Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM).

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by experts in both adult and pediatric laboratory and clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including arboviral Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also addressed. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.

Multicenter Evaluation of a Gradient Diffusion Method for Antimicrobial Susceptibility Testing of Helicobacter pylori.

Helicobacter pylori is an important human pathogen associated with peptic ulcer disease, dyspepsia, and gastric malignancy. Antimicrobial susceptibility testing (AST) is often requested for patients who fail eradication therapy. The Clinical and Laboratory Standards Institute (CLSI) reference method, agar dilution (AD), is not performed in most laboratories and maintaining organism viability during transit to a reference laboratory is difficult. We assessed the performance of the Etest (bioMérieux) as a method for H. pylori AST in comparison to AD. Etest MICs were determined for 83 H. pylori isolates at ARUP and Cleveland Clinic (CC). Categorical agreement (CA), very major, major, and minor errors (VME, ME, and mE) were determined for Etest using AD performed at Mayo Clinic Laboratories as the reference method. Testing on isolates with errors was repeated to determine final results summarized below. For clarithromycin, 66.3% of isolates were resistant (R) by AD; Etest results at each laboratory showed 1mE (1.2%) and 1 ME (3.8%). For tetracycline, only 2 isolates were R by AD; a single VME occurred at both sites (98.8% CA, 50% VME) with the same isolate. Applying EUCAST levofloxacin breakpoints to interpret ciprofloxacin results, 60.2% of isolates were R by AD; ARUP CA was 97.6% (1 ME (3%), 1 VME (2%)) and CC CA was 96.3% (1 ME (3%), 2 VMEs (4%)). Despite high error rates, the categorical agreement was acceptable (>90%) for all three antibiotics between AD and Etest. In-house susceptibility testing by gradient diffusion can allow for testing of fastidious organisms that may not survive transport to specialized laboratories; however, the method is not without technical challenges. Characterization of resistance mechanisms, increased AD dilutions, and testing from the same inoculum may determine if the observed errors reflect technical issues or breakpoints that need optimization. IMPORTANCE Routine antimicrobial susceptibility testing (AST) of Helicobacter pylori by agar dilution is difficult to perform and not practical in most clinical microbiology laboratories. The Etest gradient diffusion method can be a reliable alternative for H. pylori AST with the advantage of being a less laborious quantitative method. This work reveals that an optimized Etest method can provide acceptable performance for H. pylori AST and describes the challenges associated with this methodology.

Carbapenem-Resistant Acinetobacter baumannii in U.S. Hospitals: Diversification of Circulating Lineages and Antimicrobial Resistance.

Carbapenem-resistant Acinetobacter baumannii (CRAb) is a major cause of health care-associated infections. CRAb is typically multidrug resistant, and infection is difficult to treat. Despite the urgent threat that CRAb poses, few systematic studies of CRAb clinical and molecular epidemiology have been conducted. The Study Network of Acinetobacter as a Carbapenem-Resistant Pathogen (SNAP) is designed to investigate the clinical characteristics and contemporary population structure of CRAb circulating in U.S. hospital systems using whole-genome sequencing (WGS). Analysis of the initial 120 SNAP patients from four U.S. centers revealed that CRAb remains a significant threat to hospitalized patients, affecting the most vulnerable patients and resulting in 24% all-cause 30-day mortality. The majority of currently circulating isolates belonged to ST2Pas, a part of clonal complex 2 (CC2), which is the dominant drug-resistant lineage in the United States and Europe. We identified three distinct sublineages within CC2, which differed in their antibiotic resistance phenotypes and geographic distribution. Most concerning, colistin resistance (38%) and cefiderocol resistance (10%) were common within CC2 sublineage C (CC2C), where the majority of isolates belonged to ST2Pas/ST281Ox. Additionally, we identified ST499Pas as the most common non-CC2 lineage in our study. Our findings suggest a shift within the CRAb population in the United States during the past 10 years and emphasize the importance of real-time surveillance and molecular epidemiology in studying CRAb dissemination and clinical impact. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii (CRAb) constitutes a major threat to public health. To elucidate the molecular and clinical epidemiology of CRAb in the United States, clinical CRAb isolates were collected along with data on patient characteristics and outcomes, and bacterial isolates underwent whole-genome sequencing and antibiotic susceptibility phenotyping. Key findings included emergence of new sublineages within the globally predominant clonal complex 2 (CC2), increased colistin and cefiderocol resistance within one of the CC2 sublineages, and emergence of ST499Pas as the dominant non-CC2 CRAb lineage in U.S. hospitals.

What do positive and negative Cutibacterium culture results in periprosthetic shoulder infection mean? A multi-institutional control study.

BACKGROUND: Deep tissue culture specimens obtained at the time of revision shoulder arthroplasty are commonly positive for Cutibacterium. Clinical interpretation of positive cultures can be difficult. This was a multi-institutional study evaluating the accuracy of cultures for Cutibacterium using positive control (PC) and negative control (NC) samples. The relationship between time to culture positivity and strength of culture positivity was also studied. METHODS: Eleven different institutions were each sent 12 blinded samples (10 PC and 2 NC samples). The 10 PC samples included 2 sets of 5 different dilutions of a Cutibacterium isolate from a failed total shoulder arthroplasty with a probable periprosthetic infection. At each institution, the samples were handled as if they were received from the operating room. Specimen growth, time to culture positivity, and strength of culture positivity (based on semiquantitative assessment) were reported. RESULTS: A total of 110 PC samples and 22 NC samples were tested. One hundred percent of specimens at the 4 highest dilutions were positive for Cutibacterium. At the lowest dilution, 91% of samples showed positive findings. Cutibacterium grew in 14% of NC samples. Cutibacterium grew in PC samples at an average of 4.0 ± 1.3 days, and all of these samples showed growth within 7 days. The time to positivity was significantly shorter (P < .001) and the strength of positivity was significantly higher (P < .001) in true-positive cultures compared with false-positive cultures. CONCLUSIONS: This multi-institutional study suggests that different institutions may report highly consistent rates of culture positivity for revision shoulder arthroplasty samples with higher bacterial loads. In contrast, with lower bacterial loads, the results are somewhat less consistent. Clinicians should consider using a shorter time to positivity and a higher strength of positivity as adjuncts in determining whether a tissue culture sample is a true positive.

The Implementation and Effect of Weekend Pharmacy-Driven Antimicrobial Stewardship Services at a Large Academic Medical Center.

BACKGROUND: In September 2018, pharmacy antimicrobial stewardship (AMS) services were expanded to include weekends at this academic medical center. Activities performed by AMS pharmacists on the weekends include blood culture rapid diagnostic (RDT) review, antiretroviral therapy (ART) review, prospective audit and feedback (PAF) utilizing clinical decision support, vancomycin dosing, and operational support. The purpose of this study was to assess the operational and clinical impact of these expanded AMS services. METHODS: This single-center, quasi-experimental study included data from weekends before (9/2017-11/2017) and after (9/2018-11/2018) implementation. The descriptive primary outcome was the number of activities completed for each AMS activity type in the post-implementation group only. Secondary outcomes were time to AMS opportunity resolution, time to escalation or de-escalation following PAF or RDT alert, time to resolution of miscellaneous AMS related opportunities, length of stay (LOS), and antimicrobial use outcomes. RESULTS: During the post-implementation period 1258 activities were completed, averaging 97/weekend. Inclusion criteria for time to resolution outcomes were met by 72 patients pre-implementation and 59 patients post. The median (IQR) time to AMS opportunity resolution decreased from 18.5 hours pre-intervention (7.7-35.7) to 8.5 hours post-intervention (IQR 1.8-14.0), p < 0.01. Time to escalation was 11.6 hours compared to 1.7 hours (p = 0.1), de-escalation 16.7 hours compared to 10.8 hours (p = 0.03), and miscellaneous opportunity 40.8 hours compared to 13.2 hours (p = 0.01). No differences were observed in LOS or antimicrobial use outcomes. CONCLUSION: Presence of pharmacist-driven weekend AMS services significantly reduced time to resolution of AMS opportunities. These data support the value of weekend AMS services.

Multicenter evaluation of the VITEK MS matrix-assisted laser desorption/ionization-time of flight mass spectrometry system for identification of bacteria, including Brucella, and yeasts.

The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has proven to be rapid and accurate for the majority of clinical isolates. Some gaps remain concerning rare, emerging, or highly pathogenic species, showing the need to continuously expand the databases. In this multicenter study, we evaluated the accuracy of the VITEK MS v3.2 database in identifying 1172 unique isolates compared to identification by DNA sequence analysis. A total of 93.6% of the isolates were identified to species or group/complex level. A remaining 5.2% of the isolates were identified to the genus level. Forty tests gave a result of no identification (0.9%) and 12 tests (0.3%) gave a discordant identification compared to the reference identification. VITEK MS is also the first MALDI-TOF MS system that is able to delineate the four members of the Acinetobacter baumannii complex at species level without any specific protocol or special analysis method. These findings demonstrate that the VITEK MS v3.2 database is highly accurate for the identification of bacteria and fungi encountered in the clinical laboratory as well as emerging species like Candida auris and the highly pathogenic Brucella species.

Real-time polymerase chain reaction (PCR) cycle threshold and Clostridioides difficile infection outcomes.

OBJECTIVE: Clostridioides difficile infection (CDI) causes significant morbidity and mortality; however, the diagnosis of CDI remains controversial. The primary aim of our study was to evaluate the association of polymerase chain reaction (PCR) cycle threshold (Ct) values with CDI disease severity, recurrence, and mortality among adult patients with CDI. DESIGN: Retrospective cohort study. SETTING: Single tertiary-care hospital. PATIENTS: Adult patients diagnosed with hospital-onset, healthcare facility-associated CDI from June 2014 to September 2015. METHODS: We performed a retrospective chart review of included patients. Univariate and multivariable logistic regression methods were used to evaluate the association between Ct values and CDI severity, 8-week recurrence, and 30-day mortality. RESULTS: Among 318 included patients, 51% were male and the mean age was 62 years; ~32% of the patients developed severe CDI and 11% developed severe-complicated CDI. The 30-day all-cause mortality rate was 11% and the 8-week recurrence rate was 9.5%. The overall mean Ct value was 32.9 (range, 23-40). Multivariable analyses showed that lower values of PCR Ct were associated with increased odds of 30-day morality (odds ratio [OR] 0.83; 95% confidence interval [CI], 0.72-0.96) but were not independently associated with CDI severity (OR, 0.99; 95% CI, 0.90-1.09) or recurrence (OR, 0.88; 95% CI, 0.77-1.00). CONCLUSIONS: Our findings suggest that PCR Ct values at the time of diagnosis may have a limited predictive value and utility in clinical decision making for inpatients with CDI. Larger, prospective studies across different patient populations are needed to confirm our findings.

De-escalation of Empiric Antibiotics Following Negative Cultures in Hospitalized Patients With Pneumonia: Rates and Outcomes.

BACKGROUND: For patients at risk for multidrug-resistant organisms, IDSA/ATS guidelines recommend empiric therapy against methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas. Following negative cultures, the guidelines recommend antimicrobial de-escalation. We assessed antibiotic de-escalation practices across hospitals and their associations with outcomes in hospitalized patients with pneumonia with negative cultures. METHODS: We included adults admitted with pneumonia in 2010-2015 to 164 US hospitals if they had negative blood and/or respiratory cultures and received both anti-MRSA and antipseudomonal agents other than quinolones. De-escalation was defined as stopping both empiric drugs on day 4 while continuing another antibiotic. Patients were propensity adjusted for de-escalation and compared on in-hospital 14-day mortality, late deterioration (ICU transfer), length-of-stay (LOS), and costs. We also compared adjusted outcomes across hospital de-escalation rate quartiles. RESULTS: Of 14 170 patients, 1924 (13%) had both initial empiric drugs stopped by hospital day 4. Hospital de-escalation rates ranged from 2-35% and hospital de-escalation rate quartile was not significantly associated with outcomes. At hospitals in the top quartile of de-escalation, even among patients at lowest risk for mortality, the de-escalation rates were <50%. In propensity-adjusted analysis, patients with de-escalation had lower odds of subsequent transfer to ICU (adjusted odds ratio, .38; 95% CI, .18-.79), LOS (adjusted ratio of means, .76; .75-.78), and costs (.74; .72-.76). CONCLUSIONS: A minority of eligible patients with pneumonia had antibiotics de-escalated by hospital day 4 following negative cultures and de-escalation rates varied widely between hospitals. To adhere to recent guidelines will require substantial changes in practice.

Assessment of the Accuracy of Using ICD-9 Diagnosis Codes to Identify Pneumonia Etiology in Patients Hospitalized With Pneumonia.

Importance: Administrative databases may offer efficient clinical data collection for studying epidemiology, outcomes, and temporal trends in health care delivery. However, such data have seldom been validated against microbiological laboratory results. Objective: To assess the validity of International Classification of Diseases, Ninth Revision (ICD-9) organism-specific administrative codes for pneumonia using microbiological data (test results for blood or respiratory culture, urinary antigen, or polymerase chain reaction) as the criterion standard. Design, Setting, and Participants: Cross-sectional diagnostic accuracy study conducted between February 2017 and June 2019 using data from 178 US hospitals in the Premier Healthcare Database. Patients were aged 18 years or older admitted with pneumonia and discharged between July 1, 2010, and June 30, 2015. Data were analyzed from February 14, 2017, to June 27, 2019. Exposures: Organism-specific pneumonia identified from ICD-9 codes. Main Outcomes and Measures: Sensitivity, specificity, positive predictive value, and negative predictive value of ICD-9 codes using microbiological data as the criterion standard. Results: Of 161 529 patients meeting inclusion criteria (mean [SD] age, 69.5 [16.2] years; 51.2% women), 35 759 (22.1%) had an identified pathogen. ICD-9-coded organisms and laboratory findings differed notably: for example, ICD-9 codes identified only 14.2% and 17.3% of patients with laboratory-detected methicillin-sensitive Staphylococcus aureus and Escherichia coli, respectively. Although specificities and negative predictive values exceeded 95% for all codes, sensitivities ranged downward from 95.9% (95% CI, 95.3%-96.5%) for influenza virus to 14.0% (95% CI, 8.8%-20.8%) for parainfluenza virus, and positive predictive values ranged downward from 91.1% (95% CI, 89.5%-92.6%) for Staphylococcus aureus to 57.1% (95% CI, 39.4%-73.7%) for parainfluenza virus. Conclusions and Relevance: In this study, ICD-9 codes did not reliably capture pneumonia etiology identified by laboratory testing; because of the high specificities of ICD-9 codes, however, administrative data may be useful in identifying risk factors for resistant organisms. The low sensitivities of the diagnosis codes may limit the validity of organism-specific pneumonia prevalence estimates derived from administrative data.

Multicenter evaluation of the RAPIDEC® CARBA NP assay for the detection of carbapenemase production in clinical isolates of Enterobacterales and Pseudomonas aeruginosa.

Carbapenem-resistant Gram-negative bacilli are a major public health problem. Accurate and rapid detection of carbapenemase-producing organisms can facilitate appropriate infection prevention measures. The objective was to evaluate the performance of the RAPIDEC® CARBA NP assay (RAPIDEC), a screening assay that utilizes a pH indicator to detect carbapenem hydrolysis within 2 h. A multicenter study evaluated 306 clinical bacterial strains of Enterobacterales (n = 257) and Pseudomonas aeruginosa (n = 49). The RAPIDEC was compared to a composite reference standard-the Clinical Laboratory Standards Institute (CLSI) Carba NP assay, PCR for specific carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like, blaVIM and blaIMP), and phenotypic carbapenem susceptibility testing. The assay was evaluated using two culture incubation times for the bacterial isolates: "routine"(cultures incubated 18-24 h) and "short" (cultures incubated 4-5 h). For the routine incubation, the overall percent agreement was 98.7% with a positive percent agreement (PPA) of 99.6% and a negative percent agreement (NPA) of 97.4%; there were five false positives and one false negative. For the short incubation, the overall percent agreement was 98.0% with a PPA of 98.5% and a NPA of 97.3%; there were five false positives and four false negatives. RAPIDEC results for the P. aeruginosa isolates were 100% concordant with the reference standard for both incubation times. The RAPIDEC assay is an accurate and rapid (≤ 2 h) assay for the detection of the most common carbapenemases in clinical isolates. Growth from a short incubation culture may be used to reliably detect carbapenemase production in clinical strains.

The Pitt Bacteremia Score Predicts Mortality in Nonbacteremic Infections.

BACKGROUND: Predicting mortality risk in patients is important in research settings. The Pitt bacteremia score (PBS) is commonly used as a predictor of early mortality risk in patients with bloodstream infections (BSIs). We determined whether the PBS predicts 14-day inpatient mortality in nonbacteremia carbapenem-resistant Enterobacteriaceae (CRE) infections. METHODS: Patients were selected from the Consortium on Resistance Against Carbapenems in Klebsiella and Other Enterobacteriaceae, a prospective, multicenter, observational study. We estimated risk ratios to analyze the predictive ability of the PBS overall and each of its components individually. We analyzed each component of the PBS in the prediction of mortality, assessed the appropriate cutoff value for the dichotomized score, and compared the predictive ability of the qPitt score to that of the PBS. RESULTS: In a cohort of 475 patients with CRE infections, a PBS ≥4 was associated with mortality in patients with nonbacteremia infections (risk ratio [RR], 21.9; 95% confidence interval [CI], 7.0, 68.8) and with BSIs (RR, 6.0; 95% CI, 2.5, 14.4). In multivariable analysis, the hypotension, mechanical ventilation, mental status, and cardiac arrest parameters of the PBS were independent risk factors for 14-day all-cause inpatient mortality. The temperature parameter as originally calculated for the PBS was not independently associated with mortality. However, a temperature <36.0°C vs ≥36°C was independently associated with mortality. A qPitt score ≥2 had similar discrimination as a PBS ≥4 in nonbacteremia infections. CONCLUSIONS: Here, we validated that the PBS and qPitt score can be used as reliable predictors of mortality in nonbacteremia CRE infections.

In-Room Ultraviolet Air Filtration Units Reduce Airborne Particles During Total Joint Arthroplasty.

Reducing airborne bioburden in total joint arthroplasty (TJA) is of critical importance. The efficacy of crystalline ultraviolet-C (C-UVC) filtration in reducing bioburden in a dynamic operating room (OR) environment has not been evaluated. We assessed whether C-UVC filtration reduced (i) total particle counts (TPC); (ii) viable particle counts (VPC); and (iii) colony-forming units (CFUs). Fifty primary TJA cases were performed in a positive-pressure OR; 25 cases with the C-UVC unit and 25 cases without. The air was sampled by a particle counter and an impact air sampler to measure particle counts and CFUs, respectively. To compare TPC, VPC, and CFU/m3 between groups, independent t tests and multivariate regression, adjusted for number of OR staff and door openings, were performed. The C-UVC group had significantly lower TPC (2.6 × 106 vs. 4.7 × 106 particles, p = 0.001) and VPC (18,605 vs. 27,516 particles, p = 0.001). There were fewer CFUs in the C-UVC group (10.9 CFU/m3 vs. 13.7 CFU/m3 , p = 0.163). Multivariate analysis identified C-UVC filtration as a significant predictor of decreased TPC (ß = -0.44, p = 0.002) and VPC (ß = -0.47, p = 0.001) after accounting for door openings and number of OR staff. The reduction in CFUs was not significant on multivariate analysis. In this prospective pilot study, a C-UVC air disinfection and recirculation unit led to a significant reduction in both TPC and VPC and a non-significant reduction in CFU. Statement of clinical significance: Further studies are needed to investigate the effects of C-UVC filtration units on surgical-site infection rates. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:431-437, 2020.

Clostridium septicum-infected aortic aneurysm or graft is a deadly diagnosis.

BACKGROUND: Clostridium septicum is an anaerobic, motile, spore-forming, toxin-producing gram-positive bacillus that can lead to rapidly progressive gas gangrene due to the release of alpha toxin. Aortic aneurysm secondary to C. septicum infection is a rare condition with 60 cases reported in the literature; however, we have recently treated several patients with the condition in our large tertiary care and aortic center. METHODS: Blood and tissue culture results collected between January 2005 and January 2018 and maintained in the microbiology laboratory database at the Cleveland Clinic were reviewed to identify those with C. septicum reported. Each was reviewed to determine radiographic or histopathologic correlation with aortic disease. RESULTS: Seven cases of C. septicum aortitis were reviewed. Underlying malignant disease was found in four cases and a history of remote malignant disease in one case. The most common location for infection was the infrarenal abdominal aorta. Vascular surgery had previously been performed in three of the cases. Five of the seven patients underwent operative repair. All patients were treated with ß-lactam antibiotics. The two patients who did not undergo an operation died, which is consistent with the 100% mortality described in the literature. Of the five patients who underwent an operation, there was only one documented survivor and one was lost to follow-up. CONCLUSIONS: In the largest reported case series, only a small percentage of patients with C. septicum-infected aortic aneurysms survived >1 year. In the patients described, those who did not receive an operation had 100% mortality. Earlier recognition and prompt operation with appropriate antimicrobial therapy are needed to improve the outcome of patients diagnosed with this rare infection.

Pneumococcal Urinary Antigen Testing in United States Hospitals: A Missed Opportunity for Antimicrobial Stewardship.

BACKGROUND: The Infectious Diseases Society of America recommends pneumococcal urinary antigen testing (UAT) when identifying pneumococcal infection would allow for antibiotic de-escalation. However, the frequencies of UAT and subsequent antibiotic de-escalation are unknown. METHODS: We conducted a retrospective cohort study of adult patients admitted with community-acquired or healthcare-associated pneumonia to 170 US hospitals in the Premier database from 2010 to 2015, to describe variation in UAT use, associations of UAT results with antibiotic de-escalation, and associations of de-escalation with outcomes. RESULTS: Among 159 894 eligible admissions, 24 757 (15.5%) included UAT performed (18.4% of intensive care unit [ICU] and 15.3% of non-ICU patients). Among hospitals with ≥100 eligible patients, UAT proportions ranged from 0% to 69%. Compared to patients with negative UAT, 7.2% with positive UAT more often had a positive Streptococcus pneumoniae culture (25.4% vs 1.9%, P < .001) and less often had resistant bacteria (5.2% vs 6.8%, P < .05). Of patients initially treated with broad-spectrum antibiotics, most were still receiving broad-spectrum therapy 3 days later, but UAT-positive patients more often had coverage narrowed (38.4% vs 17.0% UAT-negative and 14.6% untested patients, P < .001). Hospital rate of UAT was strongly correlated with de-escalation following a positive test. Only 3 patients de-escalated after a positive UAT result were subsequently admitted to ICU. CONCLUSIONS: UAT is not ordered routinely in pneumonia, even in ICU. A positive UAT result was associated with less frequent resistant organisms, but usually did not lead to antibiotic de-escalation. Increasing UAT and narrowing therapy after a positive UAT result are opportunities for improved antimicrobial stewardship.

Optimal Timing of Repeat Multiplex Molecular Testing for Respiratory Viruses.

Determining whether and when multiplex nucleic acid amplification tests (NAATs) for respiratory viruses should be repeated is difficult. We analyzed 5 years of results for a multiplex NAAT targeting 14 respiratory viruses, to determine how often repeat tests were ordered and the time period in which results were likely to change. Results for NAATs performed on nasopharyngeal specimens and repeated within 90 days after initial testing were analyzed. Logistic regression models were used to compare time periods between tests with respect to the odds of a change in the sample result. During the study period, 21,819 nasopharyngeal specimens from 16,779 individuals were submitted. Of these, 8,807 samples (40%) were positive for at least one viral pathogen. Among this cohort, 2,583 specimens (12%) collected from 1,473 patients (9%) were repeat tests performed within 90 days after an initial test. If repeated within 90 days, 71% of tests (1,833 tests) did not have a change in result. Initially negative tests typically remained negative, whereas initially positive tests mostly remained positive until 11 to 15 days. The odds of result change plateaued after 20 days. The odds of result change for tests repeated within 20 days were only 0.52 times the odds (95% confidence interval, 0.43 to 0.62) for those repeated at 21 to 90 days (P < 0.001). Multiplex tests for respiratory viruses that are repeated within short periods lead to redundant results at additional costs. Repeat testing of nasopharyngeal specimens before 20 days demonstrates little change. These results provide a vital component for use in laboratory stewardship to curtail unnecessary respiratory viral testing.

Prospective Evaluation of Molecular Assays for Diagnosis of Vaginitis.

Molecular tests to diagnose conditions involving the disruption of normal microbiota are difficult to optimize. Using Nugent-scored Gram stain (NS) as the reference standard, we evaluated the performance of 3 molecular assays for the diagnosis of bacterial vaginosis (BV) and examined the impact of an incremental increase in bacterial targets. The BD Affirm assay includes a DNA probe for Gardnerella vaginalis, the Hologic transcription-mediated amplification (TMA) analyte-specific reagent (ASR) assay adds a second Lactobacillus sp. target, and the recently cleared in vitro diagnostic use (IVD) Aptima BV assay includes a third target (Atopobium vaginae). The diagnosis of vulvovaginal candidiasis (VVC) by the Affirm and Candida vaginitis Hologic TMA ASR assays was assessed using microscopy for yeast as the reference standard. From May to December 2018, 111 women with vaginitis symptoms prompting the clinician to order an Affirm test were enrolled with informed consent for the collection of additional specimens. Clinicians accurately predicted BV as the most likely diagnosis for 71% of the 45 patients with BV. Coinfection occurred in 13.5% of patients. For BV, the specificity of the Aptima IVD assay (86.3%) was higher than the Affirm assay (60.6%, P = 0.0002), but sensitivities were not significantly different. For VVC, the sensitivity of the ASR assay (100%) was higher than Affirm (75.9%; P = 0.023) and the specificity of the Affirm assay (98.8%) was higher than the ASR assay (86.6%; P = 0.004).

Implementation of a Stewardship Initiative on Respiratory Viral PCR-based Antibiotic Deescalation.

OBJECTIVE: Respiratory viral polymerase chain reaction (RV PCR) tests assist in rapidly identifying viral pathogens and differentiating viral versus bacterial causes of pneumonia. Studies evaluating the use of RV PCR tests on antibiotic use in adults have demonstrated mixed results. We implemented an antimicrobial stewardship (ASP) intervention for patients with a positive RV PCR test result who were receiving broad-spectrum antibiotics and aimed to assess the impact on antibiotic usage. METHODS: Retrospective quasi-experimental study of adult hospitalized patients comparing time to antibiotic deescalation, duration of antibiotic therapy, and antiviral use preintervention (January-March 2016) and postintervention (January-March 2017). RESULTS: Of 172 ASP alerts reviewed, 55 (32%) were considered actionable. Of these, 47% of interventions were accepted. No significant difference was observed in median time to antibiotic deescalation (pre: 2.7 days vs post: 2.3 days, p=0.88). Time to discontinuation of antimicrobial therapy pre- and postintervention was reduced from 4 to 1.9 days (p=0.057) for piperacillin-tazobactam, from 2.7 to 1.8 days (p=0.75) for ceftriaxone, and from 3.6 to 2 days (p=0.4) for levofloxacin, respectively. Time to initiation of oseltamivir for influenza was significantly shorter in the postintervention group (pre: 11.3 hrs vs post: 3.6 hrs, p=0.02). CONCLUSION: A third of patients receiving broad-spectrum antibiotics with a positive RV PCR had an opportunity for antimicrobial optimization, although this did not translate into a significant impact on the time to antibiotic deescalation or overall antibiotic use. Combination of RV PCR results with biomarkers to rule out bacterial coinfections and chest radiographic findings may help enhance the likelihood of accepted antibiotic deescalation recommendations and represents an area of future research.

A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides (Clostridium) difficile in Adults.

The evidence base for the optimal laboratory diagnosis of Clostridioides (Clostridium) difficile in adults is currently unresolved due to the uncertain performance characteristics and various combinations of tests. This systematic review evaluates the diagnostic accuracy of laboratory testing algorithms that include nucleic acid amplification tests (NAATs) to detect the presence of C. difficile The systematic review and meta-analysis included eligible studies (those that had PICO [population, intervention, comparison, outcome] elements) that assessed the diagnostic accuracy of NAAT alone or following glutamate dehydrogenase (GDH) enzyme immunoassays (EIAs) or GDH EIAs plus C. difficile toxin EIAs (toxin). The diagnostic yield of NAAT for repeat testing after an initial negative result was also assessed. Two hundred thirty-eight studies met inclusion criteria. Seventy-two of these studies had sufficient data for meta-analysis. The strength of evidence ranged from high to insufficient. The uses of NAAT only, GDH-positive EIA followed by NAAT, and GDH-positive/toxin-negative EIA followed by NAAT are all recommended as American Society for Microbiology (ASM) best practices for the detection of the C. difficile toxin gene or organism. Meta-analysis of published evidence supports the use of testing algorithms that use NAAT alone or in combination with GDH or GDH plus toxin EIA to detect the presence of C. difficile in adults. There is insufficient evidence to recommend against repeat testing of the sample using NAAT after an initial negative result due to a lack of evidence of harm (i.e., financial, length of stay, or delay of treatment) as specified by the Laboratory Medicine Best Practices (LMBP) systematic review method in making such an assessment. Findings from this systematic review provide clarity to diagnostic testing strategies and highlight gaps, such as low numbers of GDH/toxin/PCR studies, in existing evidence on diagnostic performance, which can be used to guide future clinical research studies.