PCR-based Sepsis@Quick test is superior in comparison with blood culture for identification of sepsis-causative pathogens

From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases

Infectious diseases impose a significant burden on global health systems due to high morbidity and mortality rates. According to the World Health Organization, millions die from infectious diseases annually, often due to delays in accurate diagnosis. Traditional diagnostic methods in clinical microbiology, primarily culture-based techniques, are time-consuming and may fail with hard-to-culture pathogens. Molecular biology advancements, notably the polymerase chain reaction (PCR), have revolutionized infectious disease diagnostics by allowing rapid and sensitive detection of pathogens' genetic material. PCR has become the gold standard for many infections, particularly highlighted during the COVID-19 pandemic. Following PCR, next-generation sequencing (NGS) has emerged, enabling comprehensive genomic analysis of pathogens, thus facilitating the detection of new strains and antibiotic resistance tracking. Innovative approaches like CRISPR technology are also enhancing diagnostic precision by identifying specific DNA/RNA sequences. However, the implementation of these methods faces challenges, particularly in low- and middle-income countries due to infrastructural and financial constraints. This review will explore the role of molecular diagnostic methods in infectious disease diagnosis, comparing their advantages and limitations, with a focus on PCR and NGS technologies and their future potential.

Broviac Catheter-Related Aortic Valve Infective Endocarditis Complicated With Massive Aortic Regurgitation Requiring Emergency Surgery: A Case Report

Introduction: Broviac catheter is a type of central venous catheter (CVC) used for long-term parenteral nutrition in specific patients, e.g., diagnosed with intestinal failure as short bowel syndrome (SBS). The way of the catheter insertion is conceived to minimalize the risk of infections. However, CVC-related blood stream infections (CVC-BSIs), including infective endocarditis (IE), remain most important complications associated with Broviac catheter. Staphylococcus epidermidis stands out as a prevalent pathogen. The increasing number of CVCs results in an increased incidence of healthcare-associated IE. Complete parenteral treatment is an independent risk that increases the likelihood of IE. Treatment of IE is mainly based on antibiotic therapy, but in certain cases, surgical treatment is needed. Presentation of Case: A 71-year-old female with SBS who had been receiving total parenteral nutrition through the Broviac catheter for several months was admitted in a serious condition with significant weakness, increasing shortness of breath, deteriorating cough, fever, low blood pressure, and heart palpitations. Echocardiography revealed severe aortic valve IE with a large, longitudinal, highly mobile vegetation (up to 40 mm) and massive aortic regurgitation with pulmonary edema. Fast pathogen detection in the patients' blood (S. epidermidis) was obtained using PCR-based multiplex test. Due to life-threatening conditions, emergency surgery with aortic valve replacement was performed. Consistent rehabilitation resulted in good condition achievement. Follow-up echocardiography showed normal function of the aortic valve bioprosthesis. Conclusion: The use of CVC, including Broviac catheter, is associated with an increased risk of infections, including IE. Treatment-resistant severe HF complicating IE requires emergency surgery.

Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection

Bloodstream infection is a major cause of morbidity and death worldwide. Timely and appropriate treatment can reduce mortality among critically ill patients. Current diagnostic methods are too slow to inform precise antibiotic choice, leading to the prescription of empirical antibiotics, which may fail to cover the resistance profile of the pathogen, risking poor patient outcomes. Additionally, overuse of broad-spectrum antibiotics may lead to more resistant organisms, putting further pressure on the dwindling pipeline of antibiotics, and risk transmission of these resistant organisms in the health care environment. Therefore, rapid diagnostics are urgently required to better inform antibiotic choice early in the course of treatment. Sequencing offers great promise in reducing time to microbiological diagnosis; however, the amount of host DNA compared with the pathogen in patient samples presents a significant obstacle. Various host-depletion and bacterial-enrichment strategies have been used in samples, such as saliva, urine, or tissue. However, these methods have yet to be collectively integrated and/or extensively explored for rapid bloodstream infection diagnosis. Although most of these workflows possess individual strengths, their lack of analytical/clinical sensitivity and/or comprehensiveness demands additional improvements or synergistic application. This review provides a distinctive classification system for various methods based on their working principles to guide future research, and discusses their strengths and limitations and explores potential avenues for improvement to assist the reader in workflow selection.

Identifying antibiotic-resistant strains via cell sorting and elastic-light-scatter phenotyping

The proliferation and dissemination of antimicrobial-resistant bacteria is an increasingly global challenge and is attributed mainly to the excessive or improper use of antibiotics. Currently, the gold-standard phenotypic methodology for detecting resistant strains is agar plating, which is a time-consuming process that involves multiple subculturing steps. Genotypic analysis techniques are fast, but they require pure starting samples and cannot differentiate between viable and non-viable organisms. Thus, there is a need to develop a better method to identify and prevent the spread of antimicrobial resistance. This work presents a novel method for detecting and identifying antibiotic-resistant strains by combining a cell sorter for bacterial detection and an elastic-light-scattering method for bacterial classification. The cell sorter was equipped with safety mechanisms for handling pathogenic organisms and enabled precise placement of individual bacteria onto an agar plate. The patterning was performed on an antibiotic-gradient plate, where the growth of colonies in sections with high antibiotic concentrations confirmed the presence of a resistant strain. The antibiotic-gradient plate was also tested with an elastic-light-scattering device where each colony's unique colony scatter pattern was recorded and classified using machine learning for rapid identification of bacteria. Sorting and patterning bacteria on an antibiotic-gradient plate using a cell sorter reduced the number of subculturing steps and allowed direct qualitative binary detection of resistant strains. Elastic-light-scattering technology is a rapid, label-free, and non-destructive method that permits instantaneous classification of pathogenic strains based on the unique bacterial colony scatter pattern. KEY POINTS: • Individual bacteria cells are placed on gradient agar plates by a cell sorter • Laser-light scatter patterns are used to recognize antibiotic-resistant organisms • Scatter patterns formed by colonies correspond to AMR-associated phenotypes.

Detection of Bartonella spp. in farmed deer (Artiodactyla: Cervidae) using multiplex assays in the Qinghai-Tibet Plateau, China

In this study, we investigated the prevalence of Bartonella in deer from Qilian County, Qinghai Province, China. Blood samples were collected from 69 red deer, 40 white-lipped deer, and 27 sika deer. The detection of Bartonella spp. has been conducted. The overall prevalence of Bartonella was 33.6% (46/135). Species-specific prevalence was 50.72% in red deer (35/69), 20.00% in white-lipped deer (8/40), and 11.11% in sika deer (3/27). There were significant differences in the prevalence rates among the different species of deer. The amplicon sequence comparison revealed a high homology of the ruminant-associated Bartonella spp. Nanopore sequencing further confirmed the results. Bartonella reads were presented in each of the qPCR-positive samples. Phylogenetic analysis indicated that the Bartonella sequences detected in deer blood were closely related to ruminant-borne Bartonella spp. In summary, we reported the Bartonella prevalence of different deer species in Qinghai, and there were at least one species of ruminant-associated Bartonella, B. schoenbuchensis.

IMPORTANCE

This is the first report about Bartonella infections in the deer population from China. We found that there were two species of Bartonella and an unidentified species of Bartonella among the unculturing strains carried by these deer populations. We first used Nanopore sequencing to detect Bartonella from deer blood samples and indicated that Nanopore sequencing is beneficial to detect pathogens due to its advantage of real-time and high sensitivity.

Spectrum and antimicrobial resistance in acute exacerbation of chronic obstructive pulmonary disease with pneumonia: a cross-sectional prospective study from Vietnam

BACKGROUND

Respiratory infections have long been recognized as a primary cause of acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). Additionally, the emergence of antimicrobial resistance has led to an urgent and critical situation in developing countries, including Vietnam. This study aimed to investigate the distribution and antimicrobial resistance of bacteria in patients with AE-COPD using both conventional culture and multiplex real-time PCR. Additionally, associations between clinical characteristics and indicators of pneumonia in these patients were examined.

METHODS

This cross-sectional prospective study included 92 AE-COPD patients with pneumonia and 46 without pneumonia. Sputum specimens were cultured and examined for bacterial identification, and antimicrobial susceptibility was determined for each isolate. Multiplex real-time PCR was also performed to detect ten bacteria and seven viruses.

RESULTS

The detection rates of pathogens in AE-COPD patients with pneumonia were 92.39%, compared to 86.96% in those without pneumonia. A total of 26 pathogenic species were identified, showing no significant difference in distribution between the two groups. The predominant bacteria included Klebsiella pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae, followed by Acinetobacter baumannii and Streptococcus mitis. There was a slight difference in antibiotic resistance between bacteria isolated from two groups. The frequency of H. influenzae was notably greater in AE-COPD patients who experienced respiratory failure (21.92%) than in those who did not (9.23%). S. pneumoniae was more common in patients with stage I (44.44%) or IV (36.36%) COPD than in patients with stage II (17.39%) or III (9.72%) disease. ROC curve analysis revealed that C-reactive protein (CRP) levels could distinguish patients with AE-COPD with and without pneumonia (AUC = 0.78).

CONCLUSION

Gram-negative bacteria still play a key role in the etiology of AE-COPD patients, regardless of the presence of pneumonia. This study provides updated evidence for the epidemiology of AE-COPD pathogens and the appropriate selection of antimicrobial agents in Vietnam.

Nano-Biotechnology for Bacteria Identification and Potent Anti-bacterial Properties: A Review of Current State of the Art

Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed.

Point-of-care diagnostics for sepsis using clinical biomarkers and microfluidic technology

Sepsis is a life-threatening immune response which is caused by a wide variety of sources and is a leading cause of mortality globally. Rapid diagnosis and appropriate antibiotic treatment are critical for successful patient outcomes; however, current molecular diagnostic techniques are time-consuming, costly and require trained personnel. Additionally, there is a lack of rapid point-of-care (POC) devices available for sepsis detection despite the urgent requirements in emergency departments and low-resource areas. Recent advances have been made toward developing a POC test for early sepsis detection that will be more rapid and accurate compared to conventional techniques. Within this context, this review discusses the use of current and novel biomarkers for early sepsis diagnosis using microfluidics devices for POC testing.

Antimicrobial Stewardship on Patients with Neutropenia: A Narrative Review Commissioned by Microorganisms

The emergence of antibiotic resistance poses a global health threat. High-risk patients such as those with neutropenia are particularly vulnerable to opportunistic infections, sepsis, and multidrug-resistant infections, and clinical outcomes remain the primary concern. Antimicrobial stewardship (AMS) programs should mainly focus on optimizing antibiotic use, decreasing adverse effects, and improving patient outcomes. There is a limited number of published studies assessing the impact of AMS programs on patients with neutropenia, where early appropriate antibiotic choice can be the difference between life and death. This narrative review updates the current advances in strategies of AMS for bacterial infections among high-risk patients with neutropenia. Diagnosis, drug, dose, duration, and de-escalation (5D) are the core variables among AMS strategies. Altered volumes of distribution can make standard dose regimens inadequate, and developing skills towards a personalized approach represents a major advance in therapy. Intensivists should partner antibiotic stewardship programs to improve patient care. Assembling multidisciplinary teams with trained and dedicated professionals for AMS is a priority.

Relationship between antibiotic consumption pattern and antibiotic resistance in neonatal sepsis

Background and aim

Inappropriate use of antibiotics may increase antimicrobial resistance (AMR) among different microorganisms and may lead to treatment failure in neonatal septicemia. The aim of this study was to recognize the most common microorganisms responsible for neonatal sepsis and to evaluate the trend of change of resistance pattern among microorganisms.

Methods

This study was done retrospectively on 344 cases diagnosed with neonatal sepsis, including both early and late onset cases, admitted to the tertiary care teaching hospital of southern India from January 2012 to July 2017. Accordingly, 231 culture positive neonatal sepsis cases were collected from hospital data base and analyzed. Culture positive cases within 72 hours of life were termed as early onset while after 72 hours were late onset. Antibiotics utilization during the period was calculated using WHO AMC tool and reported as (DDD)/100 bed days.

Results

Klebsiella pneumoniae with 56 (21.8%) and Coagulase negative Staphylococcus with 52 (20.2%) cases were the most frequent isolated organisms which were responsible for 55.8% and 14.6% of deaths among the study subjects respectively. Amikacin (86.7%), vancomycin (52.3%) and ampicillin (40.6%) were the most used antibiotics in terms of DDD/100 bed days.

Conclusion

The results obtained from our study have brought substantial information on the antibiotic resistance pattern among microorganisms causing neonatal sepsis. Moreover, results obtained from this study can be used for designing antibiotic stewardship policies to prevent the emergence of resistance and to improve the treatment outcome.

Predictive Score for Carbapenem-Resistant Gram-Negative Bacilli Sepsis: Single-Center Prospective Cohort Study

A clinical-epidemiological score to predict CR-GNB sepsis to guide empirical antimicrobial therapy (EAT), using local data, persists as an unmet need. On the basis of a case-case-control design in a prospective cohort study, the predictive factors for CR-GNB sepsis were previously determined as prior infection, use of mechanical ventilation and carbapenem, and length of hospital stay. In this study, each factor was scored according to the logistic regression coefficients, and the ROC curve analysis determined its accuracy in predicting CR-GNB sepsis in the entire cohort. Among the total of 629 admissions followed by 7797 patient-days, 329 single or recurrent episodes of SIRS/sepsis were enrolled, from August 2015 to March 2017. At least one species of CR-GNB was identified as the etiology in 108 (33%) episodes, and 221 were classified as the control group. The cutoff point of ≥3 (maximum of 4) had the best sensitivity/specificity, while ≤1 showed excellent sensitivity to exclude CR-GNB sepsis. The area under the curve was 0.80 (95% CI: 0.76-0.85) and the number needed to treat was 2.0. The score may improve CR-GNB coverage and spare polymyxins with 22% (95% CI: 17-28%) adequacy rate change. The score has a good ability to predict CR-GNB sepsis and to guide EAT in the future.

The characteristics of bacteremia among patients with acute febrile illness requiring hospitalization in Indonesia

Blood culturing remains the "gold standard" for bloodstream infection (BSI) diagnosis, but the method is inaccessible to many developing countries due to high costs and insufficient resources. To better understand the utility of blood cultures among patients in Indonesia, a country where blood cultures are not routinely performed, we evaluated data from a previous cohort study that included blood cultures for all participants. An acute febrile illness study was conducted from July 2013 to June 2016 at eight major hospitals in seven provincial capitals in Indonesia. All participants presented with a fever, and two-sided aerobic blood cultures were performed within 48 hours of hospital admission. Positive cultures were further assessed for antimicrobial resistance (AMR) patterns. Specimens from participants with negative culture results were screened by advanced molecular and serological methods for evidence of causal pathogens. Blood cultures were performed for 1,459 of 1,464 participants, and the 70.6% (1,030) participants that were negative by dengue NS1 antigen test were included in further analysis. Bacteremia was observed in 8.9% (92) participants, with the most frequent pathogens being Salmonella enterica serovar Typhi (41) and Paratyphi A (10), Escherichia coli (14), and Staphylococcus aureus (10). Two S. Paratyphi A cases had evidence of AMR, and several E. coli cases were multidrug resistant (42.9%, 6/14) or monoresistant (14.3%, 2/14). Culture contamination was observed in 3.6% (37) cases. Molecular and serological assays identified etiological agents in participants having negative cultures, with 23.1% to 90% of cases being missed by blood cultures. Blood cultures are a valuable diagnostic tool for hospitalized patients presenting with fever. In Indonesia, pre-screening patients for the most common viral infections, such as dengue, influenza, and chikungunya viruses, would maximize the benefit to the patient while also conserving resources. Blood cultures should also be supplemented with advanced laboratory tests when available.

Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting

Aim

The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise.

Methods

DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics.

Results

Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30).

Conclusion

Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00530-6.

Point-of-care diagnosis of invasive non-typhoidal Salmonella enterica in bloodstream infections using immunomagnetic capture and loop-mediated isothermal amplification

Invasive non-typhoidal salmonellosis is gaining worldwide attention as an emerging disease cluster among bloodstream infections. The disease has the highest burden among immunocompromised and malnourished children in resource-limited areas due to poor access to reliable and rapid diagnostics. Point-of-care (POC) diagnostics are promising for use in such low infrastructure laboratory settings. However, there still remains a major challenge for POC testing to deal with the complexity of blood matrices in rapid detection of an extremely low concentration of blood-borne pathogens. In this work, the challenges were addressed by combining magnetic bead based pathogen concentration and Loop Mediated Isothermal Amplification (LAMP) technology. Sensitivity and performance of the combined approach were determined and compared with a direct PCR method. A direct visual detection strategy, adapted using SYTO-24 DNA intercalating dye, resulted in a limit of detection (LoD) as low as 14 CFU/mL in blood samples with a total analysis time of less than 2 h, including sample preparation. This approach has the potential for wide application as a high-throughput POC testing method to analyze pathogens in clinical, food, feed and environmental samples.

Circulating miR-147b as a diagnostic marker for patients with bacterial sepsis and septic shock

BACKGROUND

Early diagnosis, precise antimicrobial treatment and subsequent patient stratification can improve sepsis outcomes. Circulating biomarkers such as plasma microRNAs (miRNAs) have proven to be surrogates for diagnosis, severity and case management of infections. The expression of four selected miRNAs (miR-146-3p, miR-147b, miR-155 and miR-223) was validated for their prognostic and diagnostic potential in a clinically defined cohort of patients with sepsis and septic shock.

METHODS

The expression of plasma miRNAs was quantified by quantitative PCR (qPCR) in patients with bacterial sepsis (n = 78), in patients with septic shock (n = 52) and in patients with dengue haemorrhagic fever (DHF; n = 69) and in healthy controls (n = 82).

RESULTS

The expression of studied miRNA was significantly increased in patients with bacterial sepsis and septic shock. The plasma miR-147b was able to differentiate bacterial sepsis from non-sepsis and septic shock (AUC = 0.77 and 0.8, respectively, p≤ 0.05), while the combination of plasma miR-147b and procalcitonin (PCT) predicted septic shock (AUC = 0.86, p≤ 0.05).

CONCLUSIONS

The plasma miR-147b may be an useful biomarker independently or in combination with PCT to support clinical diagnosis of sepsis and equally prognosis of patients with septic shock.

A simple magnetic-assisted microfluidic method for rapid detection and phenotypic characterization of ultralow concentrations of bacteria

Isolation and enumeration of bacteria at ultralow concentrations and antibiotic resistance profiling are of great importance for early diagnosis and treatment of bacteremia. In this work, we describe a simple, rapid, and versatile magnetic-assisted microfluidic method for rapid bacterial detection. The developed method enables magnetophoretic loading of bead-captured bacteria into the microfluidic chamber under external static and dynamic magnetic fields in 4 min. A shallow microfluidic chamber design that enables the monolayer orientation and transportation of the beads and a glass substrate with a thickness of 0.17 mm was utilized to allow high-resolution fluorescence imaging for quantitative detection. Escherichia coli (E. coli) with green fluorescent protein (GFP)-expressing gene and streptavidin-modified superparamagnetic microbeads were used as model bacteria and capturing beads, respectively. The specificity of the method was validated using Lactobacillus gasseri as a negative control group. The limit of detection and limit of quantification values were determined as 2 CFU/ml and 10 CFU/ml of E. coli, respectively. The magnetic-assisted microfluidic method is a versatile tool for the detection of ultralow concentrations of viable bacteria with the linear range of 5-5000 CFU/ml E. coli in 1 h, and providing growth curves and phenotypic characterization bead-captured E. coli in the following 5 h of incubation. Our results are promising for future rapid and sensitive antibiotic susceptibility testing of ultralow numbers of viable cells.

Sepsis in urology - where are we now? And where are we going?

CONTEXT

There has been heightened public awareness of the important issue of sepsis in the lay press in recent years with a focus on rapid detection and treatment. Within the field of Urology, how good are we at identifying, preventing and managing sepsis? Review: Reducing the morbidity and mortality associated with sepsis requires a multi-faceted approach including heightening awareness, prevention, early recognition of deterioration, escalation of care when necessary, implementation of antibiotic stewardship and the development of novel anti-microbial treatment strategies.

DISCUSSION

We review some of the aspects of sepsis management within our field that are working effectively and others that could potentially be optimised.

miRNAs as Biomarkers in Disease: Latest Findings Regarding Their Role in Diagnosis and Prognosis

MicroRNAs (miRNAs) represent a class of small, non-coding RNAs with the main roles of regulating mRNA through its degradation and adjusting protein levels. In recent years, extraordinary progress has been made in terms of identifying the origin and exact functions of miRNA, focusing on their potential use in both the research and the clinical field. This review aims at improving the current understanding of these molecules and their applicability in the medical field. A thorough analysis of the literature consulting resources available in online databases such as NCBI, PubMed, Medline, ScienceDirect, and UpToDate was performed. There is promising evidence that in spite of the lack of standardized protocols regarding the use of miRNAs in current clinical practice, they constitute a reliable tool for future use. These molecules meet most of the required criteria for being an ideal biomarker, such as accessibility, high specificity, and sensitivity. Despite present limitations, miRNAs as biomarkers for various conditions remain an impressive research field. As current techniques evolve, we anticipate that miRNAs will become a routine approach in the development of personalized patient profiles, thus permitting more specific therapeutic interventions.