Rapid identification of bacteria and Candida pathogens in peritoneal dialysis effluent from patients with peritoneal dialysis-related peritonitis by use of multilocus PCR coupled with electrospray ionization mass spectrometry

The Application of Bacteriophage and Photoacoustic Flow Cytometry in Bacterial Identification

Infection with resistant bacteria has become an ever-increasing problem in modern medical practice. Bacteremia is a serious and potentially lethal condition that can lead to sepsis without early intervention. Currently, broad-spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take 2-3 days and is unable to provide quantitative information. Staphylococcus aureus (S. aureus) is a leading cause of bacteremia, and methicillin-resistant S. aureus (MRSA) accounts for more than a third of the cases. Other bacteria such as Clostridium difficile, Acinetobacter baumannii, and Carbapenem-resistant Enterobacteriaceae are becoming more prevalent and antibiotic-resistant. Rapid diagnostics for each of these superbugs has been a priority for health organizations around the world. Bacteriophages have evolved for millions of years to develop exquisite specificity in target binding using their host attachment proteins. Bacteriophages are viruses that infect bacteria. Bacteriophages use tail spikes, specialized attachment proteins, to bind specifically to their target bacterial cell surface proteins. We use bacteriophages and parts of bacteriophages as specific tags coupled with photoacoustic flow cytometry for the detection and quantification of bacteria. In photoacoustic flow cytometry, laser light is absorbed by particles under flow, and the ultrasound waves generated on the release of the energy are detected. Photoacoustics involves the detection of ultrasound waves resulting from laser irradiation. In photoacoustic flow cytometry, pulsed laser light is delivered to a sample flowing past a focused transducer, and particles that absorb laser light create a photoacoustic response. Bacteria can be tagged with dyed bacteriophage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. In this chapter, we describe the procedure and methods used to accomplish this. Often the limiting factor for the treatment of patients is the time spent waiting for results. It is our hope that the work presented in this chapter can be a foundation for future work and provide an ability to detect bacterial pathogens in blood cultures. Bacterial plate cultures and Gram staining are nineteenth-century technologies that have been the gold standards for decades, but current trends in resistant bacteria have necessitated a move toward more rapid and quantifiable diagnostic tools.

Peritoneal Dialysis-Related Recurrent Rhodococcus corynebacterioides Peritonitis: A Case Report and Review of Literature

Rhodococcus corynebacterioides is a Gram-positive bacterium known to cause bacteremia and oligoarthritis. There have been only a few case reports in the literature that describe its association with peritoneal dialysis (PD)-related peritonitis. We report a case of recurrent peritonitis caused by R. corynebacterioides. The patient presented with abdominal pain, and PD fluid analysis was positive for infection, with cultures growing R. corynebacterioides. The patient was treated with multiple courses of intraperitoneal antibiotics due to recurrent episodes of PD-associated peritonitis from this bacterium, ultimately necessitating the removal of the PD catheter and the transition to hemodialysis.

Peritoneal dialysis-related peritonitis caused by Rhodococcus corynebacterioides

A 57-year-old Japanese man on peritoneal dialysis developed peritoneal dialysis-associated peritonitis caused by Rhodococcus corynebacterioides. After the introduction of peritoneal dialysis, he had experienced four episodes of peritonitis, but the causative organism was not identified in any of episode. When he was hospitalized for the fifth episode of peritonitis, Rhodococcus corynebacterioides was detected in the ascitic fluid. He improved after an intraperitoneal administration of vancomycin (VCM) that was used based on the treatment of peritonitis caused by Corynebacterium spp. However, he then had repeated flare-ups and eventually required the removal of the peritoneal dialysis catheter due to recurrent peritonitis. 16S rRNA gene sequencing is generally needed to positively identify Rhodococcus corynebacterioides. In this case, we were able to rapidly identify the organism by using mass spectrometry and then apply this knowledge to the patient's treatment. To the best of our knowledge, this is the first reported case of peritoneal dialysis-associated peritonitis caused by Rhodococcus corynebacterioides.

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

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

Continuous Ambulatory Peritoneal Dialysis Peritonitis Guidelines - Consensus Statement of Peritoneal Dialysis Society of India - 2020

Continuous ambulatory peritoneal dialysis (CAPD) related peritonitis is a major cause of technique failure, morbidity, and mortality in patients on CAPD. Its prevention and management is key to success of CAPD program. Due to variability in practice, microbiological trends and sensitivity towards antibiotics, there is a need for customized guidelines for management of CAPD related peritonitis (CAPDRP) in India. With this need, Peritoneal Dialysis Society of India (PDSI) organized a structured meeting to discuss various aspects of management of CAPDRP and formulated a consensus agreement which will help in management of patients with CAPDRP.

Peritoneal Dialysis Guidelines 2019 Part 1 (Position paper of the Japanese Society for Dialysis Therapy)

Approximately 10 years have passed since the Peritoneal Dialysis Guidelines were formulated in 2009. Much evidence has been reported during the succeeding years, which were not taken into consideration in the previous guidelines, e.g., the next peritoneal dialysis PD trial of encapsulating peritoneal sclerosis (EPS) in Japan, the significance of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs), the effects of icodextrin solution, new developments in peritoneal pathology, and a new international recommendation on a proposal for exit-site management. It is essential to incorporate these new developments into the new clinical practice guidelines. Meanwhile, the process of creating such guidelines has changed dramatically worldwide and differs from the process of creating what were “clinical practice guides.” For this revision, we not only conducted systematic reviews using global standard methods but also decided to adopt a two-part structure to create a reference tool, which could be used widely by the society’s members attending a variety of patients. Through a working group consensus, it was decided that Part 1 would present conventional descriptions and Part 2 would pose clinical questions (CQs) in a systematic review format. Thus, Part 1 vastly covers PD that would satisfy the requirements of the members of the Japanese Society for Dialysis Therapy (JSDT). This article is the duplicated publication from the Japanese version of the guidelines and has been reproduced with permission from the JSDT.

Molecular Diagnosis of Yeast Infections

PURPOSE OF REVIEW

The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing).

RECENT FINDINGS

Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny.

SUMMARY

Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.

Polymerase chain reaction/electrospray ionization-mass spectrometry (PCR/ESI-MS) is not suitable for rapid bacterial identification in peritoneal dialysis effluent

BACKGROUND

Peritoneal dialysis (PD)-related peritonitis is a serious complication of PD, but routine microbiological culture is slow and could not identify the organism in 15% cases. We examine the accuracy of polymerase chain reaction/electrospray ionization-mass spectrometry (PCR/ESI-MS), a PCR-based method developed for the direct detection of bacteria in blood, for rapid identification of microorganisms from PD effluent.

METHODS

We recruited 73 consecutive patients with PD-related peritonitis. Dialysis effluent was collected for routine bacterial culture, PCR/ESI-MS, and bacterial DNA quantification before initiation of antibiotic therapy.

RESULTS

By digital PCR with universal bacterial primers, bacterial DNA was detectable in all PD effluent specimens. For the entire cohort, taking standard bacterial culture as the gold standard, the PCR/ESI-MS assay correctly identified 34.3% of the causative organisms, failed to identify any organism in 52.1% cases, and identified a different organism in 8.2% cases. For the 14 episodes of peritonitis that were culture negative by conventional bacterial culture, the PCR/ESI-MS assay identified an organism in only four cases. The detection rate of the IRIDICA BAC BSI assay was not affected by the use of biocompatible PD solution or concomitant exit-site infection.

CONCLUSIONS

The PCR/ESI-MS assay could not identify the causative organism in over 50% of the PD effluent samples in patients with PD-related peritonitis and should be not used for such purpose. The reason for the poor performance needs further investigation.

Effluent lipopolysaccharide is a prompt marker of peritoneal dialysis-related gram-negative peritonitis

BACKGROUND

To investigate the value of effluent lipopolysaccharide (LPS) for early detection of gram-negative peritonitis (GNP) in peritoneal dialysis (PD) patients.

METHODS

PD-related peritonitis episodes occurring between January 2016 and December 2018 were included in the study. Effluent LPS and the other infectious parameters were measured at peritonitis presentation, and peritonitis was categorized as GNP, non-GNP, and culture-negative peritonitis. Receiver operating characteristic (ROC) analysis was employed to evaluate the efficacy of effluent LPS to distinguish GNP.

RESULTS

A total of 161 peritonitis episodes were analyzed, including 49 GNP episodes and 82 non-GNP episodes. In contrast with non-GNP, GNP presented with higher effluent leukocyte count (3236 (1497-6144) vs. 1904 (679-4071) cell mm^-3, p = 0.008), increased effluent LPS (1.552 (0.502-2.500) vs. 0.016 (0.010-0.030) EU mL^-1, p < 0.001), lower blood leukocyte count (9.95 ± 3.18 vs. 11.56 ± 4.37 × 10⁹ L^-1, p = 0.017), greater neutrophil predominance (87.1 ± 4.6% vs. 83.4 ± 7.7%, p = 0.001), and greater "procalcitonin" (PCT, 4.90 (2.20-12.60) vs. 1.00 (0.51-4.07) µg L^-1, p < 0.001). It took 5.2 ± 3.1 h to report the results of effluent LPS. Effluent LPS cutoff value of >0.035 EU mL^-1 showed an area under the ROC curve of 0.972 (95% CI 0.951-0.994, p < 0.001) in differentiating GNP from non-GNP with a sensitivity of 100% and a specificity of 80.5%, and its joint utilization with PCT further increased the specificity (91.4%) to discriminate GNP.

CONCLUSIONS

PD effluent LPS could be an applicable early marker of gram-negative organism-related peritonitis in PD patients.

Bacteriophage-mediated identification of bacteria using photoacoustic flow cytometry

Infection with resistant bacteria has become an ever increasing problem in modern medical practice. Currently, broad spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take two to three days and is unable to provide quantitative information. To detect and quantify bacteria rapidly in blood samples, we designed a method using labeled bacteriophage in conjunction with photoacoustic flow cytometry (PAFC). PAFC is the generation of ultrasonic waves created by the absorption of laser light in particles under flow. Bacteriophage is a virus that infects bacteria and possesses the ability to discriminate bacterial surface antigens, allowing the bacteriophage to bind only to their target bacteria. Bacteria can be tagged with dyed phage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. We demonstrate that E. coli; can be detected and discriminated from Salmonella; using this method. Our goal is to develop a method to determine bacterial content in blood samples. We hope to develop this technology into future clinical use and decrease the time required to identify bacterial species from 3 to 4 days to less than 1 hour.

Fungal peritonitis in patients undergoing peritoneal dialysis (PD) in Brazil: molecular identification, biofilm production and antifungal susceptibility of the agents

This paper presents data on fungal peritonitis (FP) in patients undergoing peritoneal dialysis (PD) at the University Hospital of Botucatu Medical School, São Paulo, Brazil. In a total of 422 patients, 30 developed FP, from which the medical records and the fungal isolates of 23 patient cases were studied. All patients presented abdominal pain, cloudy peritoneal effluent, needed hospitalization, had the catheter removed and were treated with fluconazole or fluconazole plus 5-flucitosine; six of them died due to FP. Concerning the agents, it was observed that Candida parapsilosis was the leading species (9/23), followed by Candida albicans (5/23), Candida orthopsilosis (4/23), Candida tropicalis (3/23), Candida guilliermondii (1/23), and Kodamaea ohmeri (1/23). All the isolates were susceptible to amphotericin B, voriconazole and caspofungin whereas C. albicans isolates were susceptible to all antifungals tested. Resistance to fluconazole was observed in three isolates of C. orthopsilosis, and dose-dependent susceptibility to this antifungal was observed in two isolates of C. parapsilosis and in the K. ohmeri isolate. Biofilm production estimates were high or moderate in most isolates, especially in C. albicans species, and low in C. parapsilosis species, with a marked variation among the isolates. This Brazilian study reinforces that FP in PD is caused by a diverse group of yeasts, most prevalently C. parapsilosis sensu stricto species. In addition, they present significant variation in susceptibility to antifungals and biofilm production, thus contributing to the complexity and severity of the clinical features.

Detection of fungal DNA in peritoneal fluids by a PCR DNA low-density microarray system and quantitation of serum (1-3)-β-D-glucan in the diagnosis of peritoneal candidiasis

Microbiological documentation of peritoneal candidiasis (PC) is hampered by the low numbers of yeasts observable by direct microscopic examination and recoverable by culture methods. The performance of a polymerase chain reaction (PCR) DNA Low-Density Microarray System (CLART STIs B) was compared to that of BACTEC FX automated culture method for the detection of Candida spp. in 161 peritoneal fluids (PF) from patients with peritonitis. The clinical utility of (1-3)-β-d-glucan (BDG) antigenemia in the diagnosis of PC was evaluated in 42 of these patients. The overall agreement between the PCR assay and the culture method was good (κ = 0.790), and their sensitivities were 93.5% and 74.19%, respectively. Serum BDG levels in patients with Candida spp. in PFs (median, 200.3 pg/mL; Range, 22.0-523.4 pg/mL) was significantly higher (P = 0.002) than those found in patients without the yeast (median, 25.3 pg/mL; Range, 0-523.4 pg/mL). Our study demonstrates the potential clinical utility of molecular methods and the measurement of serum BDG levels for the diagnosis of PC.