Spectrochip-based Calibration Curve Modeling (CCM) for Rapid and Accurate Multiple Analytes Quantification in Urinalysis

Most urine test strips are intended to enable the general population to rapidly and easily diagnose potential renal disorders. It is semi-quantitative in nature, and although the procedure is straightforward, certain factors will affect the judgmental outcomes. This study describes rapid and accurate quantification of twelve urine test strip parameters: leukocytes, nitrite, urobilinogen, protein, pH, occult blood, specific gravity, ketone, bilirubin, glucose, microalbumin, and creatinine using a micro-electromechanical system (MEMS)-based spectrophotometer, known as a spectrochip. For each parameter, absorption spectra were measured three times independently at eight different concentration levels of diluted standard solutions, and the average spectral intensities were calculated to establish the calibration curve under the characteristic wavelength (λ c ). Then, regression analysis on the calibration curve was performed with GraphPad Prism software, which revealed that the coefficient of determination (R 2 ) of the modeled calibration curves was greater than 0.95. This result illustrates that the measurements exceed standard levels, confirming the importance of a spectrochip for routine multi-parameter urine analysis. Thus, it is possible to obtain the spectral signal strength for each parameter at its characteristic wavelength in order to compare directly with the calibration curves in the future, even in situations when sample concentration is unknown. Additionally, the use of large testing machines can be reduced in terms of cost, time, and space by adopting a micro urine testing platform based on spectrochip, which also improves operational convenience and effectively enables point-of-care (POC) testing in urinalysis.

Barriers to implementation of rapid identification and antimicrobial susceptibility testing technologies in the clinical microbiology laboratory: an American perspective

Clinical microbiology laboratories are responsible for confirming the aetiology of infectious diseases and providing antimicrobial susceptibility testing results. Traditional culture-based testing can be augmented by more rapid testing modalities to provide clinically actionable information as quickly as possible. Despite improvements in patient outcomes, many clinical microbiology laboratories are facing challenges to in-sourcing these technologies. Depending on a multitude of factors, including size, location and patient population served, these barriers may affect some laboratories and hospital systems to greater or lesser extents than others. It will be up to each individual facility to ascertain its ability to overcome barriers. To aid in this self-assessment, we present for thoughtful consideration a discussion of the barriers to implementation of rapid identification and antimicrobial susceptibility testing technologies, with specific attention to matters of financial cost, staff expertise, operational issues and stakeholder buy-in.

Analysis and mapping of global research publications on point-of-care testing for infectious diseases

RATIONALE

This study presents the first comprehensive analysis and mapping of scientific research on point-of-care testing (POCT) in infectious diseases, filling a gap in understanding the evolving landscape of this field. The identification of research themes and global contributions offers valuable insights.

AIMS AND OBJECTIVES

This manuscript aims to analyse and map scientific research on POCT in the context of infectious diseases.

METHODS

The study employed a comprehensive search strategy using terms related to POCT and infectious diseases. The search was conducted on the Scopus database, refining results based on inclusion and exclusion criteria. The dataset of 1719 research articles was then subjected to descriptive analysis and mapping using VOSviewer.

RESULTS

The research findings indicate an exponential growth in POCT-related publications, with 46.8% published post the COVID-19 pandemic. Plos One journal led in publication frequency, and Biosensors and Bioelectronics received the highest citations per article. North America and Western Europe dominated contributions, with notable participation from China, South Africa, and India. The research landscape revealed the following research themes: detection technologies, human immunodeficiency virus (HIV)/sexually transmitted infection (STI) diagnosis, antibiotic optimisation, and schistosomiasis. Clinical trials focused on antibiotic prescribing, HIV, STIs, and specific infections. The findings suggest a shifting landscape towards POCT, emphasising the need for future planning and investment in healthcare systems. The research identifies areas for future exploration, such as the impact of POCT on antibiotic prescribing and its role in combating infectious diseases in low- and middle-income countries.

CONCLUSION

Implementation of POCT has the potential to revolutionise infectious disease management, improve patient outcomes, and reduce the global burden of diseases. Better public awareness, healthcare team management, and planning for POCT at entry points are crucial for societal benefit. Results demonstrated the evolving role of POCT in infectious disease management and prevention.

Burden and Management of Multi-Drug Resistant Organism Infections in Solid Organ Transplant Recipients Across the World: A Narrative Review

Solid organ transplant (SOT) recipients are particularly susceptible to infections caused by multidrug-resistant organisms (MDRO) and are often the first to be affected by an emerging resistant pathogen. Unfortunately, their prevalence and impact on morbidity and mortality according to the type of graft is not systematically reported from high-as well as from low and middle-income countries (HIC and LMIC). Thus, epidemiology on MDRO in SOT recipients could be subjected to reporting bias. In addition, screening practices and diagnostic resources may vary between countries, as well as the availability of new drugs. In this review, we aimed to depict the burden of main Gram-negative MDRO in SOT patients across HIC and LMIC and to provide an overview of current diagnostic and therapeutic resources.

The Complex Intracellular Lifecycle of Staphylococcus aureus Contributes to Reduced Antibiotic Efficacy and Persistent Bacteremia

Staphylococcus aureus bacteremia continues to be associated with significant morbidity and mortality, despite improvements in diagnostics and management. Persistent infections pose a major challenge to clinicians and have been consistently shown to increase the risk of mortality and other infectious complications. S. aureus, while typically not considered an intracellular pathogen, has been proven to utilize an intracellular niche, through several phenotypes including small colony variants, as a means for survival that has been linked to chronic, persistent, and recurrent infections. This intracellular persistence allows for protection from the host immune system and leads to reduced antibiotic efficacy through a variety of mechanisms. These include antimicrobial resistance, tolerance, and/or persistence in S. aureus that contribute to persistent bacteremia. This review will discuss the challenges associated with treating these complicated infections and the various methods that S. aureus uses to persist within the intracellular space.

Point of Care Molecular Testing: Current State and Opportunities for Diagnostic Stewardship

Inappropriate ordering practices, either under or over ordering of diagnostic tests, are recognized problems with possible negative downstream consequences. As the menu of clinical tests, especially molecular tests grows, it is becoming increasingly important to provide guidance to providers on the appropriate utilization. Diagnostic stewardship programs have been established at many institutions to help direct the appropriate utilization of laboratory testing to ultimately guide patient management and treatment decisions. Many molecular tests have now received Clinical Laboratory Improvement Amendments (CLIA)-waived status for use in a point-of-care (POC) setting; however, parallel diagnostic stewardship programs have not been established to help guide providers on how best to use these tests. In this article, we will discuss the available molecular POC tests and opportunities and challenges for establishing diagnostic stewardship programs for molecular testing performed in the POC setting.

Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting

In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption.

Comparison of three rapid diagnostic tests for bloodstream infections using Benefit-risk Evaluation Framework (BED-FRAME)

Rapid diagnostic tests (RDTs) for bloodstream infections have the potential to reduce time to appropriate antimicrobial therapy and improve patient outcomes. Previously, an in-house, lipid-based, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) method, Fast Lipid Analysis Technique (FLAT MS), has shown promise as a rapid pathogen identification method. In this study, FLAT MS for direct from blood culture identification was evaluated and compared to FDA-cleared identification methods using the Benefit-risk Evaluation Framework (BED-FRAME) analysis. FLAT MS was evaluated and compared to Bruker Sepsityper and bioMérieux BioFire FilmArray BCID2 using results from a previous study. For this study, 301 positive blood cultures were collected from the University of Maryland Medical Center. The RDTs were compared by their sensitivities, time-to-results, hands-on time, and BED-FRAME analysis. The overall sensitivity of all platforms compared to culture results from monomicrobial-positive blood cultures was 88.3%. However, the three RDTs differed in their accuracy for identifying Gram-positive bacteria, Gram-negative bacteria, and yeast. Time-to-results for FLAT MS, Sepsityper, and BioFire BCID2 were all approximately one hour. Hands-on times for FLAT MS, Sepsityper, and BioFire BCID2 were 10 (±1.3), 40 (±2.8), and 5 (±0.25) minutes, respectively. BED-FRAME demonstrated that each RDT had utility at different pathogen prevalence and relative importance. BED-FRAME is a useful tool that can used to determine which RDT is best for a healthcare center.

Implementation of a pharmacy-driven rapid bacteremia response program

PURPOSE

This report describes a comprehensive pharmacy-driven rapid bacteremia response program.

SUMMARY

This novel program positioned the pharmacy department at a large, community health system to receive and respond to critical microbiologic diagnostic testing results, 24/7/365. The program empowered pharmacists to provide centralized, comprehensive care including assessing blood culture Gram stain results, adjusting antibiotic therapy per protocol, ordering repeat blood cultures, analyzing and interpreting rapid molecular diagnostic test results, placing orders for contact isolation, and communicating antibiotic recommendations to the treatment team. In the first year after program implementation, 2,282 blood culture Gram stains and 2,046 rapid diagnostic test results were called in to the pharmacy department. The program reduced the median time to effective therapy in patients who did not already have active antimicrobial orders from over 10 hours to less than 1 hour. Based on the Gram stain results, antibiotics were started per protocol in 34.2% of patients. Based on the rapid molecular diagnostic test results, adjustments were made to antibiotic regimens in 55.7% of cases after discussion with a provider. Of these adjustments, 39.9% were for escalation of antibiotics and 37.7% were for de-escalation of antibiotics.

CONCLUSION

By expanding the scope of pharmacy practice, barriers to optimizing clinical care were overcome.

Primary Care Antibiotic Prescribing and Infection-Related Hospitalisation

Inappropriate prescribing of antibiotics has been widely recognised as a leading cause of antimicrobial resistance, which in turn has become one of the most significant threats to global health. Given that most antibiotic prescriptions are issued in primary care settings, investigating the associations between primary care prescribing of antibiotics and subsequent infection-related hospitalisations affords a valuable opportunity to understand the long-term health implications of primary care antibiotic intervention. A narrative review of the scientific literature studying associations between primary care antibiotic prescribing and subsequent infection-related hospitalisation was conducted. The Web of Science database was used to retrieve 252 potentially relevant studies, with 23 of these studies included in this review (stratified by patient age and infection type). The majority of studies (n = 18) were published in the United Kingdom, while the remainder were conducted in Germany, Spain, Denmark, New Zealand, and the United States. While some of the reviewed studies demonstrated that appropriate and timely antibiotic prescribing in primary care could help reduce the need for hospitalisation, excessive antibiotic prescribing can lead to antimicrobial resistance, subsequently increasing the risk of infection-related hospitalisation. Few studies reported no association between primary care antibiotic prescriptions and subsequent infection-related hospitalisation. Overall, the disparate results in the extant literature attest to the conflicting factors influencing the decision-making regarding antibiotic prescribing and highlight the necessity of adopting a more patient-focussed perspective in stewardship programmes and the need for increased use of rapid diagnostic testing in primary care.

MALDI-TOF bacterial subtyping for rapid detection of biomarkers in Staphylococcus aureus from subclinical bovine mastitis

AIMS

This study aimed to evaluate matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial subtyping for the rapid detection of biomarkers in Staphylococcus aureus from subclinical bovine mastitis.

METHODS AND RESULTS

A total of 229 S. aureus isolates were obtained from milk samples collected from cows with subclinical mastitis using microbiological culture. Staphylococcus aureus isolates were also submitted to PCR analysis targeting the mecA and mecC genes, which are indicative of methicillin resistance. Confirmation of the species was achieved through MALDI-TOF MS analysis. To analyze antimicrobial resistance patterns, the MALDI BioTyper Compass Explorer and ClinProTools Bruker software were employed, and dendrograms were generated using Bionumerics software.

CONCLUSIONS

MALDI-TOF MS successfully identified S. aureus at the species level, but no methicillin resistance was observed. Moreover, spectral typing displayed limited similarity when compared to pulsed-field gel electrophoresis (PFGE).

Clinical outcomes associated with blood-culture contamination are not affected by utilization of a rapid blood-culture identification system

OBJECTIVE

Contaminated blood cultures result in extended hospital stays and extended durations of antibiotic therapy. Rapid molecular-based blood culture testing can speed positive culture detection and improve clinical outcomes, particularly when combined with an antimicrobial stewardship program. We investigated the impact of a multiplex polymerase chain reaction (PCR) FilmArray Blood Culture Identification (BCID) system on clinical outcomes associated with contaminated blood cultures.

METHODS

We conducted a retrospective cohort study involving secondary data analysis at a single institution. In this before-and-after study, patients with contaminated blood cultures in the period before PCR BCID was implemented (ie, the pre-PCR period; n = 305) were compared to patients with contaminated blood cultures during the period after PCR BCID was implemented (ie, the post-PCR implementation period; n = 464). The primary exposure was PCR status and the main outcomes of the study were length of hospital stay and days of antibiotic therapy.

RESULTS

We did not detect a significant difference in adjusted mean length of hospital stay before (10.8 days; 95% confidence interval [CI], 9.8-11.9) and after (11.2 days; 95% CI, 10.2-12.3) the implementation of the rapid BCID panel in patients with contaminated blood cultures (P = .413). Likewise, adjusted mean days of antibiotic therapy between patients in pre-PCR group (5.1 days; 95% CI, 4.5-5.7) did not significantly differ from patients in post-PCR group (5.3 days; 95% CI, 4.8-5.9; P = .543).

CONCLUSION

The introduction of a rapid PCR-based blood culture identification system did not improve clinical outcomes, such as length of hospital stay and duration of antibiotic therapy, in patients with contaminated blood cultures.

Comparison of 3 diagnostic platforms for identification of bacteria and yeast from positive blood culture bottles

Managing bloodstream infections requires fast and accurate diagnostics. Culture-based diagnostic methods for identification from positive blood culture require 24-hour subculture, potentially delaying time to appropriate therapy. Positive blood cultures were collected (n = 301) from September 2021 to August 2022 at the University of Maryland Medical Center. Platforms compared were BioFire® BCID2, Sepsityper®, and short-term culture. For monomicrobial cultures, FilmArray® BCID2 identified 88.3% (241/273) of pathogens. Rapid Sepsityper® identified 76.9% (210/273) of pathogens. Sepsityper® extraction identified 82.4% (225/273) of pathogens. Short-term culture identified 83.5% (228/273) of pathogens. For polymicrobial cultures, Sepsityper®, short-term culture, and BioFire® BCID2 had complete identifications at 10.7% (3/28), 0%, and 92.9% (26/28), respectively. Time-to-results for Rapid Sepsityper®, Sepsityper® extraction, BioFire® BCID2, and Short-term culture were 35, 52, 65, and 306 minutes, respectively. Performance of these platforms can reduce time-to-results and may help effectively treat bloodstream infections faster. Accuracy, time-to-result, and hands-on time are important factors when evaluation diagnostic platforms.

Real-time PCR versus traditional and Nano-based ELISA in early detection of murine trichinellosis

Trichinellosis is a serious foodborne zoonosis. It poses a serious risk to public health worldwide. Early serological diagnosis of trichinellosis is influenced by an immunological 'silent' phase following infection. This highlights the necessity for developing sensitive diagnostic approaches to be employed when antibodies cannot be detected. In this work, the validity of traditional ELISA, Nano-ELISA and real time polymerase chain reaction (PCR) were evaluated in early diagnosis of Trichinella spiralis. Swiss albino mice were orally infected with 100 and 300 muscle larvae/mouse. Mice were sacrificed 4, 6, 8, 10, 15, and 28 days post-infection (dpi). Blood samples were tested for circulating antigen by traditional ELISA and Nano-ELISA using anti-rabbit polyclonal IgG conjugated with AgNPs and for Rep gene by SYBR green real-time PCR. Rep gene detection by SYBR green real-time PCR could detect T. spiralis with 100% sensitivity in the mild infection group at 8 dpi, while in the severe infection group it reached 100% sensitivity at 4 dpi. Nano-ELISA could detect T. spiralis circulating antigen from 4 dpi in both mild and severe infection and reached 100% sensitivity at 8 dpi and 6 dpi in mild and severe infection, respectively. However, traditional ELISA could detect T. spiralis circulating antigen from 6 dpi and reached maximum sensitivity at 15 dpi in the mild infection group, while in the severe infection group detection began at 4 dpi and reached 100% sensitivity at 8 dpi. Nano-ELISA and real time PCR, using Rep gene, are useful tools for the detection of early T. spiralis infection even in its mild infection state.

Comparison of Risk Stratification Approaches to Identify Patients with Clostridioides difficile Infection at Risk for Multidrug-Resistant Organism Gut Microbiota Colonization

INTRODUCTION

Multidrug-resistant organisms (MDRO) commonly colonize the gut microbiota of patients with Clostridioides difficile infection (CDI). This increases the likelihood of systemic infections with these MDROs. To help guide MDRO screening and/or empiric antibiotic therapy, we derived and compared predictive indices for MDRO gut colonization in patients with CDI.

METHODS

This was a multicenter, retrospective cohort study of adult patients with CDI from July 2017 to April 2018. Stool samples were screened for MDRO via growth and speciation on selective antibiotic media and confirmed using resistance gene polymerase chain reaction. A regression-based risk score for MDRO colonization was constructed. Predictive performance via area under the receiver operating characteristic curve (aROC) of this index was compared with two other simplified risk stratification approaches: (1) prior healthcare exposure and/or high-CDI risk antibiotics; (2) number of prior high-CDI risk antibiotics.

RESULTS

50 (20.8%) of 240 included patients had MDRO colonization; 35 (14.6%) VRE, 18 (7.5%) MRSA, 2 (0.8%) CRE. Prior fluoroquinolone (aOR 2.404, 95% CI 1.095-5.279) and prior vancomycin (1.996, 95% CI 1.014-3.932) were independently associated with MDRO colonization while prior clindamycin (aOR 3.257, 95% CI 0.842-12.597) and healthcare exposure (aOR 2.138, 95% CI 0.964-4.740) were retained as explanatory variables. The regression-based risk score significantly predicted MDRO colonization (aROC 0.679, 95% CI 0.595-0.763), but was not significantly more predictive than prior healthcare exposure + prior antibiotics (aROC 0.646, 95% CI 0.565-0.727) or number of prior antibiotic exposures (aROC 0.642, 95% CI 0.554-0.730); P > 0.05 for both comparisons.

CONCLUSION

A simplified approach using prior healthcare exposure and receipt of prior antibiotics known to increase CDI risk identified patients at risk for MDRO gut microbiome colonization as effectively as individual patient/antibiotic risk modeling.

Implementation of a Rapid Multiplex Polymerase Chain Reaction Pneumonia Panel and Subsequent Antibiotic De-escalation

Background

Net effects of implementation of a multiplex polymerase chain reaction (PCR) pneumonia panel (PNP) on antimicrobial stewardship are thus far unknown. This retrospective study evaluated the real-world impact of the PNP on time to antibiotic de-escalation in critically ill patients treated for pneumonia at an academic medical center.

Methods

This retrospective, quasi-experimental study included adult intensive care unit (ICU) patients with respiratory culture results from 1 May to 15 August 2019 (pre-PNP group) and adult ICU patients with PNP results from 1 May to 15 August 2020 (PNP group) at Nebraska Medical Center. Patients were excluded for the following reasons: any preceding positive coronavirus disease 2019 PCR test, lack of antibiotic receipt, or non-respiratory tract infection indications for antibiotics. The primary outcome was time to discontinuation of anti-methicillin-resistant Staphylococcus aureus (MRSA) therapy. Secondary outcomes included time to discontinuation of antipseudomonal therapy, frequency of early discontinuation for atypical coverage, and overall duration (in days) of antibiotic therapy for pneumonia.

Results

Sixty-six patients in the pre-PNP group and 58 in the PNP group were included. There were significant differences in patient characteristics between groups. The median time to anti-MRSA agent discontinuation was 49.1 hours in the pre-PNP and 41.8 hours in the PNP group (P = .28). The median time to discontinuation of antipseudomonal agents was 134.4 hours in the pre-PNP versus 98.1 hours in the PNP group (P = .47). Other outcomes were numerically but not significantly improved in our sample.

Conclusions

This early look at implementation of a multiplex PNP did not demonstrate a statistically significant difference in antibiotic use but lays the groundwork to further evaluate a significant real-world impact on antibiotic de-escalation in ICU patients treated for pneumonia.

Rapid antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales: an implementation study

AIMS OF THE STUDY

The goal of this descriptive study was to assess the performance as well as the extent of the clinical impact of rapid automated antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales. We also aimed to analyse how rapid automated antimicrobial susceptibility testing influences clinical decision-making.

METHODS

This single-centre study conducted at the University Hospital of Zurich included data from all consecutive patients with Enterobacterales bacteraemia from November 2019 to October 2020. There was no control group. The primary outcome was the effect of rapid automated antimicrobial susceptibility testing on antibiotic therapy (no adjustment, escalation to a broader-spectrum antibiotic or de-escalation to a narrower-spectrum antibiotic). Rapid automated antimicrobial susceptibility testing results were further compared to susceptibility tests using European Committee on Antimicrobial Susceptibility Testing (EUCAST) standard methods and erroneous results were noted. Additionally, we investigated turnaround times for rapid automated antimicrobial susceptibility testing and routine diagnostic testing.

RESULTS

We analysed 106 patients with 116 episodes of bacteraemia due to Enterobacterales, with Escherichia coli and Klebsiella pneumoniae being the most frequent isolates. Almost 8% of pathogens were multidrug resistant. Rapid automated antimicrobial susceptibility testing showed category agreement in 98.4% of all interpretable cases. A significant reduction of more than 20 h in turnaround times could be achieved with rapid automated antimicrobial susceptibility testing compared to the routine diagnostic workflow. In the majority of cases, rapid automated antimicrobial susceptibility testing had no effect, given that the empirical therapy was already correct or circumstances did not allow for de-escalation. In 38.8% of cases, antimicrobial therapy was adjusted, whereas eight cases were de-escalated based on rapid automated antimicrobial susceptibility testing alone.

CONCLUSIONS

Rapid automated antimicrobial susceptibility testing may be a valuable and safe way to accelerate diagnosis. In particular, time to suitable therapy can be shortened in cases of incorrect therapy. However, physicians are reluctant to de-escalate antibiotic therapy based on rapid automated antimicrobial susceptibility testing alone, limiting its impact in everyday clinics. To further explore the potential of rapid automated antimicrobial susceptibility testing, a stringent/compulsory antibiotic stewardship programme would be a valuable next step.

Knowledge, Attitude, and Practice (KAP) Survey on the Management of Multidrug-Resistant Gram-Negative Infections With Innovative Antibiotics: Focus on Ceftazidime-Avibactam

BACKGROUND

Antimicrobial resistance (AMR) is a major public health dilemma and a chief health concern globally. The rising incidence of resistance against carbapenems, which are considered most effective against gram-negative bacteria, has added to the concern and has limited the number of available treatment options. Newer antibiotic options may be required to tackle the mounting concern of antibiotic resistance. However, only a few antimicrobials are in the pipeline for managing infections instigated by multidrug-resistant (MDR) gram-negative bacteria. This justifies the prudent application of already available antibiotics. Among newer antibiotics available to healthcare professionals (HCPs), ceftazidime-avibactam (CAZ-AVI) has shown good efficacy in the management of MDR gram-negative infections.

METHOD

A cross-sectional survey on the knowledge, attitude, and practices (KAP) among HCPs was carried out using a questionnaire comprising 21 parameters related to AMR patterns on the need for innovative antibiotics to manage MDR gram-negative infections and the usage of CAZ-AVI by HCPs while managing such infections. The KAP scores were calculated to rank respondents' KAP levels.

RESULT

Out of the 204 study respondents, the majority (~80%) (n=160) believed that renewed efforts should be made to seek antimicrobial agents that will add to the armamentarium of treatment options for MDR gram-negative infections. CAZ-AVI is an important treatment alternative for managing MDR gram-negative infections (n=90, 45%). Further, it can be the first choice of definitive therapy for oxacillinases (OXA)-48-producing carbapenem-resistant Enterobacterales (n=84, 42%). HCPs also believed that the use of CAZ-AVI in clinical practice will require high levels of antimicrobial stewardship (n=100, 49%).

CONCLUSION

Novel and innovative antibiotics are the need of the hour in the management of MDR gram-negative infections. CAZ-AVI has established its effectiveness in treating these infections; however, the molecule must be utilized prudently while keeping stewardship principles in mind.

Implementing Alfred60AST in a clinical lab: Clinical impact on the management of septic patients and financial analysis

INTRODUCTION

Sepsis is an important cause of morbidity and mortality. An accelerated microbiology diagnosis is crucial in order to reduce the time to initiate targeted antibiotic therapy. The Alfred60AST system is able to provide phenotypic Antimicrobial Susceptibility Testing (AST) results within hours. This study has two objectives: assess the clinical impact of this technology and determine its cost-effectiveness.

METHODS

During a ten-week period, all new enterobacterial or enterococcal bloodstream infection was analyzed with the Alfred60AST system, in parallel with routine methods. Its impact on the clinician's therapeutic strategy was studied. In order to assess the financial and practical aspects of the method, an analysis of the extracosts and a survey of the technical staff were conducted.

RESULTS

Fifty-three cases of bacteriemia were included. For the Enterobacteriaceae bacteriemias, a clinical impact was shown in 18.9% of the cases (e.g, treatment modification). The financial analysis highlighted an increase in costs (+38% for Enterobacteriaceae, +50% for Enterococci), compared to the theoretical costs reported by the firm, due to the workflow and the volumes of samples used. Finally, results of the technical staff survey were favorable in terms of ease of use of the system.

CONCLUSION

In addition to its ease of use, the Alfred60AST system is able to provide an AST in a record time. This study shows a real interest of the technique in the therapeutic management of patients with enterobacterial sepsis. However, its routine implementation requires an increase of the analyzed volumes as well as a 24/7 organization of the laboratory in order to be profitable.

Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective

Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".

Antimicrobial susceptibility testing: An updated primer for clinicians in the era of antimicrobial resistance: Insights from the Society of Infectious Diseases Pharmacists

Antimicrobial susceptibility testing (AST) is a critical function of the clinical microbiology laboratory and is essential for optimizing care of patients with infectious diseases, monitoring antimicrobial resistance (AMR) trends, and informing public health initiatives. Several methods are available for performing AST including broth microdilution, agar dilution, and disk diffusion. Technological advances such as the development of commercial automated susceptibility testing platforms and the advent of rapid diagnostic tests have improved the rapidity, robustness, and clinical application of AST. Numerous accrediting and regulatory agencies are involved in the process of AST and setting and revising breakpoints, including the U.S. Food and Drug Administration and the Clinical and Laboratory Standards Institute. Challenges to optimizing AST include the emergence of new resistance mechanisms, the development of new antimicrobial agents, and generation of new data requiring updates and revisions to established methods and breakpoints. Together, the challenges in AST methods and their interpretation create important opportunities for well-informed clinicians to improve patient outcomes and provide value to antimicrobial stewardship programs, especially in the setting of rapidly changing and increasing AMR. Addressing AST challenges will involve continued development of new technologies along with collaboration between clinicians and the laboratory to facilitate optimal antimicrobial use, combat the increasing burden of AMR, and inform the development of novel antimicrobials. This updated primer serves to reinforce important principles of AST, and to provide guidance on their implementation and optimization.

Antimicrobial Stewardship Techniques for Critically Ill Patients with Pneumonia

Pneumonia is common in the intensive care unit (ICU), infecting 27% of all critically ill patients. Given the high prevalence of this disease state in the ICU, optimizing antimicrobial therapy while minimizing toxicities is of utmost importance. Inappropriate antimicrobial use can increase the risk of antimicrobial resistance, Clostridiodes difficile infection, allergic reaction, and other complications from antimicrobial use (e.g., QTc prolongation, thrombocytopenia). This review article aims to discuss methods to optimize antimicrobial treatment in patients with pneumonia, including the following: procalcitonin use, utilization of methicillin-resistant Staphylococcus aureus nares testing to determine need for vancomycin therapy, utilization of the Biofire^® FilmArray^® pneumonia polymerase chain reaction (PCR), and microbiology reporting techniques.

Molecular Rapid Diagnostics Improve Time to Effective Therapy and Survival in Patients with Vancomycin-Resistant Enterococcus Bloodstream Infections

Delays in appropriate antibiotic therapy are a key determinant for deleterious outcomes among patients with vancomycin-resistant Enterococcus (VRE) bloodstream infections (BSIs). This was a multi-center pre/post-implementation study, assessing the impact of a molecular rapid diagnostic test (Verigene® GP-BC, Luminex Corporation, Northbrook, IL, USA) on outcomes of adult patients with VRE BSIs. The primary outcome was time to optimal therapy (TOT). Multivariable logistic and Cox proportional hazard regression models were used to determine the independent associations of post-implementation, TOT, early vs. delayed therapy, and mortality. A total of 104 patients with VRE BSIs were included: 50 and 54 in the pre- and post-implementation periods, respectively. The post- vs. pre-implementation group was associated with a 1.8-fold faster rate to optimized therapy (adjusted risk ratio, 1.841 [95% CI 1.234-2.746]), 6-fold higher likelihood to receive early effective therapy (<24 h, adjusted odds ratio, 6.031 [2.526-14.401]), and a 67% lower hazards for 30-day in-hospital mortality (adjusted hazard ratio, 0.322 [0.124-1.831]), after adjusting for age, sex, and severity scores. Inversely, delayed therapy was associated with a 10-fold higher risk of in-hospital mortality (aOR 10.488, [2.497-44.050]). Reduced TOT and in-hospital mortality were also observed in subgroups of immunosuppressed patients in post-implementation. These findings demonstrate that the addition of molecular rapid diagnostic tests (mRDT) to clinical microbiology and antimicrobial stewardship practices are associated with a clinically significant reduction in TOT, which is associated with lower mortality for patients with VRE BSIs, underscoring the importance of mRDTs in the management of VRE infections.

Examining the clinical impact of rapid multiplex polymerase chain reaction-based diagnostic testing for bloodstream infections in a national cohort of the Veterans Health Administration

STUDY OBJECTIVE

Bloodstream infections (BSIs) are a significant cause of mortality. Use of a rapid multiplex polymerase chain reaction-based blood culture identification panel (BCID) may improve antimicrobial utilization and clinical outcomes by shortening the time to appropriate therapy and de-escalating antibiotics among patients on overly broad-spectrum empiric therapy. The effect of BCID on clinical outcomes across varying institutional antimicrobial stewardship program (ASP) practices is unclear. This study evaluated clinical outcomes associated with the "real-world" implementation of BCID in a national health system with varying ASP practices.

DESIGN

National, multicenter, retrospective, pre-post quasi-experimental study of hospitalized patients admitted from 2015 to 2020 to VHA facilities, which introduced the BCID for ≥1 year.

SETTING

United States Veterans Health Administration (VHA) hospitals with BCID.

PATIENTS

Hospitalized VHA patients with ≥1 blood culture positive for bacteria featured on the BCID panel.

INTERVENTION

Comparison of outcomes between the pre- and post-BCID implementation groups.

MEASUREMENTS

Outcomes evaluated included early antimicrobial de-escalation within 48 h, defined as reduction in antimicrobial spectrum scores, time to appropriate therapy, and 30-day mortality.

MAIN RESULTS

A total of 4138 patients (pre-BCID, n = 2100; post-BCID, n = 2038) met the study criteria. Implementation of BCID was associated with significant improvements in early antimicrobial de-escalation (34.6%: pre-BCID vs. 38.1%: post-BCID; p = 0.022), which persisted after adjusting for other covariates (adjusted risk ratio [aRR], 1.11; 95% confidence interval [CI], 1.02-1.20; p = 0.011). Median time to appropriate therapy was shorter in the post-BCID implementation group relative to the pre-BCID group (9 h: pre-BCID vs. 8 h: post-BCID, respectively, p = 0.005), and a greater percentage of patients received early appropriate antimicrobial therapy within 48 h in the post-BCID implementation group (91.7%: pre-BCID vs. 93.8%: post-BCID; p = 0.008). In the multivariable regression analysis, BCID implementation was significantly associated with a higher likelihood of appropriate therapy within 48 h (aRR, 1.02; 95% CI, 1.01-1.08; p = 0.020). There was no difference in 30-day mortality between groups overall (12.6% pre-BCID vs. 11.2% post-BCID; p = 0.211).

CONCLUSIONS

In a "real-world" clinical setting, the implementation of BCID was associated with clinical improvements in antimicrobial utilization. The BCID platform may serve as a useful adjunct for BSI management in facilities with ASP.

Phase Contrast Image-Based Rapid Antimicrobial Susceptibility Testing of Bacteria in Liquid Culture Media

Currently, the world is facing the problem of bacterial resistance, which threatens public health, and bacterial antimicrobial susceptibility testing (AST) plays an important role in biomedicine, dietary safety and aquaculture. Traditional AST methods take a long time, usually 16-24 h, and cannot meet the demand for rapid diagnosis in the clinic, so rapid AST methods are needed to shorten the detection time. In this study, by using an in-house built centrifuge to centrifuge bacteria in a liquid medium onto the inner wall of the bottom surface of a counting plate, and using a phase contrast microscope to track bacterial growth under the effect of different antibiotic concentrations, the results of the minimum inhibitory concentration (MIC) of bacteria under the effect of antibiotics can be obtained in as early as 4 h. We used a combination of E. coli and tigecycline and obtained MIC results that were consistent with those obtained using the gold standard broth micro-dilution method, demonstrating the validity of our method; due to the time advantage, the complete set can be used in the future for point of care and clinical applications, helping physicians to quickly obtain the MIC used to inhibit bacterial growth.

A Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Direct-from-Urine-Specimen Diagnostic for Gram-Negative Pathogens

Urinary tract infections (UTIs) pose a major public health burden. The vast majority of UTIs are caused by Gram-negative bacteria. Current culture-based pathogen identification methods may require up to 24 to 48 h of incubation. In this study, we developed and evaluated a method for Gram-negative pathogen identification direct from urine, without culture, via matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in approximately 1 h. Urine samples were collected (n = 137) from the University of Maryland Medical Center clinical microbiology laboratory. To identify bacteria direct from urine, two methods were evaluated. First, 1 μL of urine was directly spotted onto the MALDI target plate, and second, 1 mL of urine was centrifuged at 8,000 rpm for 5 min before processing using the fast lipid analysis technique (FLAT). Mass spectra were acquired on the Bruker MALDI Biotyper sirius system in the negative-ion mode. Results were compared to those of standard culture methods. When 1 μL of urine was directly spotted, positive agreement was 81.5% (101/124) and, after centrifugation, 94.4% (117/124) relative to that of standard culture methods. Negative agreement for both methods was 100% (13/13). The time to results for both of the specimen preparation methods using the FLAT extraction protocol was approximately 1 h, with minimal hands-on time required (<5 min). The ability to rapidly identify pathogens directly from urine, without the need for culture, allows for faster turnaround times and, potentially, improved patient outcomes. Overall, the FLAT extraction protocol, in combination with lipid A identification, provides a reproducible and accurate method to rapidly identify urinary pathogens. IMPORTANCE This study describes and evaluates a direct-from-urine extraction method that allows identification of Gram-negative bacteria via MALDI-TOF MS within 1 h. Currently, identification of urinary pathogens requires 24 h of culture prior to identification. While this method may not replace culture, we demonstrate its utility in screening for common urinary pathogens. By providing identifications in under 1 h, clinicians can potentially treat patients sooner with more-targeted antimicrobial therapy. In turn, earlier treatment can improve patient outcome and antimicrobial stewardship. Furthermore, MADLI-TOF MS is a readily available, easy-to-use diagnostic tool in clinical laboratories, making implementation of this method possible.

Impact of Molecular Syndromic Diagnosis of Severe Pneumonia in the Management of Critically Ill Patients

The impact of syndromic molecular diagnosis in the management of nosocomial infections caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens has been incompletely characterized. We evaluated the performance of a molecular syndromic platform (BioFire FilmArray-Pneumonia plus Panel) in patients with pneumonia in the intensive care unit (ICU) of a University Hospital in Greece over a 2-year period. We evaluated 79 consecutive patients diagnosed with pneumonia in the ICU (2018-2020), including 55 patients with ventilator associated pneumonia (VAP). We included 40 control patients diagnosed with pneumonia in the ICU the year before the study (2017-2018). We identified 16 cases of VAP due to XDR bacterial pathogens. We found an excellent agreement (89.4% 76/85 reported results) between the results of syndromic platform and conventional cultures of tracheal aspirates. The molecular syndromic test significantly improved time to diagnosis versus conventional culture (3.5 h vs 72 h, P < 0.0001), and identified new pathogens not detected by cultures in 49% of the cases. However, three cases of pneumonia with targets not included in the molecular platform, were not detected. Implementation of the molecular syndromic facilitated treatment modification from broad to narrow spectrum antimicrobial therapy, resulting in significant reductions in antibiotic consumption in the study group compared to the control group, without a negative impact in patient outcome. The implementation of syndromic molecular diagnosis in critically ill patients with pneumonia is associated with timely and improved diagnosis and has significant impact on reduction of antibiotic consumption. IMPORTANCE The impact of syndromic molecular diagnosis in the management of nosocomial infections caused by MDR/XDR pathogens has been incompletely characterized. We evaluated the performance of a molecular syndromic platform (BioFire FilmArray -Pneumonia plus Panel) in 79 patients with pneumonia in the intensive care unit (ICU) of a University Hospital in Greece over a 2-year period (2018-2020) compared to 40 control patients diagnosed with pneumonia in the ICU the year before the study (2017-2018). Importantly, implementation of syndromic pneumonia panel improved time to diagnosis, identified new pathogens not detected by cultures in 49% of the cases and resulted in a significant reduction in antibiotic consumption compared to the year before initiation of the study without a negative impact in mortality of patients. Collectively, our study demonstrates the positive value of PCR syndromic testing in the management of pneumonia in ICUs high rates of MDR/XDR nosocomial pathogens.

Time to Effective Therapy Is an Important Determinant of Survival in Bloodstream Infections Caused by Vancomycin-Resistant Enterococcus spp

Enterococcal bloodstream infections (EBSI) caused by vancomycin-resistant enterococci (VRE) are associated with a significant rate of unfavorable outcomes. No definitive data have been reported about the association between delayed antibiotic therapy and mortality. In this prospective observational study in three large hospitals in Italy (from August 2016 to April 2021), all consecutive hospitalized patients with a confirmed diagnosis of hospital-acquired monomicrobial BSI caused by VRE—with no evidence of endocarditis—were analyzed. Cox regression analysis showed that risk factors independently associated with 30-day mortality were age (HR 2.98, CI95% 1.44−6.81, p = 0.002), chronic kidney disease (HR 5.21, CI95% 1.48−22.23, p = 0.001), oncologic disease (HR 2.81, CI95% 1.45−19.8, p = 0.005), and intensive care unit admission (HR 3.71, CI95% 2.23−7.99, p < 0.001). Conversely, early effective therapy was associated with survival (HR 0.32, CI95% 0.38−0.76, p < 0.001). The administration of early effective antibiotic therapy within 48 h from blood culture collection was associated with 30-day mortality rates lower than 33%. Time from blood culture collection to appropriate therapy was an independent predictor of 30-day mortality in patients with EBSI caused by VRE. Based on these data, clinicians should start effective antibiotic therapy as soon as possible, preferably within the first 48 h from blood culture collection. Treatment strategies allowing the early delivery of in vitro active antibiotics are urgently needed, especially in critically ill patients at risk of VRE bacteremia.

Early appropriate diagnostics and treatment of MDR Gram-negative infections

The term difficult-to-treat resistance has been recently coined to identify Gram-negative bacteria exhibiting resistance to all fluoroquinolones and all β-lactam categories, including carbapenems. Such bacteria are posing serious challenges to clinicians trying to identify the best therapeutic option for any given patient. Delayed appropriate therapy has been associated with worse outcomes including increase in length of stay, increase in total in-hospital costs and ∼20% increase in the risk of in-hospital mortality. In addition, time to appropriate antibiotic therapy has been shown to be an independent predictor of 30 day mortality in patients with resistant organisms. Improving and anticipating aetiological diagnosis through optimizing not only the identification of phenotypic resistance to antibiotic classes/agents, but also the identification of specific resistance mechanisms, would have a major impact on reducing the frequency and duration of inappropriate early antibiotic therapy. In light of these considerations, the present paper reviews the increasing need for rapid diagnosis of bacterial infections and efficient laboratory workflows to confirm diagnoses and facilitate prompt de-escalation to targeted therapy, in line with antimicrobial stewardship principles. Rapid diagnostic tests currently available and future perspectives for their use are discussed. Early appropriate diagnostics and treatment of MDR Gram-negative infections require a multidisciplinary approach that includes multiple different diagnostic methods and further consensus of algorithms, protocols and guidelines to select the optimal antibiotic therapy.

A Novel GPPAS Model: Guiding the Implementation of Antimicrobial Stewardship in Primary Care Utilising Collaboration between General Practitioners and Community Pharmacists

Interprofessional collaboration between general practitioners (GPs) and community pharmacists (CPs) is central to implement antimicrobial stewardship (AMS) programmes in primary care. This study aimed to design a GP/pharmacist antimicrobial stewardship (GPPAS) model for primary care in Australia. An exploratory study design was followed that included seven studies conducted from 2017 to 2021 for the development of the GPPAS model. We generated secondary and primary evidence through a systematic review, a scoping review, a rapid review, nationwide surveys of Australian GPs and CPs including qualitative components, and a pilot study of a GPPAS submodel. All study evidence was synthesised, reviewed, merged, and triangulated to design the prototype GPPAS model using a Systems Engineering Initiative for Patient Safety theoretical framework. The secondary evidence provided effective GPPAS interventions, and the primary evidence identified GP/CP interprofessional issues, challenges, and future needs for implementing GPPAS interventions. The framework of the GPPAS model informed five GPPAS implementation submodels to foster implementation of AMS education program, antimicrobial audits, diagnostic stewardship, delayed prescribing, and routine review of antimicrobial prescriptions, through improved GP-CP collaboration. The GPPAS model could be used globally as a guide for GPs and CPs to collaboratively optimise antimicrobial use in primary care. Implementation studies on the GPPAS model and submodels are required to integrate the GPPAS model into GP/pharmacist interprofessional care models in Australia for improving AMS in routine primary care.

Early and Appropriate Use of Ceftazidime-Avibactam in the Management of Multidrug-Resistant Gram-Negative Bacterial Infections in the Indian Scenario

The increasing prevalence of antibiotic-resistant pathogens exerts a substantial burden on the healthcare infrastructure worldwide. The World Health Organization (WHO) has declared that multidrug-resistant (MDR) Gram-negative pathogens, especially, carbapenem-resistant Enterobacterales (CRE), Acinetobacter baumannii, and Pseudomonas aeruginosa as the topmost priority while developing newer antimicrobials. The increasing prevalence of infectious diseases caused by MDR Gram-negative bacteria also poses a challenge when choosing the empiric antimicrobial therapy for seriously ill hospitalized patients. The infections caused by MDR Gram-negative organisms ultimately result in increased mortality, morbidity, prolonged hospital stay, and increased cost of management. To tackle these challenges, newer antimicrobials like ceftazidime-avibactam were explored. The article also discusses the in vitro activity and therapeutic efficacy of ceftazidime-avibactam along with its pharmacokinetic properties and the role it will play in the management of MDR Gram-negative organisms in the Indian setting. Several studies have highlighted the role of early and appropriate antibiotic use in the reduction of mortality in patients with Gram-negative infections. Timely initiation of appropriate antibiotic therapy for serious infections leads to favorable clinical outcomes. Early and appropriate use of ceftazidime-avibactam while treating MDR Gram-negative infections has been associated with improved clinical outcomes. The aim of this review is to highlight the efficacy of ceftazidime-avibactam in the treatment of MDR Gram-negative infections. We have also summarized the information on outcomes achieved by early and appropriate use of ceftazidime-avibactam.

Assessing, Pricing and Funding Point-of-Care Diagnostic Tests for Community-Acquired Acute Respiratory Tract Infections-Overview of Policies Applied in 17 European Countries

Point-of-care diagnostic tests for community-acquired acute respiratory tract infections (CA-ARTI) can support doctors by improving antibiotic prescribing. However, little is known about health technology assessment (HTA), pricing and funding policies for CA-ARTI diagnostics. Thus, this study investigated these policies for this group of devices applied in the outpatient setting in Europe. Experts from competent authority responded to a questionnaire in Q4/2020. Information is available for 17 countries. Studied countries do not base their pricing and funding decision for CA-ARTI diagnostics on an HTA. While a few countries impose price regulation for some publicly funded medical devices, the prices of CA-ARTI diagnostics are not directly regulated in any of the surveyed countries. Indirect price regulation through public procurement is applied in some countries. Reimbursement lists of medical devices eligible for public funding exist in several European countries, and in some countries these lists include CA-ARTI diagnostics. In a few countries, the public payer funds the health professional for performing the service of conducting the test. Given low levels of regulation and few incentives, the study findings suggest room for strengthening pricing and funding policies of CA-ARTI diagnostics to contribute to increased acceptance and use of these point-of-care tests.

The predictive potential of different molecular markers linked to amikacin susceptibility phenotypes in Pseudomonas aeruginosa

Informed antibiotic prescription offers a practical solution to antibiotic resistance problem. With the increasing affordability of different sequencing technologies, molecular-based resistance prediction would direct proper antibiotic selection and preserve available agents. Amikacin is a broad-spectrum aminoglycoside exhibiting higher clinical efficacy and less resistance rates in Ps. aeruginosa due to its structural nature and its ability to achieve higher serum concentrations at lower therapeutic doses. This study examines the predictive potential of molecular markers underlying amikacin susceptibility phenotypes in order to provide improved diagnostic panels. Using a predictive model, genes and variants underlying amikacin resistance have been statistically and functionally explored in a large comprehensive and diverse set of Ps. aeruginosa completely sequenced genomes. Different genes and variants have been examined for their predictive potential and functional correlation to amikacin susceptibility phenotypes. Three predictive sets of molecular markers have been identified and can be used in a complementary manner, offering promising molecular diagnostics. armR, nalC, nalD, mexR, mexZ, ampR, rmtD, nalDSer32Asn, fusA1Y552C, fusA1D588G, arnAA170T, and arnDG206C have been identified as the best amikacin resistance predictors in Ps. aeruginosa while faoAT385A, nuoGA890T, nuoGA574T, lptAT55A, lptAR62S, pstBR87C, gidBE126G, gidBQ28K, amgSE108Q, and rplYQ41L have been identified as the best amikacin susceptibility predictors. Combining different measures of predictive performance together with further functional analysis can help design new and more informative molecular diagnostic panels. This would greatly inform and direct point of care diagnosis and prescription, which would consequently preserve amikacin functionality and usefulness.

Sankey diagrams can clarify 'evidence attrition': A systematic review and meta-analysis of the effectiveness of rapid diagnostic tests for antimicrobial resistance

OBJECTIVES

To demonstrate, using the example of a new systematic review of rapid diagnostic tests, how Sankey diagrams, alongside the PRISMA guidelines, can (i) facilitate reporting of the quality of the evidence base and (ii) help assess evidence syntheses when studies use heterogeneous outcomes.

METHODS

Systematic review and meta-analysis of experimental and observational studies which included at least one prescribing or clinical outcome of RDTs in hospital in-patients. Sub-group analysis was used to assess heterogeneity in summary effect estimates. A Sankey diagram was then used to show the pattern and quality of evidence on RDT outcomes.

RESULTS

57 studies from 14 countries were included. The introduction of RDTs did not significantly reduce in-hospital mortality (RR 0.83, 95% CI 0.60 - 1.15) or length of stay (weighted mean difference = -0.36, 95% CI -1.67 to 0.96). There was high heterogeneity in outcomes.

CONCLUSION

There is no clear evidence that the routine use of RDTs for bacterial identification and antibiotic susceptibility testing improves clinical outcomes in hospital in-patients. Sankey diagrams may be a useful further way succinctly to present the pattern and quality of evidence in systematic reviews, especially when it is heterogeneous and not easily amenable to meta-analysis.

Application of Fluorescent In Situ Hybridization for Quick Identification of Microorganisms from Positive Blood Cultures

AIM: The aim of this study was to evaluate the diagnostic potential of the fluorescent in situ hybridization (FISH) method for quick identification of microorganisms from positive blood cultures. MATERIALS AND METHODS: QuickFISH BC is a multicolor, qualitative nucleic acid hybridization assay using specific fluorescent-labeled probes for identification of Gram-positive bacteria (S. aureus, Coagulase-negative Staphylococcus spp. – CoNS, E. faecalis, and E. faecium); Gram-negative bacteria (E. coli, P. aeruginosa, and K. pneumoniaе), and fungi (C. albicans, C. tropicalis, and C. glabrata). This method applied to 72 positive blood cultures obtained from patients admitted at the University Hospital St. George – Plovdiv. A preliminary selection based on Gram staining was performed before the application of the FISH test. All microorganisms were subject to identification by routine biochemical tests, semi-automated and automated systems as well. Statistical data processing included descriptive statistics, nonparametric analysis for testing hypotheses by SPSS v. 22.0, and Microsoft Excel software. p < 0.05 was considered statistically significant. RESULTS: FISH detected microorganisms in 63 (87.5%) positive blood cultures, whereas no fluorescent signal was observed in 9 (12.5%). The latter was because not all the microorganisms we identified are included in the test spectrum, for example – Enterobacter spp. and Acinetobacter spp. By FISH, we found S. aureus in 10 (15.9%) cases, CoNS in 20 (31.6%), E. faecalis in 4 (6.4%), and E. faecium in 4 (6.4%). E. coli (n = 7; 11.1%) was the leading cause of bacteremia among Gram-negative bacteria, whereas C. albicans predominated (n = 4; 6.4%) among fungi. CONCLUSION: QuickFISH BC is a rapid and accurate screening method for the identification of some of the most frequent pathogens causing bacteremia. This enables the initiation of the early and adequate antimicrobial therapy. The lack of pathogen identification from positive blood cultures using this method implies the need to continue identification with other tests.

Nuclease activity: an exploitable biomarker in bacterial infections

INTRODUCTION

In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications.

AREAS COVERED

This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected.

EXPERT OPINION

Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.

Antibiotic Decision-Making in the ICU

It is well established that Intensive Care Units (ICUs) are a focal point in antimicrobial consumption with a major influence on the ecological consequences of antibiotic use. With the high prevalence and mortality of infections in critically ill patients, and the clinical challenges of treating patients with septic shock, the impact of real life clinical decisions made by intensivists becomes more significant. Both under- and over-treatment with unnecessarily broad spectrum antibiotics can lead to detrimental outcomes. Even though substantial progress has been made in developing rapid diagnostic tests that can help guide antibiotic use, there is still a time window when clinicians must decide the empiric antibiotic treatment with insufficient clinical data. The continuous streams of data available in the ICU environment make antimicrobial optimization an ongoing challenge for clinicians but at the same time can serve as the input for sophisticated models. In this review, we summarize the evidence to help guide antibiotic decision-making in the ICU. We focus on 1) deciding IF: to start antibiotics, 2) choosing the spectrum of the empiric agents to use, and 3) de-escalating the chosen empiric antibiotics. We provide a perspective on the role of machine learning and artificial intelligence models for clinical decision support systems that can be incorporated seamlessly into clinical practice in order to improve the antibiotic selection process and, more importantly, current and future patients' outcomes.

A Novel Lipid-Based MALDI-TOF Assay for the Rapid Detection of Colistin-Resistant Enterobacter Species

Enterobacter species are classified as high-priority pathogens due to high prevalence of multidrug resistance from persistent antibiotic use. For Enterobacter infections caused by multidrug-resistant isolates, colistin (polymyxin E), a last-resort antibiotic, is a potential treatment option. Treatment with colistin has been shown to lead to emergence of polymyxin resistance. The primary mechanism for colistin resistance is modification of terminal phosphate moieties of lipid A, leading to decreased membrane electronegativity and reducing colistin binding affinity. Detection of these modifications, including the addition of phosphoethanolamine and 4-amino-4-deoxy-l-arabinose (Ara4N), can be used for prediction of colistin resistance using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The objective of this study was to identify lipid A markers for colistin resistance in Enterobacter species and Klebsiella aerogenes (formerly Enterobacter aerogenes). Using a collection of Enterobacter and Klebsiella aerogenes clinical isolates, broth MICs for colistin were determined initially. Subsequently, killing assays were carried out to determine how the concentration of colistin at which there is approximately 50% survival (kill₅₀) equates to their MICs. Finally, lipid A analysis was conducted via MALDI-TOF MS using the novel rapid extraction method, termed fast lipid analysis technique (FLAT), to correlate MIC and killing efficacy with predictive lipid A modifications. Sensitivity and specificity of the MS assay compared to MIC interpretation were 100% and 53.4%, respectively. A receiver operator characteristic (ROC) demonstrated that MS was highly correlated with killing, with area under the curve of 0.97. This analysis demonstrated the potential utility of MALDI-TOF MS as a rapid diagnostic platform of colistin resistance in Enterobacter species.

IMPORTANCE In this study, we develop a novel method for identifying colistin resistance in Enterobacter species and Klebsiella aerogenes without performing antimicrobial susceptibility testing. Typically, susceptibility testing requires an additional 24 to 48 h, while the MS assay described in this study allows for resistant identifications in under 1 h after initial culture. Identification using MALDI-TOF MS would save time and prevent inappropriate use of colistin. MALDI-TOF MS is an easy-to-use, readily available, robust diagnostic tool in clinical laboratories. Furthermore, this study highlights limitations of polymyxin susceptibility testing. Use of a killing assay best captures how colistin treats infection and is shown to be highly correlated with our MS assay; thus, the MS assay in this study effectively predicts how colistin would treat a patient’s infection. Use of MALDI-TOF MS for accurate and early identification of antimicrobial resistance can improve antimicrobial stewardship and patient outcomes.

Rapid identification of mcr-1-positive Escherichia coli from patient urine using a novel lipid-based MALDI-TOF-MS assay

Mobilized colistin resistance (mcr) genes confer resistance to colistin, a last-resort antibiotic for multidrug-resistant Gram-negative infections. In this case report, we describe a novel lipid-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) diagnostic used to rapidly identify an mcr-1-positive Escherichia coli directly from a patient with a urinary tract infection without the need for ex vivo growth.

Optimizing antimicrobial use: challenges, advances and opportunities

An optimal antimicrobial dose provides enough drug to achieve a clinical response while minimizing toxicity and development of drug resistance. There can be considerable variability in pharmacokinetics, for example, owing to comorbidities or other medications, which affects antimicrobial pharmacodynamics and, thus, treatment success. Although current approaches to antimicrobial dose optimization address fixed variability, better methods to monitor and rapidly adjust antimicrobial dosing are required to understand and react to residual variability that occurs within and between individuals. We review current challenges to the wider implementation of antimicrobial dose optimization and highlight novel solutions, including biosensor-based, real-time therapeutic drug monitoring and computer-controlled, closed-loop control systems. Precision antimicrobial dosing promises to improve patient outcome and is important for antimicrobial stewardship and the prevention of antimicrobial resistance.

Antimicrobial Stewardship and the Infection Control Practitioner: A Natural Alliance

Antibiotic overuse and misuse has contributed to rising rates of multidrug-resistant organisms and Clostridioides difficile. Decreasing antibiotic misuse has become a national public health priority. This review outlines the goals of antimicrobial stewardship, essential members of the program, implementation strategies, approaches to measuring the program's impact, and steps needed to build a program. Highlighted is the alliance between antimicrobial stewardship programs and infection prevention programs in their efforts to improve antibiotic use, improve diagnostic stewardship for C difficile and asymptomatic bacteriuria, and decrease health care-associated infections and the spread of multidrug-resistant organisms.

Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles

Drug-resistant tuberculosis (TB) is a growing public health problem. There is an urgent need for information regarding cross-resistance and collateral sensitivity relationships among drugs and the genetic determinants of anti-TB drug resistance for developing strategies to suppress the emergence of drug-resistant pathogens. To identify mutations that confer resistance to anti-TB drugs in Mycobacterium species, we performed the laboratory evolution of nonpathogenic Mycobacterium smegmatis, which is closely related to Mycobacterium tuberculosis, against ten anti-TB drugs. Next, we performed whole-genome sequencing and quantified the resistance profiles of each drug-resistant strain against 24 drugs. We identified the genes with novel meropenem (MP) and linezolid (LZD) resistance-conferring mutation, which also have orthologs, in M. tuberculosis H37Rv. Among the 240 possible drug combinations, we identified 24 pairs that confer cross-resistance and 18 pairs that confer collateral sensitivity. The acquisition of bedaquiline or linezolid resistance resulted in collateral sensitivity to several drugs, while the acquisition of MP resistance led to multidrug resistance. The MP-evolved strains showed cross-resistance to rifampicin and clarithromycin owing to the acquisition of a mutation in the intergenic region of the Rv2864c ortholog, which encodes a penicillin-binding protein, at an early stage. These results provide a new insight to tackle drug-resistant TB.

Optimizing rapid diagnostics and diagnostic stewardship in Gram-negative bacteremia

Antimicrobial resistance remains a high global concern, as it is associated with prolonged hospitalizations, increased morbidity and mortality, and escalating healthcare-related costs. Rapid diagnostic technology (RDT) has become the cornerstone in achieving prompt blood culture results providing a quicker initiation of optimal therapy, decreased mortality, and decreased spread of resistance. To maximize the benefits of RDTs, antimicrobial stewardship programs must implement a diagnostic stewardship (DS) subgroup to optimize communication, education, and interpretation of RDT results within the healthcare system. The DS subgroup is necessary to evaluate the technologies available, better integrate the selected technologies into the healthcare system, and develop innovative and appropriate use to improve patient outcomes.

Impact of an Antimicrobial Stewardship Program-bundled initiative utilizing Accelerate Pheno™ system in the management of patients with aerobic Gram-negative bacilli bacteremia

PURPOSE

Gram-negative bacteria (GNB) are a leading cause of bloodstream infections (BSI) and management is complicated by antibiotic resistance. The Accelerate Pheno™ system (ACC) can provide rapid organism identification and antimicrobial susceptibility testing (AST).

METHODS

A retrospective, pre-intervention/post-intervention study was conducted to compare management of non-critically ill patients with GNB BSI before and after implementation of a bundled initiative. This bundled initiative included dissemination of a clinical decision algorithm, ACC testing on all GNB isolated from blood cultures, real-time communication of results to the Antimicrobial Stewardship Program (ASP), and prospective audit with feedback by the ASP. The pre-intervention period was January 2018 through December 2018, and the post-intervention period was May 2019 through February 2020.

RESULTS

Seventy-seven and 129 patients were included in the pre-intervention and post-intervention cohorts, respectively. When compared with the pre-intervention group, the time from Gram stain to AST decreased from 46.1 to 6.9 h (p < 0.001), and the time to definitive therapy (TTDT) improved from 32.6 to 10.5 h (p < 0.001). Implementation led to shorter median total duration of antibiotic therapy (14.2 vs 9.5 days; p < 0.001) and mean hospital length of stay (7.9 vs 5.3 days; p = 0.047) without an increase in 30-day readmissions (22.1% vs 14%; p = 0.13).

CONCLUSION

Implementation of an ASP-bundled approach incorporating the ACC aimed at optimizing antibiotic therapy in the management GNB BSI in non-critically ill patients led to reduced TTDT, shorter duration of antibiotic therapy, and shorter hospital length of stay without adversely affecting readmission rates.

Improving outcomes and antibiotic stewardship (IOAS) for patients with Gram-positive bloodstream infections through use of rapid testing: a quasi-experimental multicentre study of the Accelerate PhenoTest™ BC Kit

BACKGROUND

Data from the Improving Outcomes and Antibiotic Stewardship for Patients with Bloodstream Infections: Accelerate PhenoTest™ BC Kit (AXDX) Registry Study were analysed to determine the impact of rapid organism identification and antimicrobial susceptibility testing (AST) for Gram-positive bacteraemia.

PATIENTS AND METHODS

This multicentre, quasi-experimental study evaluated clinical and antimicrobial stewardship metrics following the implementation of AXDX. Data from hospitalized patients with bacteraemia were compared between groups, one that underwent testing on AXDX (post-AXDX) and one that underwent traditional identification and AST (pre-AXDX). An analysis of patients with Gram-positive bacteraemia was performed. The primary outcome was time to optimal therapy (TTOT). Secondary outcomes included time to first antibiotic modification (overall and Gram-positive), duration of unnecessary MRSA coverage, incidence of adverse events, length of stay and mortality.

RESULTS

A total of 219 (109 pre-AXDX, 110 post-AXDX) patients with Gram-positive bacteraemia were included. Median TTOT was 36.3 h (IQR, 16.9-56.7) in the pre-AXDX group and 20.4 h (IQR, 7.5-36.7) in the post-AXDX group (P = 0.01). Compared with pre-AXDX, median time to first antibiotic modification (29.1 versus 15.9 h; P = 0.002), time to first Gram-positive antibiotic modification (33.2 versus 17.2 h; P = 0.003) and median duration of unnecessary MRSA coverage (58.4 versus 29.7 h; P = 0.04) were reduced post-AXDX. A trend towards decreased acute kidney injury (24% versus 13%; P = 0.06) was observed in the post-AXDX group. Groups did not differ in other secondary outcomes.

CONCLUSIONS

Implementation of AXDX testing for patients with Gram-positive bacteraemia shortened the TTOT and reduced unnecessary antibiotic exposure due to faster antibiotic modifications.

Impact of Accelerate Pheno and BacT/Alert Virtuo on Clinical Processes and Outcomes in Patients with Sepsis and Concurrent Gram-Negative Bacteremia

The Accelerate Pheno and BacT/Alert Virtuo systems may improve bacteremia management. Here, we evaluated the impact of both devices on outcomes in patients with sepsis and concurrent Gram-negative bacteremia. This quasiexperimental study included a retrospective preimplementation and a prospective postimplementation group. Patients ≥18 years old with Gram-negative bacteremia were included. Patients with neutropenia, pregnant patients, those who were transferred from an outside hospital with active bloodstream infections, and those with polymicrobial bacteremia were excluded. Blood culture incubation in the BacT/Alert 3D device and microdilution antimicrobial susceptibility testing from culture plate growth were used prior to implementation of the BacT/Alert Virtuo and Accelerate Pheno systems. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identification directly from blood culture was used pre- and postimplementation. Time to Gram stain results, identification, susceptibility reporting, initiation of narrow-spectrum Gram-negative therapy at 72 h, 30-day inpatient mortality, sepsis resolution, and length of hospital stay were evaluated. A total of 116 patients were included (63 preimplementation, 53 postimplementation). Median times to Gram stain and susceptibility results were significantly shorter postimplementation (P < 0.001). The postimplementation group had an improved hazard ratio for narrow-spectrum Gram-negative therapy at 72 h (hazard ratio [HR], 2.685 [95% confidence interval {CI}, 1.348 to 5.349]), a reduced hazard ratio for 30-day inpatient mortality (adjusted HR [aHR], 0.150 [95% CI, 0.026 to 0.846]), and improved sepsis resolution (92.5% versus 77.8% [P = 0.030]). The length of hospital stay was unchanged after implementation. We conclude that implementation of the BacT/Alert Virtuo and Accelerate Pheno systems improved microbiology laboratory processes, antibiotic utilization processes, and clinical outcomes. These data support the use of rapid diagnostics in sepsis with concurrent Gram-negative bacteremia.

Rapid detection of NDM and VIM carbapenemase encoding genes by recombinase polymerase amplification and lateral flow-based detection

Carbapenemase-producing organisms (CPOs) pose a serious clinical threat and rapid detection tools are essential to aid in patient management. We developed rapid and simple molecular tests to detect bla_NDM-type and bla_VIM-type carbapenemase genes using recombinase polymerase amplification (RPA) combined with a lateral flow detection. The tests could provide results in approximately 15 min when using DNA extracts, with limits of detection of 9.2 copies/μl for the bla_NDM-type assay and 7.5 copies/μl for bla_VIM-type assay, and successfully detected all isolates harbouring the carbapenemase encoding genes in a panel of 57 isolates. These RPA tests may be suitable for use in low-resource settings to tailor rapid implementation of infection control precautions and antibiotic stewardship.

Antimicrobial stewardship and antibiograms: importance of moving beyond traditional antibiograms

The rapid evolution of resistance, particularly among Gram-negative bacteria, requires appropriate identification of patients at risk followed by administration of appropriate empiric antibiotic therapy. A primary tenet of antimicrobial stewardship programs (ASPs) is the establishment of empiric antibiotic recommendations for commonly encountered infections. An important tool in providing empiric antibiotic therapy recommendations is the use of an antibiogram. While the majority of institutions use a traditional antibiogram, ASPs have an opportunity to enhance antibiogram data. The authors provide the rationale for why ASPs should implement alternative antibiograms, and the importance of incorporating an antibiogram into clinical decision support systems with the goal of providing effective empiric antibiotic therapy.