Blood culture-based diagnosis of bacteraemia: state of the art

SERS-based approaches in the investigation of bacterial metabolism, antibiotic resistance, and species identification

Surface-enhanced Raman scattering (SERS) is an inelastic scattering phenomenon that occurs when photons interact with substances, providing detailed molecular structure information. It exhibits various advantages including high sensitivity, specificity, and multiple-detection capabilities, which make it particularly effective in bacterial detection and antibiotic resistance research. In this review, we review the recent development of SERS-based approaches in the investigation of bacterial metabolism, antibiotic resistance, and species identification. Although the promising applications have been realized in clinical microbiology and diagnostics, several challenges still limit the further development, including signal variability, the complexity of spectral data interpretation, and the lack of standardized protocols. To overcome these obstacles, more reproducible and standardized methodologies, particularly in nanomaterial design and experimental condition optimization. Furthermore, the integration of SERS with machine learning and artificial intelligence can automate spectral analysis, improving the efficiency and accuracy of bacterial species identification, resistance marker detection, and metabolic monitoring. Combining SERS with other analytical techniques, such as mass spectrometry, fluorescence microscopy, or genomic sequencing, could provide a more comprehensive understanding of bacterial physiology and resistance mechanisms. As SERS technology advances, its applications are expected to extend beyond traditional microbiology to areas like environmental monitoring, food safety, and personalized medicine. In particular, the potential for SERS to be integrated into point-of-care diagnostic devices offers significant promise for enhancing diagnostics in resource-limited settings, providing cost-effective, rapid, and accessible solutions for bacterial infection and resistance detection.

Modification of the rapid antimicrobial susceptibility testing from blood culture protocol for a resource-limited setting

Background

Sepsis is a medical emergency and rapid antimicrobial susceptibility testing (RAST) is essential for patient management. However, existing RAST protocols may be unsuitable for resource-limited settings due to the need for rapid species identification, which may require specialized equipment or expensive reagents.

Aims

To minimize the requirement of the RAST protocol while maintaining its efficacy, focusing on Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii and Staphylococcus aureus.

Methods

Positive blood cultures suspected of having these pathogens underwent RAST with three main modifications: delayed species identification, implementation of pan-species breakpoints and the change in the quality control process. Twelve antimicrobials were tested for Gram-negative bacilli, and three for S. aureus. Species identification was performed by both the MALDI-TOF MS and the rapid phenotypic tests at the final RAST time point. The categorical agreement was evaluated against the standard AST method and the RAST protocol.

Results

Among 398 samples, gentamicin, ampicillin, meropenem and trimethoprim-sulfamethoxazole met the accuracy criteria for Gram-negative bacilli. Ceftriaxone, imipenem and ciprofloxacin had slightly reduced agreement (80%-90%) due to a high false resistance. The remaining antimicrobials either had a low agreement or high false susceptibility. Only gentamicin passed the agreement criteria for S. aureus. The use of pan-species breakpoints resulted in several failed results without improvement in the concordance. The quality control process with and without sheep blood yielded comparable results.

Conclusion

RAST reduced the time-to-result for key antimicrobial agents for at least 24 h while requiring minimal workflow disruption, enabling early adjustment of antimicrobial treatment.

Multi-center evaluation of the Selux next-generation phenotyping system for gram-negative direct-from-positive blood culture antimicrobial susceptibility testing

Accurate and rapid antimicrobial susceptibility test (AST) results from positive blood cultures are crucial for patient care and combatting antimicrobial resistance. Although recent advancements in rapid direct-from-positive blood culture (PBC) identification platforms have enabled the provision of species-level identification and some resistance marker information within hours after blood culture positivity, AST results required for clinical decision-making often require 48 h after blood culture positivity. This study evaluated the Selux next-generation phenotyping system, including an automated PBC Separator and the Selux AST system in a multicenter clinical trial for their ability to perform AST directly from PBCs for gram-negative bacilli. The PBC separator produces McFarland equivalent inocula from positive blood cultures within 1 h, facilitating direct processing on the Selux AST system. The study evaluated 162 fresh clinical PBC samples, 307 seeded clinical samples, and 87 seeded challenge samples across 4 sites for each of the 17 antimicrobials included in the panel. The results demonstrate that the Selux system's clinical performance, reproducibility, and analytical performances are consistent when using positive blood cultures held for up to 16 h after positivity on the BACTEC and BacT/ALERT 3D and BacT/ALERT VIRTUO blood culture systems, including all major BACTEC and BacT/ALERT blood culture bottle types. These findings suggest that the PBC Separator with the Selux AST system is a valuable addition to the arsenal of tools available for rapid sepsis diagnosis and management.IMPORTANCETechnologies that consistently and substantially shorten the time between blood bottle positivity, organism identification, and complete AST results are crucial for ensuring that antimicrobial therapy can be tailored. The Selux PBC Separator and the Selux AST system perform rapid AST directly from positive blood culture bottles. This substantially shortens the gap between obtaining a positive blood bottle and organism identification and the availability of a fully actionable AST result.

Differentiation of Bacterial Species in Liquid Culture Using Laser Speckle Contrast Imaging

Bacterial identification is vital for healthcare and environmental quality control. Traditional bacterial identification methods require extensive sample preparation, including cultivation, staining, and microscopy, making them time-consuming and labor-intensive. This study proposes the application of Laser Speckle Contrast Imaging (LSCI) as a novel approach to capture variations in speckle patterns between the start and end of the lag caused by changes in the shape and arrangement of bacterial cells during cell division in liquid cultures at lower cell concentrations, such as in the lag phase. Our approach offers an efficient alternative to traditional methods of bacterial species identification demonstrated with Escherichia coli and Micrococcus luteus pairs. Also, the differentiation of strains ( E. coli ATCC25922 and DH5α) is carried out based on the percentage change in speckle contrast between the end of lag and mid-log phase of their growth curve.

Impact of rapid identification by MALDI-TOF MS from positive blood cultures in Enterococcus spp. bloodstream infections

PURPOSE

Regarding bloodstream infections (BSI) Enterococcus spp. rank among the top five most common organisms. Due to enterococci intrinsic resistance, empiric antibiotic therapy is often inappropriate and early identification becomes crucial. Our objective was to assess the clinical impact of MALDI-TOF identification directly from positive blood cultures (BC) in Enterococcus spp. BSI (E-BSI).

METHODS

A retrospective cohort study included all adult patients with E-BSI from 2010 to 2017 in a tertiary hospital. ID consultation within 48 h and MALDI-TOF identification directly from BC within 24 h were inclusion criteria. The primary outcome was antimicrobial treatment change following MALDI-TOF and secondary outcomes included 30-day and 1-year mortality, length of stay (LOS) and antimicrobial de-escalation.

RESULTS

Among 267 BSI episodes, E. faecalis was isolated in 130 episodes (48.7%), E. faecium in 122 (45.7%), and 104 (39%) were polymicrobial. Empiric antibiotic therapy was inappropriate in 60.3% of patients. The LOS was 36 (IQR 20-64) days, 30-day and 1-year mortality were 16.1% and 43.4%, respectively. Enterococci identification with MALDI-TOF at the species level was possible in 66.3% cases and in 73% of monomicrobial cases. Antibiotics were changed in 85.3% of the former vs. 63.3% in remaining patients (p < 10- 4), and de-escalation occurred in 35% of subjects (vs. 12.2%,p = 10- 4). Changing antibiotics after correct identification was associated with a shorter LOS. In multivariate analysis, appropriate antibiotic therapy before MALDI-TOF was protective against 30-day mortality (aOR 0.40(0.08-1.96)), and appropriate antibiotic therapy afterwards against 1-year mortality (aOR 0.21(0.05-0.84)).

CONCLUSION

In E-BSI, direct MALDI-TOF identification from positive BC has a significant clinical impact due to a more frequent antibiotic spectrum correction and de-escalation. This may improve patient outcomes, reducing LOS and potentially mortality.

CLINICAL TRIAL NUMBER

Not applicable.

In vitro and in vivo efficacy studies of an engineered endolysin targeting Gram-negative pathogens

Endolysins have drawn considerable attention as viable modalities for antibiotic use. The most significant obstacle for Gram-negative targeting endolysins is the presence of the outer membrane barrier. A heterologously expressed endolysin encoded by bacteriophage PBPA90 infecting Pseudomonas aeruginosa exhibited intrinsic antibacterial activity against P. aeruginosa. The antibacterial efficacy was improved by substituting 15 amino acids and by fusing cecropin A to the N-terminus. The resulting engineered endolysin, LNT103, demonstrated strong antibacterial activity, with minimum inhibitory concentrations as low as 4 μg/ml, against various Gram-negative pathogens in addition to P. aeruginosa, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, and Enterobacter cloacae. The engineered endolysin rendered both the outer and the inner bacterial membranes permeable. It exhibited a synergistic effect with colistin, and additive effects with carbapenem antibiotics. Bacterial resistance development to LNT103 was none to minimal in vitro. Its in vivo efficacy was verified in bacteremia models of mice infected with A. baumannii. The endolysin led to a resensitization of resistant bacteria to meropenem when used in combination in vivo.

Performance of ddPCR-GNB for microbial diagnosis of suspected bloodstream infection due to the four most common gram-negative bacteria: a prospective, multicenter study

We aimed to validate the performance of ddPCR-GNB, a plasma droplet digital PCR panel targeting the four most common gram-negative bacteria, for patients with suspected bloodstream infection (BSI). Patients suspected of having BSIs were prospectively enrolled. The results of blood culture and ddPCR-GNB were compared, and cases with discordant results were arbitrated on the basis of additional microbiological results and clinical evidence. A total of 1,041 patients were enrolled. Blood culture and ddPCR-GNB results were positive for targeted bacteria in 6.3% and 31.7% of patients, respectively. The overall per-patient sensitivity and specificity of ddPCR-GNB for proven BSIs were 98.5% (95% CI, 91.9% to 99.9%) and 72.8% (95% CI, 69.9% to 75.5%), respectively; the negative predictive value was 99.9% (95% CI, 99.2% to 100%). The discordant results included 265 cases (25.5%) with negative companion blood culture results but positive ddPCR-GNB results and one case vice versa. A total of 23.7% of the cases were attributed to probable (n = 126) or possible (n = 121) BSIs. If both probable and possible BSIs were assumed to be true positives, the per-patient specificity of ddPCR-GNB would be 97.5%. The ddPCR-GNB panel demonstrated excellent microbial diagnostic performance in identifying targeted bacteria for patients with suspected BSI.

IMPORTANCE

This is the first multicentral study to validate the clinical performance of ddPCR in etiological diagnosis of bloodstream infection. The results showed that ddPCR has high sensitivity and increased detection rate compared with blood culture. The study proved the potential of the ddPCR method in microbial diagnoses.

Dielectrophoretic Microfluidic Designs for Precision Cell Enrichments and Highly Viable Label-Free Bacteria Recovery from Blood

Conducting detailed cellular analysis of complex biological samples poses challenges in cell sorting and recovery for downstream analysis. Label-free microfluidics provide a promising solution for these complex applications. In this work, we investigate particle manipulation on two label-free microdevice designs using cDEP to enrich E. coli from whole human blood to mimic infection workflows. E. coli is still a growing source of bacteremia, sepsis, and other infections in modern countries, affecting millions of patients globally. The two microfluidic designs were evaluated for throughput, scaling, precision targeting, and high-viability recovery. While CytoChip D had the potential for higher throughput, given its continuous method of DEP-based sorting to accommodate larger clinical samples like a 10 mL blood draw, it could not effectively recover the bacteria. CytoChip B achieved a high-purity recovery of over 98% of bacteria from whole human blood, even in concentrations on the order of <100 CFU/mL, demonstrating the feasibility of processing and recovering ultra-low concentrations of bacteria for downstream analysis, culture, and drug testing. Future work will aim to scale CytoChip B for larger volume throughput while still achieving high bacteria recovery.

Investigation of methicillin, beta lactam, carbapenem, and multidrug resistant bacteria from blood cultures of septicemia suspected patients in Northwest Ethiopia

The presence of microorganisms in the bloodstream can result in severe, potentially life-threatening conditions, which are a significant cause of morbidity and mortality worldwide. The rise of antimicrobial-resistant strains further exacerbates these outcomes. However, the data concerning bacterial profiles and resistance to antimicrobials, particularly against extended-spectrum beta-lactams and carbapenems, are limited. Aimed to characterize pathogens isolated from positive blood cultures, including bacterial profiles and antibiotic susceptibility patterns, and to identify predictors of blood culture positivity in septicemia-suspected patients at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. A hospital-based cross-sectional study was conducted from February 15 to May 30, 2023. The study involved 341 patients suspected of having septicaemia who were selected consecutively through a convenience sampling technique. Blood samples were collected aseptically from each patient (10 ml from adults, 5 ml from children, and 1 ml from neonates) and inoculated into bottles containing tryptic soy broth in volumes appropriate for the patient's age. The samples were incubated at 35-37 °C for up to 7 days to detect bacterial growth. Positive blood cultures were subcultured onto various media, including chocolate agar, blood agar, modified Thayer-Martin agar, MacConkey agar, and mannitol salt agar, and incubated again at 35-37 °C for 24 h. The suspected bacteria were identified on the basis of colony morphology, Gram staining, and biochemical tests. Antimicrobial susceptibility testing was conducted via both the Kirby-Bauer and modified Kirby-Bauer disk diffusion methods. Resistance to methicillin, extended-spectrum beta-lactams, and carbapenems was determined via the cefoxitin disc test, combined-disk diffusion method, and modified carbapenem inactivation method, respectively. The data were entered into Epi-Data version 4.6 and analysed via SPSS version 25. Binary logistic regression analyses were employed to identify factors associated with bloodstream infections (BSI), with a P value of less than 0.05 considered statistically significant. Out of 341 patients suspected of septicemia, 196 (57.5%) were male and 145 (42.5%) were female, with a mean (± SD) age of 16.5 (± 7.5) years. Bloodstream infection was identified in 87 (25.5%) patients (95% CI: 21.1-30.4). Among these positive cases, 67 (77%) were from ward patients, while 20 (23%) were from those visiting outpatient departments. The primary gram-positive bacteria identified included S. aureus 27 (31.0%), CoNS 14 (16.1%), S. viridans 8 (9.2%), and S. agalactiae 4 (4.6%). The gram-negative isolates were predominantly K. pneumoniae 11 (12.6%), followed by E. coli 9 (10.3%), E. cloacae 6 (6.9%), Acinetobacter spp. 3 (3.5%), N. meningitidis 3 (3.5%), and P. aeruginosa 2 (2.3%). Methicillin resistance was detected in 17/27 (63.0%) S. aureus strains and 2/14 (14.3%) CoNS strains. Multidrug resistance was detected in 63/87 (72.4%, 95% CI: 67.2-84.7%) of the isolates. Extended-spectrum beta-lactamase and carbapenemase production were observed in 12/31 (38.7%) and 5/31 (16.1%) of isolates, respectively. The factors associated with BSI were the presence of wounds and burns (AOR = 2.103, 95% CI: 1.365-3.241, P = 0.041), length of hospital stay (≥ 5) (AOR = 2.209, 95% CI: 1.122-4.347, P = 0.022), and prior medical procedures (AOR = 1.982, 95% CI: 1.125-3.492, P = 0.018). Bloodstream infection was identified in 25.5% of suspected septicemia cases, with multidrug-resistant bacteria present in 72.4% of isolates. Gram-positive bacteria, particularly S. aureus, and gram-negative bacteria like K. pneumoniae and E. coli were predominant. High rates of methicillin, beta-lactam, and carbapenem resistance were observed, emphasizing the magnitude of antimicrobial resistance. Risk factors such as wounds, extended hospital stays, and prior medical procedures significantly increased the likelihood of culture positivity. This suggests the need for regular antimicrobial susceptibility testing to guide antibiotic selection and track resistance trends, proper wound care and medical device usage to reduce the risk of BSI in healthcare settings.

The Microbiological Background of Medication-Related Osteonecrosis of the Jaw (MRONJ): Clinical Evidence Based on Traditional Culture and Molecular Biological Detection Methods

Background: Medication-related osteonecrosis of the jaw (MRONJ) is a common adverse event following antiresorptive treatment, leading to chronic inflammation and exposed, necrotic bone surfaces in the jawbone. There is an increasing recognition of the role of compositional changes in the colonizing members of the oral microbiota implicated in triggering and/or maintaining MRONJ. The aim of our study was to characterize the culturable and non-culturable microbiota-with particular focus on Actinomyces spp. and Actinomyces-like organisms (ALOs)-from surgically removed bone samples of MRONJ patients and healthy control subjects. Methods: n = 35 patients (median age: 70 years) in various stages of MRONJ, with a history of receiving oral or intravenous antiresorptive treatment were included in the study. The controls (n = 35; median age: 35 years) consisted of otherwise healthy individuals undergoing tooth extraction. Traditional, quantitative, aerobic, and anaerobic culture, and Actinomyces-specific PCR was performed for all bone samples from patients and controls, while microbiome analyses-based on 16S rRNA sequencing-were carried out in 5-5 randomly selected samples. Mann-Whitney U test, Wilcoxon rank sum test (alpha diversity), and PERMANOVA analysis (beta diversity) were performed. Results: In MRONJ samples, 185 anaerobic isolates, corresponding to 65 different species were identified (vs. 72 isolates, corresponding to 27 different species in the control group). The detection of Actinomyces spp. and ALOs was more common in MRONJ bone samples, based on traditional culture (65.7% vs. 17.1%; p < 0.001) and PCR (82.9% vs. 37.1%; p < 0.001), respectively. The isolation of Fusobacterium spp. (22 vs. 7; p = 0.001), Prevotella spp. (22 vs. 6; p = 0.034), and Gram-positive anaerobic cocci (GPAC) (30 vs. 9; p = 0.016) was significantly more common in MRONJ patient samples. The microbiota of the controls' bone samples were characterized by a considerable dominance of Streptococcus spp. and Veillonella spp, while the bacterial abundance rates were substantially more heterogeneous in MRONJ bone samples. Notable differences were not observed among the samples related to the abundance of Actinomyces in the bone microbiota. Conclusions: According to the "infection hypothesis", alterations in the oral microbiome-with Actinomyces and ALOs being the most relevant-may play a key role in the development, aggravation, and progression of MRONJ. The timely detection of Actinomyces in necrotic bone is crucial, as it has important therapeutic implications.

Blood immune profiles reveal a CXCR3/CCR5 axis of dysregulation in early sepsis

We report on a pilot study exploring whether blood immune signatures can reveal early specific indicator profiles for patients meeting sepsis criteria upon hospital admission. We analyzed samples of sepsis-suspected patients (n = 20) and age-spanning healthy controls (n = 12) using flow cytometry-based assays. We measured inflammatory markers from plasma fractions and immunophenotyped freshly isolated unfixed peripheral blood mononucleated cells for leukocyte subset representation and expression of activation markers, including chemokine receptors. We found that besides IL-6 and sCD14, CXCR3 ligands (CXCL9 and CXCL10) separated sepsis-suspected patients from healthy controls. The abundance of CD4+ T cells was significantly reduced in patients, while they displayed substantial losses of CCR5-expressing monocytes and CXCR3/CCR5 double-positive T cells. Post hoc subgrouping of patients according to their sepsis diagnosis on discharge identified CXCR3/CCR5 double expression on T cells as a separating characteristic for confirmed cases. This work suggests a potential novel axis of dysregulation affecting CXCR3 and CCR5 in early sepsis.

Machine learning and clinician predictions of antibiotic resistance in Enterobacterales bloodstream infections

BACKGROUND

Patients with Gram-negative bloodstream infections are at risk of serious adverse outcomes without active treatment, but identifying who has antimicrobial resistance (AMR) to target empirical treatment is challenging.

METHODS

We used XGBoost machine learning models to predict antimicrobial resistance to seven antibiotics in patients with Enterobacterales bloodstream infection. Models were trained using hospital and community data from Oxfordshire, UK, for patients with positive blood cultures between 01-January-2017 and 31-December-2021. Model performance was evaluated by comparing predictions to final microbiology results in test datasets from 01-January-2022 to 31-December-2023 and to clinicians' prescribing.

FINDINGS

4709 infection episodes were used for model training and evaluation; antibiotic resistance rates ranged from 7-67%. In held-out test data, resistance prediction performance was similar for the seven antibiotics (AUCs 0.680 [95%CI 0.641-0.720] to 0.737 [0.674-0.797]). Performance improved for most antibiotics when species identifications (available ∼24 h later) were included as model inputs (AUCs 0.723 [0.652-0.791] to 0.827 [0.797-0.857]). In patients treated with a beta-lactam, clinician prescribing led to 70% receiving an active beta-lactam: 44% were over-treated (broader spectrum treatment than needed), 26% optimally-treated (narrowest spectrum active agent), and 30% under-treated (inactive beta-lactam). Model predictions without species data could have led to 79% of patients receiving an active beta-lactam: 45% over-treated, 34% optimally-treated, and 21% under-treated.

CONCLUSIONS

Predicting AMR in bloodstream infections is challenging for both clinicians and models. Despite modest performance, machine learning models could still increase the proportion of patients receiving active empirical treatment by up to 9% over current clinical practice in an environment prioritising antimicrobial stewardship.

Experimental tests challenge the evidence of a healthy human blood microbiome

The advent of next-generation sequencing (NGS) technologies has made it possible to investigate microbial communities in various environments, including different sites within the human body. Therefore, the previously established belief of the sterile nature of several body sites, including human blood, has now been challenged. However, metagenomics investigation of areas with an anticipated low microbial biomass may be susceptible to misinterpretation. Here, we critically evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples while incorporating specific negative controls aimed at addressing potential bias to supplement and strengthen the research in this area. We prepared negative controls by increasing the initial DNA quantity through sequences that can be recognized and subsequently discarded. We found that only three organisms were sporadically present among the samples, and this was mostly attributable to bacteria ubiquitously present in laboratory reagents. Despite not fully confirming or denying the existence of healthy blood microbiota, our results suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people. Finally, our study poses relevant questions on the design of controls in this research area that must be considered in order to avoid misinterpreted results that appear to contaminate current high-throughput research.

Optical Bionanosensors for Sepsis Diagnostics

Sepsis is a global health challenge, characterized by a dysregulated immune response, leading to organ dysfunction and death. Despite advances in medical care, sepsis continues to claim a significant toll on human lives, with mortality rates from 10-25% for sepsis and 30-50% for septic shock, making it a leading cause of death worldwide. Current diagnostic methods rely on clinical signs, laboratory parameters, or microbial cultures and suffer from delays and inaccuracies. Therefore, there is a pressing need for novel diagnostic tools that can rapidly and accurately identify sepsis. This review highlights advances in biosensor development that could ultimately lead to faster and more accurate sepsis diagnostics. The focus is on nanomaterial-based optical approaches that promise rapid diagnostics without the need for large equipment or trained personnel. An overview of sepsis is provided, highlighting potential molecular targets and the challenges they present for assay development. The requirements for an ideal point-of-care test (POC) are discussed, including speed, simplicity, and cost-effectiveness. Different nanomaterials suitable for various optical detection methods are reviewed and innovative nanosensors are discussed for sepsis diagnostics, focusing on chemical design and approaches to increase selectivity by multiplexing.

The trends of blood culture contamination and utilization rates in an LMIC tertiary care center from 2010 to 2022: a call for diagnostic stewardship?

Objective

At Saint George Hospital University Medical Center in Beirut, Lebanon, we determine (1) annual blood culture (BC) contamination (BCC) and utilization (BCU) rates vs international benchmarks, (2) identify blood culture contaminants, (3) bloodstream infections episodes in patients with and without COVID-19 after the pandemic onset, and (4) any epidemiologic trends in BCC and BCU.

Design

Retrospective observational study.

Setting

Private tertiary referral center, from January 1, 2010, to December 31, 2022.

Methods

We define a contaminated BC as the growth of a typical contaminant/skin flora in 1-2/4 BC bottles. We calculate BCC rates as a percentage of the contaminated BC/total BC during the period and BCU rates as the number of BC/1000 patient days (PD).

Results

The average BCU rate of 85.9/1000 PD in 2010-2019 increased to 106.6/1000 PD in 2020-2022. On average, patients with COVID-19 had a higher BCU rate of 185.9/1000 PD, corresponding to an additional 100 blood cultures/1000 PD. The average BCC rate was 7%, ranging from 6% in 2010-2019 to 8% in 2020-2022. We observed the highest BCC rate of 9% in patients with COVID-19, likely due to the higher BCU. The most frequently isolated contaminants were coagulase-negative Staphylococcus (96%), of which 65% were Staphylococcus epidermidis.

Conclusion

We saw a multifactorial, persistently elevated rate of BCC over 13 years as unaffected by strict infection control practices. We think that further research targeting a standardized, low BCU rather than inevitable BCC while advocating for diagnostic stewardship of low-middle-income countries is essential, especially where the lack of appropriate resource allocation and awareness are problematic.

Measurement of Bacterial Headspaces by FT-IR Spectroscopy Reveals Distinct Volatile Organic Compound Signatures

Ensuring prompt and precise identification of bacterial pathogens is essential for initiating appropriate antibiotic therapy and combating severe bacterial infections effectively. Traditional microbiological diagnostics, involving initial culturing and subsequent pathogen detection, are often laborious and time-consuming. Even though modern techniques such as Raman spectroscopy, MALDI-TOF, and 16S rRNA PCR have significantly expedited this process, new methods are required for the accurate and fast detection of bacterial pathogens. In this context, using bacterial metabolites for detection is promising as a future diagnostic approach. Fourier-transform infrared spectroscopy was employed in our study to analyze the biochemical composition of gas phases of bacterial isolates. We can characterize individual bacterial strains and identify specific bacteria within mixtures by utilizing volatile-metabolite-based infrared detection techniques. This approach enables rapid identification by discerning distinctive spectral features and intensities for different bacteria, offering new perspectives for bacterial pathogen diagnostics. This technique holds innovative potential to accelerate progress in the field, providing a faster and potentially more precise alternative to conventional diagnostic methods.

Examining the effect of direct-from-blood bacterial testing on antibiotic administration and clinical outcomes: a protocol and statistical analysis plan for a pragmatic randomised trial

INTRODUCTION

Patients with suspected bacterial infection frequently receive empiric, broad-spectrum antibiotics prior to pathogen identification due to the time required for bacteria to grow in culture. Direct-from-blood diagnostics identifying the presence or absence of bacteria and/or resistance genes from whole blood samples within hours of collection could enable earlier antibiotic optimisation for patients suspected to have bacterial infections. However, few randomised trials have evaluated the effect of using direct-from-blood bacterial testing on antibiotic administration and clinical outcomes. This manuscript describes the protocol and statistical analysis plan for a randomised trial designed to evaluate the effect of blood cultures plus direct-from-blood bacterial testing results compared with blood culture results alone on antibiotic administration and clinical outcomes.

METHODS AND ANALYSIS

We are conducting a prospective, single-centre, parallel-group, non-blinded, pragmatic, randomised trial. The trial will enrol 500 adult patients presenting to the emergency department at Vanderbilt University Medical Center with suspected bacterial infection who have been initiated on empiric intravenous vancomycin. Eligible patients are randomised 1:1 to receive Food and Drug Administration-approved direct-from-blood bacterial testing in addition to blood cultures or blood cultures alone. The primary outcome is the time to the last dose of intravenous vancomycin within 14 days of randomisation. The secondary outcome is the time to the last dose of systemic antipseudomonal beta-lactam antibiotics within 14 days of randomisation. Additional outcomes include highest stage of acute kidney injury, lowest platelet count and receipt of kidney replacement therapy within 14 days of randomisation, as well as hospital-free days, intensive care unit-free-days and all-cause, in-hospital mortality within 28 days of randomisation. Enrolment began on 13 December 2023.

ETHICS AND DISSEMINATION

The trial involves human participants and was approved by the Vanderbilt University Medical Center institutional review board with a waiver of informed consent (IRB#231229). Results will be submitted in a peer-reviewed journal and presented at scientific conferences.

TRIAL REGISTRATION NUMBER

NCT06069206.

Investigating the time to blood culture positivity: why does it take so long?

Introduction. Bloodstream infections (BSIs) are one of the most serious infections investigated by microbiologists. However, the time to detect a BSI fails to meet the rapidity required to inform clinical decisions in real time.Gap Statement. Blood culture (BC) is considered the gold standard for diagnosing bloodstream infections. However, the time to blood culture positivity can be lengthy. Underpinning this is the reliance on bacteria replicating to a high concentration, which is necessary for the detection using routine blood culture systems. To improve the diagnosis and management of patients with BSIs, more sensitive detection methods are required.Aim. The study aimed to answer key questions addressing the delay in BSI detection and whether the time to BSI detection could be expedited using a Scattered Light Integrated Collection (SLIC) device.Methodology. A proof-of-concept study was conducted to compare the time to positivity (TTP) of Gram-negative BCs flagging positive on BacT/ALERT with an SLIC device. An SLIC device was utilized to compare the TTP of the most prevalent BSI pathogens derived from nutrient broth and BC, the influence of bacterial load on TTP and the TTP directly from whole blood. Additionally, the overall turnaround time (TAT) of SLIC was compared with that of a standard hospital workflow.Results. Most pathogens tested took significantly longer to replicate when derived from BC than from nutrient medium. The median TTP of Gram-negative BC on BacT/ALERT was 13.56 h with a median bacterial load of 6.4×109 c.f.u. ml-1. All pathogens (7/7) derived from BC at a concentration of 105 c.f.u. ml-1 were detectable in under 70 min on SLIC. Decreasing Escherichia coli BC concentration from 105 to 102 c.f.u. ml-1 increased the TTP of SLIC from 15 to 85 min. Direct BSI detection from whole blood on SLIC demonstrated a 76% reduction in TAT when compared with the standard hospital workflow.Conclusion. An SLIC device significantly reduced the TTP of common BSI pathogens. The application of this technology could have a major impact on the detection and management of BSI.

Early detection of bacterial pneumonia by characteristic induced odor signatures

INTRODUCTION

The ability to detect pathogenic bacteria before the onsets of severe respiratory symptoms and to differentiate bacterial infection allows to improve patient-tailored treatment leading to a significant reduction in illness severity, comorbidity as well as antibiotic resistance. As such, this study refines the application of the non-invasive Secondary Electrospray Ionization-High Resolution Mass Spectrometry (SESI-HRMS) methodology for real-time and early detection of human respiratory bacterial pathogens in the respiratory tract of a mouse infection model.

METHODS

A real-time analysis of changes in volatile metabolites excreted by mice undergoing a lung infection by Staphylococcus aureus or Streptococcus pneumoniae were evaluated using a SESI-HRMS instrument. The infection status was confirmed using classical CFU enumeration and tissue histology. The detected VOCs were analyzed using a pre- and post-processing algorithm along with ANOVA and RASCA statistical evaluation methods.

RESULTS

Characteristic changes in the VOCs emitted from the mice were detected as early as 4-6 h post-inoculation. Additionally, by using each mouse as its own baseline, we mimicked the inherent variation within biological organism and reported significant variations in 25 volatile organic compounds (VOCs) during the course of a lung bacterial infection.

CONCLUSION

the non-invasive SESI-HRMS enables real-time detection of infection specific VOCs. However, further refinement of this technology is necessary to improve clinical patient management, treatment, and facilitate decisions regarding antibiotic use due to early infection detection.

Early Diagnosis of Bloodstream Infections Using Serum Metabolomic Analysis

BACKGROUND

Bloodstream infections (BSIs) pose a great challenge to treating patients, especially those with underlying diseases, such as immunodeficiency diseases. Early diagnosis helps to direct precise empirical antibiotic administration and proper clinical management. This study carried out a serum metabolomic analysis using blood specimens sampled from patients with a suspected infection whose routine culture results were later demonstrated to be positive.

METHODS

A liquid chromatograph-mass spectrometry-based metabolomic analysis was carried out to profile the BSI serum samples. The serum metabolomics data could be used to successfully differentiate BSIs from non-BSIs.

RESULTS

The major classes of the isolated pathogens (e.g., Gram-positive and Gram-negative bacteria) could be differentiated using our optimized statistical algorithms. In addition, by using different machine-learning algorithms, the isolated pathogens could also be classified at the species levels (e.g., Escherichia coli and Klebsiella pneumoniae) or according to their specific antibiotic-resistant phenotypes (e.g., extended-spectrum β-lactamase-producing and non-producing phenotypes) if needed.

CONCLUSIONS

This study provides an early diagnosis method that could be an alternative to the traditional time-consuming culture process to identify BSIs. Moreover, this metabolomics strategy was less affected by several risk factors (e.g., antibiotics administration) that could produce false culture results.

Yield of Targeted Polymerase Chain Reaction in Probable Early-Onset Sepsis: A Prospective Cohort Study in Term and Near-Term Neonates With Negative Blood Culture Results

Background

Discriminating noninfected from infected neonatal cases remains challenging, and subsequently many neonates are treated with antibiotics in the first week of life. We aimed to study the additional value of a targeted polymerase chain reaction (PCR) for group B streptococcus (GBS) and Escherichia coli on leftover blood culture media from term and near-term neonates with probable early-onset sepsis (EOS).

Methods

Leftover blood culture material from neonates participating in the RAIN study was stored after 5 days of incubation. The RAIN study evaluated intravenous-oral antibiotic switch in probable bacterial infection, defined as risk factors and/or clinical signs and elevated inflammatory parameters but negative blood culture results. We applied 2 targeted PCRs for GBS and E coli, the main pathogens in EOS, and analyzed the samples batchwise in triplicate for each PCR.

Results

PCR was performed in triplicate on blood culture media from 284 neonates. In 23 neonates, the PCR result was positive (3 cycle threshold values <37) for GBS (n = 1) or E coli (n = 22). Inflammatory parameters did not discriminate for positive PCR result, nor did risk factors for sepsis, such as maternal GBS status and prolonged rupture of membranes. However, 96% of neonates with a positive PCR result were born vaginally vs 74% in the PCR-negative group (P = .05); furthermore, 96% vs 81% (P = .21) of neonates had clinical symptoms.

Conclusions

Blood culture-negative "probable" EOS in neonates is accompanied by an 8% rate of PCR positivity, suggesting low-grade bacteriemia after birth with yet unclear clinical consequences. Further research should focus on how PCR can contribute to more targeted antibiotic use of neonates, specifically in those highly suspected of infection but in the absence of a positive blood culture result.

Assessing sepsis-induced immunosuppression to predict positive blood cultures

Introduction

Bacteremia is a life-threatening condition that can progress to sepsis and septic shock, leading to significant mortality in the emergency department (ED). The standard diagnostic method, blood culture, is time-consuming and prone to false positives and false negatives. Although not widely accepted, several clinical and artificial intelligence-based algorithms have been recently developed to predict bacteremia. However, these strategies require further identification of new variables to improve their diagnostic accuracy. This study proposes a novel strategy to predict positive blood cultures by assessing sepsis-induced immunosuppression status through endotoxin tolerance assessment.

Methods

Optimal assay conditions have been explored and tested in sepsis-suspected patients meeting the Sepsis-3 criteria. Blood samples were collected at ED admission, and endotoxin (lipopolysaccharide, LPS) challenge was performed to evaluate the innate immune response through cytokine profiling.

Results

Clinical variables, immune cell population biomarkers, and cytokine levels (tumor necrosis factor [TNFα], IL-1β, IL-6, IL-8, and IL-10) were measured. Patients with positive blood cultures exhibited significantly lower TNFα production after LPS challenge than did those with negative blood cultures. The study also included a validation cohort to confirm that the response was consistent.

Discussion

The results of this study highlight the innate immune system immunosuppression state as a critical parameter for sepsis diagnosis. Notably, the present study identified a reduction in monocyte populations and specific cytokine profiles as potential predictive markers. This study showed that the LPS challenge can be used to effectively distinguish between patients with bloodstream infection leading to sepsis and those whose blood cultures are negative, providinga rapid and reliable diagnostic tool to predict positive blood cultures. The potential applicability of these findings could enhance clinical practice in terms of the accuracy and promptness of sepsis diagnosis in the ED, improving patient outcomes through timely and appropriate treatment.

Using blood TNF-related apoptosis-inducing ligand levels to discriminate between viral and bacterial infections: A prospective observational study

OBJECTIVE

The aim of the investigation was to evaluate variations in blood TNF-related apoptosis-inducing ligand (TRAIL) levels between patients with viral and bacterial infections and the diagnostic performance of TRAIL for identifying viral and bacterial infections.

METHODS

The investigation included 169 adult (>18 years) patients presenting with medical signs of acute infections (inclusion criteria included a body temperature over 37.5 °C, an onset of symptoms no more than 12 days). Reference standard was based on a rigorous expert panel and the majority of the panel determined the infectious etiology. Finally, 104 patients with 78 bacterial and 26 viral reference standard outcomes were enrolled in this investigation (24 were eliminated depending on the exclusion criteria; 41 had indeterminate reference standard diagnosis). ELISA was employed to measure TRAIL levels in the group of 78 subjects with bacterial infections and 26 individuals with viral infections, and the diagnostic performance of TRAIL was identified by receiver operating characteristic (ROC) analysis.

RESULTS

The TRAIL level in individuals with bacterial infections was significantly lower than that in subjects with viral infections (16.59 (2.61-32.6) pg/mL vs. 97.39 (36.18-127.74) pg/mL, P < 0.05). The area under the ROC curve (AUC) of TRAIL was 0.86 (95 %CI:0.79 to 0.94) for identifying bacterial and viral infections. Combining TRAIL with C-reactive protein (CRP), the AUC was 0.94 (95 %CI:0.89 to 1.00).

CONCLUSIONS

TRAIL is diagnostic for discriminating between viral and bacterial infections. Combining TRAIL with CRP increases the AUC.

Antimicrobial resistance profile and associated factors of hospital-acquired gram-negative bacterial pathogens among hospitalized patients in northeast Ethiopia

BACKGROUND

Antimicrobial resistance is a major global public health issue. Infections caused by resistant species are associated with higher mortality rates, longer hospital stays, medication failure, and rising medical costs. The World Health Organisation has declared multidrug resistance-associated infections as an epidemic of public health concern.

OBJECTIVE

This study aimed to evaluate the antimicrobial resistance profile and associated factors of hospital-acquired Gram-negative bacterial pathogens among hospitalized patients in Northeast Ethiopia.

MATERIALS AND METHODS

A health facility-based cross-sectional study was conducted among hospitalized patients from March 2021 to February 2022. About 810 clinical specimens were collected, transported, and processed from admitted patients following the standard bacteriological procedures. The clinical samples were inoculated onto blood agar, MacConkey agar, and chocolate agar. Furthermore, the species identification was done using gram reactions, colony morphology, and color and biochemical tests. Antimicrobial susceptibility tests, extended-spectrum beta-lactamase, and carbapenemase production were performed as per the clinical laboratory standard institute guidelines. For analysis, the information was entered into Epi-data and exported to SPSS. A P value of < 0.05 with a 95% confidence interval was considered as a statistically significant association.

RESULTS

Out of 810 clinical specimens, 285/810 (35.2%) developed bacterial infections. From the isolated bacteria, E. coli was the predominant bacteria accounting for 78/285 (27.4%) followed by K. pneumoniae, 69/285(24.42%), whereas P. vulgaris accounted for the least, 7/285 (2.5%). Overall, 132/285 (46.3%) and 99/285 (34.7%) of culture-positive patients were infected by extended-spectrum beta-lactamase and carbapenemase-producing bacteria. The overall multidrug resistance rate of the isolated bacteria was 89.4%. The highest antibiotic resistance rates were detected for doxycycline (92.9%), amoxicillin-clavulanic acid (83.9%), and ampicillin (93%). The least antibiotic resistance rate was observed for meropenem at 41.1% and amikacin at 1.7%, respectively.

CONCLUSIONS AND RECOMMENDATIONS

In the study area, significant health concerns include a range of hospital-acquired bacterial infections associated with elevated rates of multidrug resistance, Extended-spectrum beta-lactamase (ESBL), and carbapenemase-producing bacterial pathogens. Consequently, it is recommended to conduct drug-susceptibility testing of isolates and molecular detection at a national level to optimize antibiotic usage for treating prevalent bacterial infections in this area.

Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Time to receive effective therapy is a primary determinant of mortality in patients with sepsis. Blood culture is the reference standard for the microbiological diagnosis of bloodstream infections, despite its low sensitivity and prolonged time to receive a pathogen detection. In recent years, rapid tests for pathogen identification, antimicrobial susceptibility, and sepsis identification have emerged, both culture-based and culture-independent methods. This rapid narrative review presents currently commercially available approved diagnostic molecular technologies in bloodstream infections, including their clinical performance and impact on patient outcome, when available. Peer-reviewed publications relevant to the topic were searched through PubMed, and manufacturer websites of commercially available assays identified were also consulted as further sources of information. We have reviewed data about the following technologies for pathogen identification: fluorescence in situ hybridization with peptide nucleic acid probes (Accelerate PhenoTM), microarray-based assay (Verigene®), multiplex polymerase chain reaction (cobas® eplex, BioFire® FilmArray®, Molecular Mouse, Unyvero BCU SystemTM), matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (Rapid MBT Sepsityper®), T2 magnetic resonance (T2Bacteria Panel), and metagenomics-based assays (Karius©, DISQVER®, Day Zero Diagnostics). Technologies for antimicrobial susceptibility testing included the following: Alfed 60 ASTTM, VITEK® REVEALTM, dRASTTM, ASTar®, Fastinov®, QuickMIC®, ResistellTM, and LifeScale. Characteristics, microbiological performance, and issues of each method are described, as well as their clinical performance, when available.

Electrochemical biosensors for clinical detection of bacterial pathogens: advances, applications, and challenges

Bacterial pathogens are responsible for a variety of human diseases, necessitating their prompt detection for effective diagnosis and treatment of infectious diseases. Over recent years, electrochemical methods have gained significant attention owing to their exceptional sensitivity and rapidity. This review outlines the current landscape of electrochemical biosensors employed in clinical diagnostics for the detection of bacterial pathogens. We categorize these biosensors into four types: amperometry, potentiometry, electrochemical impedance spectroscopy, and conductometry, targeting various bacterial components, including toxins, virulence factors, metabolic activity, and events related to bacterial adhesion and invasion. We discuss the merits and challenges associated with electrochemical methods, underscoring their rapid response, high sensitivity, and specificity, while acknowledging the necessity for skilled operators and potential interference from biological and environmental factors. Furthermore, we examine future prospects and potential applications of electrochemical biosensors in clinical diagnostics. While electrochemical biosensors offer a promising avenue for detecting bacterial pathogens, further research in optimizing the robustness and surmounting the challenges hindering their seamless integration into clinical practice is imperative.

Fast and accurate identification of pathogenic bacteria using excitation-emission spectroscopy and machine learning

Fast and reliable identification of pathogenic bacteria is of upmost importance to human health and safety. Methods that are currently used in clinical practice are often time consuming, require expensive equipment, trained personnel, and therefore have limited applications in low resource environments. Molecular identification methods address some of these shortcomings. At the same time, they often use antibodies, their fragments, or other biomolecules as recognition units, which makes such tests specific to a particular target. In contrast, array-based methods use a combination of reporters that are not specific to a single pathogen. These methods provide a more data-rich and universal response that can be used for identification of a variety of bacteria of interest. In this report, we demonstrate the application of the excitation-emission spectroscopy of an environmentally sensitive fluorescent dye for identification of pathogenic bacterial species. 2-(4'-Dimethylamino)-3-hydroxyflavone (DMAF) interacts with the bacterial cell envelope resulting in a distinct spectral response that is unique to each bacterial species. The dynamics of dye-bacteria interaction were thoroughly investigated, and the limits of detection and identification were determined. Neural network classification algorithm was used for pattern recognition analysis and classification of spectral data. The sensor successfully discriminated between eight representative pathogenic bacteria, achieving a classification accuracy of 85.8% at the species level and 98.3% at the Gram status level. The proposed method based on excitation-emission spectroscopy of an environmentally sensitive fluorescent dye is a powerful and versatile diagnostic tool with high accuracy in identification of bacterial pathogens.

Identification of sepsis-causing bacteria from whole blood without culture using primers with no cross-reactivity to human DNA

Sepsis is a major health concern globally, and identification of the causative organism usually takes several days. Furthermore, molecular amplification using whole blood from patients with sepsis remains challenging because of primer cross-reactivity with human DNA, which can delay appropriate clinical intervention. To address these concerns, we designed primers that could reduce cross-reactivity. By evaluating these primers against human DNA, we confirmed that the cross-reactivity observed with conventional primers was notably absent. In silico PCR further demonstrated the specificity and efficiency of the designed primers across 23 bacterial species that are often associated with sepsis. When tested using blood samples from sepsis patients, the designed primers showed moderate sensitivity and high specificity. Surprisingly, our method identified bacteria even in samples that were detected at other sites but tested negative using conventional blood culture methods. Although we identified some challenges, such as contamination with Acetobacter aceti due to the saponin pretreatment of samples, the developed method demonstrates remarkable potential for rapid identification of the causative organisms of sepsis and provides a new avenue for diagnosis in clinical practice.

Risk factors of bloodstream infection in erythroderma from atopic dermatitis, psoriasis, and drug reactions: a retrospective observational cohort study

Background

Atopic dermatitis (AD), psoriasis, and drug reactions associated with erythroderma are frequently complicated by infections. However, bloodstream infection (BSI) have received less research attention.

Objectives

This study aimed to investigate the clinical characteristics and risk factors associated with BSI in patients with erythroderma.

Methods

A retrospective analysis was conducted on 141 erythroderma cases. Eleven cases were identified as having BSI. Clinical records of both BSI and non-BSI groups were reviewed and compared.

Results

BSI was diagnosed in 7.80% (11/141) of erythroderma cases, with a breakdown of 7.14% in AD, 2.00% in psoriasis, and 17.14% in drug reactions. Notably, all positive skin cultures (7/7) showed bacterial isolates concordant with blood cultures. Univariate logistic regression analysis revealed several significant associations with BSI, including temperature (≤36.0 or ≥38.5 °C; odds ratio (OR) = 28.06; p < 0.001), chilling (OR = 22.10; p < 0.001), kidney disease (OR = 14.64; p < 0.001), etiology of drug reactions (OR = 4.18; p = 0.03), albumin (ALB) (OR = 0.86; p < 0.01), C-reaction protein (CRP) (OR = 1.01; p = 0.02), interleukin 6 (IL-6) (OR = 1.02; p = 0.02), and procalcitonin (PCT) (OR = 1.07; p = 0.03). Receiver operating characteristic (ROC) curves demonstrated significant associations with ALB (p < 0.001; the area under curve (AUC) = 0.80), PCT (p = 0.009; AUC = 0.74), and CRP (p = 0.02; AUC = 0.71).

Conclusions

Increased awareness of BSI risk is essential in erythroderma management. Patients with specific risk factors, such as abnormal body temperature (≤36.0 or ≥38.5 °C), chilling sensations, kidney disease, a history of drug reactions, elevated CRP (≥32 mg/L), elevated PCT (≥1.00 ng/ml), and low albumin (≤31.0 g/L), require close monitoring for BSI development.

Rapid Antimicrobial Susceptibility Testing Using the MicroScan System: Performance Evaluation of a 4-Hour Bacterial Cultivation From Positive Blood Cultures

A reliable and above all, rapid antimicrobial susceptibility test (AST) is required for the diganostics of blood stream infections (BSI). In this study, resistance testing using DxM MicroScan WalkAway (MicroScan) from a 4-h subculture is compared with the standard overnight culture (18-24 h). Randomly selected positive blood cultures (PBC, n = 102) with gram-negative bacteria were included in the study. PBC were sub-cultured onto appropriate agar plates and AST by MicroScan was performed after 4 h of incubation and repeated after incubation for 18-24 h as standard. In a total of 1909 drug-strain pairs, the 4-h subculture approach showed a very high essential agreement (EA) (98.6%) and categorical agreement (CA) (97.1%) compared with the standard. The incidence of minor error (mE), major error (ME), very major error (VME), and adjusted very major error (aVME) was 1.1%, 0.4%, 12.9%, and 5.3%, respectively. In summary, the use of 4-h subcultures for resistance testing with the MicroScan offers a very reliable and easy to realize time saving when testing positive blood cultures with gram-negative bacteria.

Utility of shaking chills as a diagnostic sign for bacteremia in adults: a systematic review and meta-analysis

BACKGROUND

Accurate prediction of bacteremia is essential for guiding blood culture collection and optimal antibiotic treatment. Shaking chills, defined as a subjective chill sensation with objective body shivering, have been suggested as a potential predictor of bacteremia; however, conflicting findings exist. To address the evidence gap, we conducted a systematic review and meta-analysis of studies to assess the diagnostic accuracy of shaking chills for predicting bacteremia among adult patients.

METHODS

We included studies reporting the diagnostic accuracy of shaking chills or chills for bacteremia. Adult patients with suspected bacteremia who underwent at least one set of blood cultures were included. Our main analysis focused on studies that assessed shaking chills. We searched these studies through CENTRAL, MEDLINE, Embase, the World Health Organization ICTRP Search Portal, and ClinicalTrials.gov. Study selection, data extraction, evaluation for risk of bias, and applicability using the QUADAS-2 tool were conducted by two independent investigators. We estimated a summary receiver operating characteristic curve and a summary point of sensitivity and specificity of the index tests, using a hierarchical model and the bivariate model, respectively.

RESULTS

We identified 19 studies with a total of 14,641 patients in which the accuracy of shaking chills was evaluated. The pooled sensitivity and specificity of shaking chills were 0.37 (95% confidence interval [CI], 0.29 to 0.45) and 0.87 (95% CI, 0.83 to 0.90), respectively. Most studies had a low risk of bias in the index test domain and a high risk of bias and a high applicability concern in the patient-selection domain.

CONCLUSIONS

Shaking chills are a highly specific but less sensitive predictor of bacteremia. Blood cultures and early initiation of antibiotics should be considered for patients with an episode of shaking chills; however, the absence of shaking chills must not lead to exclusion of bacteremia and early antibiotic treatment.

Melting temperature mapping method in children: Rapid identification of pathogenic microbes

INTRODUCTION

The melting temperature (Tm) mapping method (TM) identifies bacterial species by intrinsic patterns of Tm values in the 16S ribosomal RNA gene (16S rDNA) extracted directly from whole blood. We examined potential clinical application of TM in children with bloodstream infection (BSI).

METHODS

This was a prospective observational study at a children's hospital in Japan from 2018 to 2021. In patients with diagnosed or suspected BSI, we investigated the match rates of pathogenic bacteria identified by TM and blood culture (BC), the inspection time to identification of TM, and the amount of bacterial DNA in blood samples.

RESULTS

The median age of 81 patients (93 samples) was 3.6 years. Of 23 samples identified by TM, 11 samples matched the bacterial species with BC (positive-match rate, 48 %). Of 64 TM-negative samples, 62 samples were negative for BC (negative-match rate, 97 %). Six samples, including one containing two pathogenic bacterial species, were not suitable for TM identification. In total, the matched samples were 73 of 93 samples (match rate, 78 %). There were seven samples identified by TM in BC-negative samples from blood collected after antibiotic therapy. Interestingly, the bacteria were matched with BC before antibiotic administration. These TM samples contained as many 16S rDNA copies as the BC-positive samples. The median inspection time to identification using TM was 4.7 h.

CONCLUSIONS

In children with BSI, TM had high negative-match rates with BC, the potential to identify the pathogenic bacteria even in patients on antibiotic therapy, and more rapid identification compared to BC.

REGISTERING CLINICAL TRIALS

UMIN000041359https://center6.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000047220.

Dynamic Changes in Soluble Triggering Receptor Expressed on Myeloid Cells-1 in Sepsis with Respect to Antibiotic Susceptibility

Purpose

Proper antibiotic administration is crucial for sepsis management. Given the escalating incidence of antimicrobial resistance, there is a pressing need for indicators of antimicrobial susceptibility with short turnaround times. This study aimed to investigate the potential of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) as an early biomarker for in vivo antibiotic susceptibility in patients with sepsis.

Patients and Methods

We conducted a retrospective analysis of plasma samples from patients enrolled in a pre-established study designed to investigate prognostic biomarkers in patients with sepsis or septic shock. Baseline and 6 h sTREM-1 levels were examined using enzyme-linked immunosorbent assays. The primary outcome of the study was the comparison of percentage changes in sTREM-1 levels at the 6 h relative to baseline with respect to antibiotic susceptibility.

Results

Of the 596 patients enrolled in the pre-established study, 29 with a median age of 75.8 and a 28-day mortality rate of 17.2% were included in the present analysis. Among these patients, 24 were classified into the susceptible group, whereas the remaining five were classified into the resistant group. The trend in plasma sTREM-1 levels differed with respect to antibiotic susceptibility. Moreover, percentage change in sTREM-1 levels at the 6 h relative to baseline was significantly higher in the resistant group (P = 0.028).

Conclusion

The trend in plasma sTREM-1 levels in patients with sepsis differed with respect to antibiotic susceptibility, with a higher percentage change in patients treated with inappropriate antibiotics. These findings indicate the potential utility of sTREM-1 as an early biomarker of antibiotic susceptibility.

Rapid diagnosis of bloodstream infections using a culture-free phenotypic platform

BACKGROUND

Bloodstream infections (BSIs) are a life-threatening acute medical condition and current diagnostics for BSIs suffer from long turnaround time (TAT). Here we show the validation of a rapid detection-analysis platform (RDAP) for the diagnosis of BSIs performed on clinical blood samples METHODS: The validation was performed on a cohort of 59 clinical blood samples, including positive culture samples, which indicated confirmed bloodstream infections, and negative culture samples. The bacteria in the positive culture samples included Gram-positive and Gram-negative pathogenic species. RDAP is based on an electrochemical sandwich immunoassay with voltage-controlled signal amplification, which provides an ultra-low limit of detection (4 CFU/mL), allowing the platform to detect and identify bacteria without requiring culture and perform phenotypic antibiotic susceptibility testing (AST) with only 1-2 h of antibiotic exposure. The preliminary diagnostic performance of RDAP was compared with that of standard commercial diagnostic technologies.

RESULTS

Using a typical clinical microbiology laboratory diagnostic workflow that involved sample culture, agar plating, bacteria identification using matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry, and AST using MicroScan as a clinical diagnostic reference, RDAP showed diagnostic accuracy of 93.3% and 95.4% for detection-identification and AST, respectively. However, RDAP provided results at least 15 h faster.

CONCLUSIONS

This study shows the preliminary feasibility of using RDAP to rapidly diagnose BSIs, including AST. Limitations and potential mitigation strategies for clinical translation of the present RDAP prototype are discussed. The results of this clinical feasibility study indicate an approach to provide near real-time diagnostic information for clinicians to significantly enhance the treatment outcome of BSIs.

Performance evaluation of machine-assisted interpretation of Gram stains from positive blood cultures

Manual microscopy of Gram stains from positive blood cultures (PBCs) is crucial for diagnosing bloodstream infections but remains labor intensive, time consuming, and subjective. This study aimed to evaluate a scan and analysis system that combines fully automated digital microscopy with deep convolutional neural networks (CNNs) to assist the interpretation of Gram stains from PBCs for routine laboratory use. The CNN was trained to classify images of Gram stains based on staining and morphology into seven different classes: background/false-positive, Gram-positive cocci in clusters (GPCCL), Gram-positive cocci in pairs (GPCP), Gram-positive cocci in chains (GPCC), rod-shaped bacilli (RSB), yeasts, and polymicrobial specimens. A total of 1,555 Gram-stained slides of PBCs were scanned, pre-classified, and reviewed by medical professionals. The results of assisted Gram stain interpretation were compared to those of manual microscopy and cultural species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The comparison of assisted Gram stain interpretation and manual microscopy yielded positive/negative percent agreement values of 95.8%/98.0% (GPCCL), 87.6%/99.3% (GPCP/GPCC), 97.4%/97.8% (RSB), 83.3%/99.3% (yeasts), and 87.0%/98.5% (negative/false positive). The assisted Gram stain interpretation, when compared to MALDI-TOF MS species identification, also yielded similar results. During the analytical performance study, assisted interpretation showed excellent reproducibility and repeatability. Any microorganism in PBCs should be detectable at the determined limit of detection of 105 CFU/mL. Although the CNN-based interpretation of Gram stains from PBCs is not yet ready for clinical implementation, it has potential for future integration and advancement.

Sepsis-Related Lung Injury and the Complication of Extrapulmonary Pneumococcal Pneumonia

Globally, sepsis and pneumonia account for significant mortality and morbidity. A complex interplay of immune-molecular pathways underlies both sepsis and pneumonia, resulting in similar and overlapping disease characteristics. Sepsis could result from unmanaged pneumonia. Similarly, sepsis patients have pneumonia as a common complication in the intensive care unit. A significant percentage of pneumonia is misdiagnosed as septic shock. Therefore, our knowledge of the clinical relationship between pneumonia and sepsis is imperative to the proper management of these syndromes. Regarding pathogenesis and etiology, pneumococcus is one of the leading pathogens implicated in both pneumonia and sepsis syndromes. Growing evidence suggests that pneumococcal pneumonia can potentially disseminate and consequently induce systemic inflammation and severe sepsis. Streptococcus pneumoniae could potentially exploit the function of dendritic cells (DCs) to facilitate bacterial dissemination. This highlights the importance of pathogen-immune cell crosstalk in the pathophysiology of sepsis and pneumonia. The role of DCs in pneumococcal infections and sepsis is not well understood. Therefore, studying the immunologic crosstalk between pneumococcus and host immune mediators is crucial to elucidating the pathophysiology of pneumonia-induced lung injury and sepsis. This knowledge would help mitigate clinical diagnosis and management challenges.

Direct Species Identification in Positive Blood Culture Bottles From Patients With Hematologic Malignancies

Background In patients with hematologic malignancies, faster species identification is particularly important in the management of bloodstream infection because of their immunocompromised and neutropenic status. In the present study, we analyzed direct species identification in patients with hematologic malignancies, and the factors that might influence the results of species identification. Methods We performed direct species identification using a Sepsityper® kit (Bruker Corporation, Billerica, Massachusetts, United States) and compared the results with a conventional method in patients with hematologic malignancies. Forty-five positive blood culture bottles containing single microorganisms from 37 patients were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). And patients' clinical data were compared between the groups with spectral scores at acceptable and unacceptable levels. Results Direct species identification correctly identified 42 of 45 isolates and three were misidentified. While 35 of 45 isolates showed a spectral score ≥1.7 (acceptable identification), 10 isolates had a spectral score <1.7 (unacceptable identification) including three misidentified isolates. The group with a spectral score ≥1.7 had significantly lower white blood cell (p<0.01), neutrophil (p<0.01), and platelet (p<0.01) counts in addition to more frequent central venous (CV) line insertion (p=0.01). Multivariate analysis revealed that pathogen type (gram-positive or negative) and CV line insertion were associated with spectral scores. Conclusion Direct species identification using the Sepsityper kit is an upcoming approach for blood culture bottles, which were flagged as positive even in patients with hematologic malignancies when the spectral score was ≥ 1.7. Our study also indicates that direct identification is more accurate in patients with CV lines, and may be less accurate when gram-positive bacteria are detected.

Evaluation of the knowledge of hematologists about the management of infectious complications in hematologic patients

INTRODUCTION

Infection is a serious complication among patients with hematologic malignancies (HMs) and in hematopoietic cell transplant (HCT) recipients. In most centers, the management of these complications is provided by the hematologist in person, thus demanding a knowledge of basic aspects of infection.

METHODS

To evaluate the knowledge of the hematologist on infections, we invited clinicians to answer two questionnaires with 20 multiple-choice questions covering epidemiology, prophylaxis, diagnosis and treatment of infection in patients with HMs and HCT.

RESULTS

We obtained 289 answers: 223 in survey 1 (febrile neutropenia) and 66 in survey 2 (infection in HCT). The median score was 5.0 in both surveys (range 0.5 - 9.0). In survey 1, the questions with the lowest number of correct answers were Q3 (8%), concerning the cefepime dose, and Q1 (9%), which asked about the epidemiologic link between the use of high dose cytarabine and viridans streptococcal bacteremia. In survey 2, two questions about cytomegalovirus (CMV) infection had the lowest percentage of correct answers (Q4, 12% and Q11, 18%). Clinicians attending to HCT recipients had higher scores, compared to clinicians attending to patients with HM only (median score of 5.0 and 4.5, p = 0.03, in survey 1 and 6.0 and 4.5, p = 0.001, in survey 2). In both surveys staff clinicians, residents and professors had similar scores.

CONCLUSION

This is the first study in Brazil assessing the knowledge of hematologists on infectious complications. The low median score overall indicates an urgent need for continuous education. Such initiatives will eventually result in better patient care.

Using the Traditional Ex Vivo Whole Blood Model to Discriminate Bacteria by Their Inducible Host Responses

Whole blood models are rapid and versatile for determining immune responses to inflammatory and infectious stimuli, but they have not been used for bacterial discrimination. Staphylococcus aureus, S. epidermidis and Escherichia coli are the most common causes of invasive disease, and rapid testing strategies utilising host responses remain elusive. Currently, immune responses can only discriminate between bacterial 'domains' (fungi, bacteria and viruses), and very few studies can use immune responses to discriminate bacteria at the species and strain level. Here, whole blood was used to investigate the relationship between host responses and bacterial strains. Results confirmed unique temporal profiles for the 10 parameters studied: IL-6, MIP-1α, MIP-3α, IL-10, resistin, phagocytosis, S100A8, S100A8/A9, C5a and TF3. Pairwise analysis confirmed that IL-6, resistin, phagocytosis, C5a and S100A8/A9 could be used in a discrimination scheme to identify to the strain level. Linear discriminant analysis (LDA) confirmed that (i) IL-6, MIP-3α and TF3 could predict genera with 95% accuracy; (ii) IL-6, phagocytosis, resistin and TF3 could predict species at 90% accuracy and (iii) phagocytosis, S100A8 and IL-10 predicted strain at 40% accuracy. These data are important because they confirm the proof of concept that host biomarker panels could be used to identify bacterial pathogens.

Accurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform

Antimicrobial resistance (AMR) is a major public health threat, reducing treatment options for infected patients. AMR is promoted by a lack of access to rapid antibiotic susceptibility tests (ASTs). Accelerated ASTs can identify effective antibiotics for treatment in a timely and informed manner. We describe a rapid growth-independent phenotypic AST that uses a nanomotion technology platform to measure bacterial vibrations. Machine learning techniques are applied to analyze a large dataset encompassing 2762 individual nanomotion recordings from 1180 spiked positive blood culture samples covering 364 Escherichia coli and Klebsiella pneumoniae isolates exposed to cephalosporins and fluoroquinolones. The training performances of the different classification models achieve between 90.5 and 100% accuracy. Independent testing of the AST on 223 strains, including in clinical setting, correctly predict susceptibility and resistance with accuracies between 89.5% and 98.9%. The study shows the potential of this nanomotion platform for future bacterial phenotype delineation.

Culture-independent identification of bloodstream infections from whole blood: prospective evaluation in specimens of known infection status

Sepsis caused by bloodstream infection (BSI) is a major healthcare burden and a leading cause of morbidity and mortality worldwide. Timely diagnosis is critical to optimize clinical outcome, as mortality rates rise every hour treatment is delayed. Blood culture remains the "gold standard" for diagnosis but is limited by its long turnaround time (1-7 days depending on the organism) and its potential to provide false-negative results due to interference by antimicrobial therapy or the presence of mixed (i.e., polymicrobial) infections. In this paper, we evaluated the performance of resistance and pathogen ID/BSI, a direct-from-specimen molecular assay. To reduce the false-positivity rate common with molecular methods, this assay isolates and detects genomic material only from viable microorganisms in the blood by incorporating a novel precursor step to selectively lyse host and non-viable microbial cells and remove cell-free genomic material prior to lysis and analysis of microbial cells. Here, we demonstrate that the assay is free of interference from host immune cells and common antimicrobial agents at elevated concentrations. We also demonstrate the accuracy of this technology in a prospective cohort pilot study of individuals with known sepsis/BSI status, including samples from both positive and negative individuals.

IMPORTANCE

Blood culture remains the "gold standard" for the diagnosis of sepsis/bloodstream infection (BSI) but has many limitations which may lead to a delay in appropriate and accurate treatment in patients. Molecular diagnostic methods have the potential for markedly improving the management of such patients through faster turnaround times and increased accuracy. But molecular diagnostic methods have not been widely adopted for the identification of BSIs. By incorporating a precursor step of selective lysis of host and non-viable microorganisms, our resistance and pathogen ID (RaPID)/BSI molecular assay addresses many limitations of blood culture and other molecular assay. The RaPID/BSI assay has an approximate turnaround time of 4 hours, thereby significantly reducing the time to appropriate and accurate diagnosis of causative microorganisms in such patients. The short turnaround time also allows for close to real-time tracking of pathogenic clearance of microorganisms from the blood of these patients or if a change of antimicrobial regimen is required. Thus, the RaPID/BSI molecular assay helps with optimization of antimicrobial stewardship; prompt and accurate diagnosis of sepsis/BSI could help target timely treatment and reduce mortality and morbidity in such patients.

Passive microfluidic devices for cell separation

The separation of specific cell populations is instrumental in gaining insights into cellular processes, elucidating disease mechanisms, and advancing applications in tissue engineering, regenerative medicine, diagnostics, and cell therapies. Microfluidic methods for cell separation have propelled the field forward, benefitting from miniaturization, advanced fabrication technologies, a profound understanding of fluid dynamics governing particle separation mechanisms, and a surge in interdisciplinary investigations focused on diverse applications. Cell separation methodologies can be categorized according to their underlying separation mechanisms. Passive microfluidic separation systems rely on channel structures and fluidic rheology, obviating the necessity for external force fields to facilitate label-free cell separation. These passive approaches offer a compelling combination of cost-effectiveness and scalability when compared to active methods that depend on external fields to manipulate cells. This review delves into the extensive utilization of passive microfluidic techniques for cell separation, encompassing various strategies such as filtration, sedimentation, adhesion-based techniques, pinched flow fractionation (PFF), deterministic lateral displacement (DLD), inertial microfluidics, hydrophoresis, viscoelastic microfluidics, and hybrid microfluidics. Besides, the review provides an in-depth discussion concerning cell types, separation markers, and the commercialization of these technologies. Subsequently, it outlines the current challenges faced in the field and presents a forward-looking perspective on potential future developments. This work hopes to aid in facilitating the dissemination of knowledge in cell separation, guiding future research, and informing practical applications across diverse scientific disciplines.

Effect of nanoporous membranes thickness in electrochemical biosensing performance: application for the detection of a wound infection biomarker

Introduction: Nanoporous alumina membranes present a honeycomb-like structure characterized by two main parameters involved in their performance in electrochemical immunosening: pore diameter and pore thickness. Although this first one has been deeply studied, the effect of pore thickness in electrochemical-based nanopore immunosensors has been less taken into consideration. Methods: In this work, the influence of the thickness of nanoporous membranes in the steric blockage is studied for the first time, through the formation of an immunocomplex in their inner walls. Finally, the optimal nanoporous membranes were applied to the detection of catalase, an enzyme related with chronic wound infection and healing. Results: Nanoporous alumina membranes with a fixed pore diameter (60 nm) and variable pore thicknesses (40, 60, 100 μm) have been constructed and evaluated as immunosensing platform for protein detection. Our results show that membranes with a thickness of 40 μm provide a higher sensitivity and lower limit-of-detection (LOD) compared to thicker membranes. This performance is even improved when compared to commercial membranes (with 20 nm pore diameter and 60 μm pore thickness), when applied for human IgG as model analyte. A label-free immunosensor using a monoclonal antibody against anti-catalase was also constructed, allowing the detection of catalase in the range of 50-500 ng/mL and with a LOD of 1.5 ng/mL. The viability of the constructed sensor in real samples was also tested by spiking artificial wound infection solutions, providing recovery values of 110% and 118%. Discussion: The results obtained in this work evidence the key relevance of the nanochannel thickness in the biosensing performance. Such findings will illuminate nanoporous membrane biosensing research, considering thickness as a relevant parameter in electrochemical-based nanoporous membrane sensors.

Diagnosis of human leptospirosis: systematic review and meta-analysis of the diagnostic accuracy of the Leptospira microscopic agglutination test, PCR targeting Lfb1, and IgM ELISA to Leptospira fainei serovar Hurstbridge

BACKGROUND

Leptospirosis is an underdiagnosed infectious disease with non-specific clinical presentation that requires laboratory confirmation for diagnosis. The serologic reference standard remains the microscopic agglutination test (MAT) on paired serum samples. However, reported estimates of MAT's sensitivity vary. We evaluated the accuracy of four index tests, MAT on paired samples as well as alternative standards for leptospirosis diagnosis: MAT on single acute-phase samples, polymerase chain reaction (PCR) with the target gene Lfb1, and ELISA IgM with Leptospira fainei serovar Hurstbridge as an antigen.

METHODS

We performed a systematic review of studies reporting results of leptospirosis diagnostic tests. We searched eight electronic databases and selected studies that tested human blood samples and compared index tests with blood culture and/or PCR and/or MAT (comparator tests). For MAT selection criteria we defined a threshold for single acute-phase samples according to a national classification of leptospirosis endemicity. We used a Bayesian random-effect meta-analysis to estimate the sensitivity and specificity of MAT in single acute-phase and paired samples separately, and assessed risk of bias using the Quality Assessment of Studies of Diagnostic Accuracy Approach- 2 (QUADAS-2) tool.

RESULTS

For the MAT accuracy evaluation, 15 studies were included, 11 with single acute-phase serum, and 12 with paired sera. Two included studies used PCR targeting the Lfb1 gene, and one included study used IgM ELISA with Leptospira fainei serovar Hurstbridge as antigen. For MAT in single acute-phase samples, the pooled sensitivity and specificity were 14% (95% credible interval [CrI] 3-38%) and 86% (95% CrI 59-96%), respectively, and the predicted sensitivity and specificity were 14% (95% CrI 0-90%) and 86% (95% CrI 9-100%). Among paired MAT samples, the pooled sensitivity and specificity were 68% (95% CrI 32-92%) and 75% (95% CrI 45-93%) respectively, and the predicted sensitivity and specificity were 69% (95% CrI 2-100%) and 75% (2-100%).

CONCLUSIONS

Based on our analysis, the accuracy of MAT in paired samples was not high, but it remains the reference standard until a more accurate diagnostic test is developed. Future studies that include larger numbers of participants with paired samples will improve the certainty of accuracy estimates.

Comparison of metagenomic next-generation sequencing and blood culture for diagnosis of bloodstream infections

Objectives

This study aimed to evaluate the clinical performance of plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) for pathogen detection in patients with sepsis.

Methods

A total of 43 pairs of blood and plasma samples form 33 blood culture-positive patients were used as testing samples in metagenomic NGS (mNGS) and NGS of 16S ribosomal RNA gene amplicons (16S rRNA NGS). The results of routine tests, including microbial culture, complete blood count, and biochemical tests, were collected from electronic medical records.

Results

Using blood as an mNGS testing sample, the proportion of host DNA was 99.9%, with only three bacteria and no fungi detected. When using plasma in mNGS, the proportion of host DNA was approximately 97%, with 84 bacteria and two fungi detected. Notably, 16S rRNA NGS detected 15 and 16 bacteria in 43 pairs of blood and plasma samples, respectively. Blood culture detected 49 bacteria (23 gram-negative bacilli and 26 gram-positive cocci) and four fungi, with 14 bacteria considered contaminants by clinical microbiologists. For all blood cultures, plasma cfDNA mNGS detected 78.26% (19/23) gram-negative rods, 17% (2/12) gram-positive cocci, and no fungi. Compared to blood cultures, the sensitivity and specificity of plasma cfDNA mNGS for detecting bacteria and fungi were 62.07% and 57.14%, respectively.

Conclusion

Compared to blood, plasma is more suitable for the detection of bloodstream infections using mNGS and is less affected by host DNA. The positive detection rate of plasma cfDNA mNGS for bloodstream infections caused by gram-negative bacteria was higher than that caused by gram-positive cocci.

Machine learning and feature extraction for rapid antimicrobial resistance prediction of Acinetobacter baumannii from whole-genome sequencing data

Background

Whole-genome sequencing (WGS) has contributed significantly to advancements in machine learning methods for predicting antimicrobial resistance (AMR). However, the comparisons of different methods for AMR prediction without requiring prior knowledge of resistance remains to be conducted.

Methods

We aimed to predict the minimum inhibitory concentrations (MICs) of 13 antimicrobial agents against Acinetobacter baumannii using three machine learning algorithms (random forest, support vector machine, and XGBoost) combined with k-mer features extracted from WGS data.

Results

A cohort of 339 isolates was used for model construction. The average essential agreement and category agreement of the best models exceeded 90.90% (95%CI, 89.03-92.77%) and 95.29% (95%CI, 94.91-95.67%), respectively; the exceptions being levofloxacin, minocycline and imipenem. The very major error rates ranged from 0.0 to 5.71%. We applied feature selection pipelines to extract the top-ranked 11-mers to optimise training time and computing resources. This approach slightly improved the prediction performance and enabled us to obtain prediction results within 10 min. Notably, when employing these top-ranked 11-mers in an independent test dataset (120 isolates), we achieved an average accuracy of 0.96.

Conclusion

Our study is the first to demonstrate that AMR prediction for A. baumannii using machine learning methods based on k-mer features has competitive performance over traditional workflows; hence, sequence-based AMR prediction and its application could be further promoted. The k-mer-based workflow developed in this study demonstrated high recall/sensitivity and specificity, making it a dependable tool for MIC prediction in clinical settings.

Divergent genetic landscapes drive lower levels of AmpC induction and stable de-repression in Serratia marcescens compared to Enterobacter cloacae

The chromosomally encoded AmpC beta-lactamase is widely distributed throughout the Enterobacterales. When expressed at high levels through transient induction or stable de-repression, resistance to ceftriaxone, a commonly used antibiotic, can develop. Recent clinical guidance suggests, based on limited evidence, that resistance may be less likely to develop in Serratia marcescens compared to the better-studied Enterobacter cloacae and recommends that ceftriaxone may be used if the clinical isolate tests susceptible. We sought to generate additional data relevant to this recommendation. AmpC de-repression occurs predominantly because of mutation in the ampD peptidoglycan amidohydrolase. We find that, in contrast to E. cloacae, where deletion of ampD results in high-level ceftriaxone resistance (with ceftriaxone MIC = 96 µg/mL), in S. marcescens deletion of two amidohydrolases (ampD and amiD2) is necessary for AmpC de-repression, and the resulting ceftriaxone MIC is 1 µg/mL. Two mechanisms for this difference were identified. We find both a higher relative increase in ampC transcript level in E. cloacae ΔampD compared to S. marcescens ΔampDΔamiD2, as well as higher in vivo efficiency of ceftriaxone hydrolysis by the E. cloacae AmpC enzyme compared to the S. marcescens AmpC enzyme. We also observed higher relative levels of transient AmpC induction in E. cloacae vs S. marcescens when exposed to ceftriaxone. In time-kill curves, this difference translates into the survival of E. cloacae but not S. marcescens at clinically relevant ceftriaxone concentrations. In summary, our findings can explain the decreased propensity for on-treatment ceftriaxone resistance development in S. marcescens, thereby supporting recently issued clinical guidance.

Pathogen Discovery in the Post-COVID Era

Pathogen discovery plays a crucial role in the fields of infectious diseases, clinical microbiology, and public health. During the past four years, the global response to the COVID-19 pandemic highlighted the importance of early and accurate identification of novel pathogens for effective management and prevention of outbreaks. The post-COVID era has ushered in a new phase of infectious disease research, marked by accelerated advancements in pathogen discovery. This review encapsulates the recent innovations and paradigm shifts that have reshaped the landscape of pathogen discovery in response to the COVID-19 pandemic. Primarily, we summarize the latest technology innovations, applications, and causation proving strategies that enable rapid and accurate pathogen discovery for both acute and historical infections. We also explored the significance and the latest trends and approaches being employed for effective implementation of pathogen discovery from various clinical and environmental samples. Furthermore, we emphasize the collaborative nature of the pandemic response, which has led to the establishment of global networks for pathogen discovery.

Effect of Salicylic Acid on the gene expression of FnbA and FnbB genes in Staphylococcus hominis

BACKGROUND

Staphylococcus hominis is an opportunistic pathogen that expresses surface proteins, which are adhesive proteins that play a major role in biofilm formation. Biofilm is a protective layer that provides S. hominis bacteria with greater antibiotic resistance and promotes its adherence to biomedical surfaces, facilitating its entry into the bloodstream.

OBJECTIVE

This research aimed to investigate the activity of Salicylic Acid (SA) and its effect on the gene expression of biofilm genes (FnbA and FnbB genes).

METHODS

A total of 150 blood specimens were collected from patients. The specimens were cultured in broth media of the BacT/ALERT® system and subcultured on blood and chocolate agar. Bacteria were detected using the VITEK2 system. FnbA and FnbB genes were detected using PCR. The broth microdilution method performed the minimum inhibitory concentration (MIC) of Salicylic acid (SA) on S. hominis isolates with both genes. Detection of the gene expression levels of FnbA and FnbB genes was assessed using Real-Time PCR(RT-PCR).

RESULTS

The results showed that out of the 150 specimens collected, 35 were S. hominis. The detection of S. hominis bacteria was performed by PCR amplification of two genes FnbA and FnbB and showed 100% and 17.14% of isolates were positive for genes FnbA and FnbB, respectively. The expression of FnbA and FnbB genes was decreased in samples treated with SA compared with untreated ones.

CONCLUSION

In conclusion, there is a significant impact of SA on the prevention of biofilm formation of S. hominis through the suppression of gene expression, specifically FnbA and FnbB. This could enhance susceptibility to antimicrobial treatments. However, more research is required to determine whether SA leads to the selection of resistant bacteria.

Metagenomic identification of pathogens and antimicrobial-resistant genes in bacterial positive blood cultures by nanopore sequencing

Nanopore sequencing workflows have attracted increasing attention owing to their fast, real-time, and convenient portability. Positive blood culture samples were collected from patients with bacterial bloodstream infection and tested by nanopore sequencing. This study compared the sequencing results for pathogen taxonomic profiling and antimicrobial resistance genes to those of species identification and phenotypic drug susceptibility using traditional microbiology testing. A total of 37 bacterial positive blood culture results of strain genotyping by nanopore sequencing were consistent with those of mass spectrometry. Among them, one mixed infection of bacteria and fungi was identified using nanopore sequencing and confirmatory quantitative polymerase chain reaction. The amount of sequencing data was 21.89 ± 8.46 MB for species identification, and 1.0 MB microbial strain data enabled accurate determination. Data volumes greater than or equal to 94.6 MB nearly covered all the antimicrobial resistance genes of the bacteria in our study. In addition, the results of the antimicrobial resistance genes were compared with those of phenotypic drug susceptibility testing for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Therefore, the nanopore sequencing platform for rapid identification of causing pathogens and relevant antimicrobial resistance genes complementary to conventional blood culture outcomes may optimize antimicrobial stewardship management for patients with bacterial bloodstream infection.