Melissa B. Miller

Role of hospital surfaces in the transmission of emerging health care-associated pathogens: Norovirus, Clostridium difficile, and Acinetobacter species

Health care-associated infections (HAI) remain a major cause of patient morbidity and mortality. Although the main source of nosocomial pathogens is likely the patients endogenous flora, an estimated 20% to 40% of HAI have been attributed to cross infection via the hands of health care personnel, who have become contaminated from direct contact with the patient or indirectly by touching contaminated environmental surfaces. Multiple studies strongly suggest that environmental contamination plays an important role in the transmission of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus spp. More recently, evidence suggests that environmental contamination also plays a role in the nosocomial transmission of norovirus, Clostridium difficile, and Acinetobacter spp. All 3 pathogens survive for prolonged periods of time in the environment, and infections have been associated with frequent surface contamination in hospital rooms and health care worker hands. In some cases, the extent of patient-to-patient transmission has been found to be directly proportional to the level of environmental contamination. Improved cleaning/disinfection of environmental surfaces and hand hygiene have been shown to reduce the spread of all of these pathogens. Importantly, norovirus and C difficile are relatively resistant to the most common surface disinfectants and waterless alcohol-based antiseptics. Current hand hygiene guidelines and recommendations for surface cleaning/disinfection should be followed in managing outbreaks because of these emerging pathogens.

Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology

SUMMARY The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platforms advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.

Genotype Prevalence and Risk Factors for Severe Clinical Adenovirus Infection, United States 2004-2006

BACKGROUND Recently, epidemiological and clinical data have revealed important changes with regard to clinical adenovirus infection, including alterations in antigenic presentation, geographical distribution, and virulence of the virus. METHODS In an effort to better understand the epidemiology of clinical adenovirus infection in the United States, we adopted a new molecular adenovirus typing technique to study clinical adenovirus isolates collected from 22 medical facilities over a 25-month period during 2004-2006. A hexon gene sequence typing method was used to characterize 2237 clinical adenovirus-positive specimens, comparing their sequences with those of the 51 currently recognized prototype human adenovirus strains. In a blinded comparison, this method performed well and was much faster than the classic serologic typing method. RESULTS Among civilians, the most prevalent adenovirus types were types 3 (prevalence, 34.6%), 2 (24.3%), 1 (17.7%), and 5 (5.3%). Among military trainees, the most prevalent types were types 4 (prevalence, 92.8%), 3 (2.6%), and 21 (2.4%). CONCLUSIONS For both populations, we observed a statistically significant increasing trend of adenovirus type 21 detection over time. Among adenovirus isolates recovered from specimens from civilians, 50% were associated with hospitalization, 19.6% with a chronic disease condition, 11% with a bone marrow or solid organ transplantation, 7.4% with intensive care unit stay, and 4.2% with a cancer diagnosis. Multivariable risk factor modeling for adenovirus disease severity found that age <7 years (odds ratio [OR], 3.2; 95% confidence interval [CI], 1.4-7.4), chronic disease (OR, 3.6; 95% CI, 2.6-5.1), recent transplantation (OR, 2.7; 95% CI, 1.3-5.2), and adenovirus type 5 (OR, 2.7; 95% CI, 1.5-4.7) or type 21 infection (OR, 7.6; 95% CI, 2.6-22.3) increased the risk of severe disease.

Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP Fast Multiplex Assays for Detection of Respiratory Viruses

ABSTRACT There are several U.S. FDA-cleared molecular respiratory virus panels available today, each with advantages and disadvantages. This study compares four multiplex panels, the BioFire Diagnostics FilmArray RP (respiratory panel), the GenMark Dx eSensor RVP (respiratory viral panel), the Luminex xTAG RVPv1, and the Luminex xTAG RVP fast. Three hundred specimens (200 retrospective and 100 consecutive) were tested using all four platforms to determine performance characteristics. The overall sensitivity and specificity, respectively, and 95% confidence interval (CI; in parentheses) for each panel were as follows: FilmArray RP, 84.5% (79.2, 88.6) and 100% (96.2, 100); eSensor RVP, 98.3% (95.5, 99.5) and 99.2% (95.4, 100); xTAG RVPv1, 92.7% (88.5, 95.4) and 99.8% (96.0, 100); and xTAG RVP fast, 84.4% (78.5, 88.9) and 99.9% (96.1, 100). The sensitivity of each assay fluctuated by viral target, with the greatest discrepancies noted for adenovirus and influenza virus B detection. Hands-on time and time to result were recorded and ease of use was assessed to generate a complete profile of each assay.

Laboratory Aspects of Management of Chronic Pulmonary Infections in Patients with Cystic Fibrosis

In 1994, the U.S. Cystic Fibrosis Foundation sponsored a consensus conference (33) on microbiology and infectious disease in patients with cystic fibrosis (CF), a homozygous recessive disease in individuals of Caucasian descent. The organization of that conference followed the recognition that the discovery of the CF gene in 1989 was not going to yield a quick cure for CF and that chronic pulmonary infection was the primary culprit in the early mortality associated with this disease. The resulting document made recommendations for the detection, isolation, identification, and susceptibility testing of organisms recognized as significant or potentially significant in the lung diseases of this patient population. The microbial species that are clearly associated with lung disease in CF patients (CF lung disease) are relatively few, including Staphylococcus aureus, Pseudomonas aeruginosa, and Burkholderia cepacia complex (Table ​(Table1).1). Organisms having a secondary role in CF lung disease include respiratory viruses, such as respiratory syncytial virus and influenza virus; Haemophilus influenzae; and Aspergillus fumigatus. Mycobacterium spp. but not Mycobacterium tuberculosis, Stenotrophomonas maltophilia, and Alcaligenes xylosoxidans are being seen with increasing frequencies in CF patients, in part because of the increasing life spans of CF patients and the relentless use of antimicrobial agents in this patient population. However, the role of the latter organisms in CF lung disease has not been clearly determined. In addition, organisms that phenotypically resemble B. cepacia complex organisms (i.e., Burkholderia gladioli, Ralstonia spp., and Pandoraea spp.) are also being seen with increasing frequencies due to the use of selective media that improve the rates of recovery of B. cepacia complex isolates. These media also improve the rates of recovery of these other species. Although there are no data that suggest that these non-B. cepacia complex organisms play a role in CF lung disease, these organisms are difficult to differentiate phenotypically from B. cepacia complex. As we will review, misidentification of these seemingly harmless saprophytes as B. cepacia complex organisms may have profound consequences for the patient. This minireview discusses the state of the art in the laboratory diagnosis of the infectious agents associated with CF lung disease.

Posttransplantation Disseminated Coccidioidomycosis Acquired from Donor Lungs

ABSTRACT A North Carolinian developed fatal coccidioidomycosis immediately after bilateral lung transplantation. The donor had previously traveled to Mexico, and the recipient had no travel history to an area where Coccidioides immitis is endemic. Immunosuppresive therapy of the transplant recipient likely reactivated latent Coccidioides infection in the donor lungs, leading to posttransplant coccidioidomycosis.

Performance of Xpert MTB/RIF RUO Assay and IS6110 Real-Time PCR for Mycobacterium tuberculosis Detection in Clinical Samples

ABSTRACT The Cepheid Xpert MTB/RIF research-use-only (RUO) assay and a laboratory-developed test (LDT) targeting IS6110 were evaluated and compared to mycobacterial culture as the gold standard. The performance characteristics of both molecular assays were determined by using 112 specimens from 90 patients, including 89 pulmonary specimens and 23 extrapulmonary specimens. Of the specimens tested, 37 (33%) were culture positive for the Mycobacterium tuberculosis complex; 29 were pulmonary, and 8 were extrapulmonary. Of these culture-positive specimens, 83% of the pulmonary specimens and 50% of the extrapulmonary specimens were smear positive. There was complete concordance between the smear-positive culture-positive specimens, independent of the anatomical site (100% sensitivity). The sensitivity of the MTB/RIF RUO assay for smear-negative specimens was 60% for pulmonary and 75% for extrapulmonary specimens, while the IS6110 LDT sensitivities were 40% and 0%, respectively. There was also complete concordance among the culture-negative specimens tested. Both assays showed 95% specificity, with four culture-negative specimens testing as positive. A review of patient records indicated that there was a high likelihood of the presence of M. tuberculosis complex DNA in the false-positive specimens. Biosafety analysis was performed and showed an acceptable reduction in organism viability using the processing methods described above. Both molecular assays are suitable for the detection of M. tuberculosis isolates in smear-positive pulmonary and extrapulmonary specimens, while the sensitivity of the detection of M. tuberculosis isolates in smear-negative specimens was variable.

Comparative Evaluation of the Nanosphere Verigene RV+ Assay and the Simplexa Flu A/B & RSV Kit for Detection of Influenza and Respiratory Syncytial Viruses

ABSTRACT Using retrospective (n = 200) and prospective (n = 150) nasopharyngeal specimens, we evaluated the Nanosphere Verigene RV+ and the Focus Diagnostics Simplexa Flu A/B & RSV tests. Overall, RV+ demonstrated sensitivities and specificities of 96.6% and 100% for influenza A virus, 100% and 99.7% for influenza B virus, and 100% and 100% for respiratory syncytial virus (RSV), while the Simplexa test sensitivities and specificities were 82.8 and 99.7%, 76.2 and 100%, and 94.6 and 100%, respectively.

Prevalence of community-associated methicillin-resistant Staphylococcus aureus in patients with cystic fibrosis.

ABSTRACT We prospectively determined the prevalence of community-associated Staphylococcus aureus in a large cystic fibrosis (CF) center between October 2005 and October 2007. We found that 2.7% (19/707) of the CF patients who had cultures during the study period were infected with this organism, representing 14% of the total methicillin-resistant Staphylococcus aureus strains (n = 140) recovered from the patient population during the study period.

Impact of a rapid peptide nucleic acid fluorescence in situ hybridization assay on treatment of Candida infections.

PURPOSE The impact of a rapid peptide nucleic acid fluorescence in situ hybridization (PNA FISH) assay with an antimicrobial stewardship intervention on the treatment of Candida infections was studied. METHODS The utility of implementing the PNA FISH assay with an antimicrobial stewardship intervention in hospitalized patients with candidemia was evaluated by measuring the median time to Candida species identification, time to targeted therapy, and clinical outcomes, including time to culture clearance, hospital length of stay, and hospital mortality. Secondary objectives included determining the cost-effectiveness of the PNA FISH assay by assessing estimated antifungal drug costs (as average wholesale price) before (June 26, 2009-September 19, 2010) and after (September 20, 2010-June 13, 2011) test implementation and confirming test accuracy. For both groups, laboratory personnel notified the physician of the results of Grams stain from blood culture. RESULTS Time to targeted therapy significantly decreased after the implementation of the PNA FISH assay (p = 0.0016). The postimplementation group had a higher rate of culture clearance (p = 0.01). Median time to species identification was 0.2 day with the PNA FISH test versus 4 days with routine methods (p < 0.001). Accounting for the cost of the test itself and the cases in which patients were switched to more-expensive therapy on the basis of the test, we estimated that the PNA FISH test resulted in savings of approximately