New and novel rapid diagnostics that are impacting infection prevention and antimicrobial stewardship

The Application of Bacteriophage and Photoacoustic Flow Cytometry in Bacterial Identification

Infection with resistant bacteria has become an ever-increasing problem in modern medical practice. Bacteremia is a serious and potentially lethal condition that can lead to sepsis without early intervention. Currently, broad-spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take 2-3 days and is unable to provide quantitative information. Staphylococcus aureus (S. aureus) is a leading cause of bacteremia, and methicillin-resistant S. aureus (MRSA) accounts for more than a third of the cases. Other bacteria such as Clostridium difficile, Acinetobacter baumannii, and Carbapenem-resistant Enterobacteriaceae are becoming more prevalent and antibiotic-resistant. Rapid diagnostics for each of these superbugs has been a priority for health organizations around the world. Bacteriophages have evolved for millions of years to develop exquisite specificity in target binding using their host attachment proteins. Bacteriophages are viruses that infect bacteria. Bacteriophages use tail spikes, specialized attachment proteins, to bind specifically to their target bacterial cell surface proteins. We use bacteriophages and parts of bacteriophages as specific tags coupled with photoacoustic flow cytometry for the detection and quantification of bacteria. In photoacoustic flow cytometry, laser light is absorbed by particles under flow, and the ultrasound waves generated on the release of the energy are detected. Photoacoustics involves the detection of ultrasound waves resulting from laser irradiation. In photoacoustic flow cytometry, pulsed laser light is delivered to a sample flowing past a focused transducer, and particles that absorb laser light create a photoacoustic response. Bacteria can be tagged with dyed bacteriophage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. In this chapter, we describe the procedure and methods used to accomplish this. Often the limiting factor for the treatment of patients is the time spent waiting for results. It is our hope that the work presented in this chapter can be a foundation for future work and provide an ability to detect bacterial pathogens in blood cultures. Bacterial plate cultures and Gram staining are nineteenth-century technologies that have been the gold standards for decades, but current trends in resistant bacteria have necessitated a move toward more rapid and quantifiable diagnostic tools.

Novel Host Response-Based Diagnostics to Differentiate the Etiology of Fever in Patients Presenting to the Emergency Department

Fever is a common presentation to urgent-care services and is linked to multiple disease processes. To rapidly determine the etiology of fever, improved diagnostic modalities are necessary. This prospective study of 100 hospitalized febrile patients included both positive (FP) and negative (FN) subjects in terms of infection status and 22 healthy controls (HC). We evaluated the performance of a novel PCR-based assay measuring five host mRNA transcripts directly from whole blood to differentiate infectious versus non-infectious febrile syndromes as compared to traditional pathogen-based microbiology results. The FP and FN groups observed a robust network structure with a significant correlation between the five genes. There were statistically significant associations between positive infection status and four of the five genes: IRF-9 (OR = 1.750, 95% CI = 1.16-2.638), ITGAM (OR = 1.533, 95% CI = 1.047-2.244), PSTPIP2 (OR = 2.191, 95% CI = 1.293-3.711), and RUNX1 (OR = 1.974, 95% CI = 1.069-3.646). We developed a classifier model to classify study participants based on these five genes and other variables of interest to assess the discriminatory power of the genes. The classifier model correctly classified more than 80% of the participants into their respective groups, i.e., FP or FN. The GeneXpert prototype holds promise for guiding rapid clinical decision-making, reducing healthcare costs, and improving outcomes in undifferentiated febrile patients presenting for urgent evaluation.

Photoacoustic Flow Cytometry Using Functionalized Microspheres for Selective Detection of Bacteria

Photoacoustic flow cytometry is a method to detect rare analytes in fluids. We developed photoacoustic flow cytometry to detect pathological cells in body fluids, such as circulating tumor cells or bacteria in blood. In order to induce specific optical absorption in bacteria, we use modified bacteriophage that precisely target bacterial species or subspecies for rapid identification. In order to reduce detection variability and to halt the lytic lifescycle that results in lysis of the bacteria, we attached dyed latex microspheres to the tail fibers of bacteriophage that retained the bacterial recognition binding sites. We tested these microsphere complexes using Salmonella enterica (Salmonella) and Escherichia coli (E. coli) bacteria and found robust and specific detection of targeted bacteria. In our work we used LT2, a strain of Salmonella, against K12, a strain of E. coli. Using Det7, a bacteriophage that binds to LT2 and not to K12, we detected an average of 109.3±9.0 of LT2 versus 2.0±1.7 of K12 using red microspheres and 86.7±13.2 of LT2 versus 0.3±0.6 of K12 using blue microspheres. These results confirmed our ability to selectively detect bacterial species using photoacoustic flow cytometry.

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.

Differentiating methicillin resistant and susceptible Staphylococcus aureus from ocular infections using photoacoustic labeling

Introduction

Antibiotic resistance in bacterial species constitutes a growing problem in the clinical management of infections. Not only does it limit therapeutic options, but application of ineffective antibiotics allows resistant species to progress prior to prescribing more effective treatment to patients. Methicillin resistance in Staphylococcus aureus is a major problem in clinical infections as it is the most common hospital acquired infection.

Methods

We developed a photoacoustic flow cytometer using engineered bacteriophage as probes for rapid determination of methicillin resistance in Staphylococcus aureus with thirteen clinical samples obtained from keratitis patients. This method irradiates cells under flow with 532 nm laser light and selectively generates acoustic waves in labeled bacterial cells, thus enabling detection and enumeration of them. Staphylococcus aureus isolates were classified from culture isolation as either methicillin resistant or susceptible using cefoxitin disk diffusion testing. The photoacoustic method enumerates bacterial cells before and after treatment with antibiotics. Decreasing counts of bacteria after treatment indicate susceptible strains. We quantified the bacterial cells in the treated and untreated samples.

Results

Using k-means clustering on the data, we achieved 100% concordance with the classification of Staphylococcus aureus resistance using culture.

Discussion

Photoacoustics can be used to differentiate methicillin resistant and susceptible strains of bacteria from ocular infections. This method may be generalized to other bacterial species using appropriate bacteriophages and testing for resistance using other antibiotics.

[Rapid diagnosis of bacteremia by genomic identification]

Our objective was to make a focus on the methods for rapid diagnosis of bacteremia by genomic identification. We also aimed to evaluate the interest of using them in the laboratory practice. The different methods currently available have been presented according to their technologic approach. It is also possible to classify these methods according to the data provided, only bacterial and/or resistance gene identification or also bacterial susceptibility to antibiotics. In case of mono-microbial blood cultures, the performances recorded with these methods are very good as compared to the subcultures on agar media. Nevertheless, they are better for identifications (>90%) than for susceptibility to antibiotics (>80%). Numerous studies demonstrated the positive impact of these methods for decreasing the time necessary to the prescription of an appropriate antimicrobial treatment. However, it is noteworthy that an appropriate organization of the laboratory and a strategy of antimicrobial stewardship in the hospital are necessary. Concurrently, the impact on the patient outcome has not been clearly demonstrated. Lastly, few medico-economic studies have been reported. However, as these methods have a substantial cost, their utilization strategy must be economically viable.

Comparing the Clinical Utility of Rapid Diagnostics for Treatment of Bloodstream Infections Using Desirability of Outcome Ranking Approach for the Management of Antibiotic Therapy (DOOR-MAT)

Decisions regarding which rapid diagnostic test (RDT) for bloodstream infections to implement remain challenging given the diversity of organisms detected by different platforms. We used the desirability of outcome ranking management of antimicrobial therapy (DOOR-MAT) as a framework to compare two RDT platforms on potential desirability of antimicrobial therapy decisions. An observational study was performed at University of Maryland Medical System comparing Verigene blood culture (BC) to GenMark Dx ePlex blood culture ID (BCID) (research use only) panels on blood cultures from adult patients. Positive percent agreement (PPA) between each RDT platform and Vitek MS was calculated for comparison of on-panel targets. Theoretical antimicrobial decisions were made based on RDT results, taking into consideration patient parameters, antimicrobial stewardship practices, and local infectious diseases epidemiology. DOOR-MAT with a partial credit scoring system was applied to these decisions, and mean scores were compared across platforms using a paired t test. The study consisted of 160 unique patients. The Verigene BC PPA was 98.6% (95% confidence interval [CI], 95.1 to 99.8), and ePlex BCID PPA was 98% (95% CI, 94.3 to 99.6). Among the 31 organisms not on the Verigene BC panels, 61% were identified by the ePlex BCID panels. The mean (standard deviation [SD]) DOOR-MAT score for Verigene BC was 86.8 (28.5), while that for ePlex BCID was 91.9 (23.1) (P = 0.01). Both RDT platforms had high PPA for on-panel targets. The ePlex BCID was able to identify more organisms than Verigene, resulting in higher mean DOOR-MAT scores.

Intensivists' beliefs about rapid multiplex molecular diagnostic testing and its potential role in improving prescribing decisions and antimicrobial stewardship: a qualitative study

BACKGROUND

Rapid molecular diagnostic tests to investigate the microbial aetiology of pneumonias may improve treatment and antimicrobial stewardship in intensive care units (ICUs). Clinicians' endorsement and uptake of these tests is crucial to maximise engagement; however, adoption may be impeded if users harbour unaddressed concerns or if device usage is incompatible with local practice. Accordingly, we strove to identify ICU clinicians' beliefs about molecular diagnostic tests for pneumonias before implementation at the point-of-care.

METHODS

We conducted semi-structured interviews with 35 critical care doctors working in four ICUs in the United Kingdom. A clinical vignette depicting a fictitious patient with signs of pneumonia was used to explore clinicians' beliefs about the importance of molecular diagnostics and their concerns. Data were analysed thematically.

RESULTS

Clinicians' beliefs about molecular tests could be grouped into two categories: perceived potential of molecular diagnostics to improve antibiotic prescribing (Molecular Diagnostic Necessity) and concerns about how the test results could be implemented into practice (Molecular Diagnostic Concerns). Molecular Diagnostic Necessity stemmed from beliefs that positive results would facilitate targeted antimicrobial therapy; that negative results would signal the absence of a pathogen, and consequently that having the molecular diagnostic results would bolster clinicians' prescribing confidence. Molecular Diagnostic Concerns included unfamiliarity with the device's capabilities, worry that it would detect non-pathogenic bacteria, uncertainty whether it would fail to detect pathogens, and discomfort with withholding antibiotics until receiving molecular test results.

CONCLUSIONS

Clinicians believed rapid molecular diagnostics for pneumonias were potentially important and were open to using them; however, they harboured concerns about the tests' capabilities and integration into clinical practice. Implementation strategies should bolster users' necessity beliefs while reducing their concerns; this can be accomplished by publicising the tests' purpose and benefits, identifying and addressing clinicians' misconceptions, establishing a trial period for first-hand familiarisation, and emphasising that, with a swift (e.g., 60-90 min) test, antibiotics can be started and refined after molecular diagnostic results become available.

Update on Nocardia infections in solid-organ transplantation

PURPOSE OF REVIEW

Nocardia is a ubiquitous pathogen associated with life-threatening opportunistic infections. Organ transplant recipients are uniquely predisposed to Nocardia infections due to their iatrogenic cell-mediated immune deficit necessary to maintain allograft function. This review aims to address recent updates in the epidemiology, clinical presentation, diagnostics, treatment, and outcomes of Nocardia infections in solid-organ transplant recipients.

RECENT FINDINGS

The incidence of Nocardia infection depends on multiple patient and environmental factors. Among transplant recipients, lung recipients are most commonly affected. Species identification and antimicrobial susceptibility testing are critical for optimizing therapy as substantial variation occurs among and within Nocardia spp. This has been increasingly accomplished through advances in molecular methods leading to improved accuracy and wider accessibility to testing. There are emerging data applying novel therapeutics and short course therapy that may offer alternative management approaches for transplant associated nocardiosis to minimize drug toxicity and intolerance.

SUMMARY

Further prospective, multicenter studies are needed to better characterize the epidemiology of Nocardia in transplant recipients, as well as evaluate the impact of diagnostic advancements and new treatment strategies.

Diagnostic and antimicrobial stewardship with molecular respiratory testing across the SHEA Research Network

This survey investigated diagnostic and antimicrobial stewardship practices related to molecular respiratory panel testing in adults with lower respiratory tract infections at acute care hospitals. Most respondents reported use of rapid respiratory panels, but related stewardship practices were uncommon and the real-world impact of respiratory panels were difficult to quantify.

Laboratory evaluation of the BioFire FilmArray Pneumonia plus panel compared to conventional methods for the identification of bacteria in lower respiratory tract specimens: a prospective cross-sectional study from South Africa

Lower respiratory tract infections are important causes of morbidity and mortality. The global increase in antimicrobial resistance necessitates rapid diagnostic assays. The BioFire FilmArray Pneumonia plus (FAPP) panel is a Food and Drug Administration-approved multiplex polymerase chain reaction assay that detects the most important etiological agents of pneumonia and associated antibiotic resistance genes, in approximately 1 hour. This study assessed the diagnostic performance of this assay by comparing it to conventional culture methods in the analysis of 59 lower respiratory tract specimens. The sensitivity and specificity of the FAPP panel for bacterial detection were 92.0% (95% confidence interval [CI], 80.8% to 97.8%) and 93.8% (95% CI, 91.1% to 95.3%) respectively. For detecting antibiotic resistance, the positive- and negative percent agreement were 100% (95% CI, 81.5% to 100.0%) and 98.5% (95% CI, 216 96.7% to 99.4%) respectively. The FAPP panel was found to be highly accurate in evaluating tracheal aspirate specimens from hospitalized patients.

A multiplex polymerase chain reaction assay for antibiotic stewardship in suspected pneumonia

Background

Multiplexed molecular rapid diagnostic tests (RDTs) may allow for rapid and accurate diagnosis of the microbial etiology of pneumonia. However, little data are available on multiplexed RDTs in pneumonia and their impact on clinical practice.

Methods

This retrospective study analyzed 659 hospitalized patients for microbiological diagnosis of suspected pneumonia.

Results

The overall sensitivity of the Unyvero LRT Panel was 85.7% (95% CI 82.3–88.7) and the overall specificity was 98.4% (95% CI 98.2–98.7) with a negative predictive value of 97.9% (95% CI 97.6–98.1). The LRT Panel result predicted no change in antibiotics in 12.4% of cases but antibiotic de-escalation in 65.9% (405/615) of patients, of whom 278/405 (69%) had unnecessary MRSA coverage and 259/405 (64%) had unnecessary P. aeruginosa coverage.

Interpretation

In hospitalized adults with suspected pneumonia, use of an RDT on respiratory samples can allow for early adjustment of initial antibiotics, most commonly de-escalation.

Antimicrobial resistance in chronic liver disease

High levels of antimicrobial drug resistance deleteriously affecting the outcome of treatment with antibacterial agents are causing increasing concern worldwide. This is particularly worrying in patients with cirrhosis with a depressed immune system and heightened susceptibility to infection. Antibiotics have to be started early before results of microbiological culture are available. Current guidelines for the empirical choice of antibiotics in this situation are not very helpful, and embracing antimicrobial stewardship including rapid de-escalation of therapy are not sufficiently emphasised. Multi-drug resistant organism rates to quinolone drugs of up to 40% are recorded in patients with spontaneous bacterial peritonitis on prophylactic antibiotics, leading to a break-through recurrence of intra-peritoneal infection. Also considered in this review is the value of rifaximin-α, non-selective beta-blockers, and concerns around proton pump inhibitor drug use. Fecal microbial transplantation and other gut-targeting therapies in lessening gut bacterial translocation are a promising approach, and new molecular techniques for determining bacterial sensitivity will allow more specific targeted therapy.

Ventilator-Associated Pneumonia: Diagnostic Test Stewardship and Relevance of Culturing Practices

PURPOSE OF REVIEW

Ventilator-associated pneumonia (VAP) is one of the most common infections in the ICU. Prompt diagnosis is vital as mortality increases with delayed antibiotic therapy. However, accurate diagnosis is challenging due to non-specific clinical features in a complicated patient cohort. Microbiological culture data remains a crucial aspect in confirming diagnosis.

RECENT FINDINGS

Literature data comparing the benefit of invasive respiratory sampling to non-invasive is inconclusive. Differences in culturing practices translate in overidentification of organisms of unclear significance. Positive culture data in a low pre-test probability does not differentiate between true infection and colonization resulting in overtreatment. Furthermore, there are also opportunities for modifying the reporting of respiratory tract cultures that can better guide antimicrobial therapy. Under the umbrella of antimicrobial stewardship, diagnostic stewardship can be incorporated to create a systematic approach that would target culturing practices to match the right pre-test probability. Ideal outcome will be targeting cultures to the right patient population and minimizing unnecessary treatment.

Bacteriophage-mediated identification of bacteria using photoacoustic flow cytometry

Infection with resistant bacteria has become an ever increasing problem in modern medical practice. Currently, broad spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take two to three days and is unable to provide quantitative information. To detect and quantify bacteria rapidly in blood samples, we designed a method using labeled bacteriophage in conjunction with photoacoustic flow cytometry (PAFC). PAFC is the generation of ultrasonic waves created by the absorption of laser light in particles under flow. Bacteriophage is a virus that infects bacteria and possesses the ability to discriminate bacterial surface antigens, allowing the bacteriophage to bind only to their target bacteria. Bacteria can be tagged with dyed phage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. We demonstrate that E. coli; can be detected and discriminated from Salmonella; using this method. Our goal is to develop a method to determine bacterial content in blood samples. We hope to develop this technology into future clinical use and decrease the time required to identify bacterial species from 3 to 4 days to less than 1 hour.