New developments in the diagnosis of bloodstream infections

Electronic Skin for Health Monitoring Systems: Properties, Functions, and Applications

Electronic skin (e-skin), a skin-like wearable electronic device, holds great promise in the fields of telemedicine and personalized healthcare because of its good flexibility, biocompatibility, skin conformability, and sensing performance. E-skin can monitor various health indicators of the human body in real time and over the long term, including physical indicators (exercise, respiration, blood pressure, etc.) and chemical indicators (saliva, sweat, urine, etc.). In recent years, the development of various materials, analysis, and manufacturing technologies has promoted significant development of e-skin, laying the foundation for the application of next-generation wearable medical technologies and devices. Herein, the properties required for e-skin health monitoring devices to achieve long-term and precise monitoring and summarize several detectable indicators in the health monitoring field are discussed. Subsequently, the applications of integrated e-skin health monitoring systems are reviewed. Finally, current challenges and future development directions in this field are discussed. This review is expected to generate great interest and inspiration for the development and improvement of e-skin and health monitoring systems.

Association between blood culture turnaround time and clinical prognosis in emergency department patients with community acquired bloodstream infection: A retrospective study based on electronic medical records

Importance

Previous investigations have found that time to positive blood culture (TTP) is a prognostic factor for clinical outcomes. In fact, what the emergency physician sees from the medical information system is TAT (turnaround time) defined as time required to post a bacterial culture report. We propose a definition of blood culture TAT that more closely aligns with clinical considerations by measuring the time from starting specimen culture to the release of an official blood culture report.We were curious to know whether the duration of TAT is as intricately linked to the prognosis of bacteremia as TTP.

Objectives

To examine the association between TAT and outcomes of adult patients who present to the ED with community acquired bacteremia.

Design

Setting, and Participants: This retrospective study utilized electronic medical records from Kaohsiung Veterans General Hospital (KVGH), a 1000-bed tertiary medical center in Taiwan. Patients were adults aged 18 years and older who presented to ED (Emergency department) for initial diagnosis of community acquired bacteremia from January 1, 2016 to March 31, 2021. Data analysis was performed from December 2022 to January 2023.Main outcomes and measures.The primary outcomes included mortality in the ED, all-cause in-hospital mortality, length of hospital stay, and all-cause 30-day mortality in relation to the individual first report of positive blood culture TAT.

Results

A total of 4011 eligible patients with bacteremia were evaluated, of which 207 patients had a blood culture TAT of ≤48 h. The overall 30-day all-cause mortality rate was 13%. Contrary to expectation, no statistically significant differences were observed in clinical prognosis between the TAT groups (≤48 versus >48 h). Subgroup analyses indicated that the length of TAT did not have a significant effect on clinical prognosis in patients who underwent lactate level assessment. Furthermore, no difference in clinical outcome was noted between TAT groups (≤48 versus >48 h) in terms of Gram-negative bacilli or Gram-positive cocci bacteremia. However, in patients with delayed antibiotic treatment (>3 h), a shorter TAT was significantly associated with a fatal outcome.

Conclusion

In adults with community-acquired bacteremia, this study did not observe a significant association between blood culture TAT and clinical prognosis, except in cases of delayed antibiotic treatment.

Functional fluorescent nanomaterials for the detection, diagnosis and control of bacterial infection and biofilm formation: Insight towards mechanistic aspects and advanced applications

Infectious diseases resulting from the high pathogenic potential of several bacteria possesses a major threat to human health and safety. Traditional methods used for screening of these microorganisms face major issues with respect to detection time, selectivity and specificity which may delay treatment for critically ill patients past the optimal time. Thus, a convincing and essential need exists to upgrade the existing methodologies for the fast detection of bacteria. In this context, increasing number of newly emerging nanomaterials (NMs) have been discovered for their effective use and applications in the area of diagnosis in bacterial infections. Recently, functional fluorescent nanomaterials (FNMs) are extensively explored in the field of biomedical research, particularly in developing new diagnostic tools, nanosensors, specific imaging modalities and targeted drug delivery systems for bacterial infection. It is interesting to note that organic fluorophores and fluorescent proteins have played vital role for imaging and sensing technologies for long, however, off lately fluorescent nanomaterials are increasingly replacing these due to the latter's unprecedented fluorescence brightness, stability in the biological environment, high quantum yield along with high sensitivity due to enhanced surface property etc. Again, taking advantage of their photo-excitation property, these can also be used for either photothermal and photodynamic therapy to eradicate bacterial infection and biofilm formation. Here, in this review, we have paid particular attention on summarizing literature reports on FNMs which includes studies detailing fluorescence-based bacterial detection methodologies, antibacterial and antibiofilm applications of the same. It is expected that the present review will attract the attention of the researchers working in this field to develop new engineered FNMs for the comprehensive diagnosis and treatment of bacterial infection and biofilm formation.

Diagnostic efficiency of the FilmArray blood culture identification (BCID) panel: a systematic review and meta-analysis

Introduction. The FilmArray blood culture identification panel (BCID) panel is a multiplex PCR assay with high sensitivity and specificity to identify the most common pathogens in bloodstream infections (BSIs).Hypothesis. We hypothesize that the BCID panel has good diagnostic performance for BSIs and can be popularized in clinical application.Aim: To provide summarized evidence for the diagnostic accuracy of the BCID panel for the identification of positive blood cultures.Methodology. We searched the MEDLINE, EMBASE and Cochrane databases through March 2021 and assessed the efficacy of the diagnostic test of the BCID panel. We performed a meta-analysis and calculated the summary sensitivity and specificity of the BCID panel. Systematic review protocols were registered in the International Prospective Register of Systematic Reviews (PROSPERO) (registration number CRD42021239176).Results. A total of 16 full-text articles were eligible for analysis. The overall sensitivities of the BCID panel on Gram-positive bacteria, Gram-negative bacteria and fungi were 97 % (95 % CI, 0.96-0.98), 100 % (95 % CI, 0.98-01.00) and 99 % (95 % CI, 0.87-1.00), respectively. The pooled diagnostic specificities were 99 % (95 % CI, 0.97-1.00), 100 % (95 % CI, 1.00-1.00) and 100 % (95 % CI, 1.00-1.00) for Gram-positive bacteria, Gram-negative bacteria and fungi, respectively.Conclusions. The BCID panel has high rule-in value for the early detection of BSI patients. The BCID panel can still provide valuable information for ruling out bacteremia or fungemia in populations with low pretest probability.

Combining Acoustic Bioprinting with AI-Assisted Raman Spectroscopy for High-Throughput Identification of Bacteria in Blood

Identifying pathogens in complex samples such as blood, urine, and wastewater is critical to detect infection and inform optimal treatment. Surface-enhanced Raman spectroscopy (SERS) and machine learning (ML) can distinguish among multiple pathogen species, but processing complex fluid samples to sensitively and specifically detect pathogens remains an outstanding challenge. Here, we develop an acoustic bioprinter to digitize samples into millions of droplets, each containing just a few cells, which are identified with SERS and ML. We demonstrate rapid printing of 2 pL droplets from solutions containing S. epidermidis, E. coli, and blood; when they are mixed with gold nanorods (GNRs), SERS enhancements of up to 1500× are achieved.We then train a ML model and achieve ≥99% classification accuracy from cellularly pure samples and ≥87% accuracy from cellularly mixed samples. We also obtain ≥90% accuracy from droplets with pathogen:blood cell ratios <1. Our combined bioprinting and SERS platform could accelerate rapid, sensitive pathogen detection in clinical, environmental, and industrial settings.

Direct inoculation method for identification and antimicrobial susceptibility testing using matrix-assisted laser desorption ionization-time of flight mass spectrometry and both the Vitek 2 and MicroScan Walkaway 96 Plus systems

The aim of our study was to evaluate a protocol utilizing serum separator tubes (SST) to facilitate a faster, cost-effective, direct method for rapid sensitivity testing and identification of positive blood cultures. Spiked cultures were inoculated into either Becton Dickinson (BD) BACTEC^TM Aerobic Plus or Anaerobic/F bottles containing sterile human blood. Bottles were immediately processed when positive. A parallel study using patient isolates was used in which bacteria were pelleted by SST from positive blood cultures. For identification, a portion of the pellet was tested by matrix-assisted laser desorption/ionization as described by the manufacturer. MicroScan panels and Vitek 2 results were compared. Categorical agreement was used as comparison to standard subculture and/or polymerase chain reaction methods. No discordant identifications were observed, and 86% generated a successful identification when compared to subculture methods. For the Vitek 2, we observed a 99% essential agreement when compared to the subculture method. For the MicroScan Walkaway, we observed 94.9%, 97.4%, and 100% categorical agreement for MIC panels 53, 38, and MICroSTREP Plus 2, respectively. Turnaround times were reduced from 4 hours for identification and 11 hours for antimicrobial sensitivity testing. We conclude that the SST method results in timelier, actionable results for antimicrobial stewardship initiatives.

Epidemiology of bacteremia in a pediatric population - A 10-year study

INTRODUCTION

With the widespread introduction of conjugate meningococcal and pneumococcal vaccines, the prevalence and etiology of invasive bacterial infections have changed. We aimed to review all cases of bacteremia in a level II pediatric department over a ten-year period in the post-pneumococcal conjugate vaccine era.

METHODS

We reviewed all positive blood cultures (BC) obtained in our department between 2007 and 2016. Results were classified as contaminants, potential pathogens or confirmed pathogens, based on species, number of positive BC in the episode and the patients' medical history. Demographic and clinical data were collected for patients with identified pathogens.

RESULTS

A total of 638 positive BC were identified (6.6% of total BC); 120 (1.2%) were considered to represent true bacteremia. The most frequently identified microorganism was Streptococcus pneumoniae (29.2%), with a decrease in the number of cases between 2008 and 2015. Staphylococcus aureus was the second most common organism (19.2%) being 21.7% of these methicillin-resistant. Escherichia coli was the most common isolate in children aged less than three months.

CONCLUSION

We found a rate of true bacteremia in children similar to recent studies. Although Streptococcus pneumoniae remains the most common microorganism, its prevalence may be declining. Monitoring microbiological data in children has implications in practice, particularly in local antibiotic prescription.

Advances in image-guided drug delivery for antibacterial therapy

The emergence of antibiotic-resistant bacterial strains is seriously endangering the global healthcare system. There is an urgent need for combining imaging with therapies to realize the real-time monitoring of pathological condition and treatment progress. It also provides guidance on exploring new medicines and enhance treatment strategies to overcome the antibiotic resistance of existing conventional antibiotics. In this review, we provide a thorough overview of the most advanced image-guided approaches for bacterial diagnosis (e.g., computed tomography imaging, magnetic resonance imaging, photoacoustic imaging, ultrasound imaging, fluorescence imaging, positron emission tomography, single photon emission computed tomography imaging, and multiple imaging), and therapies (e.g., photothermal therapy, photodynamic therapy, chemodynamic therapy, sonodynamic therapy, immunotherapy, and multiple therapies). This review focuses on how to design and fabricate photo-responsive materials for improved image-guided bacterial theranostics applications. We present a potential application of different image-guided modalities for both bacterial diagnosis and therapies with representative examples. Finally, we highlighted the current challenges and future perspectives image-guided approaches for future clinical translation of nano-theranostics in bacterial infections therapies. We envision that this review will provide for future development in image-guided systems for bacterial theranostics applications.

A new application of multiplex PCR combined with membrane biochip assay for rapid detection of 9 common pathogens in sepsis

Rapid and accurate identification of specific sepsis pathogens is critical for patient treatment and disease control. This study aimed to establish a new application for the rapid identification of common pathogens in patients with suspected sepsis and evaluate its role in clinical application. A multiplex PCR assay was designed to simultaneously amplify specific conserved regions of nine common pathogenic microorganisms in sepsis, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumonia, and Candida albicans. The PCR products were analyzed by a membrane biochip. The analytical sensitivity of the assay was determined at a range of 5-100 copies/reaction for each standard strain, and the detection range was 20-200 cfu/reaction in a series dilution of simulated clinical samples at different concentrations. Out of the 179 clinical samples, the positive rate for pathogens detected by the membrane biochip assay and blood culture method was 20.11% (36/179) and 18.44% (33/179), respectively. However, by comparing the positive rate of the nine common pathogens we detected, the membrane biochip assay tended to be more sensitive than the blood culture method (20.11% vs 15.64%). The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the membrane biochip assay were 92.9%, 93.2%, 72.2% and 98.6%, respectively. Generally, this multiplex PCR combined membrane biochip assay can be used to detect major sepsis pathogens, and is useful for early initiation of effective antimicrobial treatment, and is feasible for sepsis pathogens identification in routine clinical practice.

Rapid Pathogen Identification in Aqueous Humor Samples by Combining Fc-MBL@Fe3O4 Enrichment and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Profiling

Prompt clinical diagnosis and antimicrobial therapy are key to managing infective endophthalmitis. The small volume of aqueous humor, low bacterial counts, and empirical medication by physicians make existing diagnostic methods time-consuming and imprecise. Here, we investigated the feasibility of combining Fc-containing mannose-binding lectin-coated Fe₃O₄ (Fc-MBL@Fe₃O₄) enrichment with matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) profiling to identify pathogens in aqueous humor. Aqueous humor aspirated from freshly enucleated porcine eyes was treated with different inocula of Staphylococcus aureus, Staphylococcus epidermidis, and Klebsiella pneumoniae. We performed identification directly in aqueous humor samples and after short-term culture of micro-LB broth. Aqueous humor endophthalmitis samples were enriched with Fc-MBL@Fe₃O₄ and analyzed using MALDI-TOF MS. The identification time and minimum bacterial concentration required for identification were determined. The enrichment efficiency of Fc-MBL@Fe₃O₄ for different bacteria was greater than (87.5 ± 5.0)%. The objects of direct identification include live bacteria and bacteria treated with antibiotics, which can be completed within 1.5 h. The minimum number of bacteria needed for positive identification was 2.20 × 10⁶ CFU. For micro-LB broth culture, the identification of bacteria can be completed within 6.5 to 9.5 h for aqueous humor samples with an initial bacterial count of tens to hundreds. IMPORTANCE Fc-MBL@Fe₃O₄ capture not only live bacteria in aqueous humor but also bacteria inactivated by antibiotics. Fc-MBL@Fe₃O₄ combined with micro-LB broth culture significantly reduced the turnaround time (TAT) by more than half a day by shortening the time required for bacterial identification. Our findings demonstrate that combining Fc-MBL@Fe₃O₄ enrichment with MALDI-TOF MS identification is a fast, sensitive, and efficient analytical method with great potential for identifying pathogens in aqueous humor samples.

MALDI-TOF mass spectrometry rapid pathogen identification and outcomes of patients with bloodstream infection: A systematic review and meta-analysis

There was inconsistent evidence regarding the use of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) for microorganism identification with/without antibiotic stewardship team (AST) and the clinical outcome of patients with bloodstream infections (BSI). In a systematic review and meta‐analysis, we evaluated the effectiveness of rapid microbial identification by MALDI‐TOF MS with and without AST on clinical outcomes. We searched PubMed and EMBASE databases from inception to 1 February 2022 to identify pre–post and parallel comparative studies that evaluated the use of MALDI‐TOF MS for microorganism identification. Pooled effect estimates were derived using the random‐effects model. Twenty‐one studies with 14,515 patients were meta‐analysed. Compared with conventional phenotypic methods, MALDI‐TOF MS was associated with a 23% reduction in mortality (RR = 0.77; 95% CI: 0.66; 0.90; I² = 35.9%; 13 studies); 5.07‐h reduction in time to effective antibiotic therapy (95% CI: −5.83; −4.31; I² = 95.7%); 22.86‐h reduction in time to identify microorganisms (95% CI: −23.99; −21.74; I² = 91.6%); 0.73‐day reduction in hospital stay (95% CI: −1.30; −0.16; I² = 53.1%); and US$4140 saving in direct hospitalization cost (95% CI: $‐8166.75; $‐113.60; I² = 66.1%). No significant heterogeneity sources were found, and no statistical evidence for publication bias was found. Rapid pathogen identification by MALDI‐TOF MS with or without AST was associated with reduced mortality and improved outcomes of BSI, and may be cost‐effective among patients with BSI.

Skin bioelectronics towards long-term, continuous health monitoring

Skin bioelectronics are considered as an ideal platform for personalised healthcare because of their unique characteristics, such as thinness, light weight, good biocompatibility, excellent mechanical robustness, and great skin conformability. Recent advances in skin-interfaced bioelectronics have promoted various applications in healthcare and precision medicine. Particularly, skin bioelectronics for long-term, continuous health monitoring offer powerful analysis of a broad spectrum of health statuses, providing a route to early disease diagnosis and treatment. In this review, we discuss (1) representative healthcare sensing devices, (2) material and structure selection, device properties, and wireless technologies of skin bioelectronics towards long-term, continuous health monitoring, (3) healthcare applications: acquisition and analysis of electrophysiological, biophysical, and biochemical signals, and comprehensive monitoring, and (4) rational guidelines for the design of future skin bioelectronics for long-term, continuous health monitoring. Long-term, continuous health monitoring of advanced skin bioelectronics will open unprecedented opportunities for timely disease prevention, screening, diagnosis, and treatment, demonstrating great promise to revolutionise traditional medical practices.

c-D-index at day 11 can predict febrile neutropenia during chemotherapy in acute myeloid leukemia

Acute myeloid leukemia (AML) often requires long-term intensive chemotherapy for its cure. During chemotherapy, the patient always experiences neutropenia with readings below 500 cells/μL; this is often accompanied by pyrexia with a temperature of more than 101°F. This combination of neutropenia and fever is called febrile neutropenia (FN). A tool to sum up the daily severity of a patient’s neutropenia, the “D-index,” has been validated in some specific clinical settings. In this study, we examined whether the D-index is a useful predictor of the onset of FN. We recruited consecutive patients treated with induction and consolidation chemotherapy for newly diagnosed AML. We gathered all the FN events and their clinical background data retrospectively. Patients’ background, such as pre-existing conditions and disease status before the treatment, were analyzed using multivariate methods. All FN events during chemotherapy were evaluated for infection focus and causative organism. A total cohort of 51 cases (25 women, 26 men; median age 51 years, range 18–74) was analyzed. They displayed 171 neutropenic events (115 FN and 56 afebrile episodes) during chemotherapy, and complete neutropenic events were used in this study. Sensitivity and specificity analysis showed that the most useful cutoff value to predict the onset of FN was a cumulative D-index at day 11 (c-D11-index) of 718. The cumulative incidence of FN during chemotherapy was significantly higher in the group with c-D11-index ≥710 (80%) than in the group with c-D11-index <710 (39%) (P < 0.0001). Through multivariate analysis, the presence of diabetes mellitus and the c-D11-index were extracted as contributing factors to the onset of FN (P = 0.0087 and 0.0002, respectively). In conclusion, we can predict that AML patients receiving chemotherapy will experience the complication of FN when the c-D-index at day 11 is >710, with an odds ratio of 2.1.

Recent Progress in Intelligent Wearable Sensors for Health Monitoring and Wound Healing Based on Biofluids

The intelligent wearable sensors promote the transformation of the health care from a traditional hospital-centered model to a personal portable device-centered model. There is an urgent need of real-time, multi-functional, and personalized monitoring of various biochemical target substances and signals based on the intelligent wearable sensors for health monitoring, especially wound healing. Under this background, this review article first reviews the outstanding progress in the development of intelligent, wearable sensors designed for continuous, real-time analysis, and monitoring of sweat, blood, interstitial fluid, tears, wound fluid, etc. Second, this paper reports the advanced status of intelligent wound monitoring sensors designed for wound diagnosis and treatment. The paper highlights some smart sensors to monitor target analytes in various wounds. Finally, this paper makes conservative recommendations regarding future development of intelligent wearable sensors.

Machine learning identification of specific changes in myeloid cell phenotype during bloodstream infections

The early identification of bacteremia is critical for ensuring appropriate treatment of nosocomial infections in intensive care unit (ICU) patients. The aim of this study was to use flow cytometric data of myeloid cells as a biomarker of bloodstream infection (BSI). An eight-color antibody panel was used to identify seven monocyte and two dendritic cell subsets. In the learning cohort, immunophenotyping was applied to (1) control subjects, (2) postoperative heart surgery patients, as a model of noninfectious inflammatory responses, and (3) blood culture-positive patients. Of the complex changes in the myeloid cell phenotype, a decrease in myeloid and plasmacytoid dendritic cell numbers, increase in CD14⁺CD16⁺ inflammatory monocyte numbers, and upregulation of neutrophils CD64 and CD123 expression were prominent in BSI patients. An extreme gradient boosting (XGBoost) algorithm called the “infection detection and ranging score” (iDAR), ranging from 0 to 100, was developed to identify infection-specific changes in 101 phenotypic variables related to neutrophils, monocytes and dendritic cells. The tenfold cross-validation achieved an area under the receiver operating characteristic (AUROC) of 0.988 (95% CI 0.985–1) for the detection of bacteremic patients. In an out-of-sample, in-house validation, iDAR achieved an AUROC of 0.85 (95% CI 0.71–0.98) in differentiating localized from bloodstream infection and 0.95 (95% CI 0.89–1) in discriminating infected from noninfected ICU patients. In conclusion, a machine learning approach was used to translate the changes in myeloid cell phenotype in response to infection into a score that could identify bacteremia with high specificity in ICU patients.

The Value of Interleukin-10 in the Early Diagnosis of Neonatal Sepsis: A Meta-Analysis

OBJECTIVES

Interleukin-10 is a significant marker in neonatal sepsis. This meta-analysis evaluated the accuracy of interleukin-10 expression in the diagnosis of neonatal sepsis.

DATA SOURCE

Summary of literature review.

STUDY SELECTION

A literature search strategy was developed, including PubMed, EMBASE, Web of Science, MEDLINE, and the Cochrane Library. All publications published till October 1, 2020, were retrieved; the key words were "sepsis" and "interleukin-10."

DATA EXTRACTION

The sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were used to evaluate the data, and the heterogeneity of the combined results was tested according to the I2 value.

DATA SYNTHESIS

A total of six articles involving 879 newborns were included in the study. The combined sensitivity was 0.82 (95% CI, 0.78-0.86), the specificity was 0.79 (95% CI, 0.75-0.82), the positive likelihood ratio was 4.17 (95% CI, 2.6-6.69), and the negative likelihood ratio was 0.25 (95% CI, 0.16-0.39). The area under the summary receiver operating characteristic curve was 0.88 (95% CI, 0.86-0.91), and the Q index was 0.81. The combined diagnostic odds ratio was 17.52 (95% CI, 8.95-34.29).

CONCLUSIONS

Based on the results of the meta-analysis, interleukin-10 is a useful biomarker in the early diagnosis of neonatal sepsis. Its sensitivity, specificity, and diagnostic ability are excellent. However, it needs to be combined with clinical history data for comprehensive judgment and should not be used alone for diagnosis.

Epidemiology of bacteremia in a pediatric population - A 10-year study

INTRODUCTION

With the widespread introduction of conjugate meningococcal and pneumococcal vaccines, the prevalence and etiology of invasive bacterial infections have changed. We aimed to review all cases of bacteremia in a level II pediatric department over a ten-year period in the post-pneumococcal conjugate vaccine era.

METHODS

We reviewed all positive blood cultures (BC) obtained in our department between 2007 and 2016. Results were classified as contaminants, potential pathogens or confirmed pathogens, based on species, number of positive BC in the episode and the patients' medical history. Demographic and clinical data were collected for patients with identified pathogens.

RESULTS

A total of 638 positive BC were identified (6.6% of total BC); 120 (1.2%) were considered to represent true bacteremia. The most frequently identified microorganism was Streptococcus pneumoniae (29.2%), with a decrease in the number of cases between 2008 and 2015. Staphylococcus aureus was the second most common organism (19.2%) being 21.7% of these methicillin-resistant. Escherichia coli was the most common isolate in children aged less than three months.

CONCLUSION

We found a rate of true bacteremia in children similar to recent studies. Although Streptococcus pneumoniae remains the most common microorganism, its prevalence may be declining. Monitoring microbiological data in children has implications in practice, particularly in local antibiotic prescription.

Label-free biosensor of phagocytosis for diagnosing bacterial infections

Phagocytic cells recognize and phagocytose invading microbes for destruction. However, bacterial pathogens can remain hidden at low levels from conventional detection or replicate intracellularly after being phagocytosed by immune cells. Current phagocytosis-detection approaches involve flow cytometry or microscopic search for rare bacteria-internalized phagocytes among large populations of uninfected cells, which poses significant challenges in research and clinical settings. Hence it is imperative to develop a rapid, non-disruptive, and label-free phagocytosis detection approach. Using deformability assays and microscopic imaging, we have demonstrated for the first time that the presence of intracellular bacteria in phagocytic blood cells led to aberrant physical properties. Specifically, human monocytes with internalized bacteria of various species were stiffer and larger compared with uninfected monocytes. Taking advantage of these physical differences, a novel microfluidics-based biosensor platform was developed to passively sort, concentrate and quantify rare monocytes with internalized pathogens (MIP) from uninfected monocyte populations for phagocytosis detection. The clinical utility of the MIP platform was demonstrated by enriching and detecting bacteria-internalized monocytes from spiked human blood samples within 1.5 h. Patient-derived clinical isolates were used to validate the utility of the MIP platform further. This proof-of-concept presents a phagocytosis detection platform that could be used to rapidly diagnose microbial infections, especially in bloodstream infections (BSIs), thereby improving the clinical outcomes for point-of-care management.

A new molecular method for rapid etiological diagnosis of sepsis with improved performance

The value of blood cultures for confirming the clinical diagnosis of sepsis is suboptimal. There is growing interest in the potential of real-time PCR technology by detection of minute amounts of pathogen DNA in patient blood samples with results available within 4-6 h. Adopting a two-step approach, we evaluated the compliance of two versions of the MicrobScan assay on a total of 748 patients with suspected bloodstream infections. The results obtained with a second version of the MicrobScan assay are characterized by increased specificity (from 95.1 to 98.2%) and sensitivity (from 76.7 to 85.1), increased throughput and the possibility of simultaneously testing different kinds of samples collected from the potential sites of infection and utilizing different syndromic panels.

Rapid identification of bacteria directly from blood cultures by Co-magnetic bead enrichment and MALDI-TOF MS profiling

Direct identification of bacteria in blood cultures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is interfered with by a variety of non-bacterial proteins derived from blood cells and culture media. Thus, appropriate pre-treatments are needed for successful identification. Here, the bacteria in blood culture bottles were enriched using co-magnetic beads and processed for MALDI-TOF MS profiling. In this strategy, the Fc-containing mannose-binding lectin-coated Fe₃O₄ (Fc-MBL@Fe₃O₄) is incorporated with human IgG-coated Fe₃O₄ (IgG@Fe₃O₄) to form co-magnetic beads, which can recognize both Gram-positive and Gram-negative bacteria. Compared to single magnetic beads Fc-MBL@Fe₃O₄ or IgG@Fe₃O₄, co-magnetic beads resulted in better bacterial capture efficiency and, therefore, could decrease the false-negative results. Our proposed strategy is much more suitable for enrichment of clinically unknown bacteria from blood culture bottles for MALDI-TOF MS database identification.

The Advancement in Detecting Sepsis and Its Outcome: Usefulness of Procalcitonin in Diagnosing Sepsis and Predicting Fatal Outcomes in Patients Admitted to Intensive Care Unit

Sepsis still remains a big challenge in patients admitted to intensive care units (ICUs) despite stellar advances made in the field of medicine. We can achieve better clinical outcomes in patients by diagnosing sepsis earlier. Procalcitonin (PCT), an inflammatory biomarker, has shown promising results in this regard. Therefore, this systematic review was done to assess the use of PCT in diagnosing and predicting severe outcomes in patients admitted to ICU and to assess if introducing PCT as a routine biochemical tool in hospitals would be helpful to achieve better clinical course in ICU patients. To identify relevant articles, we searched PubMed, Google Scholar, and references of included articles. Eligible studies were identified by two investigators independently and data were extracted. Original articles that evaluated the diagnostic and prognostic value of serum PCT levels in predicting sepsis, the severity of sepsis, and mortality among adult patients admitted to ICU were included in this study. A total of 2,063 citations were identified by the search, among which 10 studies (five prospective cohort, three retrospective cohort, one cross-sectional, and one case-control study) met the inclusion criteria. Most studies showed moderate-to-low risk of bias which was evaluated using the Quality in Prognosis Studies tool. All studies showed a positive correlation between initial PCT levels and detecting mortality resulting from sepsis, six studies found PCT helpful in detecting sepsis, and four studies evaluated the role of PCT in detecting severity in patients with sepsis. One study found area under the curve of serum PCT level for predicting 28-day mortality to be 0.82 (95% confidence interval [CI]: 0.70-0.94; p < 0.001) in adults and 0.83 (95% CI: 0.73-0.92; p < 0.001) in the elderly having an optimal cut-off level of serum PCT of 0.2 ng/mL in both the adult and elderly groups, with a sensitivity of 81 and 75% and specificity of 81.7 and 80.4%, respectively. PCT has shown promising results in detecting sepsis and its clinical course. For early diagnosis and management of sepsis, severe sepsis, and mortality in patients admitted to the ICU for a more favorable clinical outcome, PCT can be used.

Early prediction of blood stream infection in a prospectively collected cohort

Background

Blood stream infection (BSI) and sepsis are serious clinical conditions and identification of the disease-causing pathogen is important for patient management. The RISE (Rapid Identification of SEpsis) study was carried out to collect a cohort allowing high-quality studies on different aspects of BSI and sepsis. The aim of this study was to identify patients at high risk for BSI who might benefit most from new, faster, etiological testing using neutrophil to lymphocyte count ratio (NLCR) and Shapiro score.

Methods

Adult patients (≥ 18 years) presenting at the emergency department (ED) with suspected BSI were prospectively included between 2014 and 2016 at Örebro University Hospital. Besides extra blood sampling, all study patients were treated according to ED routines. Electronic patient charts were retrospectively reviewed. A modified Shapiro score (MSS) and NLCR were extracted and compiled. Continuous score variables were analysed with area under receiver operator characteristics curves (AUC) to evaluate the ability of BSI prediction.

Results

The final cohort consisted of 484 patients where 84 (17%) had positive blood culture judged clinically significant. At optimal cut-offs, MSS (≥3 points) and NLCR (> 12) showed equal ability to predict BSI in the whole cohort (AUC 0.71/0.74; sensitivity 69%/67%; specificity 64%/68% respectively) and in a subgroup of 155 patients fulfilling Sepsis-3 criteria (AUC 0.71/0.66; sensitivity 81%/65%; specificity 46%/57% respectively). In BSI cases only predicted by NLCR> 12 the abundance of Gram-negative to Gram-positive pathogens (n = 13 to n = 4) differed significantly from those only predicted by MSS ≥3 p (n = 7 to n = 12 respectively) (p < 0.05).

Conclusions

MSS and NLCR predicted BSI in the RISE cohort with similar cut-offs as shown in previous studies. Combining the MSS and NLCR did not increase the predictive performance. Differences in BSI prediction between MSS and NLCR regarding etiology need further evaluation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05990-3.

Validation of an Isothermal Amplification Platform for Microbial Identification and Antimicrobial Resistance Detection in Blood: A Prospective Study

Background: Recent advances in nucleic acid amplification technique (NAAT)-based identification of pathogens in blood stream infections (BSI) have revolutionized molecular diagnostics in comparison to traditional clinical microbiology practice of blood culture. Rapid pathogen detection with point-of-care diagnostic-applicable platform is prerequisite for efficient patient management. The aim of the study is to evaluate an in-house developed, lyophilized OmiX-AMP pathogen test for the detection of top six BSI-causing bacteria along with two major antimicrobial resistance (AMR) markers of carbapenem and compare it to the traditional blood culture-based detection.

Materials and methods: One hundred forty-three patients admitted to the Medical Intensive Care Unit, Narayana Hrudayalaya, Bangalore, with either suspected or proven sepsis, of either gender, of age ≥18 years were enrolled for the study. Pathogen DNA extracted from blood culture sample using OmiX pReP method was amplified at isothermal conditions and analyzed in real time using OmiX Analysis software.

Results: Among the processed 143 samples, 54 were true negative, 83 were true positive, 3 were false negative, and 2 were false positive as analyzed by OmiX READ software. Gram-negative bacteria (91.3%) and gram-positive bacteria (75%) were detected with 100% specificity and 95.6% sensitivity along with the AMR marker pattern with a turnaround time of 4 hours from sample collection to results.

Conclusion: OmiX-AMP pathogen test detected pathogens with 96.5% concordance in comparison to traditional blood culture. Henceforth, OmiX-AMP pathogen test could be used as a readily deployable diagnostic kit even in low-resource settings.

How to cite this article: Maheshwarappa HM, Guru P, Mundre RS, Lawrence N, Majumder S, Sigamani A, et al. Validation of an Isothermal Amplification Platform for Microbial Identification and Antimicrobial Resistance Detection in Blood: A Prospective Study. Indian J Crit Care Med 2021;25(3):299–304.

Clinical Utility of PNA-FISH for Burn Wound Diagnostics: A Noninvasive, Culture-Independent Technique for Rapid Identification of Pathogenic Organisms in Burn Wounds

Burn injury results in an immediate compromised skin state, which puts the affected patient at an immediate risk for infection, including sepsis. For burn patients that develop infections, it is critical to rapidly identify the etiology so that an appropriate treatment can be administered. Current clinical standards rely heavily on culture-based methods for local and systemic infection testing, which can often take days to complete. While more advanced methods (ie, MALDI or NAAT) have improved turnaround times, they may still suffer from either the need for pure culture or sensitivity and specificity issues. Peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) offers a way to reduce this time from days to hours and provide species-specific identification. While PNA-FISH has had great utility in research, its use in clinical microbiology diagnostics has been minimal (including burn wound diagnostics). This work describes a nonculture-based identification technique using commercial available U.S. FDA-approved PNA-FISH probes for the identification of common clinical pathogens, Pseudomonas aeruginosa and Staphylococcus aureus, present in burn wound infections. Additionally, calcofluor white was included for identification of Candida albicans. All three pathogens were identified from a tri-species infected deep-partial thickness rat burn wound model. These species were clearly identifiable in swab and tissue samples that were collected, with minimal autofluorescence from any species. Although autofluorescence of the tissue was present, it did not interfere or was otherwise minimized through sample preparation and analysis. The methodology developed was done so with patient care and diagnostic laboratories in mind that it might be easily transferred to the clinical setting.

Free circulating mircoRNAs support the diagnosis of invasive aspergillosis in patients with hematologic malignancies and neutropenia

Fungal infections represent a worrisome complication in hematologic cancer patients and in the absence of disease specific symptoms, it is important to establish new biological indicators, which can be used during mould-active prophylaxis. Recently, miRNAs have appeared as candidate diagnostic and prognostic markers of several diseases. A pilot clinical study was performed to evaluate the diagnostic utility of 14 microRNAs which can be related to invasive fungal infections. Based on our data miR-142-3p, miR-142-5p, miR-26b-5p and miR-21-5p showed significant overexpression (p < 0.005) due to invasive aspergillosis in hemato-oncology patients with profound neutropenia. A tetramiR assay was designed to monitor peripheral blood specimens. Optimal cut-off was estimated by using the median value (fold change 1.1) of the log10 transformed gene expressions. The biomarker panel was evaluated on two independent sample cohorts implementing different antimicrobial prophylactic strategies. The receiver operating characteristic analysis with area under the curve proved to be 0.97. Three miRNAs (miR-142-5p, miR-142-3p, miR-16-5p) showed significant expression alterations in episodes with sepsis. In summary, the tetramiR assay proved to be a promising diagnostic adjunct with sufficient accuracy and sensitivity to trace invasive aspergillosis in hemato-oncology patients.

Dried blood spots for Streptococcus pneumoniae and Haemophilus influenzae detection and serotyping among children < 5 years old in rural Mozambique

Background

Dried blood spots (DBS) have been proposed as potentially tool for detecting invasive bacterial diseases.

Methods

We evaluated the use of DBS for S. pneumoniae and H. influenzae detection among children in Mozambique. Blood for DBS and nasopharyngeal (NP) swabs were collected from children with pneumonia and healthy aged < 5 years. Bacterial detection and serotyping were performed by quantitative PCR (qPCR) (NP and DBS; lytA gene for pneumococcus and hpd for H. influenzae) and culture (NP). Combined detection rates were compared between children with pneumonia and healthy.

Results

Of 325 children enrolled, 205 had pneumonia and 120 were healthy. Pneumococci were detected in DBS from 20.5 and 64.2% of children with pneumonia and healthy, respectively; NP specimens were positive for pneumococcus in 80.0 and 80.8%, respectively. H. influenzae was detected in DBS from 22.9% of children with pneumonia and 59.2% of healthy; 81.4 and 81.5% of NP specimens were positive for H. influenzae, respectively.

Conclusion

DBS detected pneumococcal and H. influenzae DNA in children with pneumonia and healthy. Healthy children were often DBS positive for both bacteria, suggesting that qPCR of DBS specimens does not differentiate disease from colonization and is therefore not a useful diagnostic tool for children.

Radiolabeled Cationic Peptides for Targeted Imaging of Infection

Molecular probes targeting bacteria provide opportunities to target bacterial infections in vivo for both imaging and therapy. In the current study, we report the development of positron emission tomography (PET) probes for imaging of live bacterial infection based on the small molecules HLys-DOTA, a polycationic peptide synthesized as the D-isomer (RYWVAWRNRG) conjugated to 1, 4, 7, 10-tetraazacyclododecane-N',N″,N‴,N-tetraacetic acid (DOTA) and AB1-HLys-DOTA, which includes an unnatural amino acid AB1 that preferentially binds to bacteria membrane lipids with amine groups via formation of iminoboronates. HLys-DOTA and AB1-HLys-DOTA peptides were radiolabeled with ⁶⁴Cu and investigated as PET imaging agents to track bacterial infection in vitro and in intramuscularly infected (IM) mice models. Cell uptake studies at 37°C in Staphylococcus aureus (SA) show higher uptake of ⁶⁴Cu-AB1-HLys-DOTA; 98.47 ± 3.54% vs ⁶⁴Cu-HLys-DOTA; 39.12 ± 3.27% at 24 h. Standard uptake values (SUV) analysis of the PET images resulted in mean SUV of 0.70 ± 0.08, 0.49 ± 0.04, and 0.31 ± 0.01 for ⁶⁴Cu-AB1-HLys-DOTA and 0.17 ± 0.06, 0.16 ± 0.02, and 0.13 ± 0.01 for ⁶⁴Cu-HLys-DOTA at 1, 4, and 24 h post injection, respectively, in the infected muscles. Similarly, in the biodistribution studies, dose uptake in the infected muscles was 4 times higher in the targeted ⁶⁴Cu-AB1-HLys-DOTA group than in the ⁶⁴Cu-HLys-DOTA group and 2-3 times higher than in the PBS control group at 1, 4, and 24 h post injection. ⁶⁴Cu-AB1-HLys-DOTA was able to distinguish between SA-infected muscle and Pseudomonas aeruginosa (PA) infected muscle with lower mean SUV of 0.28 ± 0.10 at 1 h post injection. This illustrates the utility of the AB1 covalently targeting group in synergy with the HLys peptide, which noncovalently binds to bacterial membranes. These results suggest that ⁶⁴Cu-labeled AB1-HLys-DOTA peptide could be used as an imaging probe for detection of bacterial infection in vivo with specificity for Gram-positive bacteria.

Evaluation of two rapid molecular test systems to establish an algorithm for fast identification of bacterial pathogens from positive blood cultures

Fast identification of pathogens directly from positive blood cultures is of highest importance to supply an adequate therapy of bloodstream infections (BSI). There are several platforms providing molecular-based identification, detection of antimicrobial resistance genes, or even a full antimicrobial susceptibility testing (AST). Two of such test systems allowing rapid diagnostics were assessed in this study: The Biofire FilmArray® and the Genmark ePlex®, both fully automated test system with a minimum of hands-on time. Overall 137 BSI episodes were included in our study and compared to conventional culture–based reference methods. The FilmArray® is using one catridge including a panel for the most common bacterial and fungal BSI pathogens as well as selected resistance markers. The ePlex® offers three different cartridges for detection of Gram-positives, Gram-negatives, and fungi resulting in a broader panel including also rare pathogens, putative contaminants, and more genetic resistance markers. The FilmArray® and ePlex® were evaluated for all 137 BSI episodes with FilmArray® detecting 119 and ePlex® detecting 128 of these. For targets on the respective panel of the system, the FilmArray® generated a sensitivity of 98.9% with 100% specificity on Gram-positive isolates. The ePlex® system generated a sensitivity of 94.7% and a specificity of 90.7% on Gram-positive isolates. In each case, the two systems performed with 100% sensitivity and specificity for the detection of Gram-negative specimens covered by each panel. In summary, both evaluated test systems showed a satisfying overall performance for fast pathogen identification and are beneficial tools for accelerating blood culture diagnostics of sepsis patients.

Effect of neutrophil CD64 for diagnosing sepsis in emergency department

BACKGROUND

The aim of this study is to investigate the diagnostic and prognostic value of neutrophil CD64 (nCD64) as a novel biomarker in sepsis patients.

METHODS

One hundred fifty-one adult patients diagnosed with sepsis and 20 age-matched healthy controls were enrolled in the study. Patients with sepsis were further subdivided into a sepsis group and a septic shock group. nCD64 expression, serum procalcitonin (PCT) level, C-reactive protein (CRP) level, and white blood cell (WBC) count were obtained for each patient, and Sequential Organ Failure Assessment (SOFA) scores were calculated.

RESULTS

nCD64 expression was higher in the sepsis group with confirmed infection than in the control group. The receiver operating characteristic (ROC) curve of nCD64 was higher than those of SOFA score, PCT, CRP and WBC for diagnosing infection. The area under the curve (AUC) of nCD64 combined with SOFA score was the highest for all parameters. The AUC of nCD64 for predicting 28-day mortality in sepsis was significantly higher than those of PCT, CRP, and WBC, but slightly lower than that of SOFA score. The AUC of nCD64 or PCT combined with SOFA score was significantly higher than that of any single parameter for predicting 28-day mortality.

CONCLUSION

nCD64 expression and SOFA score are valuable parameters for early diagnosis of infection and prognostic evaluation of sepsis patients.

Evaluation of Real-Time PCR Coupled With Multiplex Probe Melting Curve Analysis for Pathogen Detection in Patients With Suspected Bloodstream Infections

Background: This study aimed to evaluate real-time polymerase chain reaction coupled with multiplex probe melting curve analysis (PCR-MCA) for pathogen detection in patients with suspected bloodstream infections (BSIs). Methods: A PCR-MCA assay was developed for simultaneous identification of 28 kinds of the most common pathogens and two resistance genes within a few hours. The diagnostic performance of the PCR-MCA assay was determined and compared to the results of blood culture. Results: A total of 2,844 consecutive new episodes of suspected BSIs in 2,763 patients were included in this study. There were 269 episodes of pathogens identified by blood culture. For all the pathogens tested, the PCR-MCA assay exhibited a sensitivity of 88.8% (239/269), specificity of 100% (2,575/2,575), and agreement of 98.9% (2,814/2,844). For the pathogens on the PCR-MCA list, the PCR-MCA results had a sensitivity of 99.2% (239/241), specificity of 100% (2,575/2,575), and agreement of 99.9% (2,814/2,816) compared with the results of blood culture. For seven samples with multiple pathogens identified simultaneously during one blood culture investigation, the PCR-MCA assay verified the results of the blood culture, with an agreement rate of 100% for each. Conclusion: The PCR-MCA assay could discover 88.8% of the pathogens in clinical practice, showing excellent diagnostic performance vs. that of blood culture for pathogen detection in patients with suspected BSIs, and would contribute to rapid diagnosis and correct antibiotic administration.

Identificación directa de microorganismos a partir de muestras de orina y hemocultivos utilizando MALDI-TOF

Objetivo: evaluar la utilidad de la identificación directa de microorganismos en muestras de orina y hemocultivos empleando la tecnología MALDI-TOF MS, me­diante el análisis de concordancia en la identificación, tiempo necesario para la obtención de un resultado y costos asociados a cada método de identificación.Materiales y métodos: estudio descriptivo de febrero de 2017 a octubre de 2017. Se seleccionaron a conveniencia 180 muestras de orinas y 129 hemocultivos de pacientes de la Clínica El Rosario, Medellín, se realizó identificación del microorganismo directamente de la muestra y a partir del cultivo por MALDI-TOF (Vitek® MS‚ bioMérieux). Se analizaron los costos y tiempo, para determinar la utilidad de esta tecnología en los procesos del laboratorio de microbiología.Resultados: En el 79,6% de las orinas positivas y en el 76% de los hemocultivos se obtuvo una identificación de microorganismos directamente por MALDI-TOF MS. El tiempo de identificación directa tuvo una media de 6 horas y por cultivo una media de 29 horas. El costo total por aislamiento identificado de forma directa (sin incluir el valor del equipo) fue de $8.200 (2,58 USD) en muestras de orina y de $9.720 (3,06 USD) en hemocultivos positivos. El equipo introduce un costo variable en cada identificación de acuerdo con el número de identificaciones que se realicen en el laboratorio.Conclusiones: Estos resultados confirman la utilidad del MALDI-TOF MS para generar identificaciones más rápidas cuando se utiliza directamente en muestras clínicas, sin embargo, tiene un bajo desempeño en la identificación directa de bacterias gram positivas, siendo necesario evaluar otros protocolos que mejoren la identificación directa. El costo de los consumibles es bajo, pero la adquisición de esta tecnología introduce un costo variable que depende del volumen de muestras identificadas en el laboratorio. 

Comparison of rapid BACpro® II, Sepsityper® kit and in-house preparation methods for direct identification of bacteria from blood cultures by MALDI-TOF MS with and without Sepsityper® module analysis

There are several approaches available for purifying microorganisms prior to matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, rapid BACpro® II (Nittobo Medical Co., Ltd., Tokyo, Japan), a new application, has been compared with Sepsityper® kit (Bruker Daltonics, Billerica, USA) and an in-house method. Samples were also tested with two modules, standard and Sepsityper®, identified in the Bruker MALDI-TOF MS. The bottles having monomicrobial growth were included in the study according to Gram staining results. In total, two hundred blood culture bottles were included but there was no growth in one of the subcultures so 199 blood culture bottles were studied prospectively. With the standard MALDI-TOF MS analysis, rapid BACpro® II could successfully identify microorganisms in 174/199 (87.4%) of the bottles where Sepsityper® kit and in-house method were successful in 136/199 (68.3%) and 114/199 (57.3%), respectively. When the MALDI-TOF MS data were analysed by Sepsityper® module, the identification rates were increased to 94.4%, 82.1% and 69.8% (p < 0.001), respectively. In the Sepsityper® module, 72/73 (98.6%) of Gram-negative and 97/106 (91.5%) of Gram-positive microorganisms were detected by rapid BACpro® II method. The present study shows that rapid BACpro® II is a reliable preparation procedure and has higher rates of identification compared with Sepsityper® kit and in-house method. The use of the Sepsityper® module in blood cultures increases the chance of identification for all three methods studied.

Assessment of a metabarcoding approach for the characterisation of vector-borne bacteria in canines from Bangkok, Thailand

BACKGROUND

Globally, bacterial vector-borne disease (VBD) exerts a large toll on dogs in terms of morbidity and mortality but nowhere is this more pronounced than in the tropics. Tropical environments permit a burgeoning diversity and abundance of ectoparasites some of which can transmit an extensive range of infectious agents, including bacteria, amongst others. Although some of these vector-borne bacteria are responsible for both animal and human diseases in the tropics, there is a scarcity of epidemiological investigation into these pathogens' prevalence. The situation is further exacerbated by frequent canine co-infection, complicating symptomatology that regular diagnostic techniques may miss or be unable to fully characterise. Such limitations draw attention to the need to develop screening tools capable of detecting a wide range of pathogens from a host simultaneously.

RESULTS

Here, we detail the employment of a next-generation sequencing (NGS) metabarcoding methodology to screen for the spectrum of bacterial VBD that are infecting semi-domesticated dogs across temple communities in Bangkok, Thailand. Our NGS detection protocol was able to find high levels of Ehrlichia canis, Mycoplasma haemocanis and Anaplasma platys infection rates as well as less common pathogens, such as "Candidatus Mycoplasma haematoparvum", Mycoplasma turicensis and Bartonella spp. We also compared our high-throughput approach to conventional endpoint PCR methods, demonstrating an improved detection ability for some bacterial infections, such as A. platys but a reduced ability to detect Rickettsia.

CONCLUSIONS

Our methodology demonstrated great strength at detecting coinfections of vector-borne bacteria and rare pathogens that are seldom screened for in canines in the tropics, highlighting its advantages over traditional diagnostics to better characterise bacterial pathogens in environments where there is a dearth of research.

New Microbiological Techniques in the Diagnosis of Bloodstream Infections

BACKGROUND

When a bloodstream infection is suspected, the preliminary and definitive results of culture-based microbiological testing arrive too late to have any influence on the initial choice of empirical antibiotic treatment.

METHODS

This review is based on pertinent publications retrieved by a selective search of the literature and on the authors' clinical and scientific experience.

RESULTS

A number of technical advances now enable more rapid microbiological diagnosis of bloodstream infections. DNA- based techniques for the direct detection of pathogenic organisms in whole blood have not yet become established in routine use because of various limitations. On the other hand, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become available for routine use in clinical laboratories and has markedly shortened the time to diagnosis after blood samples that have been cultured in automated blood-culture systems turn positive. Further developments of this technique now enable it to be used directly for blood cultures that have been flagged positive, as well as for subcultures that have been incubated for only a short time on a solid nutrient medium. The microbial biomass of the subculture can also be used in parallel for more rapid susceptibility testing with conventional methods, or, in future, with MALDI-TOF MS.

CONCLUSION

The potential of all of these new techniques will only be realizable in practice if they are optimally embedded in the diagnostic process and if sufficient attention is paid to pre-analytical issues, particularly storage and transport times.

Evaluation of blood culture epidemiology and efficiency in a large European teaching hospital

Background

Blood cultures remain the gold standard for detecting bacteremia despite their limitations. The current practice of blood culture collection is still inefficient with low yields. Limited focus has been given to the association between timing of specimen collection at different time points during admission and their yield.

Methods

We carried out a retrospective observational study by analyzing all 3,890 sets of cultures collected from the 1,962 admitted patients over the seven-month period of this study. We compared the blood culture yield between the early group (≤24 hours after admission) and the late group (> 24 hours of admission). We also investigated the effect of prehospital oral antibiotics and pre-analytical time on the first cultures in the emergency department. Epidemiology and efficiency of blood cultures were studied for each medical specialty.

Results

In total, 3,349(86.1%) blood cultures were negative and 541(13.9%) were positive for one or more microorganisms. After correcting for contamination, the overall yield was 290 (7.5%). The early group (n = 1,490) yielded significantly more true-positive cultures (10.1% versus 5.8%, P<0.001) than the late group (n = 2,400). The emergency department had a significantly higher yield than general wards, 11.2% versus 5.7% (p<0.001). Prehospital oral antibiotic use and pre-analytical time did not affect the yield of first cultures at the emergency department (p = 0.735 and 0.816 respectively). The number of tests needed to obtain one true-positive culture varied between departments, ranging from 7 to 45.

Conclusion

This study showed that blood cultures are inefficient in detecting bacteremia. Cultures collected during 24 hours after admission yielded more positive results than those collected later. Significant variations in blood culture epidemiology and efficiency per specialty suggest that guidelines should be reevaluated. Future studies should aim at improving blood culture yield, implementing educational programs to reduce contamination and cost-effective application of modern molecular diagnostic technologies.

Wearable and flexible electronics for continuous molecular monitoring

Wearable biosensors have received tremendous attention over the past decade owing to their great potential in predictive analytics and treatment toward personalized medicine. Flexible electronics could serve as an ideal platform for personalized wearable devices because of their unique properties such as light weight, low cost, high flexibility and great conformability. Unlike most reported flexible sensors that mainly track physical activities and vital signs, the new generation of wearable and flexible chemical sensors enables real-time, continuous and fast detection of accessible biomarkers from the human body, and allows for the collection of large-scale information about the individual's dynamic health status at the molecular level. In this article, we review and highlight recent advances in wearable and flexible sensors toward continuous and non-invasive molecular analysis in sweat, tears, saliva, interstitial fluid, blood, wound exudate as well as exhaled breath. The flexible platforms, sensing mechanisms, and device and system configurations employed for continuous monitoring are summarized. We also discuss the key challenges and opportunities of the wearable and flexible chemical sensors that lie ahead.

Loop-mediated isothermal amplification assays for Enterococcussp., Escherichiacoli and Staphylococcusaureus in chicken

Bacterial chondronecrosis with osteomyelitis (BCO) is a major cause of lameness in broiler chicken, and results in serious economic losses worldwide. Although the pathogenesis mechanism leading to lameness is not entirely understood, some strains of Enterococcussp., avian pathogenic Escherichia coli or Staphylococcus aureus have been long recognized as important causative pathogens. To prevent the progression of Enterococcussp., avian pathogenic E. coli or S. aureus infections, we developed rapid, sensitive and convenient diagnostic assays using loop-mediated isothermal amplification (LAMP). Entero-Common-LAMP assays were developed for simultaneous detection of eight Enterococcus species. To target specific microorganisms, seven Entero-Specific-LAMP assays for E. faecalis, E. faecium, E. hirae, E. gallinarum, E. avium, E. duransand E. cecorum were developed, as well as E. coli-LAMP and S. aureus-LAMP assays. Considering the prevalence and economic impact of Enterococcussp., E. coli and S. aureus, the 10 different LAMP assays which were developed have considerable potential as routine diagnostic methods in the field or in resource-limited environments.

Procalcitonin as a marker of Gram-negative bloodstream infections in hematological patients with febrile neutropenia

The aim of this study was to explore the predictive value of procalcitonin (PCT) in Gram-negative bloodstream infections (BSIs) in hematological patients with febrile neutropenia. A total of 1466 samples (396 blood culture (BC)-positive, 1052 BC-negative, and 18 contaminated specimens) were included, comprising 268 Gram-negative, 88 Gram-positive, 19 fungal, and 21 polymicrobial BSIs. Median PCT value (0.72 ng/mL; IQR: 0.23-3.87) was significantly higher in Gram-negative than Gram-positive (0.34 ng/mL; IQR: 0.14-2.23; p < .01), or fungal (0.27 ng/mL; IQR: 0.13-0.40; p < .01) BSIs. In mono-microbial BSIs, the best PCT cutoff distinguishing Gram-negative BSIs from all other fever causes was 0.56 ng/ml, with a specificity of 76.8%. PCT levels were significantly higher in BSIs from multidrug-resistant (MDR) Gram-negative strains than from non-MDR (p < .01). This study confirms that elevated PCT may predict Gram-negative BSIs in hematological patients with febrile neutropenia, and demonstrates higher PCT levels in MDR Gram-negative BSIs in these patients.

Substantial diagnostic impact of blood culture independent molecular methods in bloodstream infections: Superior performance of PCR/ESI-MS

This study analyzed the performance of different molecular technologies along with blood culture (BC) in the diagnosis of bloodstream infections (BSI) in patients from internal medicine wards - including intensive care units (ICUs) - and the emergency room. Patients with systemic inflammatory response syndrome were prospectively included. BCs and EDTA whole blood were obtained simultaneously. The latter was analyzed by PCR combined with electrospray ionization mass spectrometry (PCR/ESI-MS; IRIDICA BAC BSI assay, Abbott) and by SeptiFast (Roche). Cases were classified as BSI according to adapted European Centre for Disease Prevention and Control criteria. Out of 462 analyzed episodes, 193 with valid test results fulfilled the inclusion criteria and were further evaluated. Sixty-nine (35.8%) were classified as BSI. PCR/ESI-MS showed a significantly better overall performance than BC (p = 0.004) or SeptiFast (p = 0.034). Only in patients from the ICU the performance of SeptiFast was comparable to that of PCR/ESI-MS. Mainly due to the negative effect of antimicrobial pre-treatment on BC results, the cumulative performance of each of the molecular tests with BC was significantly higher than that of BC alone (p < 0.001). SeptiFast and in particular the broad-range pathogen detection system PCR/ESI-MS proved to be an essential addition to BC-based diagnostics in BSI.

Infection markers as predictors of Bacteremia in an Intensive Care Unit: A prospective study

Objective:

Although several biomarkers have been evaluated for the diagnosis and prognosis of sepsis, the gold standard biomarker has not yet been found. We aimed to evaluate the diagnostic value of neutrophil-to-lymphocyte count ratio (NLCR), neopterin, pro-adrenomedullin (pro-ADM) and the other infection markers to predict bacteremia in patients with SIRS, sepsis and severe sepsis/septic shock.

Methods:

A prospective cohort study was conducted on septic patients in a tertiary referral hospital between December 2014- July 2015. A total of 156 patients diagnosed with SIRS, sepsis and severe sepsis/septic shock in Anesthesia intensive care unit (ICU) were included in the study.

Results:

A total of 156 patients who had been diagnosed as SIRS(10.9%), sepsis (44.2%) and severe sepsis/septic shock (44.9%) were included. Positive blood cultures were obtained in 64 patients. NLCR, neopterin and pro-ADM levels were insignificant in predicting bacteremia (p>0.05). The mortality rate was significantly higher in bacteremic sepsis (43.9%) compared to non-bacteremic patients (20.8%) (p=0.001). Only procalcitonin levels were significant predictor of mortality (p<0.001).

Conclusion:

NLCR, CRP, procalcitonin, neopterin and pro-ADM levels were insignificant in diagnosis of bacteremia in critically ill patients. The gold standard method in predicting bacteremia is still blood culture positivity.

Molecular and culture based assessment of bacterial pathogens in subjects with diabetic foot ulcer

INTRODUCTION

Expeditious and precise discerning of bacterial pathogens is a fundamental grail, of clinical diagnostic microbiology. Genotypic detection is a budding substitute to recognize phenotypic culture based processes in bacterial identification.

AIMS

We report a comparative evaluation of biochemical and genomic-based assays for exploring the commonest bacterial flora of infected diabetic foot ulcers along with clinical variables of subjects enrolled.

METHODS

The pathogens selected (i) Staphylococcus aureus ii) Pseudomonas aeruginosa, iii) Escherichia coli and iv) Klebsiella pneumonia, stood for the most frequent isolates of diabetic foot infection in previous studies from Northern India. Identification of these pathogens were done by conventional assays and polymerase chain reaction.

RESULTS

Of 50 specimens obtained from infected DFUs, 74% of cases were affirmative by bacteriological assays and 90% showed positivity via polymerase chain reaction (PCR). Among processed samples 44 isolates were detectable through phenotypic analysis and 65 bacteria by species-specific PCR. Thirteen samples and 21 isolates could not be scrutinized by phenotypic identification systems. The most prevalent pathogens identifiable were Klebsiella pneumonia, followed by Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli.

CONCLUSIONS

We have shown that PCR-based diagnostic methods improved the identification compared to conventional methods and highlight the incorporation of PCR due to shorten turnaround time translating into improved clinical outcomes.

Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis

Molecular tests may enable early adjustment of antimicrobial therapy and be complementary to blood culture (BC) which has imperfect sensitivity in critically ill patients. We evaluated a novel multiplex real-time PCR assay to diagnose bloodstream pathogens directly in whole blood samples (BSI-PCR). BSI-PCR included 11 species- and four genus-specific PCRs, a molecular Gram-stain PCR, and two antibiotic resistance markers. We collected 5 mL blood from critically ill patients simultaneously with clinically indicated BC. Microbial DNA was isolated using the Polaris method followed by automated DNA extraction. Sensitivity and specificity were calculated using BC as reference. BSI-PCR was evaluated in 347 BC-positive samples (representing up to 50 instances of each pathogen covered by the test) and 200 BC-negative samples. Bacterial species-specific PCR sensitivities ranged from 65 to 100%. Sensitivity was 26% for the Gram-positive PCR, 32% for the Gram-negative PCR, and ranged 0 to 7% for yeast PCRs. Yeast detection was improved to 40% in a smaller set-up. There was no overall association between BSI-PCR sensitivity and time-to-positivity of BC (which was highly variable), yet Ct-values were lower for true-positive versus false-positive PCR results. False-positive results were observed in 84 (4%) of the 2200 species-specific PCRs in 200 culture-negative samples, and ranged from 0 to 6% for generic PCRs. Sensitivity of BSI-PCR was promising for individual bacterial pathogens, but still insufficient for yeasts and generic PCRs. Further development of BSI-PCR will focus on improving sensitivity by increasing input volumes and on subsequent implementation as a bedside test.

Evaluation of a real-time PCR assay for detection and quantification of bacterial DNA directly in blood of preterm neonates with suspected late-onset sepsis

Background

Rapid and accurate diagnosis of neonatal sepsis is highly warranted because of high associated morbidity and mortality. The aim of this study was to evaluate the performance of a novel multiplex PCR assay for diagnosis of late-onset sepsis and to investigate the value of bacterial DNA load (BDL) determination as a measure of infection severity.

Methods

This cross-sectional study was conducted in a neonatal intensive care unit. Preterm and/or very low birth weight infants suspected for late-onset sepsis were included. Upon suspicion of sepsis, a whole blood sample was drawn for multiplex PCR to detect the eight most common bacteria causing neonatal sepsis, as well as for blood culture. BDL was determined in episodes with a positive multiplex PCR.

Results

In total, 91 episodes of suspected sepsis were investigated, and PCR was positive in 53 (58%) and blood culture in 60 (66%) episodes, yielding no significant difference in detection rate (p = 0.17). Multiplex PCR showed a sensitivity of 77%, specificity of 81%, positive predictive value of 87%, and negative predictive value of 68% compared with blood culture. Episodes with discordant results of PCR and blood culture included mainly detection of coagulase-negative staphylococci (CoNS). C-reactive protein (CRP) level and immature to total neutrophil (I/T) ratio were lower in these episodes, indicating less severe disease or even contamination. Median BDL was high (4.1 log₁₀ cfu Eq/ml) with a wide range, and was it higher in episodes with a positive blood culture than in those with a negative blood culture (4.5 versus 2.5 log₁₀ cfu Eq/ml; p < 0.0001). For CoNS infection episodes BDL and CRP were positively associated (p = 0.004), and for Staphylococcus aureus infection episodes there was a positive association between BDL and I/T ratio (p = 0.049).

Conclusions

Multiplex PCR provides a powerful assay to enhance rapid identification of the causative pathogen in late-onset sepsis. BDL measurement may be a useful indicator of severity of infection.

Electronic supplementary material

The online version of this article (10.1186/s13054-018-2010-4) contains supplementary material, which is available to authorized users.

Culture-free bacterial detection and identification from blood with rapid, phenotypic, antibiotic susceptibility testing

The current culture-based approach for the diagnosis of bloodstreams infection is incommensurate with timely treatment and curbing the prevalence of multi-drug resistant organisms (MDROs) due to its long time-to-result. Bloodstream infections typically involve extremely low (e.g., <10 colony-forming unit (CFU)/mL) bacterial concentrations that require a labor-intensive process and as much as 72 hours to yield a diagnosis. Here, we demonstrate a culture-free approach to achieve rapid diagnosis of bloodstream infections. An immuno-detection platform with intrinsic signal current amplification was developed for the ultrasensitive, rapid detection, identification (ID) and antibiotic susceptibility testing (AST) of infections. With its capability of monitoring short-term (1-2 hours) bacterial growth in blood, the platform is able to provide 84-minute simultaneous detection and ID in blood samples below the 10 CFU/mL level and 204-minute AST. The susceptible-intermediate-resistant AST capacity was demonstrated.

Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing

Background

Intra-abdominal abscesses are localized collections of pus, which generally arise from a breach in the normal mucosal defense barrier that allows bacteria from gastrointestinal tract, and less commonly from the gynecologic or urinary tract, to induce inflammation, resulting in an infection. The microbiology of these abscesses is usually polymicrobial, associated with the primary disease process. However, the microbial identity, diversity and richness in intra-abdominal abscesses have not been well characterized, due in part to the difficulty in cultivating commensal organisms using standard culture-based techniques.

Methods

We used culture-independent 16S rRNA Illumina sequencing to characterize bacterial communities in intra-abdominal abscesses collected by percutaneous drainage. A total of 43 abscess samples, including 19 (44.2%) Gram stain and culture-negative specimens, were analyzed and compared with results from conventional microbiologic cultures.

Results

Microbial composition was determined in 8 of 19 culture-negative samples and 18 of 24 culture-positive samples, identifying a total of 221 bacterial taxa or operational taxonomic units (OTUs) and averaging 13.1 OTUs per sample (interquartile range, 8-16.5 OTUs). Microbial richness for monomicrobial and polymicrobial samples was significantly higher than culture-negative samples (17 and 15.2 OTUs vs 8 OTUs, respectively), with a trend toward a higher microbial diversity (Shannon diversity index of 0.87 and 1.18 vs 0.58, respectively).

Conclusions

The bacterial consortia identified by cultures correlated poorly with the microbial composition determined by 16S rRNA sequencing, and in most cases, the cultured isolates were minority constituents of the overall abscess microbiome. Intra-abdominal abscesses were generally polymicrobial with a surprisingly high microbial diversity, but standard culture-based techniques failed to reveal this diversity. These data suggest that molecular-based approaches may be helpful for documenting the presence of bacteria in intra-abdominal abscesses where standard cultures are unrevealing, particularly in the setting of prior antibiotic exposure.

Broad-Spectrum Molecular Detection of Fungal Nucleic Acids by PCR-Based Amplification Techniques

Over the past decade, the incidence of life-threatening invasive fungal infections has dramatically increased. Infections caused by hitherto rare and emerging fungal pathogens are associated with significant morbidity and mortality among immunocompromised patients. These observations render the coverage of a broad range of clinically relevant fungal pathogens highly important. The so-called panfungal or, perhaps more correctly, broad-range nucleic acid amplification techniques do not only facilitate sensitive detection of all clinically relevant fungal species but are also rapid and can be applied to analyses of any patient specimens. They have therefore become valuable diagnostic tools for sensitive screening of patients at risk of invasive fungal infections. This chapter summarizes the currently available molecular technologies employed in testing of a wide range of fungal pathogens, and provides a detailed workflow for patient screening by broad-spectrum nucleic acid amplification techniques.