Evaluation of an ethidium monoazide-enhanced 16S rDNA real-time polymerase chain reaction assay for bacterial screening of platelet concentrates and comparison with automated culture

Bacterial Analysis of the Whole Blood in Chinese Healthy Donors Using 16S rDNA-Targeted Metagenomic Sequencing

Background: The presence of bacteria in the blood of healthy individuals remains controversial. This study explored the comprehensive bacterial profiles and specific biomarkers in different components of healthy Chinese blood donors. Methods: A total of 5230 whole blood (WB) specimens were collected. Among them, 5200 random samples were pooled into 26 mixed samples for bacterial profile analysis. The remaining 30 random samples were divided into 4 groups based on components: WB, plasma, red blood cells (RBCs), and buffy coat (BC). Subsequently, the amplicons of the bacterial 16S rDNA V3-V4 fragments were sequenced to measure the diversity and composition of the bacteria using next-generation sequencing. Results: The bacterial DNAs in the blood primarily originated from the Proteobacteria phylum. A total of 301 species of bacterial DNA were found in blood specimens, with 46 species being present among all groups. A significantly higher abundance of bacterial DNA was found in the plasma and RBCs compared to those in BC and WB. However, the plasma and RBC groups showed significantly higher species diversity and richness compared to the BC and WB groups. In addition, the WB group had a significantly different community structure and composition compared to the plasma and RBC groups but was similar to the BC group. Conclusion: The presence of bacterial DNA fragments was confirmed in blood from healthy Chinese donors. The bacterial DNA fragments enriched in plasma showed the highest diversity, followed by RBC, WB, and BC. These results provide a foundation for further research on the microbiome in the blood of healthy individuals.

Current status of rapid bacterial detection methods for platelet components: A 20-year review by the ISBT Transfusion-Transmitted Infectious Diseases Working Party Subgroup on Bacteria

BACKGROUND AND OBJECTIVES

Bacterial contamination of platelet components (PCs) poses a safety challenge for transfusion patients. Despite mitigation interventions, the residual risk of transfusion-transmitted bacterial infections remains predominant. PC safety can be improved either by pathogen reduction or by implementation of bacterial detection methods. Detection methodologies include culture methods and rapid detection methods. The current review focuses on currently available rapid detection methods.

MATERIALS AND METHODS

We reviewed published manuscripts since 2000 on rapid bacterial detection methods used for PC screening with result determination within 4 h. Methods meeting this criterion included Verax PGDprime, BacTx and nucleic amplification testing. The analytical and diagnostic sensitivity and specificity of these systems were assessed.

RESULTS

The analytical sensitivity between the different detection methods ranged between 50 and 100,000 CFU/ml. The sample volume used by these testing systems varies between 0.5 and 1.0 ml of PCs. A delay of at least 48 h before sampling enhances detectability. All rapid detection methods generate results in a timely manner, allowing testing to be performed before transfusion with optimal sensitivity.

CONCLUSION

Rapid detection methods improve PC safety regarding bacterial contamination. The assays are optimal for rapidly growing bacteria, which are more likely to cause septic transfusion reactions in patients. Because of the reduced diagnostic sensitivity, the sample collection should be late in shelf-life and ideally just before transfusion. The major benefit of these methods is that the test result can be obtained before releasing PCs for transfusion or to be used in combination with other screening methods applied early during PC storage.

Optimized broad-range real-time PCR-based method for bacterial screening of platelet concentrates

Bacterial contamination of blood components remains a major challenge in transfusion medicine, particularly, platelet concentrates (PCs) due to the storage conditions that support bacterial proliferation. In this study, we develop a rapid, sensitive and specific real-time PCR protocol for bacterial screening of PCs. An internally controlled real-time PCR-based method was optimized and validated with our proprietary 16S Universal PCR Master Mix (IBMP/Fiocruz), which targets a conserved region of the bacterial 16S rRNA gene. Nonspecific background DNA was completely eliminated by treating the PCR Master Mix with ethidium monoazide (EMA). A lower limit of detection was observed for 10 genome equivalents with an observed Ct value of 34±1.07 in calibration curve generated with 10-fold serial dilutions of E. coli DNA. The turnaround time for processing, including microbial DNA purification, was approximately 4 hours. The developed method showed a high sensitivity with no non-specific amplification and a lower time-to-detection than traditional microbiological methods, demonstrating it to be an efficient means of screening pre-transfusion PCs.

Detection of bacterial contamination in platelet concentrates from Brazilian donors by molecular amplification of the ribosomal 16S gene

OBJECTIVE

The aim of our work was to establish a semi-automated high-throughput DNA amplification method for the universal screening of bacteria in platelet concentrates (PCs).

BACKGROUND

Among cases of transfusion transmission of infectious agents, bacterial contamination ranks first in the number of events, morbidity and mortality. Transmission occurs mainly by transfused PCs. Automated culture is adopted by some blood banks for screening of bacterial contamination, but this procedure is expensive and has a relatively long turnaround time.

METHODS

PCs were spiked with suspensions of five different bacterial species in a final concentration of 1 and 10 colony-forming units (CFU) per millilitre. After incubation, the presence of bacteria was investigated by real-time polymerase chain reaction (PCR) and by the Enhanced Bacterial Detection System (eBDS, Pall) assay as a reference method. Real-time PCR amplification was performed with a set of universal primers and probes targeting the 16S rRNA gene. Co-amplification of human mitochondrial DNA served as an internal control.

RESULTS

Using the real-time PCR method, it was possible to detect the presence of all bacterial species tested with an initial concentration of 10 CFU mL^-1 24 h after contamination, except for Staphylococcus hominis. The PCR assay also detected, at 24 h, the presence of Serratia marcescens and Enterobacter cloacae with an initial concentration of 1 CFU mL^-1 .

CONCLUSIONS

The real-time PCR assay may be a reliable alternative to conventional culture methods in the screening of bacterial contamination of PCs, enabling bacterial detection even with a low initial concentration of microorganisms.

Enlargement of the WHO international repository for platelet transfusion-relevant bacteria reference strains

BACKGROUND AND OBJECTIVES

Interventions to prevent and detect bacterial contamination of platelet concentrates (PCs) have reduced, but not eliminated the sepsis risk. Standardized bacterial strains are needed to validate detection and pathogen reduction technologies in PCs. Following the establishment of the First International Reference Repository of Platelet Transfusion-Relevant Bacterial Reference Strains (the 'repository'), the World Health Organization (WHO) Expert Committee on Biological Standardisation (ECBS) endorsed further repository expansion.

MATERIALS AND METHODS

Sixteen bacterial strains, including the four repository strains, were distributed from the Paul-Ehrlich-Institut (PEI) to 14 laboratories in 10 countries for enumeration, identification and growth measurement on days 2, 4 and 7 after low spiking levels [10-25 colony-forming units (CFU)/PC bag]. Spore-forming (Bacillus cereusPEI-B-P-07-S, Bacillus thuringiensisPEI-B-P-57-S), Gram-negative (Enterobacter cloacaePEI-B-P-43, Morganella morganiiPEI-B-P-74, PEI-B-P-91, Proteus mirabilisPEI-B-P-55, Pseudomonas fluorescensPEI-B-P-77, Salmonella choleraesuisPEI-B-P-78, Serratia marcescensPEI-B-P-56) and Gram-positive (Staphylococcus aureusPEI-B-P-63, Streptococcus dysgalactiaePEI-B-P-71, Streptococcus bovisPEI-B-P-61) strains were evaluated.

RESULTS

Bacterial viability was conserved after transport to the participating laboratories with one exception (M. morganiiPEI-B-P-74). All other strains showed moderate-to-excellent growth. Bacillus cereus, B. thuringiensis, E. coli, K. pneumoniae, P. fluorescens, S. marcescens, S. aureus and S. dysgalactiae grew to >10⁶ CFU/ml by day 2. Enterobacter cloacae, P. mirabilis, S. epidermidis, S. bovis and S. pyogenes achieved >10⁶ CFU/ml at day 4. Growth of S. choleraesuis was lower and highly variable.

CONCLUSION

The WHO ECBS approved all bacterial strains (except M. morganiiPEI-B-P-74 and S. choleraesuisPEI-B-P-78) for repository enlargement. The strains were stable, suitable for spiking with low CFU numbers, and proliferation was independent of the PC donor.

Development of a qualitative real-time PCR for microbiological quality control testing in mammalian cell culture production

AIMS

The aim of this study was to develop and evaluate a real-time PCR technology for microbiological control methods to examine individualized cell therapeutics, an emerging class of pharmaceutical formulations.

METHODS AND RESULTS

Oligonucleotide primers and hybridization probe for bacterial detection targeting the 16SrRNA gene were adapted based on Nadkarni et al. [Microbiology148 (2002) 257]. For detection of yeast and moulds, primers and probe were designed from conserved sequences of the 18SrRNA gene in this study. The real-time PCR assays were tested on genomic DNA of Escherichia coli and Candida albicans to assess efficiency and linear dynamic range. After successful establishment of robust real-time PCRs, applicability of the assays was evaluated by extracting microbial target DNA from cell-based preparations. Different commercial DNA extraction methods were compared identifying the MagNA Pure DNA Isolation Kit III as the method of choice. Sensitivity was examined for different strains and a detection limit of 10² -10³ CFU per ml in a sample containing ~10⁶ mammalian cells per ml was achieved.

CONCLUSIONS

This study reports the successful establishment of two qualitative real-time PCR assays, enabling in general the broad-range detection of microbial contaminants in a cell-based sample matrix.

SIGNIFICANCE AND IMPACT OF THE STUDY

Individualized cell therapeutics tend to have a short shelf life. Due to lengthy incubation periods, compendial testing according to current pharmacopoeial guidelines may not be applicable. We report a suitable alternative method upon which future microbiological quality control methods for such products could be based on. However, to implement valid rapid microbiological testing methods using real-time PCR technology, further challenges need to be addressed.

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

Background

The advent and use of highly sensitive molecular biology techniques to explore the microbiota and microbiome in environmental and tissue samples have detected the presence of contaminating microbial DNA within reagents. These microbial DNA contaminants may distort taxonomic distributions and relative frequencies in microbial datasets, as well as contribute to erroneous interpretations and identifications.

Results

We herein report on the occurrence of bacterial DNA contamination within commonly used DNA extraction kits and PCR reagents and the effect of these contaminates on data interpretation. When compared to previous reports, we identified an additional 88 bacterial genera as potential contaminants of molecular biology grade reagents, bringing the total number of known contaminating microbes to 181 genera. Many of the contaminants detected are considered normal inhabitants of the human gastrointestinal tract and the environment and are often indistinguishable from those genuinely present in the sample.

Conclusions

Laboratories working on bacterial populations need to define contaminants present in all extraction kits and reagents used in the processing of DNA. Any unusual and/or unexpected findings need to be viewed as possible contamination as opposed to unique findings.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-016-0103-7) contains supplementary material, which is available to authorized users.

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors.