Stephen A. Moser

Association Rules and Data Mining in Hospital Infection Control and Public Health Surveillance

Objectives: The authors consider the problem of identifying new, unexpected, and interesting patterns in hospital infection control and public health surveillance data and present a new data analysis process and system based on association rules to address this problem. Design: The authors first illustrate the need for automated pattern discovery and data mining in hospital infection control and public health surveillance. Next, they define association rules, explain how those rules can be used in surveillance, and present a novel process and system—the Data Mining Surveillance System (DMSS)—that utilize association rules to identify new and interesting patterns in surveillance data. Results: Experimental results were obtained using DMSS to analyze Pseudomonas aeruginosa infection control data collected over one year (1996) at University of Alabama at Birmingham Hospital. Experiments using one-, three-, and six-month time partitions yielded 34, 57, and 28 statistically significant events, respectively. Although not all statistically significant events are clinically significant, a subset of events generated in each analysis indicated potentially significant shifts in the occurrence of infection or antimicrobial resistance patterns of P. aeruginosa . Conclusion: The new process and system are efficient and effective in identifying new, unexpected, and interesting patterns in surveillance data. The clinical relevance and utility of this process await the results of prospective studies currently in progress.

Molecular Identification of Aspergillus Species Collected for the Transplant-Associated Infection Surveillance Network

ABSTRACT A large aggregate collection of clinical isolates of aspergilli (n = 218) from transplant patients with proven or probable invasive aspergillosis was available from the Transplant-Associated Infection Surveillance Network, a 6-year prospective surveillance study. To determine the Aspergillus species distribution in this collection, isolates were subjected to comparative sequence analyses by use of the internal transcribed spacer and β-tubulin regions. Aspergillus fumigatus was the predominant species recovered, followed by A. flavus and A. niger. Several newly described species were identified, including A. lentulus and A. calidoustus; both species had high in vitro MICs to multiple antifungal drugs. Aspergillus tubingensis, a member of the A. niger species complex, is described from clinical specimens; all A. tubingensis isolates had low in vitro MICs to antifungal drugs.

Patterns of Susceptibility of Aspergillus Isolates Recovered from Patients Enrolled in the Transplant-Associated Infection Surveillance Network

ABSTRACT We analyzed antifungal susceptibilities of 274 clinical Aspergillus isolates from transplant recipients with proven or probable invasive aspergillosis collected as part of the Transplant-Associated Infection Surveillance Network (TRANSNET) and examined the relationship between MIC and mortality at 6 or 12 weeks. Antifungal susceptibility testing was performed by the Clinical and Laboratory Standards Institute (CLSI) M38-A2 broth dilution method for amphotericin B (AMB), itraconazole (ITR), voriconazole (VOR), posaconazole (POS), and ravuconazole (RAV). The isolate collection included 181 Aspergillus fumigatus, 28 Aspergillus niger, 27 Aspergillus flavus, 22 Aspergillus terreus, seven Aspergillus versicolor, five Aspergillus calidoustus, and two Aspergillus nidulans isolates and two isolates identified as Aspergillus spp. Triazole susceptibilities were ≤4 μg/ml for most isolates (POS, 97.6%; ITR, 96.3%; VOR, 95.9%; RAV, 93.5%). The triazoles were not active against the five A. calidoustus isolates, for which MICs were ≥4 μg/ml. AMB inhibited 93.3% of isolates at an MIC of ≤1 μg/ml. The exception was A. terreus, for which 15 (68%) of 22 isolates had MICs of >1 μg/ml. One of 181 isolates of A. fumigatus showed resistance (MIC ≥ 4 μg/ml) to two of three azoles tested. Although there appeared to be a correlation of higher VOR MICs with increased mortality at 6 weeks, the relationship was not statistically significant (R2 = 0.61; P = 0.065). Significant relationships of in vitro MIC to all-cause mortality at 6 and 12 weeks for VOR or AMB were not found.

Epidemiology of Aspergillus terreus at a University Hospital

ABSTRACT Invasive fungal infections due to Aspergillus species have become a major cause of morbidity and mortality among immunocompromised patients. Aspergillus terreus, a less common pathogen, appears to be an emerging cause of infection at our institution, the University of Alabama hospital in Birmingham. We therefore investigated the epidemiology of A. terreus over the past 6 years by using culture data; antifungal susceptibility testing with amphotericin B, voriconazole, and itraconazole; and molecular typing with random amplification of polymorphic DNA-PCR (RAPD-PCR). During the study period, the percentage of A. terreus isolates relative to those of other Aspergillus species significantly increased, and A. terreus isolates frequently were resistant to amphotericin B. Molecular typing with the RAPD technique was useful in discriminating between patient isolates, which showed much strain diversity. Further surveillance of A. terreus may better define epidemiology and determine whether this organism is becoming more frequent in relation to other Aspergillus species.

Association of Fluconazole Pharmacodynamics with Mortality in Patients with Candidemia

ABSTRACT Recent studies of nonneutropenic patients with candidemia or candidiasis suggest that fluconazole pharmacodynamic parameters correlate with clinical outcomes; however, additional data of correlation to mortality in patients with candidemia would be valuable. We assessed the impact of MICs for Candida, fluconazole pharmacodynamics, and patient characteristics on all-cause mortality with use of a prospective cohort of 96 hospitalized patients with candidemia. Among 84 patients for whom Candida isolates were available for testing, the most frequent Candida species isolated were Candida albicans (44%), followed by Candida parapsilosis (20.2%), and Candida glabrata (20.2%). Fluconazole resistance (MIC of ≥64 μg/ml) was present in 7 (8.3%) to 10 (11.9%) of 84 isolates, depending on the MIC endpoint determination method (50% or 80% inhibition read at 24 or 48 h). Overall mortality occurred in 27 (28.1%) of 96 patients, and nonsurvivors were more likely to have fluconazole-resistant isolates (25% versus 6.7%; P = 0.02). Multivariable analysis demonstrated an association between fluconazole resistance and mortality, but it did not reach statistical significance (odds ratio, 5.3; 95% confidence interval, 0.8 to 33.4; P = 0.08). By pharmacodynamic analysis, a fluconazole area under the concentration-time curve/MIC of <11.5 or MIC of ≥64 was associated with increased patient mortality (P ≤ 0.09). These data support previous findings of an antifungal exposure-response relationship to mortality in patients with candidemia. In addition, similar MICs were obtained using a 24- or 48-h MIC endpoint determination, thus providing the opportunity to assess earlier the impact of isolate susceptibility on therapy.

Improving Molecular Detection of Fungal DNA in Formalin-Fixed Paraffin-Embedded Tissues: Comparison of Five Tissue DNA Extraction Methods Using Panfungal PCR

ABSTRACT DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissues is difficult and requires special protocols in order to extract small amounts of DNA suitable for amplification. Most described methods report an amplification success rate between 60 and 80%; therefore, there is a need to improve molecular detection and identification of fungi in FFPE tissue. Eighty-one archived FFPE tissues with a positive Gomori methenamine silver (GMS) stain were evaluated using five different commercial DNA extraction kits with some modifications. Three different panfungal PCR assays were used to detect fungal DNA, and two housekeeping genes were used to assess the presence of amplifiable DNA and to detect PCR inhibitors. The sensitivities of the five extraction protocols were compared, and the quality of DNA detection (calculated for each kit as the number of housekeeping gene PCR-positive samples divided by the total number of samples) was 60 to 91% among the five protocols. The efficiencies of the three different panfungals used (calculated as the number of panfungal-PCR-positive samples divided by the number of housekeeping gene PCR-positive samples) were 58 to 93%. The panfungal PCR using internal transcribed spacer 3 (ITS3) and ITS4 primers yielded a product in most FFPE tissues. Two of the five DNA extraction kits (from TaKaRa and Qiagen) showed similar and promising results. However, one method (TaKaRa) could extract fungal DNA from 69 of the 74 FFPE tissues from which a housekeeping gene could be amplified and was also cost-effective, with a nonlaborious protocol. Factors such as sensitivity, cost, and labor will help guide the selection of the most appropriate method for the needs of each laboratory.

Prevalence of Inducible Clindamycin Resistance among Community- and Hospital-Associated Staphylococcus aureus Isolates

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) infections have become common among both hospitalized and nonhospitalized patients. Optimal outpatient therapy for MRSA infections has yet to be determined, but this matter is complicated by the possibility of inducible macrolide-lincosamide-streptogramin B resistance (MLSBi). We studied the prevalence of MLSBi in community- and hospital-associated S. aureus isolates and the prevalence of community-associated MRSA (CA-MRSA) and identified clinical predictors of CA-MRSA and MLSBi. Among 402 S. aureus isolates, the overall prevalence of MLSBi was 52%, with 50% of MRSA and 60% of methicillin-susceptible S. aureus isolates exhibiting MLSBi. CA-MRSA represented 14% of all isolates and had a lower prevalence of MLSBi than hospital-associated MRSA (33% versus 55%). The presence of skin or soft-tissue infection was predictive for CA-MRSA, and the presence of a comorbidity was predictive for MLSBi. Due to the low prevalence of MLSBi among CA-MRSA isolates, clindamycin remains a useful option for outpatient therapy.

Genital tract methicillin-resistant Staphylococcus aureus: risk of vertical transmission in pregnant women.

OBJECTIVE: To estimate the frequency of genital tract colonization by methicillin-resistant Staphylococcus aureus (MRSA) among pregnant women and evaluate the association of such colonization with infant outcome. METHODS: Between July 2003 and July 2006, anovaginal screening cultures for group B Streptococcus (GBS) were prospectively obtained in the third trimester (35 to less than 37 weeks of gestation) and were also processed for identification of Staphylococcus aureus including methicillin-resistant strains. Maternal colonization by MRSA was linked to a computerized database of invasive neonatal infections that occurred at our center during the study period. RESULTS: Among 5,732 mothers (who delivered 5,804 infants) with GBS screening cultures and infant infection data available, 22.9% were GBS-positive and 14.5% were positive for Staphylococcus aureus. A total of 24.3% of the Staphylococcus aureus isolates were MRSA. The overall MRSA colonization rate was 3.5%. Colonization by any Staphylococcus aureus (relative risk 1.6, 95% confidence interval 1.4–1.9) as well as MRSA (relative risk 2.2, 95% confidence interval 1.6–2.8) was significantly more common among GBS-positive than among GBS-negative women. No cases of early-onset invasive neonatal infection by MRSA occurred among infants in the study. CONCLUSION: Genital tract colonization with MRSA affected 3.5% of pregnant women. Such MRSA colonization is associated with colonization by GBS but does not predispose to a high risk of early-onset neonatal MRSA infection. LEVEL OF EVIDENCE: III

Donor-Related Coccidioidomycosis in Organ Transplant Recipients

Most cases of coccidioidomycosis in organ transplant recipients arise from either primary infection with Coccidioides immitis after environmental exposure or from reactivation of latent infection. Herein, we report 2 cases of rapidly fatal, disseminated coccidioidomycosis that occurred in organ transplant recipients who had never lived in or visited an area where C. immitis is endemic. Both subjects had received a transplanted organ from the same donor, an individual with unrecognized active coccidioidomycosis at the time of his death.

Reduction of vancomycin-resistant enterococcal infections by limitation of broad-spectrum cephalosporin use in a trauma and burn intensive care unit

Both vancomycin and third-generation cephalosporin use are believed to contribute to a rise in vancomycin-resistant enterococci (VRE) infections. In 1998, the largest number of VRE infections in our hospital occurred in the trauma/burn intensive care unit (TBICU), accounting for nearly 20% of hospital infections. In an attempt to control the VRE infection rate, antibiotic protocols for prophylaxis, empiric, and definitive therapy were initiated during the final quarter of 1998 to minimize cephalosporin use by the introduction of piperacillin/tazobactam. Therefore, we undertook a study of the VRE infection rate for the TBICU in relation to vancomycin, piperacillin/tazobactam, piperacillin, third-generation cephalosporin, and total cephalosporin use before and after efforts to limit cephalosporins. These data were compared to those in the medical and surgical intensive care units. During 1998, seven VRE infections occurred in the TBICU. Following initiation of antibiotic protocols, one case of VRE infection occurred in the subsequent month and no cases in the 17 months since. The decrease in the VRE infection rate corresponded with a significant increase in the use of piperacillin/tazobactam and a reduction in third-generation and total cephalosporin use. In contrast, cephalosporin use in the medical and surgical intensive care units remains significantly higher than in the TBICU, and neither unit has had a reduction in their VRE infection rates.