Identification of bacterial pathogens in ascitic fluids from patients with suspected spontaneous bacterial peritonitis by use of broad-range PCR (16S PCR) coupled with high-resolution melt analysis. J Clin Microbiol. 2012;50:2428-2432. [PMID: 22573594 DOI: 10.1128/JCM.00345-12]

16S rRNA Next-Generation Sequencing May Not Be Useful for Examining Suspected Cases of Spontaneous Bacterial Peritonitis

Background and Objectives: Ascites, often associated with liver cirrhosis, poses diagnostic challenges, particularly in detecting bacterial infections. Traditional methods have limitations, prompting the exploration of advanced techniques such as 16S rDNA next-generation sequencing (NGS) for improved diagnostics in such low-biomass fluids. The aim of this study was to investigate whether the NGS method enhances detection sensitivity compared to a conventional ascites culture. Additionally, we aimed to explore the presence of a microbiome in the abdominal cavity and determine whether it has a sterile condition. Materials and Methods: Ten patients with clinically suspected spontaneous bacterial peritonitis (SBP) were included in this study. A traditional ascites culture was performed, and all ascites samples were subjected to 16S ribosomal RNA gene amplification and sequencing. 16S rRNA gene sequencing results were interpreted by comparing them to positive and negative controls for each sample. Results: Differential centrifugation was applied to all ascites samples, resulting in very small or no bacterial pellets being harvested. The examination of the 16S amplicon sequencing libraries indicated that the target amplicon products were either minimally visible or exhibited lower intensity than their corresponding negative controls. Contaminants present in the reagents were also identified in the ascites samples. Sequence analysis of the 16S rRNA gene of all samples showed microbial compositions that were akin to those found in the negative controls, without any bacteria isolated that were unique to the samples. Conclusions: The peritoneal cavity and ascites exhibit low bacterial biomass even in the presence of SBP, resulting in a very low positivity rate in 16S rRNA gene sequencing. Hence, the 16S RNA sequencing method does little to enhance the rate of positive samples compared to traditional culture methods, including in SBP cases.

Diagnosis of Bloodstream Infections: An Evolution of Technologies towards Accurate and Rapid Identification and Antibiotic Susceptibility Testing

Bloodstream infections (BSI) are a leading cause of death worldwide. The lack of timely and reliable diagnostic practices is an ongoing issue for managing BSI. The current gold standard blood culture practice for pathogen identification and antibiotic susceptibility testing is time-consuming. Delayed diagnosis warrants the use of empirical antibiotics, which could lead to poor patient outcomes, and risks the development of antibiotic resistance. Hence, novel techniques that could offer accurate and timely diagnosis and susceptibility testing are urgently needed. This review focuses on BSI and highlights both the progress and shortcomings of its current diagnosis. We surveyed clinical workflows that employ recently approved technologies and showed that, while offering improved sensitivity and selectivity, these techniques are still unable to deliver a timely result. We then discuss a number of emerging technologies that have the potential to shorten the overall turnaround time of BSI diagnosis through direct testing from whole blood—while maintaining, if not improving—the current assay’s sensitivity and pathogen coverage. We concluded by providing our assessment of potential future directions for accelerating BSI pathogen identification and the antibiotic susceptibility test. While engineering solutions have enabled faster assay turnaround, further progress is still needed to supplant blood culture practice and guide appropriate antibiotic administration for BSI patients.

Bacterial Pathogens, Drug-Resistance Profile and Its Associated Factors from Patients with Suspected Peritonitis in Southern Ethiopia

Background

Ascitic fluid plays a critical role in the microbiological diagnosis of peritonitis. Drug-resistant bacterial infection of the peritoneal cavity is becoming a public health threat. However, data on bacterial profile and antimicrobial-resistant pattern of isolates from the ascitic fluid are scarce. Thus, this study was aimed to assess drug-resistant bacteriological profiles and factors associated with peritonitis in southern Ethiopia.

Methods

An institutional-based cross-sectional study was conducted from March 2019 to December 2019. A semi-structured questionnaire was used to collect socio-demographic and clinical data. A total of 147 ascitic fluid samples were aseptically collected and inoculated onto blood agar, MacConkey agar, and chocolate agar. The inoculated culture media were incubated aerobically and micro-aerobically at 37°C for 48 hrs. Bacterial identification was done by standard protocols and the antimicrobial susceptibility testing by Kirby Bauer’s disk diffusion method. Logistic regression was used to identify the associated factors with bacterial peritonitis.

Results

Of the total study participants, the overall magnitude of bacterial peritonitis was 19.05% with a total of 30 bacterial isolates. Majority of the isolates were Gram negative bacteria with predominant species E. coli 36.67% followed by Gram positive S. aureus 13.33%. The multidrug resistant isolates accounts about 43.3% while a quarter of isolated S. aureus were methicillin resistant. The bacterial peritonitis was associated with recent history of surgery [AOR = 8.724, 95% CI: (2.688–28.314)], hospitalization more than seven days [AOR = 8.990, 95% CI: (2.755–29.342)], cirrhosis [AOR = 2.751, 95% CI: (1.109–6.822)] and alcoholism [AOR = 5.802, 95% CI: (1.948–17.285)].

Conclusion

Nearly half of the isolated bacteria were observed to be MDR, and this may alarm all healthcare workers and policymakers. Thus, continuous surveillance of antimicrobial resistance patterns along with associated factors is essential for regular monitoring of transmission of drug-resistant bacteria and the emergence of antibiotic resistance.

Feasibility of using the homologous parietal peritoneum as a vascular substitute for venous reconstruction during abdominal surgery: An animal model

BACKGROUND

The interest in vascular substitutes has recently increased. We evaluated the feasibility of using a homologous parietal peritoneum as a vascular substitute for venous reconstruction during abdominal surgery.

METHODS

The inferior vena cava was replaced with a homologous parietal peritoneum after cross-linking with glutaraldehyde in 36 rabbits. At 7, 14, and 28 days, the patency rate, outer and inner graft diameters, histology, and immunohistochemistry were evaluated.

RESULTS

Both the 7- and 14-day groups maintained vascular patency. Vascular patency was maintained in 3 rabbits in the 28-day group. The inner diameters of the anastomotic sites were 6.23 ± 0.18, 5.64 ± 0.16, and 2.34 ± 0.21 mm in the 7-day, 14-day, and 28-day groups, respectively. The midpoint inner diameters of the homologous parietal peritoneum grafts were 624 ± 0.46, 5.74 ± 0.26, and 2.14 ± 0.28 mm in each group, respectively. Endothelial cell proliferation on the homologous parietal peritoneum graft surfaces in all groups was based on the histological findings from the first group. Multiple neovascularizations of the homologous parietal peritoneum graft were found in the 14- and 28-day groups, indicating neo-media formation. Acute inflammation appeared to progress to the entire layer of the homologous parietal peritoneum graft without an intraluminal thrombus, but the graft was patent in the 14-day group. In the 28-day group, 6 rabbits showed near-total occlusion and a thrombus formed in the homologous parietal peritoneum graft at the anastomosis site with severe stricture; however, the rabbits were alive and had collateral vessel formation.

CONCLUSION

Using homologous parietal peritoneum is feasible for venous reconstruction in abdominal surgery.

Efficacy of 16S rRNA variable regions high-resolution melt analysis for bacterial pathogens identification in periprosthetic joint infections

BACKGROUND

Accurate and rapid identification of microorganisms causing periprosthetic joint infections (PJIs) are necessary for choosing an appropriate antibiotic therapy. Therefore, molecular techniques are suggested for diagnosis in suspected PJIs. The Broad-range PCR and High-Resolution Melt Analysis (HRMA) were evaluated for the identification of causative organisms of PJIs in this study.

RESULTS

For 47 of 63 specimens, both the culture and broad-range PCR were positive. The culture was found to be able of organism's detection in 74.6% (47/63) of patients. Of 47 positive cultures, 11 (23.4%) were polymicrobial and 36 (76.59%) were monomicrobial cultures, in which 34 (91.89%) cases were detected by HRM assay. The sensitivity, specificity of HRMA vs monomicrobial culture were 91.89, 93.75%, respectively. The sensitivity, specificity of total HRMA (mono + poly) vs culture were 82.92, 93.75%.

CONCLUSIONS

HRM assay coupled with broad-range PCR are effective screening, rapid, and relatively cost-effective methods for discrimination of PJIs especially in aiding culture method. Using computer programs such as the Matlab-2018b program for HRM data analysis is also valuable and helpful in diagnosis.

Rapid and sensitive identification of pleural and peritoneal infections by droplet digital PCR

Pleural and peritoneal infections cause substantial morbidity and mortality. Traditional diagnostic methods rely on the cultivation of clinical samples, which usually takes days to obtain report and holds a low detection sensitivity. In this study, we evaluated a 5-fluorescent-channel droplet digital PCR (ddPCR) system and 5 assay panels for culture-independent rapid pathogen detections directly from pleural and peritoneal fluid samples. Traditional culture of the same sample was used as reference. A total of 40 pleural fluid samples and 19 peritoneal fluid samples were tested in this study. Twenty-five positives including 4 polymicrobial infections by culture and 26 positives including 11 polymicrobial infections by ddPCR were detected for pleural fluid samples; 14 positives including 2 polymicrobial infections by culture and 15 positives including 3 polymicrobial infections by ddPCR were detected for peritoneal fluid samples. Klebsiella pneumoniae was the most common bacterium detected both in pleural and in peritoneal fluid samples. The sensitivity of the ddPCR assay for pleural and peritoneal fluid samples was 96% (95% confidence interval (CI) = 79.65 to 99.90%) and 92.86% (95% CI = 66.13 to 99.82%), respectively. The turnaround time of the ddPCR assay was approximately 3 h comparing with 38.30 ± 22.44 h for culture-based identifications. Our results demonstrated that the ddPCR assay is a rapid and sensitive method for identifying pathogens responsible for pleural and peritoneal infections and would be a promising approach for early diagnosis and optimizing treatment of infections.

Microbial Infections as a Trigger for Acute-on-Chronic Liver Failure: A Review

Microbial infection is an important cause of acute-on-chronic liver failure (ACLF), which is a syndrome that results in multiple organ dysfunction or failure and is accompanied by an increased short-term risk of mortality. Early detection and treatment of microbial infection can effectively reduce the mortality of patients with ACLF. However, antimicrobial resistance has recently increased due to the increased use of antimicrobial agents. Therefore, it is important to choose appropriate antibiotics and antifungal agents for early prevention or treatment of patients with microbial infection and ACLF to reduce the occurrence of drug resistance and to reduce patient mortality. This review summarizes the current status in the understanding of the epidemiology, pathogenesis, early diagnosis, treatment, and strategies for prevention of microbial infection in patients with ACLF.

Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing

In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.

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

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

Spontaneous pneumococcal peritonitis diagnosed by qPCR

Spontaneous bacterial peritonitis is an uncommon manifestation of invasive pneumococcal disease and frequently occurs when an underlying hepatic disease is present. Bacterial identification through culture can be particularly challenging in patients with prior or concurrent antimicrobial use. DNA amplification detects very few copies of target DNA under ideal conditions in CSF or pleural effusion and, therefore, can be useful in selected infections. A culture-negative spontaneous pneumococcal peritonitis without preexisting peritoneal disease diagnosed by qPCR is herein described.

Combination of vial culture and broad-range PCR for the diagnosis of spontaneous bacterial peritonitis: experience in a Greek tertiary care hospital

Spontaneous bacterial peritonitis (SBP) is often difficult to diagnose because bacteria in ascites cannot be detected accurately by conventional culture. In this study, we evaluated the use of broad-range 16S rRNA PCR, applied either directly to a total of 32 ascitic fluids (AFs) or to the AF vial cultures, after a long incubation of 14 days; the results were compared with those of AF vial cultures. Escherichia coli was isolated in four of 32 AF vial cultures (12.5%). The application of 16S rRNA PCR directly to AF detected only one of the four positive samples (sensitivity 25%, specificity 100%, positive predictive value (PPV) 100%, negative predictive value (NPV) 90.32%). However, the application of 16S rRNA PCR to AF vial cultures after 14 days of incubation correctly identified all the positive samples, including one more that was positive for Brucella mellitensis (sensitivity 100%, specificity 80%, PPV 80%, NPV 100%). The elongation of the incubation period of the AF vial cultures, combined with the use of 16S rRNA in negative vials, increases the possibility of identifying the causative agents of SBP and could be applied in the clinical laboratory.

A "Culture" Shift: Broad Bacterial Detection, Identification, and Antimicrobial Susceptibility Testing Directly from Whole Blood

BACKGROUND

The time required for bloodstream pathogen detection, identification (ID), and antimicrobial susceptibility testing (AST) does not satisfy the acute needs of disease management. Conventional methods take up to 3 days for ID and AST. Molecular diagnostics have reduced times for ID, but their promise to supplant culture is unmet because AST times remain slow. We developed a combined quantitative PCR (qPCR)-based ID+AST assay with sequential detection, ID, and AST of leading nosocomial bacterial pathogens.

METHODS

ID+AST was performed on whole blood samples by (a) removing blood cells, (b) brief bacterial enrichment, (c) bacterial detection and ID, and (d) species-specific antimicrobial treatment. Broad-spectrum qPCR of the internal transcribed spacer between the 16S and 23S was amplified for detection. High-resolution melting identified the species with a curve classifier. AST was enabled by Ct differences between treated and untreated samples.

RESULTS

A detection limit of 1 CFU/mL was achieved for Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. All species were accurately identified by unique melting curves. Antimicrobial minimum inhibitory concentrations were identified with Ct differences of ≥1 cycle. Using an RNA target allowed reduction of AST incubation time from 60 min to 5 min. Rapid-cycle amplification reduced qPCR times by 83% to 30 min.

CONCLUSIONS

Combined, sequential ID+AST protocols allow rapid and reliable detection, ID, and AST for the diagnosis of bloodstream infections, enabling conversion of empiric to targeted therapy by the second dose of antimicrobials.

Amplification of bacterial genomic DNA from all ascitic fluids with a highly sensitive polymerase chain reaction

Due to varying positive rates of polymerase chain reaction (PCR) amplification, interpretation of conventional PCR results for non-infectious ascites remains problematic. The present study developed a highly sensitive PCR protocol and investigated the positive rate of PCR for the 16S ribosomal (r)RNA gene in non-infectious ascites. Following the design of a new PCR primer pair for the 16S rRNA gene (800F and 1400R), the sequences of PCR products were analyzed and the lower limit for bacterial DNA detection evaluated. The positive rate of PCR for 16S rRNA gene in non-infectious ascites was also evaluated. PCR with the primer pair amplified the genomic DNA of 16S rRNA genes of major disease-causing bacterial strains. Additionally, PCR with this primer pair provided highly sensitive detection of bacterial genomic DNA (lower limit, 0.1 pg of template DNA). When DNA samples isolated from ascites were used, the 16S rRNA gene was amplified independently of the presence of bacterial infection. PCR products contained the genomic DNA fragments of multiple bacterial species. Bacterial genomic DNA can be amplified from all ascitic fluids using a highly sensitive PCR protocol. Careful attention is required to interpret the results based on simple amplification of 16S rRNA gene with conventional PCR.

Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling

In clinical diagnostics and pathogen detection, profiling of complex samples for low-level genotypes represents a significant challenge. Advances in speed, sensitivity, and extent of multiplexing of molecular pathogen detection assays are needed to improve patient care. We report the development of an integrated platform enabling the identification of bacterial pathogen DNA sequences in complex samples in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal PCR amplification, High Resolution Melting (HRM), and machine learning within 20,000 picoliter scale reactions, simultaneously. Clinically relevant concentrations of bacterial DNA molecules are separated by digitization across 20,000 reactions and amplified with universal primers targeting the bacterial 16S gene. Amplification is followed by HRM sequence fingerprinting in all reactions, simultaneously. The resulting bacteria-specific melt curves are identified by Support Vector Machine learning, and individual pathogen loads are quantified. The platform reduces reaction volumes by 99.995% and achieves a greater than 200-fold increase in dynamic range of detection compared to traditional PCR HRM approaches. Type I and II error rates are reduced by 99% and 100% respectively, compared to intercalating dye-based digital PCR (dPCR) methods. This technology could impact a number of quantitative profiling applications, especially infectious disease diagnostics.

Microbial Typing by Machine Learned DNA Melt Signatures

There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.

Detection of molecular bacterascites in decompensated cirrhosis defines a risk with decreased survival

BACKGROUND

The prognostic relevance of bacterial DNA (bactDNA) detection in ascitic fluid of patients with cirrhosis is still under debate. Using quantitative real-time PCR with broad-range primers targeting the V3 and V4 variable region of the 16S rRNA gene, we measured bactDNA concentrations in patients with and without leukocytic ascites and evaluated the impact on short-term survival.

PATIENTS AND METHODS

Ascites samples from 173 patients with decompensated cirrhosis were consecutively collected between February 2011 and December 2012. BactDNA-positive ascites samples were sequenced and chromatograms were identified using RipSeq. Clinical data collection and survival analyses were carried out retrospectively and correlated with ascites bactDNA levels.

RESULTS

BactDNA was detected qualitatively with a similar frequency in both nonleukocytic and leukocytic ascites [40% (57/144) and 43.5% (10/23), respectively; P=0.724]. However, the median bactDNA level was significantly higher in leukocytic ascites than in nonleukocytic ascites (1.2×10 vs. 5.7×10 copies/ml; P=0.008). Patients' survival was associated significantly with bactDNA level. The 30-day and 180-day survival was reduced if bactDNA was above the quantification limit of 520 copies/ml (84 and 63% vs. 72 and 43%, respectively; P<0.05) and worst if bactDNA was above 5000 copies/ml. The bacterial spectrum was dominated by Gram-positive strains as shown by direct sequencing.

CONCLUSION

BactDNA quantification in ascitic fluid samples using culture-independent 16S rRNA gene-based methods seems to be an interesting approach to identify patients at risk of reduced survival. Our study warrants further evaluation of antibiotic treatment in patients with molecular bacterascites.

Microwave-accelerated method for ultra-rapid extraction of Neisseria gonorrhoeae DNA for downstream detection

Nucleic acid-based detection of gonorrhea infections typically require a two-step process involving isolation of the nucleic acid, followed by detection of the genomic target often involving polymerase chain reaction (PCR)-based approaches. In an effort to improve on current detection approaches, we have developed a unique two-step microwave-accelerated approach for rapid extraction and detection of Neisseria gonorrhoeae (gonorrhea, GC) DNA. Our approach is based on the use of highly focused microwave radiation to rapidly lyse bacterial cells, release, and subsequently fragment microbial DNA. The DNA target is then detected by a process known as microwave-accelerated metal-enhanced fluorescence (MAMEF), an ultra-sensitive direct DNA detection analytical technique. In the current study, we show that highly focused microwaves at 2.45 GHz, using 12.3-mm gold film equilateral triangles, are able to rapidly lyse both bacteria cells and fragment DNA in a time- and microwave power-dependent manner. Detection of the extracted DNA can be performed by MAMEF, without the need for DNA amplification, in less than 10 min total time or by other PCR-based approaches. Collectively, the use of a microwave-accelerated method for the release and detection of DNA represents a significant step forward toward the development of a point-of-care (POC) platform for detection of gonorrhea infections.

The prognostic significance of bacterial DNA in patients with decompensated cirrhosis and suspected infection

BACKGROUND & AIMS

Circulating and peritoneal fragments of microbial DNA (bactDNA) are evidence for bacterial translocation in decompensated cirrhosis and may serve as a rational approach for antibiotic therapy when infection is suspected.

METHODS

Prospective multicenter study to investigate whether identification of bactDNA from blood or ascitic fluid (AF) by multiplex polymerase chain reaction (PCR) is associated with increased 90-day mortality in 218 patients with cirrhosis and signs of infection.

RESULTS

BactDNA in either compartment was detected in 134 (61%) patients, comprising 54 with bactDNA in blood and AF, 48 with AF bactDNA only, and 32 with blood bactDNA only. BactDNA was associated with spontaneous bacterial peritonitis and blood stream infections (SBP/BSI), acute-on-chronic liver failure (ACLF), encephalopathy and markers of inflammation. The prevalence of bactDNA in patients with proven SBP/BSI (36/49; 73%) was similar to that in patients with sterile ACLF (37/52; 71%). Actuarial 90-day survival was 56 ± 5% in the absence of bactDNA in both compartments and did not differ if bactDNA was detected in blood only (63 ± 9%), AF only (63 ± 7%), or in blood and AF (52 ± 7%). Predictors of 90-day mortality were SBP (HR = 3.10; 95% CI: 1.90-5.06), BSI (HR = 4.94; 95% CI: 2.71-9.02), and ACLF (HR = 2.20; 95% CI: 1.44-3.35). The detection of resistance genes in blood or AF in the absence of SBP/BSI (n = 11) was associated with poor 1-year survival (HR = 2.35; 95% CI: 1.03-5.35).

CONCLUSIONS

BactDNA in sterile body fluids did not indicate increased mortality in cirrhotic patients with suspected infection. Using multiplex PCR for risk stratification cannot be recommended in these patients.

Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping

High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and suggest that clinical sample testing is feasible with further optimization.

Biomarkers for the early diagnosis of bacterial infection and the surveillance of hepatocellular carcinoma in cirrhosis

The early detection of bacterial infections and hepatocellular carcinoma (HCC) could ameliorate the prognosis of cirrhosis. C-reactive protein and procalcitonin are under investigation in the setting of cirrhosis as markers of sepsis. In the attempt to discriminate bacterial infection from systemic inflammation, the role of novel biomarkers such as lypopolysaccharide binding-protein, mid-regional fragment of pro-adrenomedullin and delta neutrophil index are currently in development. Concerning HCC, many studies attempted to evaluate biomarkers in the hope of ameliorating the accuracy of the surveillance based on ultrasound. The use of α-fetoprotein (AFP) has been extensively investigated, as well as other biomarkers expressed in the serum of HCC patients like lens culinaris agglutinin-reactive fraction of AFP, des-γ-carboxy prothrombin, glypican-3, α-l-fucosidase and their combined use.

What to expect from molecular tools for non-documented pediatric infectious diseases

OBJECTIVE

Evaluation of the contribution of molecular tools to the overall diagnosis of infectious diseases in children.

METHODS

Results of 16S rDNA analysis (179 children; 228 specimens), combined to specific amplification of Kingella kingae (126 children; 166 osteoarticular specimens), were retrospectively analyzed for samples with inconclusive cultures.

RESULT

The overall positive yield in diagnosis was 12.8% of the patients for 16S rDNA PCR, 40.5% for K. kingae PCR and 45.2% for combined use of both methods. Results were related to clinical and biological data (direct examination, certainty/uncertainty of clinical diagnosis, fever, biological markers, previous antibiotics), and to the number of samples analyzed per patient, allowing the identification of specific situations with significant contribution of PCR methods.

CONCLUSION

Molecular techniques constitute valuable tools to improve the bacterial infection diagnosis in children; however, specific indications, dedicated samples, and number of analyzed samples per patient are key points to optimize their contribution.

Clinical application of 16S rRNA sequencing analysis for diagnosis of spontaneous bacterial peritonitis and evaluation of antibiotic efficacy

AIM: To explore a new method of polymerase chain reaction (PCR) based on 16S rRNA gene of bacteria with two different pairs of primers (used alone or in combination) and alignment sequencing, to improve the detection rate of bacteria in ascitic fluid and evaluate its clinical value in bacterial species identification and evaluation of antibiotic efficacy.

METHODS: Blood and ascitic fluid samples were collected from 77 spontaneous bacterial peritonitis (SBP) (n = 61) cirrhotic patients with ascites. Bacterial culture of ascitic fluid was conducted and the results were used as the gold standard in this study. Bacterial DNA in ascitic fluid was detected by PCR, based on the 16S rRNA gene, with two different pairs primers (MSQ-F/MSQ-R, 27F/1492R) and alignment sequencing assay. The results of bacterial species and positive rate between PCR method and bacterial culture of ascitic fluid were compared, and the results of bacterial species identified with different pair primers were also compared.

RESULTS: For products amplified with primers MSQ-F/MSQ-R, the coincidence rate of bacterial genus identification between PCR assay and ascitic fluid culture was 73.33% (11/15), and the coincidence rate of bacterial species identification was 66.67(10/15). For products amplified with primers27F/1492R, the coincidence rate of bacterial genus identification between PCR assay and ascitic fluid culture was 80.00% (12/15), and the coincidence rate of bacterial species identification was 73.33% (11/15). For products amplified with primers MSQ-F/MSQ-R combined with primers 27F/1492R, the coincidence rate of bacterial genus identification between PCR assay and ascitic fluid culture was 86.67% (13/15), and the coincidence rate of bacterial species identification was 80.00% (12/15). In five patients with SBP whose ascitic fluid culture was negative, PCR reaction was positive, which was consistent with clinical characteristics.

CONCLUSION: The method combining the two different pairs of primers for identifying bacteria based on the 16S rRNA gene and alignment sequencing has better identification ability and can evaluate antibiotic efficacy dynamically.

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications

Relative microorganism abundance is a parameter describing biodiversity, referring to how common a bacterial species is within the total bacterial flora. Anal, rectal, skin, mucal, and respiratory swabs are typical clinical samples where knowledge of relative bacterial abundance might make distinction between asymptomatic carriers and symptomatic cases. Assays trying to measure total bacterial load are usually based on the amplification of universal segments of 16S rRNA genes. Previous assays were not adoptable to "direct" PCR protocols, and/or they were not compatible with hydrolysis-based detection. Using the latest summary of universal 16S sequence motifs present in literature and testing our design with 500 liquid and 50 formed stool samples, we illustrate the performance characteristics of a new 16S quantitative PCR (qPCR) assay, which addresses well-known technical problems, including a) positive priming reaction in the absence of intended target due to self-priming and/or mispriming of unintended targets; b) amplification bias due to nonoptimal primer/probe coverage; and c) too large amplicons for clinical qPCR. Stool swabs ranked into bins of different bacterial loads show significant correlation with threshold cycle values of our new assay. To the best of our knowledge, this is the first description of qPCR assay measuring individual differences of total bacterial load present in human stool.

Toward culture-free Raman spectroscopic identification of pathogens in ascitic fluid

The identification of pathogens in ascitic fluid is standardly performed by ascitic fluid culture, but this standard procedure often needs several days. Additionally, more than half of the ascitic fluid cultures are negative in case of suspected spontaneous bacterial peritonitis (SBP). It is therefore important to identify and characterize the causing pathogens since not all of them are covered by the empirical antimicrobial therapy. The aim of this study is to show that pathogen identification in ascitic fluid is possible by means of Raman microspectroscopy and chemometrical evaluation with the advantage of strongly increased speed. Therefore, a Raman database containing more than 10000 single-cell Raman spectra of 34 bacterial strains out of 13 different species was built up. The performance of the used statistical model was validated with independent bacterial strains, which were grown in ascitic fluid.

Bacterial infections in cirrhosis: a position statement based on the EASL Special Conference 2013

Bacterial infections are very common and represent one of the most important reasons of progression of liver failure, development of liver-related complications, and mortality in patients with cirrhosis. In fact, bacterial infections may be a triggering factor for the occurrence of gastrointestinal bleeding, hypervolemic hyponatremia, hepatic encephalopathy, kidney failure, and development of acute-on-chronic liver failure. Moreover, infections are a very common cause of repeated hospitalizations, impaired health-related quality of life, and increased healthcare costs in cirrhosis. Bacterial infections develop as a consequence of immune dysfunction that occurs progressively during the course of cirrhosis. In a significant proportion of patients, infections are caused by gram-negative bacteria from intestinal origin, yet gram-positive bacteria are a frequent cause of infection, particularly in hospitalized patients. In recent years, infections caused by multidrug-resistant bacteria are becoming an important clinical problem in many countries. The reduction of the negative clinical impact of infections in patients with cirrhosis may be achieved by a combination of prophylactic measures, such as administration of antibiotics, to reduce the occurrence of infections in high-risk groups together with early identification and management of infection once it has developed. Investigation on the mechanisms of altered gut microflora, translocation of bacteria, and immune dysfunction may help develop more effective and safe methods of prevention compared to those that are currently available. Moreover, research on biomarkers of early infection may be useful in early diagnosis and treatment of infections. The current manuscript reports an in-depth review and a position statement on bacterial infections in cirrhosis.

Nonculture techniques for the detection of bacteremia and fungemia

ABSTRACT: 

Bacteremia and fungemia account for a substantial proportion of all cases of severe sepsis. Antibiotic resistance is a contributing factor in many hospital-acquired infection deaths. Traditional phenotypic methods for the identification of bacteria and yeasts from positive blood cultures and determining antimicrobial susceptibility require 48–72 h, delaying optimal therapy and negatively impacting patient outcomes. Molecular methods, including nonamplified DNA probe panels and peptide nucleic acid probes, and nucleic acid amplification methods such as PCR, proteomic methods (matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry) and direct biochemical tests provide more rapid identification of bacteria and fungi, and in some cases antimicrobial resistance markers, from positive blood cultures, as well as directly from whole blood. These methods vary in the breadth of organisms that they detect, and equally important, their ease of use. This article examines the principles, performance and practicality of the various rapid, nonculture techniques for the detection of bacteremia and fungemia.

Application of qualitative and quantitative real-time PCR, direct sequencing, and terminal restriction fragment length polymorphism analysis for detection and identification of polymicrobial 16S rRNA genes in ascites

Qualitative and quantitative 16S rRNA gene-based real-time PCR and direct sequencing were applied for rapid detection and identification of bacterial DNA (bactDNA) in 356 ascites samples. bactDNA was detected in 35% of samples, with a mean of 3.24 log copies ml(-1). Direct sequencing of PCR products revealed 62% mixed chromatograms predominantly belonging to Gram-positive bacteria. Terminal restriction fragment length polymorphism (T-RFLP) results of a sample subset confirmed sequence data showing polymicrobial DNA contents in 67% of bactDNA-positive ascites samples.

Laboratory diagnostics of spontaneous bacterial peritonitis

The term peritonitis indicates an inflammatory process involving the peritoneum that is most frequently infectious in nature. Primary or spontaneous bacterial peritonitis (SBP) typically occurs when a bacterial infection spreads to the peritoneum across the gut wall or mesenteric lymphatics or, less frequently, from hematogenous transmission in combination with impaired immune system and in absence of an identified intra-abdominal source of infection or malignancy. The clinical presentation of SBP is variable. The condition may manifest as a relatively insidious colonization, without signs and symptoms, or may suddenly occur as a septic syndrome. Laboratory diagnostics play a pivotal role for timely and appropriate management of patients with bacterial peritonitis. It is now clearly established that polymorphonuclear leukocyte (PMN) in peritoneal fluid is the mainstay for the diagnosis, whereas the role of additional biochemical tests is rather controversial. Recent evidence also suggests that automatic cell counting in peritoneal fluid may be a reliable approach for early screening of patients. According to available clinical and laboratory data, we have developed a tentative algorithm for efficient diagnosis of SBP, which is based on a reasonable integration between optimization of human/economical resources and gradually increasing use of invasive and expensive testing. The proposed strategy entails, in sequential steps, serum procalcitonin testing, automated cell count in peritoneal fluid, manual cell count in peritoneal fluid, peritoneal fluid culture and bacterial DNA testing in peritoneal fluid.

Sensitive detection and serovar differentiation of typhoidal and nontyphoidal Salmonella enterica species using 16S rRNA Gene PCR coupled with high-resolution melt analysis

Salmonella enterica species infections are a significant public health problem causing high morbidity rates worldwide and high mortality rates in the developing world. These infections are not always rapidly diagnosed as a cause of bloodstream infections because of the limitations of blood culture, which greatly affects clinical care as a result of treatment delays. A molecular diagnostic assay that could rapidly detect and identify S. enterica species infections as a cause of sepsis is needed. Nine typhoidal and nontyphoidal S. enterica serovars were used to establish the limit of detection (LOD) of a previously published 16S rRNA gene PCR (16S PCR) in mock whole blood specimens. In addition, 16 typhoidal and nontyphoidal S. enterica serovars were used to evaluate the serovar differentiation capability of 16S PCR coupled with high-resolution melt analysis. The overall LOD of 16S PCR for the nine typhoidal and nontyphoidal S. enterica serovars analyzed was <10 colony-forming units per milliliter (CFU/mL) in mock whole blood specimens, with the lowest and highest LOD at <1 CFU/mL and 9 CFU/mL, respectively. By high-resolution melt analysis, the typhoidal and nontyphoidal S. enterica serovar groups analyzed each generated a unique grouping code, allowing for serovar-level identification. 16S PCR coupled with high-resolution melt analysis could be a useful molecular diagnostic that could enhance the current diagnostic, treatment, and surveillance methods of S. enterica bloodstream infections.