Evaluation of Abbott ID NOW COVID-19 POC test performance characteristics and integration in the regional health network workflows to improve health care delivery.

With the recent global surge of SARS-CoV-2 Delta variant, there continues to be high demand for COVID-19 diagnostic testing. Abbott ID NOW is a rapid, CLIA-waived, COVID-19 diagnostic test ideally suited for use in urgent care settings or where access to diagnostic testing is limited. In this study we describe the results of rigorous validation of ID NOW and post-implementation study of POC test utilization patterns within community hospitals and clinics. Performance of ID NOW was validated by comparison of the results from 207 consecutive, paired, specimens tested on the ID NOW and on the m2000/Alinity m platforms. Once validated, ID NOW devices were placed for clinical use at four regional hospitals and clinics. We found that the ID NOW and m2000/Alinity m positive and negative percent agreement were 94.5% (95% CI, 85.1% to 98.1%) and 99.3% (95% CI, 96.4% to 99.9%), respectively. As of August 2021, a total of 2,301 tests were performed by ID NOW at individual regional network sites. The population tested consisted of 55.5% White and 42.9% Black patients, with Black patients presenting predominantly in the hospitals, while White patients were more evenly distributed between hospital and clinic sites. Disease prevalence observed among patients tested by ID NOW (12.3%) was aligned with overall prevalence seen at regional sites (11.3%). In summary, the ID NOW test can provide rapid and accurate results in a variety of near-to-patient and POC settings. If used correctly, it could serve as a valuable diagnostic tool to enable equal access to care and improve healthcare delivery within large health network systems.

Pseudo-outbreak of Legionella pneumophila serogroup 8 infection associated with a contaminated ice machine in a bronchoscopy suite.

OBJECTIVE: To investigate the marked increase noted over an 8-month period in the number of Legionella pneumophila isolates recovered from bronchoalveolar lavage fluid specimens obtained during bronchoscopy in our healthcare system. SETTING: Bronchoscopy suite that serves a 580-bed tertiary care center and a large, multisite, faculty practice plan with approximately 2 million outpatient visits per year. METHODS: Cultures of environmental specimens from the bronchoscopy suite were performed, including samples from the air and water filters, bronchoscopes, and the ice machine, with the aim of identifying Legionella species. Specimens were filtered and acid-treated and then inoculated on buffered charcoal yeast extract agar. Serogrouping was performed on all isolates recovered from patient and environmental samples. RESULTS: All L. pneumophila isolates recovered from patients were serogroup 8, a serogroup that is not usually recovered in our facility. An epidemiologic investigation of the bronchoscopy suite revealed the ice machine to be contaminated with L. pneumophila serogroup 8. Patients were exposed to the organism as a result of a recently adopted practice in the bronchoscopy suite that involved directly immersing uncapped syringes of sterile saline in contaminated ice baths during the procedures. At least 1 patient was ill as a result of the pseudo-outbreak. Molecular typing of isolates recovered from patient and environmental samples revealed that the isolates were indistinguishable. CONCLUSIONS: Extensive cleaning of the ice machine and replacement of the machine's water filter ended the pseudo-outbreak. This episode emphasizes the importance of using aseptic technique when performing invasive procedures, such as bronchoscopies. It also demonstrates the importance of reviewing procedures in all patient areas to ensure compliance with facility policies for providing a safe patient environment.

Posaconazole treatment for Apophysomyces elegans rhino-orbital zygomycosis following trauma for a male with well-controlled diabetes.

We report a case of rhino-orbital zygomycosis in a 43-year-old male with well-controlled diabetes mellitus. The patient initially received liposomal amphotericin B, but the infection continued to progress, so posaconazole treatment was begun and eventually led to the cure of his infection. The causative agent was identified as Apophysomyces elegans, an emerging cause of zygomycosis in immunocompetent hosts.

Acanthamoeba castellani encephalitis following partially mismatched related donor peripheral stem cell transplantation.

We describe a case of Acanthamoeba encephalitis in a 45-year-old Caucasian male with acute myelogenous leukemia, who was 140 days status post partially mismatched related donor peripheral blood stem cell transplant. The patient had been transplanted with a highly T-cell-depleted graft, and was not taking any immunosuppressive drugs, and had no history of graft-versus-host disease. He complained of nausea, vomiting, and occasional episodes of confusion; he also had a chronic cough since transplantation. Physical examination was unremarkable except for orthostatic hypotension. Neurologic examination was within normal limits. Laboratory values including electrolytes, white blood cells and platelet counts were normal. Computed tomographic scan of the brain showed a pansinusitis and a hyperdense lesion along the corona radiata suggestive of a fungal abscess. Magnetic resonance imaging showed multifocal areas with mass effect in the posterior fossa and parietal and occipital lobes. The patient had worsening respiratory failure and died three days after admission. At autopsy, specific immunofluorescent staining identified Acanthamoeba castellani in the brain and lungs.

Prospective multicenter clinical evaluation of AMPLICOR and COBAS AMPLICOR hepatitis C virus tests.

We conducted a multicenter clinical evaluation of the second versions of the manual AMPLICOR and the semiautomated COBAS AMPLICOR tests for hepatitis C virus (HCV) RNA (Roche Molecular Systems, Inc., Pleasanton, Calif.). The performance characteristics of these HCV RNA tests for diagnosis of active viral infection were determined by comparison to anti-HCV serological test results, alanine aminotransferase levels, and liver biopsy histology results. A total of 878 patients with clinical or biochemical evidence of liver disease were enrolled at four hepatology clinics. A total of 1,089 specimens (901 serum and 188 plasma) were tested with the AMPLICOR test. Sensitivity compared to serology was 93.1% for serum and 90.6% for plasma. The specificity was 97% for serum and 93.1% for plasma. A total of 1,084 specimens (896 serum and 188 plasma) were tested with the COBAS test. Sensitivities for serum and plasma were the same as with the AMPLICOR test. The specificity was 97.8% for serum and 96.6% for plasma. Of the 69 specimens with false-positive and false-negative AMPLICOR test results relative to those of serology, alternative primer set (APS) reverse transcription (RT)-PCR analysis showed that the AMPLICOR test provided the correct result relative to the specimens containing HCV RNA in 64 (92.7%) specimens. Similarly, 66 of 67 (98.5%) false-positive and false-negative COBAS test results were determined to be correct by APS RT-PCR analysis. There were no substantive differences in clinical performances between study sites, patient groups, specimen types, storage conditions (-20 to -80 degrees C versus 2 to 8 degrees C), or anticoagulants (EDTA versus acid citrate dextrose) for either test. Both tests showed >99% reproducibility within runs, within sites, and overall. We conclude that these tests can reliably detect the presence of HCV RNA, as evidence of active infection, in patients with clinical or biochemical evidence of liver disease.

Hepatitis C virus genotyping: clinical implications and methods.

Hepatitis C virus (HCV) chronically infects at least 1% of the world's population and is a leading cause of end-stage liver disease. HCV displays a remarkable degree of genomic diversity, with the six major genotypes and numerous subtypes differing in geographic distribution. The ability of this virus to cause persistent infections is a direct result of its genomic plasticity and the evolution of quasispecies within an infected individual. HCV genotype has emerged as an important factor both in predicting a sustained response to, and in determining the duration of, antiviral therapy. Although a variety of methods have been used for genotyping HCV, nucleotide sequencing of a phylogenetically informative region remains the gold standard.

Detection and typing of hepatitis C virus.

For more than two decades prior to the discovery of the hepatitis C virus (HCV), posttransfusion non-A, non-B (NANB) hepatitis was thought to have a viral etiology. In 1989, the virus was finally identified through a unique application of molecular cloning techniques by investigators at the Centers for Disease Control, and the Chiron Corporation (1). In a reversal of the usual sequence of events, HCV was identified and defined before its existence was substantiated through tissue culture growth, electron microscopic observation, or serologic detection. Molecular cloning of HCV preceded the use of any of the conventional methods of viral identification and serologic detection then evolved from the blind immunoscreening of millions of clones with serum from a patient who had NANB hepatitis (2). The peptide expressed in a single reactive clone (5-1-1) served as the basis for the first Food and Drug Administration (FDA)-licensed diagnostic test for detection of antibodies to HCV (3).

Diagnosis and monitoring of hepatic injury. I. Performance characteristics of laboratory tests.

PURPOSE: To review information on performance characteristics for tests that are commonly used to identify acute and chronic hepatic injury. DATA SOURCES AND STUDY SELECTION: A MEDLINE search was performed for key words related to hepatic tests, including quality specifications, aminotransferases, alkaline phosphatase, gamma-glutamyltransferase, bilirubin, albumin, ammonia, and viral markers. Abstracts were reviewed, and articles discussing performance of laboratory tests were selected for review. Additional articles were selected from the references. Guideline Preparation and Review: Drafts of the guidelines were posted on the Internet, presented at the AACC Annual Meeting in 1999, and reviewed by experts. Areas requiring further amplification or literature review were identified for further analysis. Specific recommendations were made based on analysis of published data and evaluated for strength of evidence and clinical impact. The drafts were also reviewed by the Practice Guidelines Committee of the American Association for the Study of Liver Diseases and approved by the committee and the Association's Council. RECOMMENDATIONS: Although many specific recommendations are made in the guidelines, some summary recommendations are discussed here. Alanine aminotransferase is the most important test for recognition of acute and chronic hepatic injury. Performance goals should aim for total error of <10% at the upper reference limit to meet clinical needs in monitoring patients with chronic hepatic injury. Laboratories should have age-adjusted reference limits for enzymes in children, and gender-adjusted reference limits for aminotransferases, gamma-glutamyltransferase, and total bilirubin in adults. The international normalized ratio should not be the sole method for reporting results of prothrombin time in liver disease; additional research is needed to determine the reporting mechanism that best correlates with functional impairment. Harmonization is needed for alanine aminotransferase activity, and improved standardization for hepatitis C viral RNA measurements.

Diagnosis and monitoring of hepatic injury. II. Recommendations for use of laboratory tests in screening, diagnosis, and monitoring.

PURPOSE: To review information on the use of laboratory tests in screening, diagnosis, and monitoring of acute and chronic hepatic injury. DATA SOURCES AND STUDY SELECTION: A MEDLINE search was performed for key words related to hepatic diseases, including acute hepatitis, chronic hepatitis, alcoholic hepatitis, cirrhosis, hepatocellular carcinoma, and etiologic causes. Abstracts were reviewed, and articles discussing use of laboratory tests selected for review. Additional articles were selected from the references. Guideline Preparation and Review: Drafts of the guidelines were posted on the Internet, presented at the AACC Annual Meeting in 1999, and reviewed by experts. Areas requiring further amplification or literature review were identified for further analysis. Specific recommendations were made based on analysis of published data and evaluated for strength of evidence and clinical impact. RECOMMENDATIONS: Although many specific recommendations are made in the guidelines, only some summary recommendations are listed here. In acute hepatic injury, prothrombin time and, to a lesser extent, total bilirubin are the best indicators of severity of disease. Although ALT is useful for detecting acute and chronic hepatic injury, it is not related to severity of acute hepatic injury and only weakly related to severity of chronic hepatic injury. Specific tests of viral markers should be the initial differential tests in both acute and chronic hepatic injury; when positive, they are also useful for monitoring recovery from hepatitis B and C.

A multicenter, randomized trial of daily high-dose interferon-alfa 2b for the treatment of chronic hepatitis c: pretreatment stratification by viral burden and genotype.

OBJECTIVES: The aim of this study was to determine prospectively whether an intensive regimen of daily, high-dose interferon would improve the response rate for the treatment of chronic hepatitis C in patients with unfavorable virological characteristics. METHODS: A total of 104 patients with chronic hepatitis C were randomized at eight centers to receive interferon alfa-2b at a dose of 5 million units (MU) daily or 3 MU t.i.w. for a period of 24 wk. Patients were prospectively randomized by low or high viral burden and stratified by genotype. HCV RNA was measured by quantitative polymerase chain reaction, and response rates were compared between the dosage regimens. RESULTS: HCV RNA levels dropped more rapidly to lower levels in the group treated with 5 MU daily. In this group, the initial virological response (IR) at wk 12 and the end-of-treatment response (ETR) at wk 24 were double that of patients treated with standard interferon (66% vs 33% and 48% vs 24%, p < 0.01). Sustained response rates were low for both dose groups (14% vs 4%, p = 0.08). Genotype-related differences in initial response rates were present in the standard dose group (63% non-1 genotype vs 24% genotype 1; p = 0.005) but not in those treated with 5 MU daily (66% vs 67%, p = NS). Using multivariate analysis, only the interferon dose was associated with IR and ETR (p = 0.002). CONCLUSIONS: Daily, high dose interferon rapidly dropped HCV RNA and increased initial and end-of-treatment response rates when compared to t.i.w. regimens. This effect, independent of viral burden and genotype, suggests that patients with unfavorable viral characteristics might benefit from an intensive regimen that promotes rapid viral clearance. These data support further study of the use of high-dose induction regimens. However, improvements in sustained response rates will require additional therapeutic maneuvers such as prolonged therapy or the adjunctive use of ribavirin.

Impact of viral load testing on patient care.

Quantitative human immunodeficiency virus (HIV) type 1 RNA tests have been essential tools in increasing our understanding of HIV pathogenesis and antiretroviral therapy. The plasma HIV RNA level is among the most powerful predictive tests in modern medicine for disease progression and has rapidly become the standard of practice for guiding clinicians in initiating, monitoring, and changing antiretroviral therapy. In this article the scientific rationale and clinical indications for viral load testing in HIV infection are reviewed.

Rapid identification of up to three Candida species in a single reaction tube by a 5' exonuclease assay using fluorescent DNA probes.

We used fungus-specific PCR primers and species-specific DNA probes to detect up to three Candida species in a single reaction tube by exploiting the 5' to 3' exonuclease activity of Taq DNA polymerase. Probes to the internal transcribed spacer region of the rRNA gene were labeled at the 5' end with one of three fluorescent reporter dyes, 6-carboxy-fluorescein (FAM), tetrachloro-6-carboxy-fluorescein (TET), or hexachloro-6-carboxy-fluorescein (HEX), and at the 3' end with a quencher dye, 6-carboxy-tetramethyl-rhodamine. During PCR amplification, each reporter dye emits a characteristic wavelength as it is cleaved from its specific target DNA and from the quencher dye. Therefore, signals from up to three probes can be detected simultaneously during the PCR assay. Six probes were designed for use in this study: CA-FAM, CT-TET, and CP-HEX were added to one tube to simultaneously detect the typically fluconazole-sensitive species C. albicans, C. tropicalis, and C. parapsilosis, respectively. CG-FAM and CK-TET were added to a second tube to simultaneously detect the typically more innately fluconazole-resistant species C. glabrata and C. krusei, respectively. All-CAN-TET, a Candida genus probe, was added to a third tube to detect DNAs from all Candida species tested. DNAs recovered from 61 blood culture bottles, including 23 positive for C. albicans, 18 positive for C. glabrata, 6 positive for C. tropicalis, 6 positive for C. krusei, 5 positive for C. parapsilosis, and 3 positive for mixed fungemias, were tested. Control samples included those from blood culture bottles with no growth (n = 10) or from patients with confirmed bacteremia (n = 10). Probes detected and correctly identified the organisms in 58 of 61 specimens (95.1%) and gave no false-positive results. This method is simple and rapid and does not require post-PCR hybridization and incubation steps. It is sensitive and specific for the detection and identification of Candida species from blood culture bottles, including those containing mixtures of Candida species, and should facilitate an earlier specific diagnosis, leading to more appropriately targeted antifungal drug therapy.

Clinical comparison of an enhanced-sensitivity branched-DNA assay and reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma.

The performance characteristics of an enhanced-sensitivity branched-DNA assay (bDNA) (Quantiplex HIV-1 version 2.0; Chiron Corp., Emeryville, Calif.) and a reverse transcription (RT)-PCR assay (AMPLICOR HIV-1 Monitor; Roche Diagnostic Systems, Inc., Branchburg, N.J.) were compared in a molecular diagnostic laboratory. Samples used in this evaluation included linearity and reproducibility panels made by dilution of a human immunodeficiency virus type 1 (HIV-1) stock culture of known virus particle count in HIV-1-negative plasma, a subtype panel consisting of HIV-1 subtypes A through F at a standardized level, and 64 baseline plasma specimens from HIV-1-infected individuals. Plots of log10 HIV RNA copies per milliliter versus log10 nominal virus particles per milliliter demonstrated that both assays were linear over the stated dynamic ranges (bDNA, r = 0.98; RT-PCR, r = 0.99), but comparison of the slopes of the regression lines (bDNA, m = 0.96; RT-PCR, m = 0.83) suggested that RT-PCR had greater proportional systematic error. The between-run coefficients of variation for bDNA and RT-PCR were 24.3 and 34.3%, respectively, for a sample containing 1,650 nominal virus particles/ml and 44.0 and 42.7%, respectively, for a sample containing 165 nominal virus particles/ml. Subtypes B, C, and D were quantitated with similar efficiencies by bDNA and RT-PCR; however, RT-PCR was less efficient in quantitating subtypes A, E, and F. One non-B subtype was recognized in our clinical specimens based on the ratio of values obtained with the two methods. HIV-1 RNA was quantitated in 53 (83%) baseline plasma specimens by bDNA and in 55 (86%) specimens by RT-PCR. RT-PCR values were consistently greater than bDNA values, with population means of 142,419 and 67,580 copies/ml, respectively (P < 0.01). The results were highly correlated (r = 0.91), but the agreement was poor (mean difference in log10 copies per milliliter +/- 2 standard deviations, 0.45 +/- 0.61) for the 50 clinical specimens that gave discrete values with both methods.

Aureobacterium resistens sp. nov., exhibiting vancomycin resistance and teicoplanin susceptibility.

Two similar strains of a coryneform bacterium were isolated from human clinical material. Both strains were resistant to vancomycin but susceptible to teicoplanin. Detailed biochemical, chemotaxonomical, and molecular genetic investigations revealed that both isolates were members of a hitherto undescribed species of genus Aureobacterium. The name Aureobacterium resistens sp. nov. is proposed for the new bacterium and the type strain is CCUG 38312.

Branched DNA signal amplification for direct quantitation of nucleic acid sequences in clinical specimens.

In this chapter I have reviewed the development of bDNA as a method for quantitation of nucleic acid targets and the application of this technology to the study of infectious diseases and cell biology. The ability to quantify viral nucleic acids in clinical specimens has led to a better understanding of the pathogenesis of chronic viral infections such as HIV-1, HCV, and HBV. The information provided by these methods can also be important in the management of patients with these infections. The prognostic value of a single baseline HIV-1 RNA level rivals that surgical staging procedures for cancer, which are among the most powerfully predictive tests in medicine (Mellors et al., 1996). These methods have been used to assess rapidly the effects of antiviral therapy, which has both expedited the development of antiviral drugs and improved the management of patients with HIV-1 and HCV infections. bDNA has several characteristics that distinguish it from the quantitative target amplification systems, including better tolerance of target sequence variability, more direct measurement of target, simpler sample preparation, and less sample-to-sample variation. However, the first- and second-generation bDNA assays lacked sensitivity compared with the target amplifications systems. The changes incorporated into the third-generation assays have effectively increased the signal-to-noise ratio to such a high level that the analytical sensitivity of system 8 bDNA approaches that of PCR. In theory, bDNA can be made even more sensitive by increasing both the sample volume and the signal-to-noise ratio. Nonspecific hybridization can be further reduced by finding more effective blockers for the solid phase or by redesigning the amplifier molecule or the solid phase itself. The increased sensitivity may create new applications for the technology in filter and in situ hybridization assays.

Detection of vancomycin-resistant enterococci in fecal samples by PCR.

Surveillance cultures for vancomycin-resistant enterococci (VRE) are time-consuming and expensive for the laboratory to perform. Therefore, we investigated the use of PCR as an alternative method of detecting and identifying VRE directly in fecal samples. PCR primers directed to vanA, vanB, vanC1, vanC2, and enterococcal ligase genes were used to detect and identify VRE in fecal material obtained by rectal or perirectal swabbing. Although PCR-inhibitory substances were present in DNA prepared directly from the swabs, the inhibitory substances could be reduced by processing the nucleic acid with two commercially available DNA preparation columns. Fecal material from 333 swabs was cultured on several selective agar media before and after broth enrichment. DNA was extracted from the fecal material and was analyzed by PCR. By using all four primer sets, only 59 (67.8%) of the samples were positive for vanA. However, after retesting the negative samples with only the vanA primer set, 77 (88.5%) of 87 specimens that were culture positive for Enterococcus faecium containing vanA were positive by PCR. One specimen was PCR positive for the vanA gene but culture negative for enterococci. The specificity of the vanA assay was 99.6%. PCR analysis of enrichment broth samples with all four primers sets after 15 to 18 h of incubation detected 74 (85.1%) of the 87 culture-positive specimens. The specificity of the vanA assay after the enrichment step was 100%. No vanB-containing enterococci were recovered by culture. Since 16 samples can be tested by PCR in 4 h (including electrophoresis), identification of VRE is possible within 8 h of specimen submission at a cost of approximately $10.12/assay. Thus, PCR may be a cost-effective alternative to culture for surveillance of VRE in some hospitals.

Rapid identification of Candida species in blood cultures by a clinically useful PCR method.

Widespread use of fluconazole for the prophylaxis and treatment of candidiasis has led to a reduction in the number of cases of candidemia caused by Candida albicans but has also resulted in the emergence of candidemias caused by innately fluconazole-resistant, non-C. albicans Candida species. Given the fulminant and rapidly fatal outcome of acute disseminated candidiasis, rapid identification of newly emerging Candida species in blood culture is critical for the implementation of appropriately targeted antifungal drug therapy. Therefore, we used a PCR-based assay to rapidly identify Candida species from positive blood culture bottles. This assay used fungus-specific, universal primers for DNA amplification and species-specific probes to identify C. albicans, C. krusei, C. parapsilosis, C. tropicalis, or C. glabrata amplicons. It also used a simpler and more rapid (1.5-h) sample preparation technique than those described previously and used detergent, heat, and mechanical breakage to recover Candida species DNA from blood cultures. A simple and rapid (3.5-h) enzyme immunosorbent assay (EIA)-based format was then used for amplicon detection. One hundred fifty blood culture bottles, including 73 positive blood culture bottle sets (aerobic and anaerobic) from 31 patients with candidemia, were tested. The combined PCR and EIA methods (PCR-EIA) correctly identified all Candida species in 73 blood culture bottle sets, including bottles containing bacteria coisolated with yeasts and 3 cultures of samples from patients with mixed candidemias originally identified as single-species infections by routine phenotypic identification methods. Species identification time was reduced from a mean of 3.5 days by routine phenotypic methods to 7 h by the PCR-EIA method. No false-positive results were obtained for patients with bacteremias (n = 18), artificially produced non-Candida fungemias (n = 3), or bottles with no growth (n = 20). Analytical sensitivity was 1 cell per 2-microl sample. This method is simpler and more rapid than previously described molecular identification methods, can identify all five of the most medically important Candida species, and has the potential to be automated for use in the clinical microbiology laboratory.