Benefits Derived from Full Laboratory Automation in Microbiology: a Tale of Four Laboratories.

Automation in clinical microbiology is starting to become more commonplace and reportedly offers several advantages over the manual laboratory. Most studies have reported on the rapid turnaround times for culture results, including times for identification of pathogens and their respective antimicrobial susceptibilities, but few have studied the benefits from a laboratory efficiency point of view. This is the first large, multicenter study in North America to report on the benefits derived from automation measured in full-time equivalents (FTE), FTE reallocation, productivity, cost per specimen, and cost avoidance. Pre- and post-full automation audits were done at 4 laboratories that have vastly different culture volumes, and results show that regardless of the size of the facility, improved efficiencies can be realized after implementation of full laboratory automation.

Current State of Laboratory Automation in Clinical Microbiology Laboratory.

BACKGROUND: Although it has been 30 years since the first automation systems were introduced in the microbiology laboratory, total laboratory automation (TLA) has only recently been recognized as a valuable component of the laboratory. A growing number of publications illustrate the potential impact of automation. TLA can improve standardization, increase laboratory efficiency, increase workplace safety, and reduce long-term costs. CONTENT: This review provides a preview of the current state of automation in clinical microbiology and covers the main developments during the last years. We describe the available hardware systems (that range from single function devices to multifunction workstations) and the challenging alterations on workflow and organization of the laboratory that have to be implemented to optimize automation. SUMMARY: Despite the many advantages in efficiency, productivity, and timeliness that automation offers, it is not without new and unique challenges. For every advantage that laboratory automation provides, there are similar challenges that a laboratory must face. Change management strategies should be used to lead to a successful implementation. TLA represents, moreover, a substantial initial investment. Nevertheless, if properly approached, there are a number of important benefits that can be achieved through implementation of automation in the clinical microbiology laboratory. Future developments in the field of automation will likely focus on image analysis and artificial intelligence improvements. Patient care, however, should remain the epicenter of all future directions and there will always be a need for clinical microbiology expertise to interpret the complex clinical and laboratory information.

Digital Image Analysis for the Detection of Group B Streptococcus from ChromID Strepto B Medium Using PhenoMatrix Algorithms.

Group B Streptococcus (GBS) can be found to colonize about 25% of all healthy, adult women and is the leading infectious cause of early neonatal morbidity and mortality in the United States. This study evaluated the clinical performance of PhenoMatrix (PM) chromogenic detection module (CDM) digital imaging software in detection of GBS from LIM broth plated on ChromID Strepto B chromogenic medium (ChromID) using the WASP automated processor. The performance of the PM CDM was compared to manual culture review of the digital images and molecular detection of GBS. ChromID alone had a sensitivity and specificity of 84.5% and 94.7%, respectively, after 48 h compared to nucleic acid amplification testing (NAAT). Compared to the composite reference for positivity, when PM CDM was used to detect GBS from ChromID, the sensitivity was 100%, with no true-positive GBS isolates missed by 48 h of incubation. Overall, evaluating all three methods for the detection of GBS, the sensitivities of NAAT, ChromID plus PM CDM at 48 h, and ChromID alone at 48 h were 96.8%, 95.5%, and 90.3%, respectively. The specificities of NAAT, ChromID plus PM CDM, and ChromID alone were 97.7%, 63.0%, and 95.4%, respectively. The sensitivity of ChromID in combination with the PM CDM was similar to the sensitivity of molecular detection. Further, the algorithm never called a culture negative that was determined to be positive by manual reading, and it identified an additional eight true positive specimens that were missed by manual digital image culture reading.

Diagnostic performance of two molecular assays for the detection of vaginitis in symptomatic women.

The three main causes of vaginitis are bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), and trichomoniasis (TV). Two multiplex assays are commercially available for detection of DNA from organisms associated with vaginitis: BD Affirm™ VPIII Microbial Identification Test (Affirm) and BD MAX™ Vaginal Panel (MAX VP). Here, the performance of MAX VP was compared to that of Affirm, which was considered the standard of care. Four vaginal swabs were collected from each subject with the following: BD Affirm™ VPIII Ambient Temperature Transport System (ATTS), BD MAX™ UVE Specimen Collection Kit, Hologic Aptima® Vaginal Swab Specimen Collection Kit, and BD ESwab™ collection and transport system (ESwab). Candida culture, Gram stain followed by Nugent scoring, and the Hologic Aptima® Trichomonas vaginalis assay were used for discordant analysis. Results were considered true positive if there were at least two tests positive for any vaginitis target. A total of 200 symptomatic women were evaluated in the study. The sensitivity and specificity of MAX VP for BV was 96.2% and 96.1%, respectively, compared to 96.2% and 81.6% for Affirm. The sensitivity and specificity of MAX VP for Candida spp. was 98.4% and 95.4%, respectively, compared to 69.4% and 100% for Affirm. MAX VP and Affirm showed 100% concordance for detection of TV. These results demonstrate improved accuracy of MAX VP compared to Affirm for the detection of BV and Candida spp. and no difference for detection of TV between the two tests.

Carbapenem-Resistant Pseudomonas aeruginosa at US Emerging Infections Program Sites, 2015.

Pseudomonas aeruginosa is intrinsically resistant to many antimicrobial drugs, making carbapenems crucial in clinical management. During July-October 2015 in the United States, we piloted laboratory-based surveillance for carbapenem-resistant P. aeruginosa (CRPA) at sentinel facilities in Georgia, New Mexico, Oregon, and Tennessee, and population-based surveillance in Monroe County, NY. An incident case was the first P. aeruginosa isolate resistant to antipseudomonal carbapenems from a patient in a 30-day period from any source except the nares, rectum or perirectal area, or feces. We found 294 incident cases among 274 patients. Cases were most commonly identified from respiratory sites (120/294; 40.8%) and urine (111/294; 37.8%); most (223/280; 79.6%) occurred in patients with healthcare facility inpatient stays in the prior year. Genes encoding carbapenemases were identified in 3 (2.3%) of 129 isolates tested. The burden of CRPA was high at facilities under surveillance, but carbapenemase-producing CRPA were rare.

Imported Toxin-Producing Cutaneous Diphtheria - Minnesota, Washington, and New Mexico, 2015-2018.

From September 2015 to March 2018, CDC confirmed four cases of cutaneous diphtheria caused by toxin-producing Corynebacterium diphtheriae in patients from Minnesota (two), Washington (one), and New Mexico (one). All patients had recently returned to the United States after travel to countries where diphtheria is endemic. C. diphtheriae infection was not clinically suspected in any of the patients; treating institutions detected the organism through matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF) testing of wound-derived coryneform isolates. MALDI-TOF is a rapid screening platform that uses mass spectrometry to identify bacterial pathogens. State public health laboratories confirmed C. diphtheriae through culture and sent isolates to CDC's Pertussis and Diphtheria Laboratory for biotyping, polymerase chain reaction (PCR) testing, and toxin production testing. All isolates were identified as toxin-producing C. diphtheriae. The recommended public health response for cutaneous diphtheria is similar to that for respiratory diphtheria and includes treating the index patient with antibiotics, identifying close contacts and observing them for development of diphtheria, providing chemoprophylaxis to close contacts, testing patients and close contacts for C. diphtheriae carriage in the nose and throat, and providing diphtheria toxoid-containing vaccine to incompletely immunized patients and close contacts. This report summarizes the patient clinical information and response efforts conducted by the Minnesota, Washington, and New Mexico state health departments and CDC and emphasizes that health care providers should consider cutaneous diphtheria as a diagnosis in travelers with wound infections who have returned from countries with endemic diphtheria.

Improved Phenotype-Based Definition for Identifying Carbapenemase Producers among Carbapenem-Resistant Enterobacteriaceae.

Preventing transmission of carbapenemase-producing, carbapenem-resistant Enterobacteriaceae (CP-CRE) is a public health priority. A phenotype-based definition that reliably identifies CP-CRE while minimizing misclassification of non-CP-CRE could help prevention efforts. To assess possible definitions, we evaluated enterobacterial isolates that had been tested and deemed nonsusceptible to >1 carbapenem at US Emerging Infections Program sites. We determined the number of non-CP isolates that met (false positives) and CP isolates that did not meet (false negatives) the Centers for Disease Control and Prevention CRE definition in use during our study: 30% (94/312) of CRE had carbapenemase genes, and 21% (14/67) of Klebsiella pneumoniae carbapenemase-producing Klebsiella isolates had been misclassified as non-CP. A new definition requiring resistance to 1 carbapenem rarely missed CP strains, but 55% of results were false positive; adding the modified Hodge test to the definition decreased false positives to 12%. This definition should be considered for use in carbapenemase-producing CRE surveillance and prevention.

Reflect urine culture cancellation in the emergency department.

BACKGROUND: The yield of urine culture testing in the emergency department (ED) is often low, resulting in wasted laboratory and ED resources. Use of a reflex culture cancellation protocol, in which urine cultures are canceled when automated urinalysis results predict that culture yield will be low, may help to conserve these resources. STUDY OBJECTIVES: To identify a reflex culture cancellation protocol consisting of urinalysis-based criteria to limit urine culture over-utilization. METHODS: We studied patients aged 5 years and older whose ED evaluation included both an automated urinalysis and urine culture. Logistic regression models incorporating individual urinalysis components were used to predict culture growth. Receiver operating characteristic curves corresponding to each model were constructed, and the area under the curve was used to identify the model that best predicted positive urine culture growth. RESULTS: There were 1546 ED patients who met study inclusion criteria. Of these, 314 (20%) had positive urine cultures. Restriction of culture testing to samples with white blood cells > 10 per high-power field, positive nitrites, positive leukocyte esterase, or positive bacteria provided a sensitivity of 96.5% (95% confidence interval [CI] 93.6-98.1%) and specificity of 48.1% (95% CI 45.3-51.0%) for positive urine culture. Implementation of a reflex culture cancellation protocol based on these criteria would have eliminated 604 of 1546 cultures (39%); 11 of 314 positive cultures (3.5%) would have been missed. CONCLUSION: These results suggest that a substantial reduction in urine culture testing might be achievable by implementing this protocol. Confirmation of these findings in a validation cohort is necessary.

Hierarchical AI enables global interpretation of culture plates in the era of digital microbiology.

Full Laboratory Automation is revolutionizing work habits in an increasing number of clinical microbiology facilities worldwide, generating huge streams of digital images for interpretation. Contextually, deep learning architectures are leading to paradigm shifts in the way computers can assist with difficult visual interpretation tasks in several domains. At the crossroads of these epochal trends, we present a system able to tackle a core task in clinical microbiology, namely the global interpretation of diagnostic bacterial culture plates, including presumptive pathogen identification. This is achieved by decomposing the problem into a hierarchy of complex subtasks and addressing them with a multi-network architecture we call DeepColony. Working on a large stream of clinical data and a complete set of 32 pathogens, the proposed system is capable of effectively assist plate interpretation with a surprising degree of accuracy in the widespread and demanding framework of Urinary Tract Infections. Moreover, thanks to the rich species-related generated information, DeepColony can be used for developing trustworthy clinical decision support services in laboratory automation ecosystems from local to global scale.

Evolution of testing algorithms at a university hospital for detection of Clostridium difficile infections.

We present the evolution of testing algorithms at our institution in which the C. Diff Quik Chek Complete immunochromatographic cartridge assay determines the presence of both glutamate dehydrogenase and Clostridium difficile toxins A and B as a primary screen for C. difficile infection and indeterminate results (glutamate dehydrogenase positive, toxin A and B negative) are confirmed by the GeneXpert C. difficile PCR assay. This two-step algorithm is a cost-effective method for highly sensitive detection of toxigenic C. difficile.

Educating health professionals about COVID-19 with ECHO telementoring.

BACKGROUND: When the COVID-19 pandemic began, primary care clinicians had almost no knowledge regarding best practices COVID-19 treatment. Project ECHO developed a COVID-19 Infectious Disease Office Hours (Office Hours) program to respond to the needs of clinicians seeking COVID-19 information. METHODS: This mixed-methods evaluation analyzed weekly post-session data and focus group results from the weekly Office Hours ECHO sessions during June 1, 2020- May 31, 2021. RESULTS: A total of 1,421 participants attended an average of 4.9 sessions during the 45 Office Hours sessions studied. The most common specialties included: nurses= 530 (37%), physicians= 284 (20%), and 493 (34%) having other degrees. The participants stated that they were definitely (68.2%) or probably (22.0%) going to use what they learned in their work, especially vaccination information. Focus group results identified these themes: 1) quality information, 2) community of practice, 3) interprofessional learning, and 4) increased knowledge, confidence, and practice change. CONCLUSIONS: This evaluation demonstrates that the Office Hours program was successful in bringing a large group of health professionals together each week in a virtual community of practice. The participants acknowledged their plans to use the information gained with their patients. This diffusion of knowledge from clinician to patient amplifies the response of the program, changes practice behavior and may improve patient care.

Detection of rapidly growing mycobacteria in routine cultures of samples from patients with cystic fibrosis.

Rapidly growing mycobacteria (RGM) are respiratory pathogens in patients with cystic fibrosis (CF), but detection generally requires specialized cultures for acid-fast bacilli (AFB; AFB cultures). We determined that RGM could be recovered from routine cultures of samples from patients with CF by extending incubation of the Burkholderia cepacia selective agar (BCSA) from 5 to 14 days. To explore the impact of this modification, we compared results from routine and AFB cultures of samples from CF patients for 2 years before (4,212 samples by routine culture, 1,810 samples by AFB culture, 670 patients) and 2 years after (4,720 samples by routine culture, 2,179 samples by AFB culture, 695 patients) the change. Clinical relevance was assessed with samples from a subgroup of 340 patients followed regularly throughout both periods. Extending incubation of BCSA enhanced RGM recovery from routine cultures (0.7% before, 2.8% after; P < 0.001); recovery from AFB cultures was unchanged (5.5% before, 5.7% after). Estimates of RGM detection sensitivity by culture or patient-based methods ranged from ∼65 to 75% for routine cultures (nonsignificantly lower than the ∼80 to 85% for AFB cultures) and were adversely affected by coculture with mold or nonpseudomonal, nonfermenting Gram-negative rods. In the after period, 16 CF patients met the criteria for RGM infection by routine culture, including 4 who did not meet the criteria for RGM infection by AFB culture. We conclude that a simple methodological change enhanced recovery of RGM from routine cultures. The modified culture method could be utilized to improve screening for RGM in CF patients or as a simpler method to follow patients with known RGM infection. However, this method should be used cautiously in patients with certain coinfections.

Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids.

Next-generation sequencing-based 16S rRNA gene metagenomic sequencing (16S MG) technology has tremendous potential for improving diagnosis of bacterial infections given its quantitative capability and culture-independent approach. We validated and used a quantitative 16S MG assay to identify and quantify bacterial species in clinical samples from a wide spectrum of infections, including meningitis, septic arthritis, brain abscess, intra-abdominal abscess, soft tissue abscess, and pneumonia. Twenty clinical samples were tested, and 16S MG identified a total of 34 species, compared with 22 species and three descriptive findings identified by culture. 16S MG results matched culture results in 75% (15/20) of the samples but detected at least one more species in five samples, including one culture-negative cerebrospinal fluid sample that was found to contain Streptococcus intermedius. Shotgun metagenomic sequencing verified the presence of all additional species. The 16S MG assay is highly sensitive, with a limit of detection of 10 to 100 colony-forming units/mL. Other performance characteristics, including linearity, precision, and specificity, all met the requirements for a clinical test. This assay showed the advantages of accurate identification and quantification of bacteria in culture-negative and polymicrobial infections for which conventional microbiology methods are limited. It also showed promises to serve unmet clinical needs for solving difficult infectious diseases cases.

Clinical Impact of a Rapid Streptococcal Antigen Test on Antibiotic Use in Adult Patients.

INTRODUCTION: Adult pharyngitis is rarely attributable to group A streptococci. Utilization of a rapid streptococcal antigen test (RADT) may improve appropriate prescribing for bacterial pharyngitis. METHODS: Clinic 1 performed RADTs with subsequent Group A DNA probe test (GADNA) from November 2014-March 2015 and November 2015-March 2016 while Clinic 2 was the control clinic, then implemented the RADT with a GADNA from November 2015-March 2016. All GADNA results were obtained for each clinic from October 2013-March 2016. RESULTS: At Clinic 1, 22.2% versus 8.5% of patients received inappropriately prescribed antibiotics for a GADNA or RADT result, respectively (p=0.048). For Clinic 2, 51.1% compared to 21.4% of patients were inappropriately prescribed antibiotic for a GADNA or RADT result, respectively (p=0.038). Overall, the total GADNA without RADT testing or RADTs with subsequent GADNA testing, 41.6% versus 11% of patients were inappropriately prescribed antibiotics, respectively (p=<0.0001). CONCLUSION: Utilizing the RADT prevented unnecessary prescribing of antibiotics in adults.

Unusual carbapenem resistant but ceftriaxone and cefepime susceptible Klebsiella oxytoca isolated from a blood culture: Case report and whole-genome sequencing investigation.

A carbapenem resistant but ceftriaxone and cefepime susceptible Klebsiella oxytoca was isolated from the blood of a patient with polymicrobial bacteremia after 2 weeks of ertapenem treatment. Whole-genome sequencing identified no carbapenemase gene nor plasmid, but only blaOXY-2-8 gene with a mutation in the promoter that's been reported to increase its expression. Two other specific carbapenem resistance mechanisms including mutated porin genes and the AcrAB-TolC efflux system genes were also identified. Clinicians need to be aware of such unusual antibiogram and should not assume carbapenems are always broader spectrum antibiotics than expanded-spectrum cephalosporins.

An Introduction to Research Work, Scholarship, and Paving a Way to a Career in Academic Medicine.

Introduction: Despite high faculty attrition and challenges to expanding the number of clinician-researchers, career development to heighten trainees' pursuit of an academic research career remains a relatively understudied topic. Completing peer-reviewed publications during medical school increases a trainee's likelihood of becoming a future faculty member. There is a lack of educational content to guide trainees in selecting research activities, publishing, and gaining self-efficacy to pave a path towards a clinician-researcher track. Methods: The Kern model was applied to create a multimodal workshop that would heighten trainee awareness of various research opportunities, skills for conducting research, best practices in publishing, and also help them develop a personal plan to pursue research. The workshop included a presentation, reflection exercises, and a case scenario. The workshop was implemented among trainees attending professional development conferences at nine medical schools. A questionnaire assessed participants' change in self-efficacy in completing research scholarship and pursuing an academic research career. Results: Sixty medical students and seven residents participated in the workshops. Paired-sample t tests indicated a statistically significant increase in participants' perception that academic medicine would allow them to engage in research work, and in their self-efficacy to publish and succeed along a clinician-researcher track. Discussion: The workshop not only exposed participants to a variety of research activities but also provided a sense that all research types are valid, aiding some participants to identify new research opportunities. In addition, participants gained clarity on how to publish and develop a research path, which may help maintain interest in a clinician-researcher track.

Diversity and Inclusion in the Academic Medicine Workforce: Encouraging Medical Students and Residents to Consider Academic Careers.

Introduction: The expansion of medical schools and increased faculty attrition call for heightened efforts to encourage medical students and residents to consider academic careers. As diversity serves as a driver of institutional excellence, special attention to the ongoing underrepresentation of certain groups in academia, such as racial and ethnic minorities, women, and lesbian, gay, bisexual, and transgender individuals, is warranted. Methods: We developed a 90-minute workshop to raise medical student and resident awareness of academic medicine careers, and the benefits and challenges of having a diverse faculty. The workshop consists of a didactic PowerPoint presentation and a reflection exercise, shared in small- and large-group format, discussing facilitators and barriers to pursuing academia. The workshop was implemented at nine regional conferences. Results: There were 165 diverse participants. In comparing pre- and postworkshop responses of learners using the sample t test, there was a statistically significant increase in confidence to succeed in academic medicine given learners' gender (2.69 vs. 3.34, p < .001), race and ethnicity (2.53 vs. 3.24, p < .001), or sexual orientation (3.04 vs. 3.42, p < .001). Approximately 95% of learners felt that each of the workshop's learning objectives had been achieved. Participants considered the workshop to be enlightening, motivational, realistic, and validating. Discussion: This workshop was effective in providing an interactive format for medical students and residents to gain awareness of the state, benefits, and challenges of diversity and inclusion in academic medicine, and can affect their perception of being a future faculty member.