A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity.

BACKGROUND: Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In areas with adequate cold chain facilities, large volumes of leukocyte-depleted patient blood can be frozen for use in parasite genomic analyses. In more remote endemic areas smaller volumes of infected blood are taken by finger prick, and dried and stored on filter paper. These dried blood spots do not generally yield enough concentrated parasite DNA for whole-genome sequencing. RESULTS: A DNA microarray was designed for use on field samples to type a genome-wide set of SNPs which prior sequencing had shown to be variable in Africa, Southeast Asia, and Papua New Guinea. An algorithm was designed to call SNPs in samples with low parasite DNA. With this new algorithm SNP-calling accuracy of 98% was measured by hybridizing purified DNA from malaria lab strains and comparing calls with SNPs called from full genome sequences. An average accuracy of >98% was likewise obtained for DNA extracted from malaria field samples collected in studies in Southeast Asia, with an average call rate of > 82%. CONCLUSION: This new high-density microarray provided high quality SNP calls from a wide range of parasite DNA quantities, and represents a robust tool for genome-wide analysis of malaria parasites in diverse settings.

Sensitivity of surveillance testing for multidrug-resistant Gram-negative bacteria in the intensive care unit.

We tested intensive care unit patients for colonization with multidrug-resistant Gram-negative bacilli (MDR GNB) and compared the results with those of concurrent clinical cultures. The sensitivity of the surveillance test for detecting MDR GNB was 58.8% (95% confidence interval, 48.6 to 68.5%). Among 133 patients with positive surveillance tests, 61% had no prior clinical culture with MDR GNB.

Nontuberculous mycobacterial infection after fractionated CO(2) laser resurfacing.

Nontuberculous mycobacteria are increasingly associated with cutaneous infections after cosmetic procedures. Fractionated CO2 resurfacing, a widely used technique for photorejuvenation, has been associated with a more favorable side effect profile than alternative procedures. We describe 2 cases of nontuberculous mycobacterial infection after treatment with a fractionated CO2 laser at a private clinic. Densely distributed erythematous papules and pustules developed within the treated area within 2 weeks of the laser procedure. Diagnosis was confirmed by histologic analysis and culture. Both infections responded to a 4-month course of a multidrug regimen. An environmental investigation of the clinic was performed, but no source of infection was found. The case isolates differed from each other and from isolates obtained from the clinic, suggesting that the infection was acquired by postprocedure exposure. Papules and pustules after fractionated CO2 resurfacing should raise the suspicion of nontuberculous mycobacterial infection.

Acute eosinophilic pneumonia secondary to daptomycin: a report of three cases.

We describe 3 cases of daptomycin-induced pulmonary toxic effects that are consistent with drug-induced acute eosinophilic pneumonia. Patients presented similarly with dyspnea, cough, hypoxia, and diffuse ground-glass opacities at chest computed tomography. Clinical suspicion for this adverse drug event and cessation of daptomycin until definitive diagnosis can be made is crucial.

Central line-associated infections as defined by the Centers for Medicare and Medicaid Services' Hospital-acquired condition versus standard infection control surveillance: why hospital compare seems conflicted.

OBJECTIVE: To evaluate the concordance of case-finding methods for central line-associated infection as defined by Centers for Medicare and Medicaid Services (CMS) hospital-acquired condition (HAC) compared with traditional infection control (IC) methods. SETTING: One tertiary care and 2 community hospitals in North Carolina. PATIENTS: Adult and pediatric hospitalized patients determined to have central line infection by either case-finding method. METHODS: We performed a retrospective comparative analysis of infection detected using HAC versus standard IC central line-associated bloodstream infection surveillance from October 1, 2007, through December 31, 2009. One billing and 2 IC databases were queried and matched to determine the number and concordance of cases identified by each method. Manual review of 25 cases from each discordant category was performed. Sensitivity and positive predictive value (PPV) were calculated using IC as criterion standard. RESULTS: A total of 1,505 cases were identified: 844 by International Classification of Diseases, Ninth Revision (ICD-9), and 798 by IC. A total of 204 cases (24%) identified by ICD-9 were deemed not present at hospital admission by coders. Only 112 cases (13%) were concordant. HAC sensitivity was 14% and PPV was 55% compared with IC. Concordance was low regardless of hospital type. Primary reasons for discordance included differences in surveillance and clinical definitions, clinical uncertainty, and poor documentation. CONCLUSIONS: The case-finding method used by CMS HAC and the methods used for traditional IC surveillance frequently do not agree. This can lead to conflicting results when these 2 measures are used as hospital quality metrics.

Observing and improving hand hygiene compliance: implementation and refinement of an electronic-assisted direct-observer hand hygiene audit program.

We implemented a direct-observer hand hygiene audit program that used trained observers, wireless data entry devices, and an intranet portal. We improved the reliability and utility of the data by standardizing audit processes, regularly retraining auditors, developing an audit guidance tool, and reporting weighted composite hand hygiene compliance scores.

The impact of depth of infection and postdischarge surveillance on rate of surgical-site infections in a network of community hospitals.

OBJECTIVE: To describe the epidemiology of surgical-site infections (SSIs) in community hospitals and to explore the impact of depth of SSI, healthcare location at the time of diagnosis, and variations in surveillance practices on the overall rate of SSI. DESIGN: Retrospective cohort study. SETTING: Thirty-seven community hospitals in the southeastern United States. PATIENTS: Consecutive sample of patients undergoing surgical procedures between July 1, 2007, and December 31, 2008. METHODS: ANOVA was used to compare rates of SSIs, and the F test was used to compare the distribution of rates of SSIs. Wilcoxon Signed Rank test [corrected] was used to test for differences in performance rankings of hospitals. RESULTS: Following 177,706 surgical procedures, 1,919 SSIs were identified (incidence, 1.08 per 100 procedures). Sixty-four percent (1,223 of 1,919) of these were identified as complex SSIs; 87% of the complex SSIs were diagnosed in inpatient settings. The median proportion of superficial-incisional SSIs was 37% (interquartile range, 29.6%-49.5%). Postdischarge SSI surveillance was variable, with 58% of responding hospitals using surgeon letters. As reporting focus was narrowed from all SSIs to complex SSIs (incidence, 0.69 per 100 procedures) and, finally, to complex SSIs diagnosed in the inpatient setting (incidence, 0.51 per 100 procedures), variance in rates changed significantly ([Formula: see text]). Performance ranking of individual hospitals, based on rates of SSIs, differed significantly, depending on the reporting method utilized ([Formula: see text]). CONCLUSIONS: Inconsistent reporting methods focused on variable depths of infection and healthcare location at time of diagnosis significantly impact rates of SSI, distribution of rates of SSI, and hospital comparative-performance rankings. We believe that public reporting of SSI rates should be limited to complex SSIs diagnosed in the inpatient setting.

"What the eyes don't see, the heart doesn't grieve over": epidemiology and risk factors for bloodstream infections following cardiac catheterization.

No standard definition exists for surveillance and characterization of the epidemiology of bloodstream infections (BSIs) after cardiac catheterization (CC) procedures. We proposed a novel case definition and determined the epidemiology and risk factors of BSIs after CC procedure using this new definition.

A major genome region underlying artemisinin resistance in malaria.

Evolving resistance to artemisinin-based compounds threatens to derail attempts to control malaria. Resistance has been confirmed in western Cambodia and has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CRs) after treatment. We used a two-phase strategy to identify genome region(s) underlying this ongoing selective event. Geographical differentiation and haplotype structure at 6969 polymorphic single-nucleotide polymorphisms (SNPs) in 91 parasites from Cambodia, Thailand, and Laos identified 33 genome regions under strong selection. We screened SNPs and microsatellites within these regions in 715 parasites from Thailand, identifying a selective sweep on chromosome 13 that shows strong association (P = 10(-6) to 10(-12)) with slow CRs, illustrating the efficacy of targeted association for identifying the genetic basis of adaptive traits.

Comparison of the burdens of hospital-onset, healthcare facility-associated Clostridium difficile Infection and of healthcare-associated infection due to methicillin-resistant Staphylococcus aureus in community hospitals.

We sought to determine the burden of nosocomial Clostridium difficile infection in comparison to other healthcare-associated infections (HAIs) in community hospitals participating in an infection control network. Our data suggest that C. difficile has replaced MRSA as the most common etiology of HAI in community hospitals in the southeastern United States.

A case-control study of community-associated Clostridium difficile infection: no role for proton pump inhibitors.

BACKGROUND: The epidemiology of community-associated Clostridium difficile infection is not well known. We performed a multicenter, case-control study to further describe community-associated C. difficile infection and assess novel risk factors. METHODS: We conducted this study at 5 sites from October 2006 through November 2007. Community-associated C. difficile infection included individuals with diarrhea, a positive C. difficile toxin, and no recent (12 weeks) discharge from a health care facility. We selected controls from the same clinics attended by cases. We collected clinical and exposure data at the time of illness and cultured residual stool samples and performed ribotyping. RESULTS: Of 1041 adult C. difficile infections, 162 (15.5%) met criteria for community-associated: 66 case and 114 control patients were enrolled. Case patients were relatively young (median 64 years), female (56%), and frequently required hospitalization (38%). Antimicrobials, malignancy, exposure to high-risk persons, and remote health care exposure were independently associated with community-associated C. difficile infection. In 40% of cases, we could not confirm recent antibiotic exposure. Stomach-acid suppressants were not associated with community-associated infection, and 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors appeared protective. Prevalence of the hypervirulent NAP-1/027 strain was infrequent (17%). CONCLUSIONS: Community-associated C. difficile infection resulted in a substantial health care burden. Antimicrobials are a significant risk factor for community-associated infection. However, other unique factors also may contribute, including person-to-person transmission, remote health care exposures, and 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors. A role for stomach-acid suppressants in community-associated C. difficile infection is not supported.

The network approach for prevention of healthcare-associated infections: long-term effect of participation in the Duke Infection Control Outreach Network.

OBJECTIVE: To describe the rates of several key outcomes and healthcare-associated infections (HAIs) among hospitals that participated in the Duke Infection Control Outreach Network (DICON). DESIGN AND SETTING: Prospective, observational cohort study of patients admitted to 24 community hospitals from 2003 through 2009. METHODS: The following data were collected and analyzed: incidence of central line-associated bloodstream infections (CLABSIs), ventilator-associated pneumonia (VAP), catheter-associated urinary tract infections (CAUTIs), and HAIs caused by methicillin-resistant Staphylococcus aureus (MRSA); employee exposures to bloodborne pathogens (EBBPs); physician EBBPs; patient-days; central line-days; ventilator-days; and urinary catheter-days. Poisson regression was used to determine whether incidence rates of these HAIs and exposures changed during the first 5 and 7 years of participation in DICON; nonrandom clustering of each outcome was controlled for. Cost saved and lives saved were calculated on the basis of published estimates. RESULTS: In total, we analyzed 6.5 million patient-days, 4,783 EBPPs, 2,948 HAIs due to MRSA, and 2,076 device-related infections. Rates of employee EBBPs, HAIs due to MRSA, and device-related infections decreased significantly during the first 5 years of participation in DICON (P< .05 for all models; average decrease was approximately 50%); in contrast, physician EBBPs remained unchanged. In aggregate, 210 CLABSIs, 312 cases of VAP, 332 CAUTIs, 1,042 HAIs due to MRSA, and 1,016 employee EBBPs were prevented. Each hospital saved approximately $100,000 per year of participation, and collectively the hospitals may have prevented 52-105 deaths from CLABSI or VAP. The 7-year analysis demonstrated that these trends continued with further participation. CONCLUSIONS: Hospitals with long-term participation in an infection control network decreased rates of significant HAIs by approximately 50%, decreased costs, and saved lives.

An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations.

We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.

Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae).

Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.