Emerging technologies for rapid identification of bloodstream pathogens

From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification

One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences. Diagnostic sensitivity to the single molecular level is critical, particularly when identifying bloodstream infections. In cases of clinically manifest sepsis, the concentration of bacteria in the blood may reach as low as one bacterial cell/CFU per mL of blood. Therefore, it is crucial to achieve the highest level of sensitivity for accurate detection. In the present study, we have established a method that fills the analytical gap between low concentrations of molecular markers and the minimum requirements for molecular testing. For this purpose, a sample preparation of whole blood samples with a directly downstream pre-amplification was developed, which amplifies specific species and resistance markers in a multiplex procedure. When applying pre-amplification techniques, the sensitivity of the pathogen detection in whole blood samples was up to 100 times higher than in non-pre-amplified samples. The method was tested with blood samples that were spiked with several Gram-positive and Gram-negative bacterial pathogens. By applying this method to artificial spiked blood samples, it was possible to demonstrate a sensitivity of 1 colony-forming unit (CFU) per millilitre of blood for S. aureus and E. faecium. A detection limit of 28 and 383 CFU per ml of blood was achieved for E. coli and K. pneumoniae, respectively. If the sensitivity is also confirmed for real clinical blood samples from septic patients, the novel technique can be used for pathogen detection without cultivation, which might help to accelerate diagnostics and, thus, to decrease sepsis mortality rates.

Clostridium septicum infection complicating Hemolytic-Uremic Syndrome: a case report and review of the literature

Clostridium septicum (C. septicum) is a zoonotic bacillus found in 2.8% of healthy human stools. In humans, it can cause serious infections such as bacteremia, myonecrosis, and encephalitis by spreading through the bloodstream. Reports of Shiga toxin-producing Escherichia Coli-related hemolytic-uremic syndrome complicated by C. septicum superinfection are rare, likely because colonic microangiopathic lesions by Shiga toxin-producing Escherichia Coli facilitate bacterial dissemination. Only 13 cases of Shiga toxin-producing Escherichia Coli-related hemolytic-uremic syndrome with C. septicum superinfection have been reported to date, according to our litterature review, with a 50% mortality rate. The lack of clinico-laboratory clues suggesting this condition makes the diagnosis challenging. For these reasons C. septicum superinfection usually goes undiagnosed in patients with Shiga toxin-producing Escherichia Coli-related hemolytic-uremic syndrome, and results in unfavorable outcomes. In this paper, we describe the case of a 5-year-old girl admitted for Shiga toxin-producing Escherichia Coli-related hemolytic-uremic syndrome who developed C. septicum coinfection leading to a fatal outcome. We carried out a review of the available literature on C. septicum infection complicating Shiga toxin-producing Escherichia Coli-related hemolytic-uremic syndrome and we compared the clinical features of the observed cases with those of an historical cohort of uncomplicated Shiga toxin-producing Escherichia Coli-related hemolytic-uremic syndrome. The mechanisms of superinfection are still unclear and clinical features are indistinguishable from those of uncomplicated Shiga toxin-producing Escherichia Coli-related hemolytic-uremic syndrome. However, rapid deterioration of clinical conditions and evidence of neurological involvement, associated with abnormal radiological findings, require immediate management. Although therapeutic approaches have not been directly compared, neurosurgical treatment of amenable lesions may improve the clinical outcome of patients with C. septicum-hemolytic-uremic syndrome.

Refractory Bilateral Tubo-Ovarian Abscesses in a Patient with Iatrogenic Hypogammaglobulinemia

Genital mycoplasmas are sexually transmitted Mollicutes with a high prevalence of urogenital tract colonization among females of reproductive age. Current guidelines recommend against routine screening for these organisms, since their role in the pathogenesis of pelvic inflammatory disease and tubo-ovarian abscesses (TOAs) remains unclear. However, genital mycoplasmas harbor pathogenic potential in immunocompromised hosts, especially patients with hypogammaglobulinemia. It is important to identify such infections early, given their potential for invasive spread and the availability of easily accessible treatments. We present a young adult female with multiple sclerosis and iatrogenic hypogammaglobulinemia, with refractory, bilateral pelvic inflammatory disease and TOAs due to Ureaplasma urealyticum, identified as a single pathogen via three distinct molecular tests. To our knowledge, this is the second case of TOAs caused by U. urealyticum in the literature, and the first diagnosed by pathogen cell-free DNA metagenomic next-generation sequencing in plasma.

Clinical value of droplet digital PCR in the diagnosis and dynamic monitoring of suspected bacterial bloodstream infections

BACKGROUND

Bloodstream infections (BSIs) represent a significant public health challenge due to their high morbidity and mortality. The clinical prognosis of BSIs is closely related to the timely and accurate diagnosis and the rational use of initial antimicrobials. We aimed to evaluate the clinical value of droplet digital PCR (ddPCR) in rapid diagnosis and dynamic monitoring of BSIs.

METHODS

In this prospective study, using a ddPCR-based approach which detects 18 common pathogens, we compared the detection results and clinical concordance rates of ddPCR with blood culture (BC) in 211 patients with suspected BSIs. Further, the inflammatory profile of BSIs with Gram-negative bacteria was analyzed by Olink proteomics platform.

RESULTS

Our data showed that the positive detection rate of ddPCR was 48.82%, which was higher than that of BC (9.48%). For BC-validated BSIs, ddPCR had a sensitivity of 90.00% and a specificity of 55.50%. When considering clinically-validated BSIs, the diagnostic value of ddPCR improved with a sensitivity of 92.59% and a specificity of 78.46%.The bacterial load detected by ddPCR was correlated with traditional clinical inflammatory indicators such as interleukin-6 (IL-6) and C-reactive protein (CRP). In addition, using Olink proteomics platform, we revealed that serological osteoprotegerin (OPG), interleukin-8 (IL-8), interleukin-18 receptor 1 (IL-18R1), C-C motif chemokine 20 (CCL20) and IL-6 were substantially elevated in Gram-negative bacteria-associated BSIs, which could serve as novel auxiliary diagnostic indicators for Gram-negative bacteria BSIs.

CONCLUSION

ddPCR has the potential to provide early pathogen diagnosis, dynamic monitoring, and treatment regimen optimization for patients with BSIs.

Performance of automated antimicrobial susceptibility testing for the detection of antimicrobial resistance in gram-negative bacteria: a NordicAST study

Automated testing of antimicrobial susceptibility is common in clinical microbiology laboratories but their ability to detect low-level resistance has been questioned. This Nordic multicentre study aimed to evaluate the performance of commercially available automated AST systems. A phenotypically well-characterised collection of gram-negative bacilli (Escherichia coli (n = 7), Klebsiella pneumoniae (n = 6) and Pseudomonas aeruginosa (n = 7)) with and without resistance mechanisms was examined by Danish (n = 1), Finnish (n = 6), Norwegian (n = 16) and Swedish (n = 5) laboratories. Minimum inhibitory concentrations (MICs) were determined for 12 antimicrobials with automated systems and compared with MICs obtained with gold standard broth microdilution. The automated systems used were VITEK 2 (n = 23), Phoenix (n = 4), MicroScan (n = 1), and ARIS (n = 1). Very major errors were identified for six antimicrobials; cefotaxime (6.9%), meropenem (0.4%), ciprofloxacin (0.7%), ertapenem (4.3%), amikacin (3.4%) and colistin (6.4%). Categorical agreement of MIC for the automated systems compared to broth microdilution ranged from 83% for imipenem to 100% for ampicillin and trimethoprim-sulfamethoxazole. The analysis revealed several important antimicrobials where resistance was underestimated, potentially with significant consequences in patient treatment. The results cast doubt on the use of automated AST in the management of patients with serious infections and suggests that more work is needed to define their limitations.

Efficient filter-in-centrifuge separation of low-concentration bacteria from blood

Separating bacteria from infected blood is an important step in preparing samples for downstream bacteria detection and analysis. However, the extremely low bacteria concentration and extremely high blood cell count make efficient separation challenging. In this study, we introduce a method for separating bacteria from blood in a single centrifugation step, which involves sedimentation velocity-based differentiation followed by size-based cross-flow filtration over an inclined filter. Starting from 1 mL spiked whole blood, we recovered 32 ± 4% of the bacteria (Escherichia coli, Klebsiella pneumonia, or Staphylococcus aureus) within one hour while removing 99.4 ± 0.1% of the red blood cells, 98.4 ± 1.4% of the white blood cells, and 90.0 ± 2.6% of the platelets. Changing the device material could further increase bacteria recovery to >50%. We demonstrated bacterial recovery from blood spiked with 10 CFU mL-1. Our simple hands-off efficient separation of low-abundant bacteria approaches clinical expectations, making the new method a promising candidate for future clinical use.

Society for Maternal-Fetal Medicine Consult Series #67: Maternal sepsis

Maternal sepsis is a significant cause of maternal morbidity and mortality, and is a potentially preventable cause of maternal death. This Consult aims to summarize what is known about sepsis and provide guidance for the management of sepsis during pregnancy and the postpartum period. Most studies cited are from the nonpregnant population, but where available, pregnancy data are included. The following are the Society for Maternal-Fetal Medicine recommendations: (1) we recommend that clinicians consider the diagnosis of sepsis in pregnant or postpartum patients with otherwise unexplained end-organ damage in the presence of a suspected or confirmed infectious process, regardless of the presence of fever (GRADE 1C); (2) we recommend that sepsis and septic shock in pregnancy be considered medical emergencies and that treatment and resuscitation begin immediately (Best Practice); (3) we recommend that hospitals and health systems use a performance improvement program for sepsis in pregnancy with sepsis screening tools and metrics (GRADE 1B); (4) we recommend that institutions develop their own procedures and protocols for the detection of maternal sepsis, avoiding the use of a single screening tool alone (GRADE 1B); (5) we recommend obtaining tests to evaluate for infectious and noninfectious causes of life-threatening organ dysfunction in pregnant and postpartum patients with possible sepsis (Best Practice); (6) we recommend that an evaluation for infectious causes in pregnant or postpartum patients in whom sepsis is suspected or identified includes appropriate microbiologic cultures, including blood, before starting antimicrobial therapy, as long as there are no substantial delays in timely administration of antibiotics (Best Practice); (7) we recommend obtaining a serum lactate level in pregnant or postpartum patients in whom sepsis is suspected or identified (GRADE 1B); (8) in pregnant or postpartum patients with septic shock or a high likelihood of sepsis, we recommend administration of empiric broad-spectrum antimicrobial therapy, ideally within 1 hour of recognition (GRADE 1C); (9) after a diagnosis of sepsis in pregnancy is made, we recommend rapid identification or exclusion of an anatomic source of infection and emergency source control when indicated (Best Practice); (10) we recommend early intravenous administration (within the first 3 hours) of 1 to 2 L of balanced crystalloid solutions in sepsis complicated by hypotension or suspected organ hypoperfusion (GRADE 1C); (11) we recommend the use of a balanced crystalloid solution as a first-line fluid for resuscitation in pregnant and postpartum patients with sepsis or septic shock (GRADE 1B); (12) we recommend against the use of starches or gelatin for resuscitation in pregnant and postpartum patients with sepsis or septic shock (GRADE 1A); (13) we recommend ongoing, detailed evaluation of the patient's response to fluid resuscitation guided by dynamic measures of preload (GRADE 1B); (14) we recommend the use of norepinephrine as the first-line vasopressor during pregnancy and the postpartum period with septic shock (GRADE 1C); (15) we suggest using intravenous corticosteroids in pregnant or postpartum patients with septic shock who continue to require vasopressor therapy (GRADE 2B); (16) because of an increased risk of venous thromboembolism in sepsis and septic shock, we recommend the use of pharmacologic venous thromboembolism prophylaxis in pregnant and postpartum patients in septic shock (GRADE 1B); (17) we suggest initiating insulin therapy at a glucose level >180 mg/dL in critically ill pregnant patients with sepsis (GRADE 2C); (18) if a uterine source for sepsis is suspected or confirmed, we recommend prompt delivery or evacuation of uterine contents to achieve source control, regardless of gestational age (GRADE 1C); and (19) because of an increased risk of physical, cognitive, and emotional problems in survivors of sepsis and septic shock, we recommend ongoing comprehensive support for pregnant and postpartum sepsis survivors and their families (Best Practice).

Insight Into Neonatal Sepsis: An Overview

There are approximately 1.3 million cases of neonatal sepsis reported worldwide with deaths occurring more commonly in preterm and low-weight newborns. Neonatal sepsis is the third major cause of neonatal deaths resulting in 203,000 deaths per year. It is divided into two subtypes based on time of occurrence: early-onset neonatal sepsis (ENS), occurring within the first 72 hours of birth usually due to perinatal risk factors, and late-onset neonatal sepsis (LOS) usually occurring after the first week of life and up to 28th day of life. There are many complications associated with neonatal sepsis including septic shock, multiple organ failure, and death. It is vital for clinicians to know the signs and symptoms of neonatal sepsis in order to diagnose it early. Preventive measures, early diagnosis, appropriate antibiotic administration, timely supportive management, and the establishment of efficient management are vital in the prevention of severe complications or death. In this review, we aim to provide the most up-to-date information regarding risk factors, pathophysiology, signs and symptoms, diagnosis, and treatment of neonatal sepsis. We discuss the maternal and neonatal risk factors involved in the pathogenesis of neonatal sepsis and the signs and symptoms of early and late neonatal sepsis. We focus on the different pathogens involved and the markers used in the diagnosis and treatments available for each.

Rapid identification of sepsis in the emergency department

Objectives

Recent research has helped define the complex pathways in sepsis, affording new opportunities for advancing diagnostics tests. Given significant advances in the field, a group of academic investigators from emergency medicine, intensive care, pathology, and pharmacology assembled to develop consensus around key gaps and potential future use for emerging rapid host response diagnostics assays in the emergency department (ED) setting.

Methods

A modified Delphi study was conducted that included 26 panelists (expert consensus panel) from multiple specialties. A smaller steering committee first defined a list of Delphi statements related to the need for and future potential use of a hypothetical sepsis diagnostic test in the ED. Likert scoring was used to assess panelists agreement or disagreement with statements. Two successive rounds of surveys were conducted and consensus for statements was operationally defined as achieving agreement or disagreement of 75% or greater.

Results

Significant gaps were identified related to current tools for assessing risk of sepsis in the ED. Strong consensus indicated the need for a test providing an indication of the severity of dysregulated host immune response, which would be helpful even if it did not identify the specific pathogen. Although there was a relatively high degree of uncertainty regarding which patients would most benefit from the test, the panel agreed that an ideal host response sepsis test should aim to be integrated into ED triage and thus should produce results in less than 30 minutes. The panel also agreed that such a test would be most valuable for improving sepsis outcomes and reducing rates of unnecessary antibiotic use.

Conclusion

The expert consensus panel expressed strong consensus regarding gaps in sepsis diagnostics in the ED and the potential for new rapid host response tests to help fill these gaps. These finding provide a baseline framework for assessing key attributes of evolving host response diagnostic tests for sepsis in the ED.

The Role of Coagulase-Negative Staphylococci Biofilms on Late-Onset Sepsis: Current Challenges and Emerging Diagnostics and Therapies

Infections are one of the most significant complications of neonates, especially those born preterm, with sepsis as one of the principal causes of mortality. Coagulase-negative staphylococci (CoNS), a group of staphylococcal species that naturally inhabit healthy human skin and mucosa, are the most common cause of late-onset sepsis, especially in preterms. One of the risk factors for the development of CoNS infections is the presence of implanted biomedical devices, which are frequently used for medications and/or nutrient delivery, as they serve as a scaffold for biofilm formation. The major concerns related to CoNS infections have to do with the increasing resistance to multiple antibiotics observed among this bacterial group and biofilm cells’ increased tolerance to antibiotics. As such, the treatment of CoNS biofilm-associated infections with antibiotics is increasingly challenging and considering that antibiotics remain the primary form of treatment, this issue will likely persist in upcoming years. For that reason, the development of innovative and efficient therapeutic measures is of utmost importance. This narrative review assesses the current challenges and emerging diagnostic tools and therapies for the treatment of CoNS biofilm-associated infections, with a special focus on late-onset sepsis.

Rapid and precise identification of bloodstream infections using a pre-treatment protocol combined with high-throughput multiplex genetic detection system

Background

Bloodstream infection (BSI) is a life-threatening condition with high morbidity and mortality rates worldwide. Early diagnosis of BSI is critical to avoid the unnecessary application of antimicrobial agents and for proper treatment. However, the current standard methods based on blood culture are time-consuming, thus failing to provide a timely etiological diagnosis of BSI, and common PCR-based detection might be inhibited by matrix components.

Methods

The current study explored an integrated pre-analytical treatment protocol for whole blood samples, wherein pathogens are enriched and purified by incubation and concentration, and inhibitors are inactivated and removed. Further, this study developed and evaluated a novel high-throughput multiplex genetic detection system (HMGS) to detect 24 of the most clinically prevalent BSI pathogens in blood culture samples and pre-treated whole blood samples. The specificity and sensitivity were evaluated using related reference strains and quantified bacterial/fungal suspensions. The clinical utility of BSI-HMGS combined with the pre-analytical treatment protocol was verified using blood cultures and whole blood samples.

Results

The combined pre-treatment protocol and BSI-HMGS was highly specific for target pathogens and possessed a low detection limit for clinical whole blood samples. The pre-treatment protocol could deplete the PCR inhibitors effectively. For blood culture samples, the current method showed 100.0% negative percent agreements and > 87.5% positive percent agreements compared to the reference results based on blood culture findings. For whole blood samples, the current method showed 100.0% negative percent agreements and > 80.0% positive percent agreements compared to the reference results for most pathogens. The turnaround time was ≤ 8 h, and all the procedures could be conducted in a general clinical laboratory.

Conclusion

The BSI-HMGS combined with the pre-treatment protocol was a practical and promising method for early and precise detection of BSIs, especially for areas without access to advanced medical facilities.

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.

Clinical validation of a multiplex droplet digital PCR for diagnosing suspected bloodstream infections in ICU practice: a promising diagnostic tool

Background

Droplet digital PCR (ddPCR) has emerged as a promising tool of pathogen detection in bloodstream infections (BSIs) in critical care medicine. However, different ddPCR platforms have variable sensitivity and specificity for diverse microorganisms at various infection sites. There is still a lack of prospective clinical studies aimed at validating and interpreting the discrepant ddPCR results for diagnosing BSI in intensive care unit (ICU) practice.

Methods

A prospective diagnostic study of multiplex ddPCR panels was conducted in a general ICU from May 21, 2021, to December 22, 2021. Paired blood cultures (BCs) and ddPCRs (2.5 h) were obtained synchronously to detect the 12 most common BSI pathogens and three antimicrobial resistance (AMR) genes. Firstly, ddPCR performance was compared to definite BSI. Secondly, clinical validation of ddPCR was compared to composite clinical diagnosis. Sensitivity, specificity, and positive and negative predictive values were calculated. Thirdly, the positive rate of AMR genes and related analysis was presented.

Results

A total of 438 episodes of suspected BSIs occurring in 150 critical patients were enrolled. BC and ddPCR were positive for targeted bacteria in 40 (9.1%) and 180 (41.1%) cases, respectively. There were 280 concordant and 158 discordant. In comparison with BCs, the sensitivity of ddPCR ranged from 58.8 to 86.7% with an aggregate of 72.5% in different species, with corresponding specificity ranging from 73.5 to 92.2% with an aggregate of 63.1%. Furthermore, the rate of ddPCR+/BC− results was 33.6% (147/438) with 87.1% (128 of 147) cases was associated with probable (n = 108) or possible (n = 20) BSIs. When clinically diagnosed BSI was used as true positive, the final sensitivity and specificity of ddPCR increased to 84.9% and 92.5%, respectively. In addition, 40 blaKPC, 3blaNDM, and 38 mecA genes were detected, among which 90.5% were definitely positive for blaKPC. Further, 65.8% specimens were predicted to be mecA-positive in Staphylococcus sp. according to all microbiological analysis.

Conclusions

The multiplexed ddPCR is a flexible and universal platform, which can be used as an add-on complementary to conventional BC. When combined with clinical infection evidence, ddPCR shows potential advantages for rapidly diagnosing suspected BSIs and AMR genes in ICU practice.

Rapid Fluorescence Sensor Guided Detection of Urinary Tract Bacterial Infections

Introduction

Urinary tract infections (UTI) are one of the most serious human bacterial infections affecting millions of people every year. Therefore, simple and reliable identification of the urinary tract pathogenic bacteria within a few minutes would be of great significance for diagnosis and treatment of clinical patients with UTIs. In this study, the fluorescence sensor was reported to guide the detection of urinary tract bacterial infections rapidly.

Methods

The Ami-AuNPs-DNAs sensor was fabricated by the amino-modified Au nanoparticles (Ami-AuNPs) and six DNAs signal molecules, which bound to the urinary tract pathogenic bacteria and generated corresponding response signals. Further, based on the collected response signals, identification was performed by principal component analysis (PCA) and linear discriminant analysis (LDA). The Ami-AuNPs and Ami-AuNPs-DNAs were characterized by transmission electron microscopy, UV−vis absorption spectrum, Fourier transform infrared spectrum, dynamic light scattering and zeta potentials. Thereafter, the Ami-AuNPs-DNAs sensor was used to discriminate and identify five kinds of urinary tract pathogenic bacteria. Moreover, the quantitative analysis performance towards individual bacteria at different concentrations were also evaluated.

Results

The Ami-AuNPs-DNAs sensor were synthesized successfully in terms of spherical, well-dispersed and uniform in size, which could well discriminate five main urinary tract pathogenic bacteria with unique fingerprint-like patterns and was sufficiently sensitive to determine individual bacteria with a detection limit to 1×10⁷ cfu/mL. Furthermore, the sensor had also been successfully applied to identify bacteria in urine samples collected from clinical UTIs.

Conclusion

The developed fluorescence sensor could be applied to rapid and accurate discrimination of urinary tract pathogenic bacteria and holds great promise for the diagnosis of the disease caused by bacterial infection.

Prognostic Effects of Delayed Administration of Appropriate Antimicrobials in Bacteraemic Adults Initially Presenting with Various Body Temperatures

Purpose

To investigate the different impact of delayed administration of appropriate antimicrobial therapy (AAT) on short-term mortality of bacteraemia patients initially presenting with various body temperatures (BTs).

Materials and Methods

A six-year, two-center cohort consisting of adults with community-onset bacteraemia in emergency departments (EDs) was retrospectively collected. Through the multivariable analyses, clinical impacts of delayed AAT, assessed by the time gap between the first dose of AAT and ED arrival, on 30-day mortality (primary outcomes) were respectively examined in the different groups of initial BTs (iBTs).

Results

Of the 3171 adults, despite the similarities of delayed AAT in six iBT categories, hourly AAT delay was associated with an average increase in 30-day mortality rates of 0.24% in the group of iBT <36.0℃, 0.40% in the 36.0℃–36.9℃ group, 0.48% in the 37.0℃–37.9℃ group, 0.59% in the 38.0℃–38.9℃ group, 0.58% in the 39.0℃–39.9℃ group, and 0.71% in the ≥40.0℃ group, after respective adjusting independent predictors of mortality. Furthermore, for 589 patients who inappropriately received empirical antimicrobial treatment (ie, delayed AAT ≥ 24 hours), with a cutoff of 34.0℃, each 1℃ increase in iBTs was independently associated with an average increase in 30-day mortality rates of 42%.

Conclusion

For adults with community-onset bacteraemia, the iBT-related differences in the prognostic impacts of delayed administration of appropriate antimicrobials might be evident.

A Refunding Scheme to Incentivize Narrow-Spectrum Antibiotic Development

The rapid rise of antibiotic resistance is a serious threat to global public health. The situation is exacerbated by the “antibiotics dilemma”: Developing narrow-spectrum antibiotics against resistant bacteria is most beneficial for society, but least attractive for companies, since their usage and sales volumes are more limited than for broad-spectrum drugs. After developing a general mathematical framework for the study of antibiotic resistance dynamics with an arbitrary number of antibiotics, we identify efficient treatment protocols. Then, we introduce a market-based refunding scheme that incentivizes pharmaceutical companies to develop new antibiotics against resistant bacteria and, in particular, narrow-spectrum antibiotics that target specific bacterial strains. We illustrate how such a refunding scheme can solve the antibiotics dilemma and cope with various sources of uncertainty that impede antibiotic R &D. Finally, connecting our refunding approach to the recently established Antimicrobial Resistance (AMR) Action Fund, we discuss how our proposed incentivization scheme could be financed.

Current commercial dPCR platforms: technology and market review

Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.

Diagnosis and Management of Invasive Candida Infections in Critically Ill Patients

Invasive candidiasis (IC) has become a serious problem in the intensive care unit patients with an attributable mortality rate that can reach up to 51%. Multiple global surveillance studies have shown an increasing incidence of candidemia. Despite their limited sensitivity (21-71%), cultures remain the gold standard for the diagnosis of IC associated with candidemia. Many adjunct laboratory tests exist to support or rule out the diagnosis, each with its indications and limitations, including procalcitonin, 1,3-β-D-glucan, mannan and anti-mannan antibodies, and Candida albicans germ tube antibody. In addition, polymerase chain reaction-based methods could expedite species identification in positive blood cultures, helping in guiding early empirical antifungal therapy. The management of IC in critically ill patients can be classified into prophylactic, preemptive, empiric, and directed/targeted therapy of a documented infection. There is no consensus concerning the benefit of prophylactic therapy in critically ill patients. While early initiation of appropriate therapy in confirmed IC is an important determinant of survival, the selection of candidates and drug of choice for empirical systemic antifungal therapy is more controversial. The choice of antifungal agents is determined by many factors, including the host, the site of infection, the species of the isolated Candida, and its susceptibility profile. Echinocandins are considered initial first-line therapy agents. Due to the conflicting results of the various studies on the benefit of preemptive therapy for critically ill patients and the lack of robust evidence, the Infectious Diseases Society of America (IDSA) omitted this category from its updated guidelines and the European Society of Intensive Care Medicine (ESICM) and the Critically Ill Patients Study Group of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) do not recommend it.

Managing sepsis in the era of precision medicine: challenges and opportunities

INTRODUCTION

Precision medicine is a medical model in which decisions, practices, interventions and therapies are tailored to the individual patient based on their predicted response or risk of disease. Sepsis is a life-threatening condition characterized by immune system dysregulation whose pathophysiology remains incompletely understood. There is much hope that precision medicine can lead to better outcomes in patients with sepsis.

AREAS COVERED

In this review from a comprehensive literature search in PubMed for English-language studies conducted in adults, we highlight recent advances in the diagnosis and treatment of sepsis of bacterial origin in adults using precision medicine approaches including rapid diagnostic tests, predictive biomarkers, genomic methods, rapid antimicrobial susceptibility testing, and monitoring cell mediated immunity. Challenges and directions for future research are also discussed.

EXPERT OPINION

Current diagnostic testing in sepsis relies primarily on conventional cultures (e.g. blood cultures), which are time-consuming and may delay critical therapeutic decisions. Nonculture-based techniques including nucleic acid amplification technologies (NAAT), other molecular methods (biomarkers), and genomic sequencing offer promise to overcome some of the inherent limitations seen with culture-based techniques.

Recent advances in novel diagnostic testing for peritoneal dialysis-related peritonitis

Peritoneal dialysis-related peritonitis remains a significant complication and an important cause of technique failure. Based on current International Society for Peritoneal Dialysis guidelines, diagnosis of peritonitis is made when two of the three following criteria are met: 1) clinical features consistent with peritonitis; 2) dialysis effluent white blood cell count of >100 cells/μL; 3) positive effluent culture. However, early and accurate diagnosis can still be faulty, and emphasis has been placed on improving the timeliness and accuracy of diagnosis to facilitate early effective treatment. There have been advances in the novel diagnostic tests such as point-of-care molecular tests, genetics sequencing, mass spectrometry, and machine learning algorithm with immune fingerprinting. This article will discuss the latest evidence and updates of these tests in the management of peritoneal dialysis-related peritonitis.

Diagnosis of neonatal sepsis: the past, present and future

Sepsis remains a significant cause of neonatal mortality and morbidity, especially in low- and middle-income countries. Neonatal sepsis presents with nonspecific signs and symptoms that necessitate tests to confirm the diagnosis. Early and accurate diagnosis of infection will improve clinical outcomes and decrease the overuse of antibiotics. Current diagnostic methods rely on conventional culture methods, which is time-consuming, and may delay critical therapeutic decisions. Nonculture-based techniques including molecular methods and mass spectrometry may overcome some of the limitations seen with culture-based techniques. Biomarkers including hematological indices, cell adhesion molecules, interleukins, and acute-phase reactants have been used for the diagnosis of neonatal sepsis. In this review, we examine past and current microbiological techniques, hematological indices, and inflammatory biomarkers that may aid sepsis diagnosis. The search for an ideal biomarker that has adequate diagnostic accuracy early in sepsis is still ongoing. We discuss promising strategies for the future that are being developed and tested that may help us diagnose sepsis early and improve clinical outcomes. IMPACT: Reviews the clinical relevance of currently available diagnostic tests for sepsis. Summarizes the diagnostic accuracy of novel biomarkers for neonatal sepsis. Outlines future strategies including the use of omics technology, personalized medicine, and point of care tests.

Cost-effectiveness of rapid laboratory-based mass-spectrometry diagnosis of bloodstream infection: evidence from the RAPIDO randomised controlled trial

OBJECTIVES AND INTERVENTION

Bloodstream infection, the presence of viable micro-organisms in the blood, is a prevalent clinical event associated with substantial mortality. Patient outcomes may be improved when the causative micro-organism is identified quickly. We assessed the cost-effectiveness of rapid microbial identification by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry.

DESIGN

Economic evaluation alongside a randomised multicentre trial (RAPIDO: RAPId Diagnosis on Outcome) assessing the impact of rapid identification by MALDI-TOF spectrometry.

SETTING

Adult inpatients with bloodstream infections at seven National Health Service hospital trusts in England and Wales.

PRIMARY OUTCOME

Net monetary benefit, estimated as incremental costs compared with incremental 28-day survival, of rapid identification by MALDI-TOF spectrometry compared with conventional identification.

METHODS

Patients were randomised (1:1) to receive diagnosis by conventional methods of microbial identification (conventional arm) only or by MALDI-TOF spectrometry in addition to conventional identification (RAPIDO arm).

RESULTS

Data from 5550 patients were included in primary analysis. Mean imputed costs in 2018/2019 prices per patient were lower by £126 in the RAPIDO arm (95% CI -£784 to £532) but the proportion of patients alive at day 28 was lower (81.4% vs 82.3%). The probability of cost-effectiveness of MALDI-TOF was <0.5 at cost-effectiveness thresholds between £20 000 and £50 000.

CONCLUSIONS

Adjunctive MALDI-TOF diagnosis was unlikely to be cost-effective when measured as cost per death avoided at 28 days. However, the differences between arms in cost and effect were modest, associated with uncertainty and may not accurately reflect 'real-world' routine use of MALDI-TOF technology in this patient group.

TRIAL REGISTRATION NUMBERS

ISRCTN97107018/UKCRN 11978.

Novel electronic biosensor for automated inoculum preparation to accelerate antimicrobial susceptibility testing

A key predictor of morbidity and mortality for patients with a bloodstream infection is time to appropriate antimicrobial therapy. Accelerating antimicrobial susceptibility testing from positive blood cultures is therefore key to improving patient outcomes, yet traditional laboratory approaches can require 2–4 days for actionable results. The eQUANT—a novel instrument utilizing electrical biosensors—produces a standardized inoculum equivalent to a 0.5 McFarland directly from positive blood cultures. This proof-of-concept study demonstrates that eQUANT inocula prepared from clinically significant species of Enterobacterales were comparable to 0.5 McF inocula generated from bacterial colonies in both CFU/ml concentration and performance in antimicrobial susceptibility testing, with ≥ 95% essential and categorical agreement for VITEK2 and disk diffusion. The eQUANT, combined with a rapid, direct from positive blood culture identification technique, can allow the clinical laboratory to begin antimicrobial susceptibility testing using a standardized inoculum approximately 2–3 h after a blood culture flags positive. This has the potential to improve clinical practice by accelerating conventional antimicrobial susceptibility testing and the resulting targeted antibiotic therapy.

Artificial neural networks combined multi-wavelength transmission spectrum feature extraction for sensitive identification of waterborne bacteria

Present research is focused on the rapid and accurate identification of bacterial species based on artificial neural networks combined with spectral data processing technology. The spectra of different bacterial species in the logarithmic growth phase were obtained. Model input features were extracted from the raw spectra using signal processing techniques, including normalization, principal component analysis (PCA) and area-based feature value extraction. The identification models based on artificial neural network of back propagation neural networks (BPNN), generalized regression neural networks (GRNN) and probabilistic neural networks (PNN) were developed using the extracted features in order to ascertain whether the different species of bacteria could be differentiated. The performance of developed models and its corresponding signal processing techniques is tested by the recognition accuracy of validation set and test set, and model error. The maximum recognition accuracy of normalized spectrum combined with BPNN was 95.5% (error: 10%, test accuracy: 100%). The total recognition accuracy of PCA-reduced features (200-400 nm) combined with GRNN resulted in 96.3%~96.8% (error: 3.3%~6.7%, test accuracy: 97.5%~100%). While the overall recognition accuracy of area-based features combined with GRNN reached 97.3% with test accuracy of 100% (model error: 5.0%). Choosing of model and signal processing techniques has a positive influence on improving classification accuracy, so as to make it possible to realize the rapid detection and online monitoring of waterborne microbial contamination.

Monocyte distribution width (MDW) parameter as a sepsis indicator in intensive care units

OBJECTIVES

Patients in Intensive Care Units (ICU) are a high-risk population for sepsis, recognized as a major cause of admission and death. The aim of the current study was to evaluate the diagnostic accuracy and prognostication of monocyte distribution width (MDW) in sepsis for patients admitted to ICU.

METHODS

Between January and June 2020, we conducted a prospective observational study during the hospitalization of 506 adult patients admitted to the ICU. MDW was evaluated in 2,367 consecutive samples received for routine complete blood counts (CBC) performed once a day and every day during the study. Sepsis was diagnosed according to Sepsis-3 criteria and patients enrolled were classified in the following groups: no sepsis, sepsis and septic shock.

RESULTS

MDW values were significantly higher in patients with sepsis or septic shock in comparison to those within the no sepsis group [median 26.23 (IQR: 23.48-29.83); 28.97 (IQR: 21.27-37.21); 21.99 (IQR: 19.86-24.36) respectively]. ROC analysis demonstrated that AUC is 0.785 with a sensitivity of 66.88% and specificity of 77.79% at a cut-off point of 24.63. In patients that developed an ICU-acquired sepsis MDW showed an increase from 21.33 [median (IQR: 19.47-21.72)] to 29.19 [median (IQR: 27.46-31.47)]. MDW increase is not affected by the aetiology of sepsis, even in patients with COVID-19. In sepsis survivors a decrease of MDW values were found from the first time to the end of their stay [median from 29.14 (IQR: 26.22-32.52) to 25.67 (IQR: 22.93-30.28)].

CONCLUSIONS

In ICU, MDW enhances the sepsis detection and is related to disease severity.

Clinical Impact of Rapid Species Identification From Positive Blood Cultures With Same-day Phenotypic Antimicrobial Susceptibility Testing on the Management and Outcome of Bloodstream Infections

BACKGROUND

Timely availability of microbiological results from positive blood cultures is essential to enable early pathogen-directed therapy. The Accelerate Pheno system (ADX) is a novel technology using fluorescence in situ hybridization for rapid species identification (ID) and morphokinetic bacterial analysis for phenotypic antimicrobial susceptibility testing (AST), with promising results. Yet the impact of this technology on clinical management and patient outcome remains unclear.

METHODS

We conducted a quasiexperimental before-and-after observational study and analyzed 3 groups with different diagnostic and therapeutic pathways following recent integration of ADX: conventional microbiological diagnostics with and without antimicrobial stewardship program (ASP) intervention, and rapid diagnostics (ADX in addition to conventional standard) with ASP intervention. Primary endpoints were time to adequate, to optimal and to step-down antimicrobial therapy. Secondary endpoints were antimicrobial consumption, in-hospital mortality, length of stay (LOS), and the incidence of Clostridioidesdifficile infection (CDI).

RESULTS

Two hundred four patients (conventional diagnostics, n = 64; conventional diagnostics + ASP, n = 68; rapid diagnostics + ASP; n = 72) were evaluated. The use of ADX significantly decreased time from Gram stain to ID (median, 23 vs 2.2 hours, P < .001) and AST (median, 23 vs 7.4 hours, P < .001), from Gram stain to optimal therapy (median, 11 vs 7 hours, P = .024) and to step-down antimicrobial therapy (median, 27.8 vs 12 hours, P = .019). However, groups did not differ in antimicrobial consumption, duration of antimicrobial therapy, mortality, LOS, or incidence of CDI.

CONCLUSIONS

Use of ADX significantly reduced time to ID and AST as well as time to optimal antimicrobial therapy but did not affect antimicrobial consumption and clinical outcome.

Identification of Staphylococci by Polymerase Chain Reaction Directly from a Positive Blood Culture and Effect on Patient Care

BACKGROUND

As one of the most common bloodstream infections worldwide, Staphylococcus aureus bacteremia places a major burden on health care. Implementation of a rapid, genetic-based diagnostic test may have important implications in the clinical management of patients with S. aureus bacteremia.

OBJECTIVES

The primary objective was to assess concordance between testing based on polymerase chain reaction (PCR) and the current gold standard, culture and sensitivity testing; the secondary objective was to assess the impact of this technology on patient care.

METHODS

A pre-post intervention retrospective chart review was used to document the hospital course of patients with a diagnosis of S. aureus bacteremia before and after implementation of the PCR-based diagnostic system. Laboratory results from all patient samples subjected to PCR-based analysis following implementation of this system were compared with culture and sensitivity data for the same samples to determine accuracy of the new system. In addition, time to optimal therapy for each patient was calculated as the interval between the initiation of empiric and terminal therapies. The appropriateness of antimicrobial treatment was characterized as guideline-concordant, nonconcordant with the guidelines, or nonconcordant yet still clinically appropriate.

RESULTS

In total, 98 and 99 patients met the inclusion criteria before and after implementation of the PCR-based diagnostic system, respectively. PCR-based results displayed 99.8% concordance (440/441 total samples) with results from culture and sensitivity testing. The time to optimal therapy was significantly shorter after implementation, by a mean of 22.8 h (p < 0.001). Overall, 97% of empiric and 99% of terminal antimicrobial regimens were either guideline-concordant or clinically appropriate for treatment of S. aureus bacteremia; 3% of empiric and 1% of terminal antimicrobial regimens were nonconcordant with clinical guidelines without any explanation based on other clinical considerations.

CONCLUSIONS

The study findings support the utility of using a direct-from-positive-blood-culture PCR-based diagnostic tool as the primary method of identifying S. aureus bacteremia in patients, as well as the acceptance of and acting upon the new assay's results by our local clinicians. PCR-based assays can help reduce the time to optimal terminal therapy for patients with bacteremia.

Dose Optimization of Vancomycin Using a Mechanism-based Exposure-Response Model in Pediatric Infectious Disease Patients

PURPOSE

This study aimed to determine the appropriate vancomycin dosage, considering patient size and organ maturation, by simulating the bacterial count and biomarker level for drug administration in pediatric patients with gram-positive bacterial (GPB) infections.

METHODS

Natural language processing for n-gram analysis was used to detect appropriate pharmacodynamic (PD) markers in infectious disease patients. In addition, a mechanism-based model was established to describe the systemic exposure and evaluate the PD marker simultaneously in pediatric patients. A simulation study was then conducted by using a mechanism-based model to evaluate the optimal dose of vancomycin in pediatric patients.

FINDINGS

C-reactive protein (CRP) was selected as a PD marker from an analysis of ~270,000 abstracts in PubMed. In addition, clinical results, including the vancomycin plasma concentrations and CRP levels of pediatric patients (n = 93), were collected from electronic medical records. The vancomycin pharmacokinetic model with allometric scaling and a maturation function was built as a one-compartment model, with an additional compartment for bacteria. Both the effects of vancomycin plasma concentrations on the destruction of bacteria and those of bacteria on CRP production rates were represented by using a maximum achievable effect model (E_max model). Simulation for dose optimization was conducted not only by using the final model but also by exploring the possibility of therapeutic failure based on the MICs of vancomycin for GPB. Clinical cure was defined as when the CRP level fell below the upper limit of the normal range. Our dose optimization simulations suggested a vancomycin dosage of 10 mg/kg every 8 h as the optimal maintenance dose for pediatric patients with a postconceptual age <30 weeks and 10 mg/kg every 6 h for older children, aged up to 12 years. In addition, the MIC of 3 μg/mL was assessed as the upper concentration limit associated with successful vancomycin treatment of GPB infections.

IMPLICATIONS

This study confirmed that the changes in bacterial counts and CRP levels were well described with mechanistic exposure-response modeling of vancomycin. This model can be used to determine optimal empiric doses of vancomycin and to improve therapeutic outcomes in pediatric patients with GPB.

High concentration of Cas12a effector tolerates more mismatches on ssDNA

Rapid pathogen detection is critical for prompt treatment, interrupting transmission routes, and decreasing morbidity and mortality. The V-type CRISPR system had been used for rapid pathogen detection. However, whether single-stranded DNA in CRISPR system can cause false positives remains undetermined. Herein, we show that high molar concentration of Cas12a effector tolerated more mismatches on ssDNA and activated its trans-cleavage activity at six base matches. Reducing Cas12a and crRNA molar concentration increased the minimal base-match number required for Cas12a ssDNA activation to 11, which reducing nonspecific activation. We then established a Cas12a-based M tuberculosis detection system with a primer having an 8 bp overlap with crRNA. This system did not exhibit primer-induced false positives, and minimum detection copy reached 1 copy/uL (inputting 1-μL sample) in standard strains. The Cas12a-based M tuberculosis detection system showed 80.0% sensitivity and 100.0% specificity in verification using clinical specimens, compared with Xpert MTB/RIF, which showed 72.0% sensitivity and 90.9% specificity. All these results prove that appropriate concentration of cas12a effector can effectively perform nucleic acid detection.

The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update

The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.

Innovative optofluidics and microscopy-based rapid analysis of pathogens

The timely knowledge and prescription of the most suitable antibiotic to treat bacterial infections is critical for the recovery of patients battling life-threatening bacterial infections. Unfortunately, current standard-of-care approaches relies on the empiric prescription of an antibiotic, as determination of the most effective antibiotic requires multiple time-consuming steps. These steps often include culturing of the bacterium responsible for infection and subsequent antibiotic susceptibility testing. Here we introduce an optofluidic technology that allows us to capture bacterial cells efficiently and rapidly from different biological samples and use the captured cells for rapid antibiotic selection thereby bypassing the need to culture the bacterium.

The hypothetical impact of Accelerate Pheno™ system on time to effective therapy and time to definitive therapy in an institution with an established antimicrobial stewardship programme currently utilizing rapid genotypic organism/resistance marker identification

Background

Rapid organism identification and antimicrobial susceptibility testing (AST) can optimize antimicrobial therapy in patients with bacteraemia. The Accelerate Pheno™ system (ACC) can provide identification and AST results within 7 h of a positive culture.

Objectives

To assess the hypothetical impact of ACC on time to effective therapy (TTET), time to definitive therapy (TTDT) and antimicrobial usage at the Detroit Medical Center (DMC).

Methods

Patients with positive blood cultures from 29 March to 24 June 2016 were included. ACC was performed in parallel with normal laboratory procedures, but results were not made available to the clinicians. The potential benefit of having ACC results was determined if clinicians modified therapy based on actual AST results. Potential changes in TTET, TTDT and antibiotic usage were calculated.

Results

One hundred and sixty-seven patients were included. The median TTET was 2.4 h (IQR 0.5, 15.1). Had ACC results been available, TTET could have been improved in four patients (2.4%), by a median decrease of 18.9 h (IQR 11.3, 20.4). The median TTDT was 41.4 h (IQR 21.7, 73.3) and ACC results could have improved TTDT among 51 patients (30.5%), by a median decrease of 25.4 h (IQR 18.7, 37.5). ACC implementation could have led to decreases in usage of cefepime (16% reduction), aminoglycosides (23%), piperacillin/tazobactam (8%) and vancomycin (4%).

Conclusions

ACC results could potentially improve time to de-escalation and reduce use of antimicrobials. The impact of ACC on TTET was small, likely related to the availability of other rapid diagnostic tests at DMC.

Clinical Impact of Accelerate PhenoTM Rapid Blood Culture Detection System in Bacteremic Patients

BACKGROUND

Accelerate Pheno blood culture detection system (AXDX) provides identification (ID) and antimicrobial susceptibility testing (AST) results within 8h of blood culture growth. Limited data exists regarding its clinical impact. Other rapid platforms coupled with antimicrobial stewardship program (ASP) real-time notification (RTN) have shown improved length of stay (LOS) in bacteremia.

METHODS

A single-center, quasi-experimental study of adult bacteremic inpatients before/after AXDX implementation was conducted comparing clinical outcomes from 1 historical and 2 intervention cohorts (AXDX and AXDX+RTN). Primary outcome was LOS.

RESULTS

Of 830 bacteremic episodes, 188 (77%) of 245 historical and 308 (155 AXDX, 153 AXDX+RTN; 65%) of 585 intervention episodes were included. Median LOS was shorter with AXDX (6.3d) and AXDX+RTN (6.7d) compared to historical (8.1d; P=0.001). Achievement of optimal therapy (AOT) was more frequent (93.6% and 95.4%) and median time to optimal therapy (TTOT) was faster (1.3d and 1.4d) in AXDX and AXDX+RTN compared to historical (84.6%, P≤0.001 and 2.4d; P≤0.001) respectively. Median antimicrobial days of therapy (DOT) was shorter in both intervention arms compared to historical (6d each vs 7d; P=0.011). Median LOS benefit was most pronounced in patients with coagulase negative Staphylococcus bacteremia (5.5d and 4.5d vs 7.2d; P=0.003) in AXDX, AXDX+RTN, and historical cohorts respectively.

CONCLUSIONS

LOS, AOT, TTOT, and total DOT significantly improved after AXDX implementation. Addition of RTN did not show further improvement over AXDX and an already active ASP. These results suggest AXDX can be integrated into healthcare systems with an active ASP even without the resources to include RTN.

Microfluidic enrichment of bacteria coupled to contact-free lysis on a magnetic polymer surface for downstream molecular detection

We report on a microsystem that couples high-throughput bacterial immunomagnetic capture to contact-free cell lysis using an alternating current magnetic field (AMF) to enable downstream molecular characterization of bacterial nucleic acids. Traditional methods for cell lysis rely on either dilutive chemical methods, expensive biological reagents, or imprecise physical methods. We present a microchip with a magnetic polymer substrate (Mag-Polymer microchip), which enables highly controlled, on-chip heating of biological targets following exposure to an AMF. First, we present a theoretical framework for the quantitation of power generation for single-domain magnetic nanoparticles embedded in a polymer matrix. Next, we demonstrate successful bacterial DNA recovery by coupling (1) high-throughput, sensitive microfluidic immunomagnetic capture of bacteria to (2) on-chip, contact-free bacterial lysis using an AMF. The bacterial capture efficiency exceeded 76% at 50 ml/h at cell loads as low as ∼10 CFU/ml, and intact DNA was successfully recovered at starting bacterial concentrations as low as ∼1000 CFU/ml. Using the presented methodology, cell lysis becomes non-dilutive, temperature is precisely controlled, and potential contamination risks are eliminated. This workflow and substrate modification could be easily integrated in a range of micro-scale diagnostic systems for infectious disease.

Prevalence of Antibiotic-Resistant Pathogens in Culture-Proven Sepsis and Outcomes Associated With Inadequate and Broad-Spectrum Empiric Antibiotic Use

IMPORTANCE

Broad-spectrum antibiotics are recommended for all patients with suspected sepsis to minimize the risk of undertreatment. However, little is known regarding the net prevalence of antibiotic-resistant pathogens across all patients with community-onset sepsis or the outcomes associated with unnecessarily broad empiric treatment.

OBJECTIVE

To elucidate the epidemiology of antibiotic-resistant pathogens and the outcomes associated with both undertreatment and overtreatment in patients with culture-positive community-onset sepsis.

DESIGN, SETTING, AND PARTICIPANTS

This cohort study included 17 430 adults admitted to 104 US hospitals between January 2009 and December 2015 with sepsis and positive clinical cultures within 2 days of admission. Data analysis took place from January 2018 to December 2019.

EXPOSURES

Inadequate empiric antibiotic therapy (ie, ≥1 pathogen nonsusceptible to all antibiotics administered on the first or second day of treatment) and unnecessarily broad empiric therapy (ie, active against methicillin-resistant Staphylococcus aureus [MRSA]; vancomycin-resistant Enterococcus [VRE]; ceftriaxone-resistant gram-negative [CTX-RO] organisms, including Pseudomonas aeruginosa; or extended-spectrum β-lactamase [ESBL] gram-negative organisms when none of these were isolated).

MAIN OUTCOMES AND MEASURES

Prevalence and empiric treatment rates for antibiotic-resistant organisms and associations of inadequate and unnecessarily broad empiric therapy with in-hospital mortality were assessed, adjusting for baseline characteristics and severity of illness.

RESULTS

Of 17 430 patients with culture-positive community-onset sepsis (median [interquartile range] age, 69 [57-81] years; 9737 [55.9%] women), 2865 (16.4%) died in the hospital. The most common culture-positive sites were urine (9077 [52.1%]), blood (6968 [40.0%]), and the respiratory tract (2912 [16.7%]). The most common pathogens were Escherichia coli (5873 [33.7%]), S aureus (3706 [21.3%]), and Streptococcus species (2361 [13.5%]). Among 15 183 cases in which all antibiotic-pathogen susceptibility combinations could be calculated, most (12 398 [81.6%]) received adequate empiric antibiotics. Empiric therapy targeted resistant organisms in 11 683 of 17 430 cases (67.0%; primarily vancomycin and anti-Pseudomonal β-lactams), but resistant organisms were uncommon (MRSA, 2045 [11.7%]; CTX-RO, 2278 [13.1%]; VRE, 360 [2.1%]; ESBLs, 133 [0.8%]). The net prevalence for at least 1 resistant gram-positive organism (ie, MRSA or VRE) was 13.6% (2376 patients), and for at least 1 resistant gram-negative organism (ie, CTX-RO, ESBL, or CRE), it was 13.2% (2297 patients). Both inadequate and unnecessarily broad empiric antibiotics were associated with higher mortality after detailed risk adjustment (inadequate empiric antibiotics: odds ratio, 1.19; 95% CI, 1.03-1.37; P = .02; unnecessarily broad empiric antibiotics: odds ratio, 1.22; 95% CI, 1.06-1.40; P = .007).

CONCLUSIONS AND RELEVANCE

In this study, most patients with community-onset sepsis did not have resistant pathogens, yet broad-spectrum antibiotics were frequently administered. Both inadequate and unnecessarily broad empiric antibiotics were associated with higher mortality. These findings underscore the need for better tests to rapidly identify patients with resistant pathogens and for more judicious use of broad-spectrum antibiotics for empiric sepsis treatment.

Impact of rapid microbial identification on clinical outcomes in bloodstream infection: the RAPIDO randomized trial

OBJECTIVES

Bloodstream infection has a high mortality rate. It is not clear whether laboratory-based rapid identification of the organisms involved would improve outcome.

METHODS

The RAPIDO trial was an open parallel-group multicentre randomized controlled trial. We tested all positive blood cultures from hospitalized adults by conventional methods of microbial identification and those from patients randomized (1:1) to rapid diagnosis in addition to matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) performed directly on positive blood cultures. The only primary outcome was 28-day mortality. Clinical advice on patient management was provided to members of both groups by infection specialists.

RESULTS

First positive blood culture samples from 8628 patients were randomized, 4312 into rapid diagnosis and 4136 into conventional diagnosis. After prespecified postrandomization exclusions, 2740 in the rapid diagnosis arm and 2810 in the conventional arm were included in the mortality analysis. There was no significant difference in 28-day survival (81.5% 2233/2740 rapid vs. 82.3% 2313/2810 conventional; hazard ratio 1.05, 95% confidence interval 0.93-1.19, p 0.42). Microbial identification was quicker in the rapid diagnosis group (median (interquartile range) 38.5 (26.7-50.3) hours after blood sampling vs. 50.3 (47.1-72.9) hours after blood sampling, p < 0.01), but times to effective antimicrobial therapy were no shorter (respectively median (interquartile range) 24 (2-78) hours vs. 13 (2-69) hours). There were no significant differences in 7-day mortality or total antibiotic consumption; times to resolution of fever, discharge from hospital or de-escalation of broad-spectrum therapy or 28-day Clostridioides difficile incidence.

CONCLUSIONS

Rapid identification of bloodstream pathogens by MALDI-TOF MS in this trial did not reduce patient mortality despite delivering laboratory data to clinicians sooner.

Differences and overlaps between Phd studies in diagnostic microbiology in industrial and academic settings

Industrial and academic needs for innovation and fundamental research are essential and not widely different. Depending on the industrial setting, research and development (R&D) activities may be more focused on the developmental aspects given the need to ultimately sell useful products. However, one of the biggest differences between academic and industrial R&D will usually be the funding model applied and the priority setting between innovative research and product development. Generalizing, companies usually opt for development using customer- and consumer-derived funds whereas university research is driven by open innovation, mostly funded by taxpayer’s money. Obviously, both approaches require scientific rigor and quality, dedication and perseverance and obtaining a PhD degree can be achieved in both settings. The formal differences between the two settings need to be realized and students should make an educated choice prior to the start of PhD-level research activities. Intrinsic differences in scientific approaches between the two categories of employers are not often discussed in great detail. We will here document our experience in this field and provide insights into the need for purely fundamental research, industrial R&D and current mixed models at the level of European funding of research. The field of diagnostics in clinical bacteriology and infectious diseases will serve as a source of reference.

Automatically Controlled Microfluidic System for Continuous Separation of Rare Bacteria from Blood

Bloodstream infection by microorganisms is a major public health concern worldwide. Millions of people per year suffer from microbial infections, and current blood culture-based diagnostic methods are time-consuming because of the low concentration of infectious microorganisms in the bloodstream. In this study, we introduce an efficient automated microfluidic system for the continuous isolation of rare infectious bacteria (Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa) from blood. Bacteria received a balanced force between a fluidic drag force and a periodically controlled dielectrophoretic (DEP) force from tilted electrodes to minimize cell adhesion to the electrodes, which prevented the loss of rare infectious bacteria. Target bacteria were efficiently segregated from the undesired blood cells to ensure that only the bacteria received the DEP force under the hypotonic condition, while the blood cells received no DEP force and exited the channel via a laminar flow. Thus, the bacteria were successfully extracted from the blood with a high recovery yield of 91.3%, and the limit of the bacteria concentration for isolation was 100 cfu/ml. We also developed an automated system that performed every step from blood-sample loading to application of electricity to the microfluidic chip for bacteria separation. It reduced the standard deviation of the bacteria recovery yield from 6.16 to 2.77 compared with the conventional batch process, providing stable bacteria-extraction performance and minimizing errors and bacteria loss caused by user mistakes. © 2019 International Society for Advancement of Cytometry.

A Healthcare Improvement Intervention Combining Nucleic Acid Microarray Testing With Direct Physician Response for Management of Staphylococcus aureus Bacteremia

Background

Nucleic acid microarray (NAM) testing for detection of Staphylococcus aureus bacteremia (SAB) and S. aureus resistance gene determinants can reduce time to targeted antibiotic administration. Evidence-based management of SAB includes bedside infectious diseases (ID) consultation. As a healthcare improvement initiative at our institution, with the goal of improving management and outcomes for subjects with SAB, we implemented NAM with a process for responding to positive NAM results by directly triggered, mandatory ID consultation.

Methods

Preintervention, SAB was identified by traditional culture and results passively directed to antibiotic stewardship program (ASP) pharmacists. Postintervention, SAB in adult inpatients was identified by Verigene Gram-Positive Blood Culture test, results paged directly to ID fellow physicians, and consultation initiated immediately. In the new process, ASP assisted with management after the initial consultation. A single-center, retrospective, pre-/postintervention analysis was performed.

Results

One hundred six preintervention and 120 postintervention subjects were assessed. Time to ID consultation after notification of a positive blood culture decreased 26.0 hours (95% confidence interval [CI], 45.1 to 7.1 hours, P < .001) postintervention compared with preintervention. Time to initiation of targeted antibiotic decreased by a mean of 21.2 hours (95% CI, 31.4 to 11.0 hours, P < .001) and time to targeted antibiotics for methicillin-sensitive S. aureus decreased by a mean of 40.7 hours (95% CI, 58.0 to 23.5 hours, P < .001). The intervention was associated with lower in-hospital (13.2% to 5.8%, P = .047) and 30-day (17.9% to 8.3%, P = .025) mortality.

Conclusions

Compared with an ASP-directed response to traditionally detected SAB, an efficient physician response to NAM was associated with improved care and outcomes for SAB.

Clinical Utility of Advanced Microbiology Testing Tools

Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies.

Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies. While select stakeholders have an appreciation of the value/importance of improvements in the microbial diagnostic field, there remains a disconnect between clinicians and some payers and hospital administrators in terms of understanding the potential clinical utility of these novel technologies. Therefore, a key challenge for the clinical microbiology community is to clearly articulate the value proposition of these technologies to encourage payers to cover and hospitals to adopt advanced microbiology tests. Specific guidance on how to define and demonstrate clinical utility would be valuable. Addressing this challenge will require alignment on this topic, not just by microbiologists but also by primary care and emergency room (ER) physicians, infectious disease specialists, pharmacists, hospital administrators, and government entities with an interest in public health. In this article, we discuss how to best conduct clinical studies to demonstrate and communicate clinical utility to payers and to set reasonable expectations for what diagnostic manufacturers should be required to demonstrate to support reimbursement from commercial payers and utilization by hospital systems.

Diagnosing and Managing Sepsis by Probing the Host Response to Infection: Advances, Opportunities, and Challenges

Sepsis is a major source of mortality and morbidity globally. Accurately diagnosing sepsis remains challenging due to the heterogeneous nature of the disease, and delays in diagnosis and intervention contribute to high mortality rates. Measuring the host response to infection enables more rapid diagnosis of sepsis than is possible through direct detection of the causative pathogen, and recent advances in host response diagnostics and prognostics hold promise for improving outcomes. The current review discusses recent advances in the technologies used to probe the host response to infection, particularly those based on transcriptomics. These are discussed in the context of contemporary approaches to diagnosing and prognosing sepsis, and recommendations are made for successful development and validation of host response technologies.

Cost-effectiveness of molecular diagnostic assays for the therapy of severe sepsis and septic shock in the emergency department

Objectives

Sepsis presents a major burden to the emergency department (ED). Because empiric inappropriate antimicrobial therapy (IAAT) is associated with increased mortality, rapid molecular assays may decrease IAAT and improve outcomes. We evaluated the cost-effectiveness of molecular testing as an adjunct to blood cultures in patients with severe sepsis or septic shock evaluated in the ED.

Methods

We developed a decision analysis model with primary outcome the incremental cost-effectiveness ratio expressed in terms of deaths averted. Costs were dependent on the assay price and the patients’ length of stay (LOS). Three base-case scenarios regarding the difference in LOS between patients receiving appropriate (AAT) and IAAT were described. Sensitivity analyses regarding the assay cost and sensitivity, and its ability to guide changes from IAAT to AAT were performed.

Results

Under baseline assumptions, molecular testing was cost-saving when the LOS differed by 4 days between patients receiving IAAT and AAT (ICER -$7,302/death averted). Our results remained robust in sensitivity analyses for assay sensitivity≥52%, panel efficiency≥39%, and assay cost≤$270. In the extreme case that the LOS of patients receiving AAT and IAAT was the same, the ICER remained≤$20,000/death averted for every studied sensitivity (i.e. 0.5–0.95), panel efficiency≥34%, and assay cost≤$313. For 2 days difference in LOS, the bundle approach was dominant when the assay cost was≤$135 and the panel efficiency was≥77%.

Conclusions

The incorporation of molecular tests in the management of sepsis in the ED has the potential to improve outcomes and be cost-effective for a wide range of clinical scenarios.

A 'culture' shift: Application of molecular techniques for diagnosing polymicrobial infections

With the advancement of microbiological discovery, it is evident that many infections, particularly bloodstream infections, are polymicrobial in nature. Consequently, new challenges have emerged in identifying the numerous etiologic organisms in an accurate and timely manner using the current diagnostic standard. Various molecular diagnostic methods have been utilized as an effort to provide a fast and reliable identification in lieu or parallel to the conventional culture-based methods. These technologies are mostly based on nucleic acid, proteins, or physical properties of the pathogens with differing advantages and limitations. This review evaluates the different molecular methods and technologies currently available to diagnose polymicrobial infections, which will help determine the most appropriate option for future diagnosis.

Microfluidics-Based Organism Isolation from Whole Blood: An Emerging Tool for Bloodstream Infection Diagnosis

The diagnosis of bloodstream infections presents numerous challenges, in part, due to the low concentration of pathogens present in the peripheral bloodstream. As an alternative to existing time-consuming, culture-based diagnostic methods for organism identification, microfluidic devices have emerged as rapid, high-throughput and integrated platforms for bacterial and fungal enrichment, detection, and characterization. This focused review serves to highlight and compare the emerging microfluidic platforms designed for the isolation of sepsis-causing pathogens from blood and suggest important areas for future research.

SMFM Consult Series #47: Sepsis during pregnancy and the puerperium

Maternal sepsis is a significant cause of maternal morbidity and mortality and is a preventable cause of maternal death. The purpose of this guideline is to summarize what is known about sepsis and to provide guidance for the management of sepsis in pregnancy and the postpartum period. The following are SMFM recommendations: (1) we recommend that sepsis and septic shock be considered medical emergencies and that treatment and resuscitation begin immediately (GRADE 1B); (2) we recommend that providers consider the diagnosis of sepsis in pregnant patients with otherwise unexplained end-organ damage in the presence of an infectious process, regardless of the presence of fever (GRADE 1B); (3) we recommend that empiric broad-spectrum antibiotics be administered as soon as possible, ideally within 1 hour, in any pregnant woman in whom sepsis is suspected (GRADE 1B); (4) we recommend obtaining cultures (blood, urine, respiratory, and others as indicated) and serum lactate levels in pregnant or postpartum women in whom sepsis is suspected or identified, and early source control should be completed as soon as possible (GRADE 1C); (5) we recommend early administration of 1-2 L of crystalloid solutions in sepsis complicated by hypotension or suspected organ hypoperfusion (GRADE 1C); (6) we recommend the use of norepinephrine as the first-line vasopressor during pregnancy and the postpartum period in sepsis with persistent hypotension and/or hypoperfusion despite fluid resuscitation (GRADE 1C); (7) we recommend against immediate delivery for the sole indication of sepsis and that delivery should be dictated by obstetric indications (GRADE 1B).

Cost-effectiveness of rapid diagnostic assays that perform directly on blood samples for the diagnosis of septic shock

Molecular diagnostic assays that test directly whole blood provide the ability to decrease inappropriate antimicrobial therapy and improve survival in patients with septic shock. We developed a decision analysis model to evaluate the cost-effectiveness of the addition of molecular assays to blood cultures in adults admitted to medical ICUs with septic shock. Under baseline assumptions, the use of molecular diagnostic methods was cost-saving in all cases that the length of hospital stay differed by 2 and 4 days between patients receiving appropriate and inappropriate antimicrobial therapy. In the case that the length of stay was the same, the use of molecular methods was cost-effective with an estimated incremental cost-effectiveness ratio (ICER) < $3000 per death averted. In the extreme that the length of stay between the 2 groups was the same, the highest cost reached was when the cost of the assay was $1000, with the estimated ICER being < $20,000 per death averted.