed to promote sporulation by directly phosphorylating Spo0A. We found that deletion of CD1492 resulted in increased sporulation, indicating that CD1492 is a negative regulator of sporulation. Accordingly, we observed increased transcription of Spo0A-dependent genes in the CD1492 mutant. Deletion of CD1492 also resulted in decreased toxin production in vitro and in decreased virulence in the hamster model of CDI. Further, the CD1492 mutant demonstrated effects on gene expression that are not associated with Spo0A activation, including lower sigD and rstA transcription, suggesting that this protein interacts with factors other than Spo0A. Altogether, the data indicate that CD1492 negatively affects sporulation and positively influences motility and virulence. These results provide further evidence that C. difficile sporulation is regulated differently from that of other endospore-forming species.

  View details for DOI 10.1128/IAI.00735-16

  View details for Web of Science ID 000390128700017

  View details for PubMedID 27647869

  View details for PubMedCentralID PMC5116721

• The Clostridium difficile Dlt Pathway Is Controlled by the Extracytoplasmic Function Sigma Factor σV in Response to Lysozyme. Infection and immunity Woods, E. C., Nawrocki, K. L., Suárez, J. M., McBride, S. M. 2016; 84 (6): 1902-1916

  Abstract

  Clostridium difficile (also known as Peptoclostridium difficile) is a major nosocomial pathogen and a leading cause of antibiotic-associated diarrhea throughout the world. Colonization of the intestinal tract is necessary for C. difficile to cause disease. Host-produced antimicrobial proteins (AMPs), such as lysozyme, are present in the intestinal tract and can deter colonization by many bacterial pathogens, and yet C. difficile is able to survive in the colon in the presence of these AMPs. Our prior studies established that the Dlt pathway, which increases the surface charge of the bacterium by addition of d-alanine to teichoic acids, is important for C. difficile resistance to a variety of AMPs. We sought to determine what genetic mechanisms regulate expression of the Dlt pathway. In this study, we show that a dlt null mutant is severely attenuated for growth in lysozyme and that expression of the dltDABC operon is induced in response to lysozyme. Moreover, we found that a mutant lacking the extracytoplasmic function (ECF) sigma factor σ(V) does not induce dlt expression in response to lysozyme, indicating that σ(V) is required for regulation of lysozyme-dependent d-alanylation of the cell wall. Using reporter gene fusions and 5' RACE (rapid amplification of cDNA ends) analysis, we identified promoter elements necessary for lysozyme-dependent and lysozyme-independent dlt expression. In addition, we observed that both a sigV mutant and a dlt mutant are more virulent in a hamster model of infection. These findings demonstrate that cell wall d-alanylation in C. difficile is induced by lysozyme in a σ(V)-dependent manner and that this pathway impacts virulence in vivo.

  View details for DOI 10.1128/IAI.00207-16

  View details for PubMedID 27068095

  View details for PubMedCentralID PMC4907151

• An alkaline phosphatase reporter for use in Clostridium difficile ANAEROBE Edwards, A. N., Pascual, R. A., Childress, K. O., Nawrocki, K. L., Woods, E. C., McBride, S. M. 2015; 32: 98–104

  Abstract

  Clostridium difficile is an anaerobic, Gram-positive pathogen that causes severe gastrointestinal disease in humans and other mammals. C. difficile is notoriously difficult to work with and, until recently, few tools were available for genetic manipulation and molecular analyses. Despite the recent advances in the field, there is no simple or cost-effective technique for measuring gene transcription in C. difficile other than direct transcriptional analyses (e.g., quantitative real-time PCR and RNA-seq), which are time-consuming, expensive and difficult to scale-up. We describe the development of an in vivo reporter assay that can provide qualitative and quantitative measurements of C. difficile gene expression. Using the Enterococcus faecalis alkaline phosphatase gene, phoZ, we measured expression of C. difficile genes using a colorimetric alkaline phosphatase assay. We show that inducible alkaline phosphatase activity correlates directly with native gene expression. The ability to analyze gene expression using a standard reporter is an important and critically needed tool to study gene regulation and design genetic screens for C. difficile and other anaerobic clostridia.

  View details for DOI 10.1016/j.anaerobe.2015.01.002

  View details for Web of Science ID 000353427200018

  View details for PubMedID 25576237

  View details for PubMedCentralID PMC4385412