Scholars@Duke
Jeffrey Daniel Jenks

Jeffrey Daniel Jenks

Adjunct Associate Professor in the Department of Medicine
Medicine, Infectious Diseases

Selected Publications

Global guideline for the diagnosis and management of candidiasis: an initiative of the ECMM in cooperation with ISHAM and ASM.

Journal Article Lancet Infect Dis · May 2025 Candida species are the predominant cause of fungal infections in patients treated in hospital, contributing substantially to morbidity and mortality. Candidaemia and other forms of invasive candidiasis primarily affect patients who are immunocompromised o ... Full text Open Access Link to item Cite

Mpox Vaccination and the Role of Social Vulnerability in Durham County, North Carolina, USA.

Journal Article J Racial Ethn Health Disparities · December 2024 BACKGROUND: Disparities in vaccine coverage among groups in the USA is common, possibly due to higher vaccine hesitancy in certain populations, difficulty accessing vaccines, and underlying social vulnerability. METHODS: The aim of this study was to invest ... Full text Open Access Link to item Cite

Novel antifungals and treatment approaches to tackle resistance and improve outcomes of invasive fungal disease.

Journal Article Clin Microbiol Rev · June 13, 2024 SUMMARYFungal infections are on the rise, driven by a growing population at risk and climate change. Currently available antifungals include only five classes, and their utility and efficacy in antifungal treatment are limited by one or more of innate or a ... Full text Open Access Link to item Cite

Universal digital high-resolution melting for the detection of pulmonary mold infections.

Journal Article J Clin Microbiol · June 12, 2024 UNLABELLED: Invasive mold infections (IMIs) are associated with high morbidity, particularly in immunocompromised patients, with mortality rates between 40% and 80%. Early initiation of appropriate antifungal therapy can substantially improve outcomes, yet ... Full text Open Access Link to item Cite

Impact of climate change and natural disasters on fungal infections.

Journal Article Lancet Microbe · June 2024 The effects of climate change and natural disasters on fungal pathogens and the risks for fungal diseases remain incompletely understood. In this literature review, we examined how fungi are adapting to an increase in the Earth's temperature and are becomi ... Full text Open Access Link to item Cite

Study protocol: A randomized, double-blind, placebo-controlled trial of isavuconazole prophylaxis for the prevention of covid-19-associated pulmonary aspergillosis.

Journal Article Contemp Clin Trials Commun · June 2024 BACKGROUND: During the early stages of the coronavirus disease 2019 (COVID-19) pandemic, those with severe COVID-19 infection were at risk for a number of opportunistic infections including COVID-19-associated pulmonary aspergillosis (CAPA). We initiated a ... Full text Open Access Link to item Cite

Trichomoniasis and retesting in Durham County, North Carolina, United States, 2021 - 2022.

Journal Article Int J STD AIDS · May 2024 BACKGROUND: The Centers for Disease Control and Prevention recommends universal retesting within 3 months after treatment of Trichomonas vaginalis infection given high rates of persistent infection or reinfection, or if this is not possible, within 12 mont ... Full text Open Access Link to item Cite

Combating COVID-19 Vaccine Inequity During the Early Stages of the COVID-19 Pandemic.

Journal Article J Racial Ethn Health Disparities · April 2024 Throughout the COVID-19 pandemic, populations of color have been disproportionately impacted, with higher rates of infection, hospitalization, and mortality, compared to non-Hispanic whites. These disparities in health outcomes are likely related to a comb ... Full text Open Access Link to item Cite

Treatment of Fusarium Infection of the Central Nervous System: A Review of Past Cases to Guide Therapy for the Ongoing 2023 Outbreak in the United States and Mexico.

Journal Article Mycopathologia · December 2023 INTRODUCTION: Fusariosis of the central nervous system (CNS) is extremely uncommon. Treatment and outcome data from previously published cases may provide some guidance in light of the ongoing fungal meningitis outbreak in 2023 involving Fusarium spp. in t ... Full text Open Access Link to item Cite

Social determinants of health as drivers of fungal disease.

Journal Article EClinicalMedicine · December 2023 Disparities in social determinants of health (SDOH) play a significant role in causing health inequities globally. The physical environment, including housing and workplace environment, can increase the prevalence and spread of fungal infections. A number ... Full text Open Access Link to item Cite

Universal Digital High Resolution Melt for the detection of pulmonary mold infections.

Journal Article bioRxiv · November 9, 2023 BACKGROUND: Invasive mold infections (IMIs) such as aspergillosis, mucormycosis, fusariosis, and lomentosporiosis are associated with high morbidity and mortality, particularly in immunocompromised patients, with mortality rates as high as 40% to 80%. Outc ... Full text Open Access Link to item Cite

Fungal Endocarditis: Pathophysiology, Epidemiology, Clinical Presentation, Diagnosis, and Management.

Journal Article Clin Microbiol Rev · September 21, 2023 Fungal endocarditis accounts for 1% to 3% of all infective endocarditis cases, is associated with high morbidity and mortality (>70%), and presents numerous challenges during clinical care. Candida spp. are the most common causes of fungal endocarditis, im ... Full text Open Access Link to item Cite

Relationship Between Sexually Transmitted Infections and Social Determinants of Health in Durham County, North Carolina, United States.

Journal Article Open Forum Infect Dis · July 2023 BACKGROUND: Sexually transmitted infections (STIs) are increasing in the United States, and certain populations are more at risk than others. One explanation for this is inequities in underlying social determinants of health (SDOH). METHODS: We analyzed ch ... Full text Open Access Link to item Cite

Race and ethnicity: Risk factors for fungal infections?

Journal Article PLoS Pathog · January 2023 Racial and ethnic identities, largely understood as social rather than biologic constructs, may impact risk for acquiring infectious diseases, including fungal infections. Risk factors may include genetic and immunologic differences such as aberrations in ... Full text Open Access Link to item Cite

An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections.

Journal Article Expert Rev Mol Diagn · 2023 BACKGROUND: Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized a ... Full text Open Access Link to item Cite

Test-of-Cure After Treatment of Pharyngeal Gonorrhea in Durham, North Carolina, 2021-2022.

Journal Article Sex Transm Dis · October 1, 2022 BACKGROUND: In December 2020, the Centers for Disease Control and Prevention updated its treatment guidelines for gonococcal infection and, for the first time, recommended universal test-of-cure for all individuals treated for pharyngeal gonorrhea. After t ... Full text Open Access Link to item Cite

Antimicrobial-Resistant Shigella spp. in San Diego, California, USA, 2017-2020.

Journal Article Emerg Infect Dis · June 2022 Annually, Shigella spp. cause ≈188 million cases of diarrheal disease globally, including 500,000 cases in the United States; rates of antimicrobial resistance are increasing. To determine antimicrobial resistance and risk factors in San Diego, California, ... Full text Open Access Link to item Cite

Let's talk about sex characteristics-As a risk factor for invasive fungal diseases.

Journal Article Mycoses · June 2022 Biological sex, which comprises differences in host sex hormone homeostasis and immune responses, can have a substantial impact on the epidemiology of infectious diseases. Comprehensive data on sex distributions in invasive fungal diseases (IFDs) are lacki ... Full text Open Access Link to item Cite

Performance of the Euroimmun Aspergillus Antigen ELISA for the Diagnosis of Invasive Pulmonary Aspergillosis in Bronchoalveolar Lavage Fluid.

Journal Article J Clin Microbiol · April 20, 2022 Invasive pulmonary aspergillosis (IPA) is a life-threatening disease that affects mainly immunocompromised hosts. Galactomannan testing from serum and bronchoalveolar lavage fluid (BALF) represents a cornerstone in diagnosing the disease. Here, we evaluate ... Full text Open Access Link to item Cite

Risk factors and outcome of pulmonary aspergillosis in critically ill coronavirus disease 2019 patients-a multinational observational study by the European Confederation of Medical Mycology.

Journal Article Clin Microbiol Infect · April 2022 OBJECTIVES: Coronavirus disease 2019 (COVID-19) -associated pulmonary aspergillosis (CAPA) has emerged as a complication in critically ill COVID-19 patients. The objectives of this multinational study were to determine the prevalence of CAPA in patients wi ... Full text Open Access Link to item Cite

Reply to Mikulska et al.

Journal Article Clin Infect Dis · October 5, 2021 Full text Open Access Link to item Cite

Performance of the Bronchoalveolar Lavage Fluid Aspergillus Galactomannan Lateral Flow Assay With Cube Reader for Diagnosis of Invasive Pulmonary Aspergillosis: A Multicenter Cohort Study.

Journal Article Clin Infect Dis · October 5, 2021 BACKGROUND: The Aspergillus Galactomannan Lateral Flow Assay (LFA) is a rapid test for the diagnosis of invasive aspergillosis (IA) that has been almost exclusively evaluated in patients with hematologic malignancies. An automated digital cube reader that ... Full text Open Access Link to item Cite

Serum Lateral Flow assay with digital reader for the diagnosis of invasive pulmonary aspergillosis: A two-centre mixed cohort study.

Journal Article Mycoses · October 2021 BACKGROUND: Detection of galactomannan (GM) from bronchoalveolar lavage fluid (BALF) or serum is broadly used for diagnosis of invasive aspergillosis (IA), although the sensitivity of GM from serum is lower in non-neutropenic patients. We evaluated the Asp ... Full text Open Access Link to item Cite

The Antifungal Pipeline: Fosmanogepix, Ibrexafungerp, Olorofim, Opelconazole, and Rezafungin.

Journal Article Drugs · October 2021 The epidemiology of invasive fungal infections is changing, with new populations at risk and the emergence of resistance caused by the selective pressure from increased usage of antifungal agents in prophylaxis, empiric therapy, and agriculture. Limited an ... Full text Open Access Link to item Cite

Invasive aspergillosis in critically ill patients: Review of definitions and diagnostic approaches.

Journal Article Mycoses · September 2021 Invasive aspergillosis (IA) is an increasingly recognised phenomenon in critically ill patients in the intensive care unit, including in patients with severe influenza and severe coronavirus disease 2019 (COVID-19) infection. To date, there are no consensu ... Full text Open Access Link to item Cite

Aspergillus fumigatus and aspergillosis: From basics to clinics.

Journal Article Stud Mycol · September 2021 The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employ ... Full text Open Access Link to item Cite

Global guideline for the diagnosis and management of rare mould infections: an initiative of the European Confederation of Medical Mycology in cooperation with the International Society for Human and Animal Mycology and the American Society for Microbiology.

Journal Article Lancet Infect Dis · August 2021 With increasing numbers of patients needing intensive care or who are immunosuppressed, infections caused by moulds other than Aspergillus spp or Mucorales are increasing. Although antifungal prophylaxis has shown effectiveness in preventing many invasive ... Full text Open Access Link to item Cite

Do high MICs predict the outcome in invasive fusariosis?

Journal Article J Antimicrob Chemother · March 12, 2021 BACKGROUND: Invasive fusariosis (IF) affects mostly severely immunocompromised hosts and is associated with poor outcome. Since Fusarium species exhibit high MICs for most antifungal agents, this could explain the poor prognosis. However, a clear-cut corre ... Full text Open Access Link to item Cite

Drug-Resistant Fungi: An Emerging Challenge Threatening Our Limited Antifungal Armamentarium.

Journal Article Antibiotics (Basel) · December 8, 2020 The high clinical mortality and economic burden posed by invasive fungal infections (IFIs), along with significant agricultural crop loss caused by various fungal species, has resulted in the widespread use of antifungal agents. Selective drug pressure, fu ... Full text Open Access Link to item Cite

Needles in a haystack: Extremely rare invasive fungal infections reported in FungiScopeⓇ-Global Registry for Emerging Fungal Infections.

Journal Article J Infect · November 2020 OBJECTIVES: Emerging invasive fungal infections (IFI) have become a notable challenge. Apart from the more frequently described fusariosis, lomentosporiosis, mucormycosis, scedosporiosis, and certain dematiaceae or yeasts, little is known about extremely r ... Full text Open Access Link to item Cite

Diagnosis of Breakthrough Fungal Infections in the Clinical Mycology Laboratory: An ECMM Consensus Statement.

Journal Article J Fungi (Basel) · October 11, 2020 Breakthrough invasive fungal infections (bIFI) cause significant morbidity and mortality. Their diagnosis can be challenging due to reduced sensitivity to conventional culture techniques, serologic tests, and PCR-based assays in patients undergoing antifun ... Full text Open Access Link to item Cite

Breakthrough invasive fungal infections: Who is at risk?

Journal Article Mycoses · October 2020 The epidemiology of invasive fungal infections (IFIs) in immunocompromised individuals has changed over the last few decades, partially due to the increased use of antifungal agents to prevent IFIs. Although this strategy has resulted in an overall reducti ... Full text Open Access Link to item Cite

Point-of-care diagnostics for invasive aspergillosis: nearing the finish line.

Journal Article Expert Rev Mol Diagn · October 2020 INTRODUCTION: The spectrum of disease caused by Aspergillus spp. is dependent on the immune system of the host, with invasive aspergillosis (IA) its most severe manifestation. Early and reliable diagnosis of Aspergillus disease is important to decrease ass ... Full text Open Access Link to item Cite

Latent Tuberculosis Screening Using Electronic Health Record Data.

Journal Article Emerg Infect Dis · September 2020 Screening for latent tuberculosis infection is recommended for foreign-born persons in the United States. We used proxy data from electronic health records to determine that 17.5% of foreign-born outpatients attending the UC San Diego Health clinic (San Di ... Full text Open Access Link to item Cite

Invasive Aspergillosis as an Under-recognized Superinfection in COVID-19.

Journal Article Open Forum Infect Dis · July 2020 Pulmonary aspergillosis has been increasingly reported following severe respiratory viral infections. Millions have been infected by SARS-CoV-2, placing large numbers of patients at-risk for COVID-19 associated pulmonary aspergillosis (CAPA). Prompt recogn ... Full text Open Access Link to item Cite

COVID-19 Associated Pulmonary Aspergillosis (CAPA)-From Immunology to Treatment.

Journal Article J Fungi (Basel) · June 24, 2020 Like severe influenza, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome (ARDS) has emerged as an important disease that predisposes patients to secondary pulmonary aspergillosis, with 35 cases of COVID-19 associated pulmon ... Full text Open Access Link to item Cite

Risk factors and outcomes of culture-proven acute Coccidioides spp. infection in San Diego, California, United States.

Journal Article Mycoses · June 2020 BACKGROUND: Coccidioides spp. are dimorphic fungi endemic to parts of the United States, Mexico, Central and South America. Infection can cause a range of disease from self-limited acute pneumonia to severe disseminated disease. METHODS: We performed a ret ... Full text Open Access Link to item Cite

Voriconazole plus terbinafine combination antifungal therapy for invasive Lomentospora prolificans infections: analysis of 41 patients from the FungiScope® registry 2008-2019.

Journal Article Clin Microbiol Infect · June 2020 OBJECTIVES: Lomentospora prolificans is an emerging cause of serious invasive fungal infections. Optimal treatment of these infections is unknown, although voriconazole-containing treatment regimens are considered the treatment of choice. The objective of ... Full text Open Access Link to item Cite

Clinical characteristics and outcomes of invasive Lomentospora prolificans infections: Analysis of patients in the FungiScope® registry.

Journal Article Mycoses · May 2020 OBJECTIVES: Invasive fungal infections caused by Lomentospora prolificans are associated with very high mortality rates and can be challenging to treat given pan-drug resistance to available antifungal agents. The objective of this study was to describe th ... Full text Open Access Link to item Cite

Blood Aspergillus PCR: The Good, the Bad, and the Ugly.

Journal Article J Fungi (Basel) · January 27, 2020 Invasive Aspergillosis (IA) is one of the most common invasive fungal diseases and is accompanied by high morbidity and mortality. In order to maximize patient outcomes and survival, early and rapid diagnosis has been shown to be pivotal. Hence, diagnostic ... Full text Open Access Link to item Cite

The Aspergillus Lateral Flow Assay for the Diagnosis of Invasive Aspergillosis: an Update.

Journal Article Curr Fungal Infect Rep · 2020 PURPOSE OF REVIEW: To review the data on the Aspergillus lateral flow assay for the diagnosis of invasive Aspergillosis. RECENT FINDINGS: Aspergillus spp. cause a wide spectrum of disease with invasive aspergillosis (IA) as its most severe manifestation. E ... Full text Open Access Link to item Cite

Immune Parameters for Diagnosis and Treatment Monitoring in Invasive Mold Infection.

Journal Article J Fungi (Basel) · December 16, 2019 Infections caused by invasive molds, including Aspergillus spp., can be difficult to diagnose and remain associated with high morbidity and mortality. Thus, early diagnosis and targeted systemic antifungal treatment remains the most important predictive fa ... Full text Open Access Link to item Cite

9th Trends in Medical Mycology Held on 11–14 October 2019, Nice, France, Organized under the Auspices of EORTC-IDG and ECMM

Journal Article Journal of Fungi · October 8, 2019 Dear Friends and Colleagues,It is a great honor and pleasure for us to invite you cordially to participate in the 9th Congress on Trends in Medical Mycology (TIMM-9) [...] ... Full text Open Access Cite

Correction to: (New) Methods for Detection of Aspergillus fumigatus Resistance in Clinical Samples (Current Fungal Infection Reports, (2019), 13, 3, (129-136), 10.1007/s12281-019-00342-w)

Journal Article Current Fungal Infection Reports · September 15, 2019 Funding information was incomplete. The correct information is given below. ... Full text Open Access Cite

(New) Methods for Detection of Aspergillus fumigatus Resistance in Clinical Samples.

Journal Article Curr Fungal Infect Rep · September 2019 PURPOSE OF REVIEW: The incidence of invasive aspergillosis has increased substantially over the past few decades, accompanied by a change in susceptibility patterns of Aspergillus fumigatus with increasing resistance observed against triazole antifungals, ... Full text Open Access Link to item Cite

Broad spectrum triazoles for invasive mould infections in adults: Which drug and when?

Journal Article Med Mycol · April 1, 2019 Invasive mould infections are an increasing cause of morbidity and mortality globally, mainly due to increasing numbers of immunocompromised individuals at risk for fungal infections. The introduction of broad spectrum triazoles, which are much better tole ... Full text Open Access Link to item Cite

Point-of-care diagnosis of invasive aspergillosis in non-neutropenic patients: Aspergillus Galactomannan Lateral Flow Assay versus Aspergillus-specific Lateral Flow Device test in bronchoalveolar lavage.

Journal Article Mycoses · March 2019 BACKGROUND: We compared new Aspergillus Galactomannan Lateral Flow Assay with the newly formatted Aspergillus-specific Lateral Flow device tests for the diagnosis of invasive pulmonary aspergillosis (IPA) in non-neutropenic patients. METHODS: We performed ... Full text Open Access Link to item Cite

Using Interleukin 6 and 8 in Blood and Bronchoalveolar Lavage Fluid to Predict Survival in Hematological Malignancy Patients With Suspected Pulmonary Mold Infection.

Journal Article Front Immunol · 2019 Background: Molds and other pathogens induce elevated levels of several cytokines, including interleukin (IL)-6 and IL-8. The objective of this study was to investigate the prognostic value of IL-6 and IL-8 as well as fungal biomarkers in blood and broncho ... Full text Open Access Link to item Cite

Improving the rates of Aspergillus detection: an update on current diagnostic strategies.

Journal Article Expert Rev Anti Infect Ther · January 2019 The spectrum of disease caused by Aspergillus spp. is dependent on the immune system of the host, and ranges from invasive aspergillosis (IA) to chronic pulmonary aspergillosis (CPA). Early and reliable diagnosis of Aspergillus disease is important to decr ... Full text Open Access Link to item Cite

Rare mould infections caused by Mucorales, Lomentospora prolificans and Fusarium, in San Diego, CA: the role of antifungal combination therapy.

Journal Article Int J Antimicrob Agents · November 2018 Non-Aspergillus invasive mould infections (IMIs) are associated with devastating morbidity and mortality rates and are increasingly diagnosed in immunocompromised hosts. The aim of this study was to describe the epidemiology and outcomes of non-Aspergillus ... Full text Open Access Link to item Cite

Treatment of Aspergillosis.

Journal Article J Fungi (Basel) · August 19, 2018 Infections caused by Aspergillus spp. remain associated with high morbidity and mortality. While mold-active antifungal prophylaxis has led to a decrease of occurrence of invasive aspergillosis (IA) in those patients most at risk for infection, breakthroug ... Full text Open Access Link to item Cite

Spotlight on isavuconazole in the treatment of invasive aspergillosis and mucormycosis: design, development, and place in therapy.

Journal Article Drug Des Devel Ther · 2018 In recent decades, important advances have been made in the diagnosis and treatment of invasive aspergillosis (IA) and mucormycosis. One of these advances has been the introduction of isavuconazole, a second-generation broad spectrum triazole with a favora ... Full text Open Access Link to item Cite

Early cerebritis resulting in a first-time seizure in an otherwise healthy young man.

Journal Article Infect Dis Clin Pract (Baltim Md) · November 2016 We report the case of an otherwise healthy 28-year-old-man who presented with a first-time seizure. Computed tomography (CT) and magnetic resonance imaging (MRI) revealed a circumscribed left frontal lobe heterogeneous mass most consistent with a neoplasm. ... Full text Open Access Link to item Cite

Improved tuberculosis outcomes with daily vs. intermittent rifabutin in HIV-TB coinfected patients in India.

Journal Article Int J Tuberc Lung Dis · September 2016 SETTING: Y R Gaitonde Centre for AIDS Research and Education, Chennai, India. OBJECTIVE: To compare anti-tuberculosis treatment outcomes in individuals with human immunodeficiency virus (HIV) and tuberculosis (TB) co-infection on atazanavir/ritonavir (ATV/ ... Full text Open Access Link to item Cite

Persistent Bacillus cereus Bacteremia in 3 Persons Who Inject Drugs, San Diego, California, USA.

Journal Article Emerg Infect Dis · September 2016 Bacillus cereus is typically considered a blood culture contaminant; however, its presence in blood cultures can indicate true bacteremia. We report 4 episodes of B. cereus bacteremia in 3 persons who inject drugs. Multilocus sequence typing showed that th ... Full text Open Access Link to item Cite

A challenging case of invasive pulmonary aspergillosis after near-drowning: a case report and literature review.

Journal Article Infect Dis Clin Pract (Baltim Md) · September 1, 2015 Near-drowning, a relatively common event, is often complicated by subsequent pneumonia. While endogenous and exogenous bacteria are typical pathogens, rarely fungi are as well. We report a complicated case of invasive pulmonary aspergillosis in a 30-year-o ... Full text Open Access Link to item Cite

Development and validation of the San Diego Early Test Score to predict acute and early HIV infection risk in men who have sex with men.

Journal Article Clin Infect Dis · August 1, 2015 BACKGROUND: Although men who have sex with men (MSM) represent a dominant risk group for human immunodeficiency virus (HIV), the risk of HIV infection within this population is not uniform. The objective of this study was to develop and validate a score to ... Full text Open Access Link to item Cite

A Case of Plasmodium falciparum Malaria in a Man 6 Months after Visiting a Malaria-Endemic Region

Journal Article Infectious Diseases in Clinical Practice · May 1, 2012 Unlike other malaria-causing species of the genus Plasmodium, Plasmodium falciparum normally manifests symptoms of malaria within weeks of exposure. We report the unusual case of symptomatic malaria in a previously healthy individual 6 months after staying ... Full text Open Access Cite

Suppurative parotitis Due to Candida glabrata: Case report and review of the literature

Journal Article Infectious Diseases in Clinical Practice · May 1, 2010 We report the case of an insulin-dependent diabetic woman with chronic renal insufficiency who developed Candida glabrata suppurative parotitis. Infectious inflammation of the parotid gland is typically bacterial in etiology, and candidal parotitis is a ra ... Full text Open Access Cite