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1.  Dihydropteroate Synthase Mutations in Pneumocystis Pneumonia: Impact of Applying Different Definitions of Prophylaxis, Mortality Endpoints and Mutant in a Single Cohort 
Medical mycology  2013;51(6):568-575.
Pneumocystis jirovecii dihydropteroate synthase (DHPS) gene mutations are well-reported. Although sulfa prophylaxis generally is associated with DHPS mutant infection, whether mutant infection is associated with poorer clinical outcomes is less clear. The differing definitions of sulfa prophylaxis and the different mortality endpoints used in these studies may be one explanation for the conflicting study results. Applying different definitions of prophylaxis, mortality endpoints and DHPS mutant to 301 HIV-infected patients with Pneumocystis pneumonia, we demonstrate that prophylaxis, irrespective of definition, increased the risk of infection with pure mutant (any prophylaxis: AOR 4.00, 95% CI: 1.83–8.76, p<0.001) but not mixed genotypes (any prophylaxis: AOR 0.78, 95% CI: 0.26–2.36, p=0.65). However, infection with mutant DHPS, irrespective of definition, was not associated with increased mortality (all-cause or PCP death) at the three time-intervals examined (all p>0.05). Future studies should standardize key variables associated with DHPS mutant infection as well as examine DHPS mutant subtypes (pure mutant vs. mixed infections) – perhaps even individual DHPS mutant genotypes – so that data can be pooled to better address this issue.
PMCID: PMC4008324  PMID: 23470037
Pneumocystis jirovecii; PCP; dihydropteroate synthase; DHPS; DHPS mutant
2.  Environmental Risk Factors for Pneumocystis Pneumonia Hospitalizations in HIV Patients 
This report identifies both climatological and air pollution constituents as independent risk factors for hospitalization of HIV-positive patients with Pneumocystis pneumonia (PcP). These findings may lead to new insights about the epidemiology and pathogenesis of PcP.
Background. Pneumocystis pneumonia (PcP) is the second leading cause of morbidity and mortality in human immunodeficiency virus (HIV)–infected patients in the United States. Although the host risk factors for the development of PcP are well established, the environmental (climatological, air pollution) risk factors are poorly understood. The major goal of this study was to determine the environmental risk factors for admissions of HIV-positive patients with PcP to a single medical center.
Methods. Between 1997 and 2008, 457 HIV-positive patients with microscopically confirmed PcP were admitted to the San Francisco General Hospital. A case-crossover design was applied to identify environmental risk factors for PcP hospitalizations. Climatological and air pollution data were collected from the Environmental Protection Agency and Weather Warehouse databases. Conditional logistic regression was used to evaluate the association of each environmental factor and PcP hospital admission.
Results. Hospital admissions were significantly more common in the summer than in the other seasons. Increases in temperature and sulfur dioxide levels were independently associated with hospital admissions for PcP, but the effects of sulfur dioxide were modified by increasing carbon monoxide levels.
Conclusions. This study identifies both climatological and air pollution constituents as independent risk factors for hospitalization of HIV-positive patients with PcP in San Francisco. Thus, the environmental effects on PcP are more likely complex than previously thought. Further studies are needed to understand how these factors exert their effects and to determine if these factors are associated with PcP in other geographic locations.
PMCID: PMC3571628  PMID: 23042978
Pneumocystis; PcP; environmental factors; HIV
3.  Antibody Responses against Pneumocystis jirovecii in Health Care Workers Over Time 
Emerging Infectious Diseases  2013;19(10):1613-1620.
In a previous cross-sectional study, we showed that clinical staff working in a hospital had significantly higher antibody levels than nonclinical staff to Pneumocystis jirovecii. We conducted a longitudinal study, described here, to determine whether occupation and self-reported exposure to a patient with P. jirovecii pneumonia were associated with antibody levels to P. jirovecii over time. Baseline and quarterly serum specimens were collected and analyzed by using an ELISA that targeted different variants of the Pneumocystis major surface glycoprotein (MsgA, MsgB, MsgC1, MsgC3, MsgC8, and MsgC9). Clinical staff had significantly higher estimated geometric mean antibody levels against MsgC1 and MsgC8 than did nonclinical staff over time. Significant differences were observed when we compared the change in antibody levels to the different MsgC variants for staff who were and were not exposed to P. jirovecii pneumonia–infected patients. MsgC variants may serve as indicators of exposure to P. jirovecii in immunocompetent persons.
PMCID: PMC3810734  PMID: 24048016
Pneumocystis jirovecii; transmission; health care worker–patient; human immunodeficiency virus; HIV; major surface glycoprotein; pneumonia; respiratory diseases; fungi; HIV/AIDS and other retroviruses
4.  Severity and outcomes of Pneumocystis pneumonia in patients newly diagnosed with HIV infection: an observational cohort study 
It is unclear whether patients who are unaware of their HIV infection have different severity or outcomes of Pneumocystis pneumonia (PCP) compared to patients who have been previously diagnosed with HIV. In this retrospective observational cohort study of consecutive HIV-infected patients with microscopically diagnosed PCP at San Francisco General Hospital between 1997 and 2006, 121 of 522 patients (23%) were unaware of their HIV infection prior to their diagnosis of PCP. The proportion of patients with concurrently diagnosed HIV and PCP each year remained unchanged during the study period. Patients with newly diagnosed HIV had a significantly higher alveolar-arterial oxygen gradient at presentation (median 51 versus 45 mm Hg, p=0.03), but there were no differences in mortality, frequency of mechanical ventilation, or admission to intensive care compared to patients with previously diagnosed HIV infection. In multivariate analysis, patients who reported a sexual risk factor for HIV infection were more likely to be newly diagnosed with HIV than patients who reported injection drug use as their only HIV risk factor (odds ratio = 3.14, 95% confidence interval 1.59–6.18, p = 0.001). This study demonstrates a continued need for HIV education and earlier HIV testing, particularly in patients with high-risk sexual behavior.
PMCID: PMC2806953  PMID: 19521925
5.  Predicting mortality from HIV-associated Pneumocystis pneumonia at illness presentation: an observational cohort study 
Thorax  2009;64(12):1070-1076.
Although the use of antiretroviral therapy has led to dramatic declines in AIDS-associated mortality, Pneumocystis pneumonia (PCP) remains a leading cause of death in HIV-infected patients.
To measure mortality, identify predictors of mortality at time of illness presentation, and derive a PCP mortality prediction rule that stratifies patients by risk for mortality.
Observational cohort study with case note review of all HIV-infected persons with a laboratory diagnosis of PCP at San Francisco General Hospital from 1997–2006.
451 patients were diagnosed with PCP on 524 occasions. In-hospital mortality was 10.3%. Multivariate analysis identified five significant predictors of mortality: age (adjusted odds ratio [AOR] per 10-year increase, 1.69; 95% confidence interval [CI] 1.08–2.65; p=0.02); recent injection drug use (AOR 2.86; 95% CI 1.28–6.42; p=0.01); total bilirubin >0.6 mg/dL (AOR 2.59; 95% CI 1.19–5.62; p=0.02); serum albumin <3 g/dL (AOR 3.63; 95% CI 1.72–7.66; p=0.001); and alveolar-arterial oxygen gradient ≥50 mm Hg (AOR 3.02; 95% CI 1.41–6.47; p=0.004). Using these five predictors, we derived a six point PCP mortality prediction rule that stratifies patients according to increasing risk of mortality: score 0–1, 4%; score 2–3, 12%; score 4–5, 48%.
Our PCP mortality prediction rule stratifies patients by mortality risk at the time of illness presentation and should be validated as a clinical tool.
PMCID: PMC2788120  PMID: 19825785
Pneumonia; Pneumocystis; HIV/AIDS; antiretroviral therapy; highly active
6.  A Hydrophilic-interaction Chromatography Tandem Mass Spectrometry Method for Quantitation of Serum s-Adenosylmethionine in Patients Infected with Human Immunodeficiency Virus 
S-adenosylmethionine (SAM)1 has been suggested as a diagnostic test and surrogate marker for Pneumocystis jirovecii pneumonia (PCP) in HIV-positive patients. In this study, we report a robust hydrophilic-interaction liquid chromatography tandem mass spectrometry (LC-MS/MS) assay that can be used to quantitate serum SAM in clinical laboratories.
Proteins in serum samples were precipitated using trichloroacetic acid. The supernatant was separated after centrifugation. D3-SAM was added as the internal standard. SAM and d3-SAM were extracted using a mixed-mode cation exchange column. Extracts were dried under nitrogen and reconstituted in H2O and acetonitrile (1:9, vol:vol). HPLC-tandem mass spectrometry analysis was performed with a silica column and multiple reaction monitoring for SAM and d3-SAM.
The limit of quantitation (LOQ) for SAM was 10 ng/mL. The assay was linear between 10–500 ng/mL. Intra-assay coefficient of variation (CV) was 8% and inter-assay CV was 17% at the LOQ. Turnaround time for each specimen was approximately 1 hour. Using this method, we found that serum SAM concentration was correlated with fasting status, especially methionine intake. We also measured acute and convalescent serum SAM levels of 8 HIV-positive patients with PCP and non-PCP pneumonia. SAM concentrations in convalescent samples were significantly increased compared to acute levels only in patients with PCP.
The LC-MS/MS method had sufficient analytical sensitivity for detecting low levels of SAM found in HIV-infected patients and can be used for quantitative measurements in a clinical laboratory. This method facilitates research and possible clinical application of SAM as a marker for PCP.
PMCID: PMC2575815  PMID: 18619430
7.  Healthcare Worker Occupation and Immune Response to Pneumocystis jirovecii 
Emerging Infectious Diseases  2009;15(10):1590-1597.
Humans may be a reservoir for this pathogen and transmit it from person to person.
The reservoir and mode of transmission of Pneumocystis jirovecii remain uncertain. We conducted a cross-sectional study of 126 San Francisco General Hospital staff in clinical (n = 103) and nonclinical (n = 23) occupations to assess whether occupational exposure was associated with immune responses to P. jirovecii. We examined antibody levels by ELISA for 3 overlapping fragments that span the P. jirovecii major surface glycoprotein (Msg): MsgA, MsgB, and MsgC1. Clinical occupation participants had higher geometric mean antibody levels to MsgC1 than did nonclinical occupation participants (21.1 vs. 8.2, p = 0.004); clinical occupation was an independent predictor of higher MsgC1 antibody levels (parameter estimate = 0.89, 95% confidence interval 0.29–1.48, p = 0.003). In contrast, occupation was not significantly associated with antibody responses to either MsgA or MsgB. Healthcare workers may have occupational exposure to P. jirovecii. Humans may be a reservoir for P. jirovecii and may transmit it from person to person.
PMCID: PMC2866396  PMID: 19861050
Pneumocystis; health personnel; HIV/AIDS and other retroviruses; opportunistic infections; antibodies; fungal; fungi; serologic tests; research

Results 1-7 (7)