Dynamics and predisposition of respiratory viral co-infections in children and adults.

OBJECTIVES: The epidemiology of respiratory co-infection pairings is poorly understood. Here we assess the dynamics of respiratory viral co-infections in children and adults and determine predisposition for or against specific viral pairings. METHODS: Over five respiratory seasons from 30 November 2013 through 6 June 2018, the mono-infection and co-infection prevalence of 13 viral pathogens was tabulated at The Cleveland Clinic. Employing a model to proportionally distribute viral pairs using individual virus co-infection rate with prevalence patterns of concurrent co-circulating viruses, we compared predicted occurrence with observed occurrence of 132 viral pairing permutations using binomial analysis. RESULTS: Of 30 535 respiratory samples, 9843 (32.2%) were positive for at least one virus and 1018 (10.8%) of these were co-infected. Co-infected samples predominantly originated from children. Co-infection rate in paediatric population was 35.0% (2068/5906), compared with only 5.8% (270/4591) in adults. Adenovirus C (ADVC) had the highest co-infection rate (426/623, 68.3%) while influenza virus B had the lowest (55/546, 10.0%). ADVC-rhinovirus (HRV), respiratory syncytial virus A (RSVA)-HRV and RSVB-HRV pairings occurred at significantly higher frequencies than predicted by the proportional distribution model (p < 0.05). Additionally, several viral pairings had fewer co-infections than predicted by our model: notably metapneumovirus (hMPV)-parainfluenza virus 3, hMPV-RSVA and RSVA-RSVB. CONCLUSIONS: This is one of the largest studies on respiratory viral co-infections in children and adults. Co-infections are substantially more common in children, especially under 5 years of age, and the most frequent pairings occurred at a higher frequency than would be expected by random. Specific pairings occur at altered rates compared with those predicted by proportional distribution, suggesting either direct or indirect interactions result between specific viral pathogens.

Implementation of a Clinical Decision Support Tool for Stool Cultures and Parasitological Studies in Hospitalized Patients.

There is substantial evidence that stool culture and parasitological examinations are of minimal to no value after 3 days of hospitalization. We implemented and studied the impact of a clinical decision support tool (CDST) to decrease the number of unnecessary stool cultures (STCUL), ova/parasite (O&P) examinations, and Giardia/Cryptosporidium enzyme immunoassay screens (GC-EIA) performed for patients hospitalized >3 days. We studied the frequency of stool studies ordered before or on day 3 and after day 3 of hospitalization (i.e., categorical orders/total number of orders) before and after this intervention and denoted the numbers and types of microorganisms detected within those time frames. This intervention, which corresponded to a custom-programmed hard-stop alert tool in the Epic hospital information system, allowed providers to override the intervention by calling the laboratory, if testing was deemed medically necessary. Comparative statistics were employed to determine significance, and cost savings were estimated based on our internal costs. Before the intervention, 129/670 (19.25%) O&P examinations, 47/204 (23.04%) GC-EIA, and 249/1,229 (20.26%) STCUL were ordered after 3 days of hospitalization. After the intervention, 46/521 (8.83%) O&P examinations, 27/157 (17.20%) GC-EIA, and 106/1,028 (10.31%) STCUL were ordered after 3 days of hospitalization. The proportions of reductions in the number of tests performed after 3 days and the associated P values were 54.1% for O&P examinations (P < 0.0001), 22.58% for GC-EIA (P = 0.2807), and 49.1% for STCUL (P < 0.0001). This was estimated to have resulted in $8,108.84 of cost savings. The electronic CDST resulted in a substantial reduction in the number of evaluations of stool cultures and the number of parasitological examinations for patients hospitalized for more than 3 days and in a cost savings while retaining the ability of the clinician to obtain these tests if clinically indicated.

Impact of antimicrobial stewardship and rapid microarray testing on patients with Gram-negative bacteremia.

A rapid microarray assay, Nanosphere Verigene® Gram-negative blood culture test (BC-GN), detects four Gram-negative species, four Gram-negative genera, and six resistance genes directly from positive blood culture samples, shortening the time from Gram stain to pathogen and resistance-gene identification. The purpose of this study was to determine the impact of the BC-GN paired with an antimicrobial stewardship intervention on antimicrobial and clinical outcomes. Patients with Gram-negative bacteremia were compared before (n = 456) and after (n = 421) BC-GN implementation. The primary objective was to compare time from Gram stain to antimicrobial switch pre- and post-implementation. Time from Gram stain to effective treatment, in-hospital mortality, and hospital length of stay were also compared. The number and type of antimicrobial switches were similar between groups. Median (IQR) time from Gram stain to antimicrobial switch was significantly decreased in the post group, 28.6 (8.6-56.9) h vs 44.1 (18.9-64.6) h, p = 0.004. In patients on ineffective antimicrobial therapy at the time of result, median time to effective therapy was lower in the post group, 8.8 (5.5-18.4) h vs 24.5 (4.9-44.3) h, p = 0.034. Median (IQR) hospital length of stay was also decreased in the post group, 7 (5-15) days vs 9 (4.5-21) days, p = 0.001. The rate of in-hospital mortality was similar between groups, 11.6% (pre) vs 11.4% (post), p = 0.87. Rapid microarray testing on blood cultures combined with active antimicrobial stewardship intervention was associated with decreased time to antimicrobial switch, time to effective therapy, and hospital length of stay.

Progress in Quantitative Viral Load Testing: Variability and Impact of the WHO Quantitative International Standards.

It has been hoped that the recent availability of WHO quantitative standards would improve interlaboratory agreement for viral load testing; however, insufficient data are available to evaluate whether this has been the case. Results from 554 laboratories participating in proficiency testing surveys for quantitative PCR assays of cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK virus (BKV), adenovirus (ADV), and human herpesvirus 6 (HHV6) were evaluated to determine overall result variability and then were stratified by assay manufacturer. The impact of calibration to international units/ml (CMV and EBV) on variability was also determined. Viral loads showed a high degree of interlaboratory variability for all tested viruses, with interquartile ranges as high as 1.46 log10 copies/ml and the overall range for a given sample up to 5.66 log10 copies/ml. Some improvement in result variability was seen when international units were adopted. This was particularly the case for EBV viral load results. Variability in viral load results remains a challenge across all viruses tested here; introduction of international quantitative standards may help reduce variability and does so more or less markedly for certain viruses.

Multicenter evaluation of the new Vitek 2 yeast susceptibility test using new CLSI clinical breakpoints for fluconazole.

A fully automated antifungal susceptibility test system recently updated to reflect the new species-specific clinical breakpoints (CBPs) of fluconazole for Candida (Vitek 2 AF03 yeast susceptibility test; bioMérieux, Inc., Durham, NC) was compared in three different laboratories with the Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution (BMD) method by testing 2 quality control strains, 10 reproducibility strains (4 Candida species and 6 Cryptococcus neoformans strains), and 746 isolates of Candida species (702 isolates, 13 species) and 44 isolates of C. neoformans against fluconazole. Excellent essential agreement (EA) (within 2 dilutions) between the reference and Vitek 2 MICs was observed for fluconazole and Candida species (94.0%). The EA was lower for fluconazole and C. neoformans at 86.4%. The mean times to a result with the Vitek 2 test were 9.1 h for Candida species and 12.1 h for C. neoformans. Categorical agreement (CA) between the two methods was assessed by using the new species-specific CBPs. For less common species without fluconazole CBPs, the epidemiological cutoff values (ECVs) were used to differentiate wild-type (WT; MIC, ≤ ECV) from non-WT (MIC, >ECV) strains. The CAs between the two methods were 92.0% for Candida species (0.3% very major errors [VME] and 2.6% major errors [ME]) and 84.1% for C. neoformans (4.5% VME and 11.4% ME). The updated Vitek 2 AF03 IUO yeast susceptibility system is comparable to the CLSI BMD reference method for testing the susceptibility of clinically important yeasts to fluconazole when using the new (lower) CBPs and ECVs.

Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system.

Accurate and timely identification of anaerobic bacteria is critical to successful treatment. Classic phenotypic methods for identification require long turnaround times and can exhibit poor species level identification. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an identification method that can provide rapid identification of anaerobes. We present a multi-centre study assessing the clinical performance of the VITEK(®) MS in the identification of anaerobic bacteria. Five different test sites analysed a collection of 651 unique anaerobic isolates comprising 11 different genera. Multiple species were included for several of the genera. Briefly, anaerobic isolates were applied directly to a well of a target plate. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry. Mass spectra results were generated with the VITEK(®) MS, and the comparative spectral analysis and organism identification were determined using the VITEK(®) MS database 2.0. Results were confirmed by 16S rRNA gene sequencing. Of the 651 isolates analysed, 91.2% (594/651) exhibited the correct species identification. An additional eight isolates were correctly identified to genus level, raising the rate of identification to 92.5%. Genus-level identification consisted of Actinomyces, Bacteroides and Prevotella species. Fusobacterium nucleatum, Actinomyces neuii and Bacteroides uniformis were notable for an increased percentage of no-identification results compared with the other anaerobes tested. VITEK(®) MS identification of clinically relevant anaerobes is highly accurate and represents a dramatic improvement over other phenotypic methods in accuracy and turnaround time.

Multi-center evaluation of the VITEK® MS system for mass spectrometric identification of non-Enterobacteriaceae Gram-negative bacilli.

Studies have demonstrated that matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, accurate method for the identification of clinically relevant bacteria. The purpose of this study was to evaluate the performance of the VITEK MS v2.0 system (bioMérieux) for the identification of the non-Enterobacteriaceae Gram-negative bacilli (NEGNB). This multi-center study tested 558 unique NEGNB clinical isolates, representing 18 genera and 33 species. Results obtained with the VITEK MS v2.0 were compared with reference 16S rRNA gene sequencing and when indicated recA sequencing and phenotypic analysis. VITEK MS v2.0 provided an identification for 92.5 % of the NEGNB isolates (516 out of 558). VITEK MS v2.0 correctly identified 90.9 % of NEGNB (507 out of 558), 77.8 % to species level and 13.1 % to genus level with multiple species. There were four isolates (0.7 %) incorrectly identified to genus level and five isolates (0.9 %), with one incorrect identification to species level. The remaining 42 isolates (7.5 %) were either reported as no identification (5.0 %) or called "mixed genera" (2.5 %) since two or more different genera were identified as possible identifications for the test organism. These findings demonstrate that the VITEK MS v2.0 system provides accurate results for the identification of a challenging and diverse group of Gram-negative bacteria.

Identification of Enterobacteriaceae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using the VITEK MS system.

This multicenter study evaluated the accuracy of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry identifications from the VITEK MS system (bioMérieux, Marcy l'Etoile, France) for Enterobacteriaceae typically encountered in the clinical laboratory. Enterobacteriaceae isolates (n = 965) representing 17 genera and 40 species were analyzed on the VITEK MS system (database v2.0), in accordance with the manufacturer's instructions. Colony growth (≤72 h) was applied directly to the target slide. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry before mass spectrometry analysis. On the basis of the confidence level, the VITEK MS system provided a species, genus only, or no identification for each isolate. The accuracy of the mass spectrometric identification was compared to 16S rRNA gene sequencing performed at MIDI Labs (Newark, DE). Supplemental phenotypic testing was performed at bioMérieux when necessary. The VITEK MS result agreed with the reference method identification for 96.7% of the 965 isolates tested, with 83.8% correct to the species level and 12.8% limited to a genus-level identification. There was no identification for 1.7% of the isolates. The VITEK MS system misidentified 7 isolates (0.7 %) as different genera. Three Pantoea agglomerans isolates were misidentified as Enterobacter spp. and single isolates of Enterobacter cancerogenus, Escherichia hermannii, Hafnia alvei, and Raoultella ornithinolytica were misidentified as Klebsiella oxytoca, Citrobacter koseri, Obesumbacterium proteus, and Enterobacter aerogenes, respectively. Eight isolates (0.8 %) were misidentified as a different species in the correct genus. The VITEK MS system provides reliable mass spectrometric identifications for Enterobacteriaceae.

Should varicella-zoster virus culture be eliminated? A comparison of direct immunofluorescence antigen detection, culture, and PCR, with a historical review.

A comparison of direct fluorescent-antibody assay (DFA), culture, and two PCR assays disclosed sensitivities of 87.8%, 46.3%, and 97.6% and 100%, respectively. We reviewed 1,150 results for clinical specimens submitted for DFA and culture and found that only 17 were culture positive/DFA negative. The incremental cost to detect these 17 positives was $3,078/specimen.

Immuno-flow cytometry for the rapid identification of Staphylococcus aureus and the detection of methicillin resistance.

Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) can be reliably differentiated by flow cytometry when labeled with nucleic acid dyes. The purpose of this study was to determine if this differentiation can be achieved while labeling with a S. aureus-specific anti-staphylococcal protein A antibody instead of nucleic acid dyes. A total of 103 S. aureus isolates were incubated for 4 h at 37°C in Mueller Hinton broth with and without oxacillin, then stained with anti-staphylococcal protein A antibody, and analyzed by flow cytometry using the Micro PRO™ instrument. Dot plots (side scatter vs. fluorescence intensity) of isolates exposed to oxacillin were examined to define two gates encompassing the majority of MSSA and MRSA signal events, respectively. The ratio of signal event counts in the two gates was called the gate signal count ratio (GSCR), and its performance was evaluated using receiver operating characteristic (ROC) curves. The GSCR could differentiate MRSA from MSSA with 98% sensitivity and 100% specificity using a cut-off of 0.6868 when the two gates were defined as follows: gate 1, fluorescence intensity 2-10, side scatter 5-70; gate 2, fluorescence intensity 7-700, side scatter 70-500. MRSA and MSSA can be accurately detected and differentiated by flow cytometry after 4 h of oxacillin exposure when labeled with anti-staphylococcal protein A antibody.

Detection of group B Streptococcus bacteria in LIM enrichment broth by peptide nucleic acid fluorescent in situ hybridization (PNA FISH) and rapid cycle PCR.

The sensitivity, specificity, and negative and positive predictive values for the detection of group B Streptococcus (GBS) in 206 LIM enrichment broths by the use of subculture, GBS peptide nucleic acid fluorescent in situ hybridization (PNA FISH), and GBS PCR were 96.9%, 100%, 98.6%, and 100%; 98.4%, 100%, 99.3%, and 100%; and 100%, 100%, 100%, and 100%, respectively.

Use of a high-resolution melt assay to characterize codon 54 of the cyp51A gene of Aspergillus fumigatus on a Rotor-Gene 6000 instrument.

A high-resolution melt (HRM) assay using a Rotor-Gene 6000 instrument was developed to characterize the codon for glycine 54 in the cyp51A genes from 13 reference isolates and 12 clinical isolates of Aspergillus fumigatus. Mutations in this codon confer reduced susceptibility to itraconazole and posaconazole. The assay is simple to perform, and a result of "wild type" or "mutant" is available after approximately 1 h following DNA extraction using commercially available reagents and conventional primers.

Mycobacterium abscessus infection in solid organ transplant recipients: report of three cases and review of the literature.

Mycobacterium abscessus is an ubiquitous organism found in the environment. This rapidly growing mycobacterium infrequently causes disease in humans; however, in immunocompromised hosts, disease can range from localized cutaneous lesions to disseminated infection. The organism is resistant to most antimycobacterial drugs and therapy can be limited by drug interactions. The exact incidence of M. abscessus infection among solid organ transplant (SOT) recipients is unknown; data are only available from previously reported cases in the literature. We describe 3 cases of M. abscessus infection in SOT recipients diagnosed within a 5-month period. One of the cases followed multi-visceral transplantation, the first such case to be reported in the literature. An epidemiological investigation did not reveal significant commonalities among the cases, and pulsed-field gel electrophoresis of genomic DNA of the case isolates confirmed their non-identity. All cases improved with antibiotic therapy, most notably with the new glycylcycline, tigecycline, along with surgical intervention in 2 of the cases. In addition, we review features and characteristics of M. abscessus infections in recipients of SOT reported in the literature from 1992 to 2008 and summarize some selected therapeutic concerns and issues related to treatment.

A case of subcutaneous Mycoleptodiscus indicus infection in a liver transplant recipient successfully treated with antifungal therapy.

Mycoleptodiscus indicus, a dematiaceous mold, occurs on the leaves of a number of different host plants and has been only recently described as a cause of human infection. Immunosuppressed individuals are at risk for developing infections with opportunistic fungal pathogens, which are a major cause of morbidity and mortality in this population. In addition, the treatment of infections caused by these fungi is frequently challenging. We report a case of M. indicus subcutaneous infection in a 51-year-old man with human immunodeficiency virus and hepatitis C co-infection, who had a liver transplant. He developed skin nodules with a sporotrichoid lymphangitic distribution. Histopathology demonstrated unusual fungal elements with angioinvasion. Mycology cultures isolated a dematiaceous mold with the characteristic curved hyaline conidia of M. indicus. Initial treatment involved a combination of amphotericin B lipid complex and voriconazole, followed by monotherapy with voriconazole. The subcutaneous lesions resolved completely after 4 months of antifungal therapy.

Multicenter comparison of the VITEK 2 antifungal susceptibility test with the CLSI broth microdilution reference method for testing amphotericin B, flucytosine, and voriconazole against Candida spp.

A fully automated commercial antifungal susceptibility test system (VITEK 2; bioMérieux, Inc., Hazelwood, MO) was compared in three different laboratories with the Clinical and Laboratory Standards Institute (formerly the NCCLS) reference broth microdilution method (BMD) by testing 2 quality control strains, 10 reproducibility strains, and 426 isolates of Candida spp. against amphotericin B, flucytosine, and voriconazole. Reference BMD MIC endpoints were established after 24 and 48 h of incubation. VITEK 2 system MIC endpoints were determined spectrophotometrically after 9.1 to 27.1 h of incubation (mean, 12 to 14 h). Excellent essential agreement (within 2 dilutions) between the VITEK 2 system and the 24- and 48-h BMD MICs was observed for all three antifungal agents: amphotericin B, 99.1% and 97%, respectively; flucytosine, 99.1% and 98.8%, respectively; and voriconazole, 96.7% and 96%, respectively. Both intra- and interlaboratory agreements were >98% for all three drugs. The overall categorical agreements between the VITEK 2 system and BMD for flucytosine and voriconazole were 98.1 to 98.6% at the 24-h BMD time point and 96.9 to 97.4% at the 48-h BMD time point. The VITEK 2 system reliably detected flucytosine and voriconazole resistance among Candida spp. and demonstrated excellent quantitative and qualitative agreement with the reference BMD method.

Rapid detection of Panton-Valentine leukocidin-positive Staphylococcus aureus by real-time PCR targeting the lukS-PV gene.

In order to assess the speed and accuracy of a real-time PCR assay targeting the lukS-PV gene of Panton-Valentine leukocidin (PVL)-positive Staphylococcus aureus, 700 S. aureus strains were tested and the results were compared to those achieved with block cycler PCR. Cross-reactivity was tested with 166 other bacterial species. Using this homogeneous real-time PCR assay format, the presence or absence of genetic information for PVL, which is also found in community-associated methicillin-resistant S. aureus, was correctly identified from pure culture and directly in various types of clinical specimens.

Multicenter comparison of the VITEK 2 yeast susceptibility test with the CLSI broth microdilution reference method for testing fluconazole against Candida spp.

A fully automated commercial antifungal susceptibility test system (VITEK 2 yeast susceptibility test; bioMerieux, Inc., Hazelwood, Mo.) was compared in three different laboratories with Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution (BMD) method by testing two quality control strains and a total of 426 isolates of Candida spp. (103 to 135 clinical isolates in each laboratory plus 80 challenge isolates in one laboratory) against fluconazole. Reference BMD MIC endpoints were established after 24 and 48 h of incubation. VITEK 2 endpoints were determined spectrophotometrically after 10 to 26 h of incubation (mean, 13 h). Excellent essential agreement (within two dilutions) between the VITEK 2 and the 24- and 48-h BMD MICs was observed. The overall agreement values were 97.9 and 93.7%, respectively. Both intra- and interlaboratory agreement was 100%. The overall categorical agreement between VITEK 2 and BMD was 97.2% at the 24-h BMD time point and 88.3% at the 48-h BMD time point. Decreased categorical agreement at 48 h was attributed to trailing growth observed with Candida glabrata. The VITEK 2 system reliably detected fluconazole resistance among Candida spp. and demonstrated excellent quantitative and qualitative agreement with the reference BMD method.

Use of partial 16S rRNA gene sequencing for identification of Legionella pneumophila and non-pneumophila Legionella spp.

We examined 49 Legionella species, 26 L. pneumophila and 23 non-pneumophila Legionella spp., using partial 16S rRNA gene sequencing. This approach accurately identified all the L. pneumophila isolates, characterized all non-pneumophila Legionella isolates as such within this genus, and classified most (20/23; 87%) of the non-pneumophila Legionella isolates to the species level.

Multicenter evaluation of a Candida albicans peptide nucleic acid fluorescent in situ hybridization probe for characterization of yeast isolates from blood cultures.

We evaluated aliquots from 244 clinical blood culture bottles that demonstrated yeasts on Gram stain using a Candida albicans peptide nucleic acid (PNA) fluorescent in situ hybridization (FISH) probe. The sensitivity, specificity, positive predictive value, and negative predictive value of the C. albicans PNA FISH test in this study were 99%, 100%, 100%, and 99.3%, respectively.