Proceedings of the Clinical Microbiology Open 2023: discussions about pandemic preparedness.

The 4th Clinical Microbiology Open (CMO) took place in Carlsbad, California, on 10 and 11 February 2023. This event facilitated discussion between clinical and public health laboratory directors, government agencies, and industry representatives from the companies that make up ASM's Corporate Council. While many topics were discussed, much of the discussion focused on pandemic preparedness. There were four major questions addressed: (i) When is the perfect the enemy of good in pandemic testing? (ii) What other types of pathogens might cause another pandemic and how would this affect laboratory response? (iii) What research is needed to better understand the effectiveness of the pandemic response? (iv) What have we learned about the utility of self and at-home testing in future pandemics? This review serves as a summary of these discussions.

Politics and health care spending in the United States: A case study from the passage of the 2003 Medicare Modernization Act.

This paper analyzes the interplay between congressional politics, the actions of the executive branch, and hospitals' regulated Medicare payments. We focus on the 2003 Medicare Modernization Act (MMA) and analyze a provision in the law - Section 508 - that raised certain hospitals' regulated payments. We show, via our analysis of the Section 508 program, that Medicare payments are malleable and can be influenced by political dynamics. In the cross-section, hospitals represented by members of Congress who voted "yea" on the MMA were more likely to receive Section 508 payment increases. We interviewed the Secretary of Health and Human Services who oversaw the MMA, and he described how these payment increases were designed to win support for the law. The Section 508 payment increases raised hospitals' activity and spending. Members of Congress representing recipient hospitals received increased campaign contributions after the Section 508 payment increases were extended. Ultimately, our analysis highlights how Medicare payment increases can serve as an appealing tool for legislative leaders working to win votes for wider pieces of legislation.

Clinical utility of multiplex PCR in the detection of pathogens from sterile body fluids.

Rapid identification of pathogens in normally sterile body fluid (NSBF) is essential for appropriate patient management, specifically antimicrobial therapy. Limited sensitivity and increased time to detection of traditional culture prompted us to evaluate additional testing to contribute to the diagnosis of infection. The purpose of this study was to evaluate the GenMark Dx ePlex Blood Culture Identification (BCID) Panels on positive body fluids inoculated into blood culture bottles for the detection of microorganisms. A total of 88 positive body fluids from blood culture bottles were analyzed using a Gram-Positive, Gram-Negative, and/or Fungal pathogen BCID Panel based on the Gram stain result. Each result was compared to routine culture performed from the positive bottle. When using culture as a reference standard, we found the ePlex multiplex panel performed with a positive percent agreement of 96.5% and a negative percent agreement of 99.8%. The use of multiplex PCR may be a useful supplement to routine culture for NSBF in blood culture bottles. IMPORTANCE: The identification of pathogens in normally sterile body fluid (NSBF) is performed using routine culture, the current gold standard. Limitations of this method include sensitivity and increased turnaround times which could potentially delay vital patient care, especially antimicrobial therapy. Adaptations of NSBF in blood culture bottles prompted us to consider the utility of additional methods to bridge the gap in diagnostic challenges for these life-threatening infections. Multiplex molecular panels have been manufactured for use with multiple specimen types including blood, cerebral spinal fluid, stool, and respiratory. Therefore, the purpose of this study was to evaluate the off-label use of ePlex Blood Culture Identification Panels on positive body fluids grown in blood culture bottles for the detection of microorganisms for research purposes.

Transcranial magnetic stimulation over supramarginal gyrus stimulates primary motor cortex directly and impairs manual dexterity: implications for TMS focality.

Based on human motor cortex, the effective spatial resolution of transcranial magnetic stimulation (TMS) is often described as 5-20 mm, because small changes in TMS coil position can have large effects on motor-evoked potentials (MEPs). MEPs are often studied at rest, with muscles relaxed. During muscle contraction and movement, corticospinal excitability is higher, thresholds for effective stimulation are lower, and MEPs can be evoked from larger regions of scalp, so the effective spatial resolution of TMS is larger. We found that TMS over the supramarginal gyrus (SMG) impaired manual dexterity in the grooved pegboard task. It also resulted in short-latency MEPs in hand muscles, despite the coil being 55 mm away from the motor cortex hand area (M1). MEPs might be evoked by either a specific corticospinal connection from SMG or a remote but direct electromagnetic stimulation of M1. To distinguish these alternatives, we mapped MEPs across the scalp during rest, isotonic contraction, and manual dexterity tasks and ran electric field simulations to model the expected M1 activation from 27 scalp locations and four coil orientations. We also systematically reviewed studies using TMS during movement. Across five experiments, TMS over SMG reliably evoked MEPs during hand movement. These MEPs were consistent with direct M1 stimulation and substantially decreased corticospinal thresholds during natural movement. Systematic review suggested that 54 published experiments may have suffered from similar motor activation confounds. Our results have implications for the assumed spatial resolution of TMS, and especially when TMS is presented within 55 mm of the motor cortex.NEW & NOTEWORTHY Transcranial magnetic stimulation (TMS) is often described as having an effective spatial resolution of ∼10 mm, because of the limited area of the scalp on which TMS produces motor-evoked potentials (MEPs) in resting muscles. We find that during natural hand movement TMS evokes MEPs from a much larger scalp area, in particular when stimulating over the supramarginal gyrus 55 mm away. Our results show that TMS can be effective at much larger distances than generally assumed.

Preanalytical Challenges of Molecular Microbiology Tests.

As infectious disease diagnostics increasingly incorporates molecular techniques, there are unique preanalytical concerns that must be considered. First, noninvasive specimen types that may be inadequate for culture-based diagnostics may be acceptable when using molecular tests. Second, specimen containers must be evaluated for the presence of substances that may interfere with amplification or sequencing reactions. Finally, the capacity of transport, storage, and processing conditions to maintain nucleic acid integrity and avoid contamination must be assessed. This review explores these issues and the effects they may have on result quality.

Viral pathogen detection using multiplex gastrointestinal molecular panels: The pros and cons of viral target inclusion.

Diagnosis of gastrointestinal infections has been revolutionized by the development of in vitro diagnostic (IVD) multiplex molecular panels for the detection of viral nucleic acids. In addition to a high degree of accuracy, these panels are commercially available and relatively simple to perform in the clinical laboratory. However, use of these panels must be carefully considered owing to the laboratory costs of the test, limited reimbursement, and potential for overuse. In this review from the Pan American Society for Clinical Virology, we focus on the viral components of GI multiplex panels (GIPs), presenting a brief overview of pathogens included on most panels and a discussion of advantages and challenges of the inclusion of viral targets on GIPs that should be considered before implementation in the clinical laboratory.

Utility and Recommendations for the Use of Multiplex Molecular Gastrointestinal Pathogen Panels.

BACKGROUND: Many molecular gastrointestinal pathogen panels (GIPs) are Food and Drug Administration (FDA) cleared but it is still unclear how to best utilize these new diagnostic tools. GIPs are highly sensitive and specific, simultaneously detect multiple pathogens in one reaction, and can shorten the overall time of diagnosis for infectious gastroenteritis but are also expensive with relatively poor insurance reimbursement. CONTENT: In this review, we take a comprehensive approach to discuss issues with utilization of GIPs from a physician perspective, and implementation from a laboratory perspective. The information presented is to assist physicians in deciding on appropriate use of GIPs in diagnostic algorithms for their patients, and to provide information to laboratories that may be considering the addition of these powerful diagnostic assays to their test menu. Some of the important topics discussed are inpatient vs outpatient use, the appropriate panel size and organisms to include, interpretation of results, laboratory validation, and reimbursement. SUMMARY: The information in this review provides clear guidance to both clinicians and laboratories in deciding the best use of GIPs for a specific patient population. While this technology provides many benefits over traditional methods, it can also complicate result interpretation and comes with a high cost, which necessitates the need for use recommendations.

In silico analysis of mutations associated with occult hepatitis B virus (HBV) infection in South Africa.

Occult hepatitis B virus (OBI) infection is defined by the presence of viral DNA in the liver and/or serum in absence of hepatitis B surface antigen (HBsAg). While multiple studies have identified mutations that are associated with OBI, only a small portion of these mutations have been functionally characterized in vitro. Using complementary in silico approaches, the effects of OBI-associated amino acid mutations on HBV protein function in HBV/HIV-positive ART-naïve South Africans were evaluated. Two OBI-associated mutations in the PreS1 region, one in the PreS2 region, and seven in the surface region of subgenotype A1 sequences were identified as deleterious. In subgenotype A2 sequences, 11 OBI-associated mutations in the PreS1 region, seven in the PreS2 region, and 31 in the surface region were identified as deleterious. In the polymerase region, 14 OBI-associated mutations in subgenotype A1 and 71 OBI-associated mutations in subgenotype A2 were identified as deleterious. This study utilized in silico approaches to characterize the likely impact of OBI-associated mutations on viral function, thereby identifying and prioritizing candidates and reducing the significant cost associated with functional studies that are essential for mechanistic studies of the OBI phenotype.

Predicting Oral Beta-lactam susceptibilities against Streptococcus pneumoniae.

BACKGROUND: Oral beta-lactam antimicrobials are not routinely tested against Streptococcus pneumoniae due to presumed susceptibility based upon penicillin minimum inhibitory concentration (MIC) testing. Currently, Clinical and Laboratory Standards Institute provides comments to use penicillin MIC ≤0.06 to predict oral cephalosporin susceptibility. However, no guidance is provided when cefotaxime MIC is known, leading to uncertainty with interpretation. The purpose of this study was to evaluate cefotaxime and penicillin MICs and their respective correlation to oral beta-lactam categorical susceptibility patterns. METHODS: 249 S. pneumoniae isolates were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF) and then tested by broth microdilution method to penicillin, cefotaxime, amoxicillin, cefdinir, cefpodoxime, and cefuroxime. RESULTS: Using Clinical and Laboratory Standards Institute (CLSI) non-meningitis breakpoints for cefotaxime, 240/249 isolates were classified as susceptible. Of the cefotaxime susceptible isolates, 23% of the isolates are misrepresented as cefdinir susceptible. Amoxicillin correlated well with penicillin MIC breakpoints with only 1 discordant isolate out of 249. CONCLUSION: The correlation between amoxicillin and penicillin creates a very reliable predictor to determine categorical susceptibility. However oral cephalosporins were not well predicted by either penicillin or cefotaxime leading to the possible risk of treatment failures. Caution should be used when transitioning to oral cephalosporins in cefotaxime susceptible isolates, especially with higher cefotaxime MICs.

Use of High-fidelity simulation training for radiology healthcare professionals in the management of acute medical emergencies.

OBJECTIVES: Life-threatening emergencies are relatively uncommon in the radiology department, but when encountered, require timely intervention. With an increasing number of critically unwell patients visiting the radiology department each year for both diagnostic and interventional procedures, it is vital that radiology staff are trained to provide basic resuscitation before further assistance arrives. Simulation training is a well-validated, effective method for rehearsing low-frequency, high-acuity events in a supportive and safe environment. The aim of our study was to investigate whether the introduction of a focussed, multidisciplinary simulation course would improve healthcare professional's knowledge and confidence when managing common medical emergencies; including cardiac arrest, anaphylaxis and airway obstruction. METHODS: A multidisciplinary group of radiology staff attended a dedicated simulation teaching course. Participants completed a pre- and post-test questionnaire which assessed a range of knowledge domains and their perceived confidence with dealing with the clinical scenarios. The delegates were then asked to repeat this questionnaire 6 months after taking part in the course to assess their retention of skills and knowledge. RESULTS: Knowledge scores increased by a mean difference of 4 points (p < 0.001). The mean pre- and post-course perceived confidence scores were 4.4/10 and 8/10, respectively. ADVANCES IN KNOWLEDGE: This study suggests that embedding simulation training into the radiology curriculum improves healthcare professional's knowledge and perceived confidence when dealing with common medical emergencies. Although previous studies have looked at the use of simulation training for radiology trainees in the management of selected medical emergencies, to the authors' knowledge, this is the first study to demonstrate these benefits across a range of clinical scenarios, within an interprofessional environment.

Clinical features and laboratory diagnosis of emerging arthropod-transmitted viruses: A Report from the Pan American Society for Clinical Virology Clinical Practice Committee.

Arthropod-borne viruses (arboviruses) are an increasing global threat due to their ability to cause human disease and their expanding geographical distribution. They circulate in nature between arthropod vectors and vertebrate hosts. Infection of susceptible human hosts leads to harmful developmental and neurological manifestations. Arboviruses have caused recent outbreaks with significant public health implications, such as the Zika virus outbreak in the western hemisphere which caused fetal abnormalities in some infected pregnant women, or Eastern Equine Encephalitis which caused 15 deaths in 2019. This review discusses several arboviral infections and their clinical manifestations while highlighting the importance of laboratory diagnostics to detect infections and current attempts at vaccine development. The ability to accurately diagnose an arbovirus infection is critical for initiating a timely response to infections in order to improve patient outcomes.

Combined Molecular and Phenotypic Antimicrobial Susceptibility Testing Is Beneficial in Detection of ESBL and AmpC Beta-Lactamase Producing Isolates of Enterobacteriaceae in Pediatric Patients with Bloodstream Infections.

Objectives: The aim was to assess the potential advantage of combined genotypic testing with phenotypic antimicrobial susceptibility testing (AST) to detect AmpC ß-lactamases (AmpC) and extended-spectrum ß-lactamases (ESBL) producing Enterobacteriaceae isolated from blood cultures in a pediatric population. Materials and Methods: All first-time Enterobacteriaceae isolates recovered from blood cultures of pediatric patients at the Cincinnati Children's Hospital Medical Center between January 2017 and December 2018 were evaluated. The Check-MDR CT103XL ß-lactamase assay was used to determine the presence of AmpC and ESBL, while AST was performed using the VITEK 2 platform. Phenotypic ESBL resistance was defined by resistance to either ceftriaxone or ceftazidime using Clinical and Laboratory Standards Institute breakpoints, while combined cefoxitin resistance with ceftriaxone or ceftazidime resistance was used to detect AmpCs (as per European Committee on Antimicrobial Susceptibility Testing standards). Results: Overall, there were 170 isolates. Genotypically, 21 (12.4%) had AmpC and 18 (10.6%) had ESBL genes detected. Phenotypically, 11 (6.5%) isolates were AmpC and 26 (15.3%) were ESBL producing organisms. Genotypic testing identified an additional 14 AmpC and two ESBL isolates that failed to meet phenotypic criteria. Conclusions: Using combined genotypic and phenotypic methods to detect AmpC and ESBL producing organisms increased the identification of resistant organism and provided potentially clinical relevant data to guide the treatment of resistant organisms.

Accelerating Initiation of Adequate Antimicrobial Therapy Using Real-Time Decision Support and Microarray Testing.

INTRODUCTION: Bloodstream infections (BSI) represent a common cause of sepsis and mortality in children. Early and adequate empirical antimicrobial therapy is a critical component of successful treatment of BSI. Rapid PCR-based diagnostic technologies, such as nucleic acid microarrays, can decrease the time needed to identify pathogens and antimicrobial resistance and have the potential to ensure patients are started on adequate antibiotics as early as possible. However, without appropriate processes to support timely and targeted interpretation of these results, these advantages may not be realized in practice. METHODS: Our Antimicrobial Stewardship Program (ASP) implemented a quality improvement initiative using the Institute for Healthcare Improvement's Model for Improvement to decrease the time between a nucleic acid microarray result for Gram-positive bacteremia and the time a patient was placed on adequate antimicrobial therapy. The primary effective intervention was a near real-time notification system to the managing physicians of inadequate antimicrobial therapy via a call from the ASP team. RESULTS: Following the intervention, the average time to adequate antimicrobial therapy in patients with Gram-positive BSI and inadequate coverage decreased from 38 hours with the nucleic acid microarray result alone to 4.7 hours when results were combined with an ASP clinical decision support intervention, an 87% reduction. CONCLUSIONS: The positive effects of rapid-detection technologies to improve patient care are enhanced when combined with clinical decision support tools that can target inadequate antimicrobial treatments in near real time.

Frequency of Hepatitis B Virus Resistance Mutations in Women Using Tenofovir Gel as Pre-Exposure Prophylaxis.

Intermittent use of a single antiretroviral agent in the presence of a replicating virus could potentially increase the development of antiviral resistance. The pericoital, before-and-after sex, dosing regimen used in the Centre for the AIDS Programme of Research in South Africa (CAPRISA) 004 tenofovir gel trial meant that women who were infected with hepatitis B virus (HBV) were exposed intermittently to tenofovir during their participation. The impact of this dosing regimen on HBV resistance was assessed by amplification of the HBV polymerase region from 37 stored plasma samples of women who were HBV surface antigen positive. All samples belonged to HBV genotype A. None of the known tenofovir resistance mutations (M240V/I, L180M, A194T, V214A, N238T) were identified in any individuals. While it is reassuring that no resistance mutations were found among women using topical tenofovir, the rapidly expanding access to oral tenofovir-containing HIV pre-exposure prophylaxis (PrEP), with higher systemic exposure to the drug, makes monitoring for potential HBV drug resistance important.

Association of systemic antimicrobials with the expression of beta-lactamases in bacteria cultured from urological patients.

BACKGROUND: Patients with abnormalities of the genitourinary tract are at high risk for infections with antimicrobial-resistant pathogens. METHODS: All urine cultures ordered by members of the Division of Urology from four quarterly one-week periods were included. All gram-negative bacilli isolated were analyzed using the Check-Points Check-MDR CT103XL assay to identify the presence of genes associated with resistance to beta-lactam antibiotics. Association between the days of antibiotics and the presence of an ESBL-producing organism was determined. RESULTS: One hundred eleven positive cultures were included in this analysis, of which 5 (4.5%) contained ESBL-producing species. Days of systemic antibiotics within 30 days of urine culture was associated with an increased risk of isolating an ESBL-producing pathogen. CONCLUSION: The overall prevalence of ESBL-producing organisms is low in this cohort. The number of days of systemic antibiotics within 30 days of a urine culture was significantly associated with increased risk of isolating an ESBL-producing organism.

Rapid resolution of extreme gallbladder wall thickening in a patient with acute hepatitis C.

Diffuse gallbladder wall thickening is a common radiological finding with a wide range of differential diagnoses, many of which are not due to primary cholecystic disease. We report an unusual case of extreme diffuse gallbladder thickening in a 39-year-old lady, subsequently diagnosed with hepatitis C virus, and with complete resolution of her radiological appearances within 6 weeks-before commencing any treatment.

The Perils of Multiplex Gastrointestinal Pathogen Panels: Pseudo-outbreaks of Salmonellae and Entamoeba histolytica in Immunocompromised Hosts.

Two distinct clusters of gastroenteritis due to Salmonellae and Entamoeba histolytica (EH) were identified using a multiplex gastrointestinal pathogen panel (GPP) at a tertiary-care cancer center. Despite temporo-spatial overlap, our investigation did not corroborate transmission or true infection. In clinical practice, GPPs may render false-positive results.Infect Control Hosp Epidemiol 2018;867-870.

A sequential case series of 23 intubations in a rural emergency department in New Zealand.

OBJECTIVE: To describe the practice and procedure of emergency intubation in Whanganui Emergency Department, New Zealand and determine whether intubation can be carried out effectively in the rural setting. METHOD: A prospective observational study using the Australia and New Zealand Airway Registry proforma to collect data on the indication, lead intubator, first-pass success rate and peri-procedural complications. Data were also collected on whether a formal airway assessment was carried out and whether a checklist was used. RESULTS: Twenty-three patients were intubated in the emergency department over a 12-month period. Sixty-two percent (14/23 cases) were medical encounters and the remaining 38% of indications due to a trauma. Head injury was the most common indication (23%). Ninety-two percent of primary intubators were emergency department-based Fellowship of the Australasian College for Emergency Medicine or resident medical officers, while anaesthetic-trained operators accounted for just 8%. Our first-pass intubation success rate was 87% and 16% of cases had procedural complications. Sixty-five percent (15/23) carried out a formal airway assessment and a checklist was only used in 23% of cases. CONCLUSION: This sequential case series is the first study looking at airway management in rural New Zealand emergency department airway practice. Overall intubation success rates were comparable to larger tertiary centres across Australasia. We have demonstrated that with adequate resources and adherence to interventions, a rural emergency department can provide effective airway management.