Cindy M Liu

Cindy M Liu
George Washington University | GW · Department of Environmental and Occupational Health

MD, MPH, PhD

About

112
Publications
13,795
Reads
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3,822
Citations
Additional affiliations
July 2012 - June 2015
Johns Hopkins University
Position
  • Residency in Clinical Pathology
February 2009 - June 2012
Northern Arizona University
Position
  • Research Associate
February 2009 - June 2012
Translational Genomics Research Institute
Position
  • Professor (Associate)
Education
July 2009 - December 2013
Northern Arizona University
Field of study
  • Biology
June 2005 - May 2006
Johns Hopkins Bloomberg School of Public Health
Field of study
  • Concentration in Epidemiological & Biostatistics Methods for Public Health and Clinical Research
June 2002 - May 2007
New York University
Field of study
  • Medicine

Publications

Publications (112)
Article
Full-text available
Semen is a major vector for HIV transmission, but the semen HIV RNA viral load (VL) only correlates moderately with the blood VL. Viral shedding can be enhanced by genital infections and associated inflammation, but it can also occur in the absence of classical pathogens. Thus, we hypothesized that a dysregulated semen microbiome correlates with lo...
Article
Full-text available
Unlabelled: Male circumcision reduces female-to-male HIV transmission. Hypothesized mechanisms for this protective effect include decreased HIV target cell recruitment and activation due to changes in the penis microbiome. We compared the coronal sulcus microbiota of men from a group of uncircumcised controls (n = 77) and from a circumcised interv...
Article
Full-text available
Background Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for new broad-coverage techniques. Methods We analyzed 2,085 18S rRNA gene sequences from the SILVA database for assay design. We generated and q...
Article
Full-text available
Bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. Based on our analysis of a diverse collection of 16 S rRNA gene sequences, we designed a broad-coverage quantitative real-time PCR (qPCR) assay-BactQuant-for quantif...
Article
Full-text available
Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men and significant reductions in bacterial vaginosis among their female partners. We assessed the penile (coronal sulci) microbiota in 12 HIV-negative Ugandan men before and after circumcision. Microbiota were characterized using sequence-tagged 16S rRNA...
Article
Objective: Previous studies have reported high rates of inappropriate antibiotic prescriptions in urgent care (UC). Specific prescribing patterns for the most common diagnoses are not known. The aim of the study is to determine the diagnoses for which antibiotics are prescribed in pediatric UC settings. Methods: We recruited pediatric UC provide...
Article
Background: Outpatient antibiotic prescribing for acute respiratory conditions is highest in urgent care settings; however, this has not been studied among pediatric urgent cares. The objective of this study was to evaluate pediatric urgent care providers' perceptions of antibiotic stewardship. Methods: Members of the Society for Pediatric Urgen...
Article
Background: Urgent care (UC; a convenient site to receive care for ambulatory-sensitive) centers conditions; however, UC clinicians showed the highest rate of inappropriate antibiotic prescriptions among outpatient settings according to national billing data. Antibiotic prescribing practices in pediatric-specific UC centers were not known but assu...
Article
Full-text available
Globally, most Human Immunodeficiency Virus type 1 (HIV) transmission occurs through vaginal–penile sex (heterosexual transmission). The local immune environment at the site of HIV exposure is an important determinant of whether exposure during sex will lead to productive infection, and the vaginal and penile immune milieus are each critically shap...
Article
Objective: The George Washington University (GW) in Washington, D.C., USA established the Public Health Laboratory and Campus COVID-19 Support Team (CCST) to develop and implement its SARS-CoV-2 surveillance testing and outbreak response for the 2020-2021 academic year. Participants and methods: Approximately 4,000 GW members had access to campu...
Article
Full-text available
Background Coronal sulcus (CS) anaerobe abundance and IL-8 levels are linked to HIV acquisition, and are dramatically reduced after penile circumcision (PC). The distal urethra may be the site of some HIV acquisition before PC, and presumably most acquisition post PC. We describe the immune milieu and microbiome of the distal urethra in uncircumcis...
Article
This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter dista...
Article
In this retrospective cohort study of patients presenting to a national direct-to-consumer medical practice, we found that provider geographic location is a stronger driver of antibiotic prescribing than patient location. Physicians in the Northeast and South are significantly more likely than physicians in the West to prescribe antibiotics for upp...
Article
The foreskin is a site of heterosexual acquisition of HIV-1 among uncircumcised men. However, some men remain HIV-negative despite repeated, unprotected vaginal intercourse with HIV-positive partners, while others become infected after few exposures. The foreskin microbiome includes a diverse group of anaerobic bacteria that have been linked to HIV...
Preprint
Full-text available
International efforts to curb antimicrobial resistance have focused on drug development and limiting unnecessary use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, and where biosecurity in food-animal production is poor, pathogen-flow between humans and animals could exacerbate the emergence and spread of resista...
Preprint
Full-text available
S ummary This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shor...
Article
Full-text available
Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant us...
Article
Full-text available
Objective Male circumcision (MC) reduces acquisition of HIV-1 in heterosexual men by at least 60%, but the biological mechanism for this protection is incompletely understood. Previous studies have shown that a larger foreskin size, increased abundance of anaerobic bacteria in the sub-preputial space, and higher levels of pro-inflammatory cytokines...
Article
Full-text available
Background Klebsiella pneumoniae is a frequent cause of neonatal sepsis and carries a high mortality rate in lower and middle-income countries (LMICs). From March-November 2015, two Jamaican hospitals experienced K. pneumoniae outbreaks in their Special Care Nurseries (SCNs). New admissions to both SCNs were temporarily halted while additional infe...
Article
Background The impact of antiretroviral therapy (ART) initiation on the vaginal microbiome is unknown, this is of particular importance among women living in sub-Saharan Africa. Understanding this relationship will help elucidate if and how the host immune system interacts with the vaginal microbiome. Methods The vaginal microbiome of HIV-1/HSV-2...
Article
Full-text available
Background We sought to determine if the prevalence of antibiotic-resistant Escherichia coli differed across retail poultry products and among major production categories, including organic, “raised without antibiotics”, and conventional. Results We collected all available brands of retail chicken and turkey—including conventional, “raised without...
Article
Full-text available
Escherichia coli sequence type 131 (ST131) has emerged rapidly to become the most prevalent extraintestinal pathogenic E. coli clones in circulation today. Previous investigations appeared to exonerate retail meat as a source of human exposure to ST131; however, these studies focused mainly on extensively multidrug-resistant ST131 strains, which ty...
Article
Full-text available
Leaf litter provides an important resource to forested stream ecosystems. During leaf fall a significant amount of dissolved organic carbon (DOC) enters streams as leaf leachate. We compared the effects of plant species and leaf leachate bioavailability on the composition of stream bacterial communities and rates of DOC decomposition. We used four...
Article
Full-text available
Sexual transmission of HIV requires exposure to the virus and infection of activated mucosal immune cells, specifically CD4⁺ T cells or dendritic cells. The foreskin is a major site of viral entry in heterosexual transmission of HIV. Although the probability of acquiring HIV from a sexual encounter is low, the risk varies even after adjusting for k...
Article
Full-text available
Objective To characterize parameters associated with semen HIV-1 RNA viral load variability in HIV-infected, therapy-naive men. Methods Paired blood and semen samples were collected from thirty HIV-infected, therapy-naive men who have sex with men (MSM), and thirteen participants were followed longitudinally for up to a year. HIV RNA, bacterial lo...
Article
Full-text available
Individual susceptibility to HIV is heterogeneous, but the biological mechanisms explaining differences are incompletely understood. We hypothesized that penile inflammation may increase HIV susceptibility in men by recruiting permissive CD4 T cells, and that male circumcision may decrease HIV susceptibility in part by reducing genital inflammation...
Data
Comparison of the frequency of detection of each cytokine between circumcised and uncircumcised men, performed cross-sectionally at each time point. (PDF)
Data
Demographics of Rakai RCT participants (longitudinal study of circumcision). (PDF)
Data
Participant demographics (case-control study of HIV seroconverters), stratified by presence of IL-8. (PDF)
Data
Participant demographics (case-control study of HIV seroconverters), stratified by presence of MIG. (PDF)
Data
Demographic of participants enrolled through the Rakai Circumcision Service Program (n = 89). (PDF)
Article
Full-text available
We report here the complete genome sequence, including five plasmid sequences, of Escherichia coli sequence type 131 (ST131) strain JJ1887. The strain was isolated in 2007 in the United States from a patient with recurrent cystitis, whose caregiver sister died from urosepsis caused by a nearly identical strain.
Article
Full-text available
The PrePex circumcision device causes ischemic necrosis of the foreskin raising concerns of anaerobic overgrowth. We compared the sub-preputial microbiome of 22 men seven days after PrePex device placement to 145 uncircumcised men in Rakai, Uganda using 16S rRNA gene-based qPCR and sequencing. PrePex users had increased absolute abundance of all ba...
Article
Full-text available
Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremon...
Article
Full-text available
Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more com...
Article
Full-text available
Bacteria grow and transform elements at different rates, yet quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to Stable Isotope Probing (SIP) that enables determining...
Preprint
Full-text available
Bacteria grow and transform elements at different rates, yet quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to Stable Isotope Probing (SIP) that enables determining...
Preprint
Full-text available
Bacteria grow and transform elements at different rates, yet quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to Stable Isotope Probing (SIP) that enables determining...
Article
Full-text available
Background: Klebsiella pneumoniae is a common colonizer of the gastrointestinal tract of humans, companion animals, and livestock. To better understand potential contributions of foodborne K. pneumoniae to human clinical infections, we compared K. pneumoniae isolates from retail meat products and human clinical specimens to assess their similarity...
Article
Full-text available
Unlabelled: Bacterial vaginosis (BV) is a common vaginal bacterial imbalance associated with risk for HIV and poor gynecologic and obstetric outcomes. Male circumcision reduces BV-associated bacteria on the penis and decreases BV in female partners, but the link between penile microbiota and female partner BV is not well understood. We tested the...
Article
Full-text available
The human microbiome can play a key role in host susceptibility to pathogens, including in the nasal cavity, a site favored by Staphylococcus aureus. However, what determines our resident nasal microbiota-the host or the environment-and can interactions among nasal bacteria determine S. aureus colonization? Our study of 46 monozygotic and 43 dizygo...
Article
Full-text available
The human microbiome can play a key role in host susceptibility to pathogens, including in the nasal cavity, a site favored by Staphylococcus aureus. However, what determines our resident nasal microbiota-the host or the environment-and can interactions among nasal bacteria determine S. aureus colonization? Our study of 46 monozygotic and 43 dizygo...
Article
Background Topical treatments with nasal saline irrigation, topical steroid sprays, or corticosteroid rinses can improve sinonasal symptoms in chronic rhinosinusitis (CRS). However, the impact of these therapies on commensals (Corynebacterium) and on biofilm pathogens associated with CRS (Staphylococcus aureus and Pseudomonas) is not well character...
Article
Full-text available
Microbial communities are complex and dynamic systems that are primarily structured according to their members' ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial...
Article
Full-text available
Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced...
Article
The human microbiome represents the collective genomes and gene products of microbes living within and on humans. The objective of this review is to provide a summary of the current microbiome literature pertaining to otolaryngology-head and neck surgery. Ovid Medline. Scientific publications with clinical correlates. Human microbiome studies have...
Article
Full-text available
Coxiella burnetii causes Q fever in humans and Coxiellosis in animals; symptoms range from general malaise to fever, pneumonia, endocarditis and death. Livestock are a significant source of human infection as they shed C. burnetii cells in birth tissues, milk, urine and feces. Although prevalence of C. burnetii is high, few Q fever cases are report...
Article
Full-text available
Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition o...
Article
Chronic rhinosinusitis (CRS) is a highly prevalent and heterogeneous condition frequently treated with antibiotics and corticosteroid therapy. However, the effect of medical therapy on sinus microbiota remains unknown. We enrolled CRS patients (n = 6) with patent maxillary antrostomies and active mucosal inflammation, who had not received antibioti...
Article
Full-text available
Few investigators have examined simultaneous bacterial and fungal responses to leaf-litter chemistry in fresh water. We tested the hypothesis that bacteria would be more abundant on labile litter with lower concentrations of defensive compounds, whereas fungi would be more abundant on recalcitrant litter. We used quantitative-polymerase chain react...
Article
Full-text available
Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. Disproportionately affecting women, UTIs exact a substantial public burden each year in terms of direct medical expenses, decreased quality of life, and lost productivity. Increasing antimicrobial resistance among strains of extraintestinal pathogenic Escheric...