Detection of nucleic acid sequences from bacterial species with molecular genetic methods

Implementation of Bacterial Detection Methods into Blood Donor Screening - Overview of Different Technologies

SUMMARY: BACKGROUND: Through the implementation of modern technology, such as nucleic acid testing, over the last two decades, blood safety has improved considerably in that the risk of viral infection is less than 1 in a million blood transfusions. By contrast, the residual risk of transfusion-associated bacterial infection is stable at approximately 1 in 2,000 to 1 in 3,000 in platelets. To improve blood safety with regard to bacterial infections, many countries have implemented bacterial screening methods as part of their blood donor screening programmes. METHODS: BACTERIAL DETECTION METHODS ARE CLUSTERED INTO THREE GROUPS: i) culture methods in combination with the 'negative-to-date' concept, ii) rapid detection systems with a late sample collection, and iii) bedside screening tests. RESULTS: The culture methods are convincing because of their very high analytical sensitivity. Nevertheless, false-negative culture results and subsequent fatalities were reported in several countries. Rapid bacterial systems are characterised as having short testing time but reduced sensitivity. Sample errors are prevented by late sample collection. Finally, bedside tests reduce the risk for sample errors to a minimum, but testing outside of blood donation services may have risks for general testing failures. CONCLUSION: Bacterial screening of blood products, especially platelets, can be performed using a broad range of technologies. Each system exhibits advantages and disadvantages and offers only a temporary solution until a general pathogen inactivation technology is available for all blood components.

Direct detection of the bacterial stress response in intact samples of platelets by differential impedance

BACKGROUND

We have previously described a new rapid approach that relies on monitoring intentionally stressed bacteria in contaminated platelet concentrates (PCs). This earlier work included human cell lysis with Triton X-100 and filtration as steps in the sample preparation. This study was undertaken to develop an improved and time-saving protocol that enables direct bacterial detection in PCs without lysis and filtration.

STUDY DESIGN AND METHODS

Apheresis- or whole blood-derived PCs were spiked with 17 model bacteria and tested at final concentrations from 10(3) to 10(6) colony-forming units (CFUs)/mL. The contaminated PCs were treated with a chemical compound that induces a stress response in bacteria and monitored using differential impedance sensing to detect and record subtle changes in the dielectric permittivities of the contaminated platelet (PLT) samples.

RESULTS

No measurable responses from sterile PLT samples were observed during exposure to the compounds used as stressors. In contrast, distinct response profiles were obtained without exception for all 17 bacterial species for all bacterial concentrations tested. Bacterial presence was established within 5 to 10 minutes for high inocula (10(6) and 10(5) CFUs/mL) while low inocula (10(4) and 10(3) CFUs/mL) were usually detectable within 20 minutes. The entire testing process routinely took less than 30 minutes from the point of sampling to the time that the final results are available.

CONCLUSIONS

The results described here demonstrate that monitoring the development of stress in bacteria is a fast and simple way to detect 10(3) CFUs/mL or more bacteria in complex cellular blood products such as PCs.

Obstacles of Multiplex Real-Time PCR for Bacterial 16S rDNA: Primer Specifity and DNA Decontamination of Taq Polymerase

BACKGROUND: The detection of a broad range of bacteria by PCR is applied for the screening of blood and blood products with special attention to platelet concentrates. For practical use it is desirable that detection systems include Gram-positive, Gram-negative and non-Gram-stainable bacteria. It is quite challenging to achieve high sensitivity along with a clear negative control with PCR reagents, because especially Taq polymerase is contaminated with traces of bacterial DNA. METHODS: Bacterial DNA decontamination of Taq polymerase was attempted by two different methods using the restriction enzyme Sau 3A1 and microfiltration. Additionally a commercially available Taq polymerase depleted of bacterial DNA was included. A published real-time PCR specific for Gram-negative bacteria was adapted for Gram-positive bacteria, including certain Staphylococcus species and Mycobacteria, and was used to charge the three Taq polymer-ases depleted of bacterial DNA contamination RESULTS: Despite published reports about successful DNA decontamination, all three approaches performed poorly in experiments done in this study. Sensitivity ranged at approximately 50-100 colony forming units (CFU) per PCR reaction for Escherichia coli and Staphylococcus epidermidis, corresponding to 1,250-2,500 CFU/ml sample material. Conclusion: It seems unsatisfying to accept detection limits that high for diagnostic bacterial PCR even if highly multiplexed. Reliable methods for DNA decontamination of Taq polymerase are needed and would present one important step towards bacterial DNA detection with high sensitivity.

Methods for the detection of bacterial contamination in blood products

Culture-based and molecular assays have been developed for the screening of platelet concentrates and other blood components for bacterial contaminations. In this review, the principles of the assays are outlined. The focus of this review is the assessment of the analytical qualities of the methods. Spiking studies by adding defined levels of a wide range of bacteria to the complex biological matrix provide the first basis to evaluate and compare the qualities of methods for bacterial detection. The sensitivity acceptable for reliable screening for bacteria critically depends on the timing of either early sampling (within a period of up to 24 h after preparation of the blood component) or late sampling (a few hours before issuing the blood component). Large screening studies are essential to confirm both adequate sensitivity and specificity of the testing. In the ideal setting, these studies are prospectively planned and include systematic surveillance of adverse events in response to the administration of the screened products. The findings from sterility testing (predominantly with automated systems for detection of bacteria based on CO(2) generation) of more than 550,000 platelet concentrates in 13 studies are summarised. The limitations of the early sampling and the "negative-to-date" strategy to issue platelet concentrates are addressed. A few reported cases of probable transmission of bacteria by platelet transfusion despite negative screening tests emphasise the need to further develop optimised methods for testing of bacteria blood components.

Strategies of bacteria screening in cellular blood components

Since the impressive reduction of transfusion-transmitted virus infections, bacterial infections by blood transfusion represent the most important infection risk. Platelet concentrates are the current focus of attention, as they are stored under temperature conditions which allow growth of contaminating bacteria up to 10(10) and more microbes per platelet bag. This paper does not consider the pathogen reduction methods but will assess suitable screening methods. Beside conventional microbiological approaches or surrogate markers, several efficient methods able to detect bacterial contamination in platelets are available on the market. They need to be divided into two different methodological principles: the cultivation methods and rapid methods. Cultivation or incubation methods require some time for signal production as they depend on growth of microbes. Thus, they have to be combined with early sampling, i.e., the sample to be examined has to be drawn from the blood component 1 day after donation. Their advantage is the relatively uncomplicated implementation into the logistics of blood banks. Because of the initially very low count of bacteria after donation, a certain small sampling error in application of that strategy remains. Rapid methods are able to produce the diagnosis within a short time. Therefore, they allow postponing of sample drawing, ideally up to the time immediately before transfusion. However, this procedure causes logistic complications. On the other hand, late sampling combined with a rapid method will prevent the transfusion of highly contaminated platelet concentrates leading to acute septic shock up to the death of the patient. Considering the sum of different aspects including the supply of patients, the potential improvement of microbial safety of platelet concentrates is comparable in both strategies.

Quantitative PCR for detection and discrimination of the bloodborne pathogen Staphylococcus epidermidis in platelet preparations using divIVA and icaA as target genes

Bacterial contamination of blood components is the major microbiological cause of transfusion-associated morbidity, with Staphylococcus epidermidis being the most frequently isolated organism from contaminated platelet preparations (PPs). We have recently shown that S. epidermidis forms biofilms during platelet storage, which might account for reported missed detection during routine screening. In this study, we developed a highly sensitive and specific multiplex quantitative PCR (QPCR) assay to detect S. epidermidis in PPs at levels of 102–103 cfu/mL. A specific primer pair and hydrolysis probe were designed to amplify an internal region of the cell division divIVA gene that is unique to S. epidermidis. In addition, an internal sequence of the virulence gene icaA, which is involved in the synthesis of the S. epidermidis biofilm matrix, was selected to allow for differentiation of potentially biofilm-forming S. epidermidis isolates. A conserved region of the 8 alleles of the HLA-DQα1 locus present in residual white blood cells in PPs was selected as an internal control for the assay. The specificity of this assay was confirmed, as other staphylococcal species that were tested with the optimized parameters were not detected. This QPCR assay could be adaptable for the detection of other bloodborne bacterial pathogens.

Microcalorimetry: a novel method for detection of microbial contamination in platelet products

BACKGROUND

Measuring heat from replicating microorganisms in culture may be a rapid, accurate, and simple screening method for platelets (PLTs). Microcalorimetry for detection of microorganisms in in vitro contaminated PLT products was evaluated.

STUDY DESIGN AND METHODS

Staphylococcus epidermidis, Staphylococcus aureus, Streptococcus sanguinis, Escherichia coli, Propionibacterium acnes, and Candida albicans were inoculated in single-donor apheresis PLTs to achieve target concentrations of 10(5), 10(3), 10, or 1 colony-forming units (CFU) per mL of PLTs. Contaminated PLTs in growth medium were incubated at 37 degrees C for 5 days in a calorimeter. Positivity was defined as heat flow of at least 10 microW above the lowest value of the power-time curve.

RESULTS

With microcalorimetry, inocula of 10 CFUs per mL PLTs could be detected with the following detection times: S. epidermidis (31.65 hr), S. aureus (24.24 hr), S. sanguinis (7.82 hr), E. coli (7.53 hr), P. acnes (73.57 hr), and C. albicans (43.77 hr). The detection time was less than 4 hr at 10(5) CFUs per mL PLTs for S. aureus, S. sanguinis, and E. coli. Noncontaminated PLTs remained negative. The total heat ranged from 2.8 (S. sanguinis) to 8.3 J (E. coli). The shape of the power-time curve was species-specific and independent from the initial concentration of microorganisms.

CONCLUSION

The detection limit of microcalorimetry was 1 to 10 CFUs per mL PLTs. Microcalorimetry is a promising novel method for detection of contaminated PLTs. Applying this method to all PLT products could reduce the frequency of transfusion-related sepsis and prolong the shelf life of PLTs.

Real-Time Polymerase Chain Reaction in Transfusion Medicine: Applications for Detection of Bacterial Contamination in Blood Products

Bacterial contamination of blood components, particularly of platelet concentrates (PCs), represents the greatest infectious risk in blood transfusion. Although the incidence of platelet bacterial contamination is approximately 1 per 2,000 U, the urgent need for a method for the routine screening of PCs to improve safety for patients had not been considered for a long time. Besides the culturing systems, which will remain the criterion standard, rapid methods for sterility screening will play a more important role in transfusion medicine in the future. In particular, nucleic acid amplification techniques (NATs) are powerful potential tools for bacterial screening assays. The combination of excellent sensitivity and specificity, reduced contamination risk, ease of performance, and speed has made real-time polymerase chain reaction (PCR) technology an appealing alternative to conventional culture-based testing methods. When using real-time PCR for the detection of bacterial contamination, several points have to be considered. The main focus is the choice of the target gene; the assay format; the nucleic acid extraction method, depending on the sample type; and the evaluation of an ideal sampling strategy. However, several factors such as the availability of bacterial-derived nucleic acid amplification reagents, the impracticability, and the cost have limited the use of NATs until now. Attempts to reduce the presence of contaminating nucleic acids from reagents in real-time PCR have been described, but none of these approaches have proven to be very effective or to lower the sensitivity of the assay. Recently, a number of broad-range NAT assays targeting the 16S ribosomal DNA or 23S ribosomal RNA for the detection of bacteria based on real-time technology have been reported. This review will give a short survey of current approaches to and the limitations of the application of real-time PCR for bacterial detection in blood components, with emphasis on the bacterial contamination of PCs.

False-positive alarms for bacterial screening of platelet concentrates with BacT/ALERT new-generation plastic bottles: a multicenter pilot study

BACKGROUND

The microbial detection system BacT/ALERT (bioMérieux) is widely used to monitor bacterial contamination of platelet concentrates (PCs). Recently, the manufacturer introduced polycarbonate culture bottles and a modified pH-sensitive liquid emulsion sensor as microbial growth indicator. This reconfigured assay was investigated in a routine setting.

STUDY DESIGN AND METHODS

In each of eight transfusion centers, samples from 500 consecutive PCs were monitored for 1 week. For all PCs with a positive BacT/ALERT signal, retained samples and, if available, original PC containers and concomitant red blood cell concentrates were analyzed independently. Initially BacT/ALERT-positive PCs without bacterial identification in any sample were defined as false-positive. BacT/ALERT-positive PCs with bacteria in the first sample only were called potentially positive. PCs with bacteria in the first sample and the same strain in at least one additional sample were accepted as positive.

RESULTS

Five PCs (0.13%) were positive, 9 PCs (0.23%) were potentially positive, and 35 PCs (0.9%) were false-positive. The rate of false-positive BacT/ALERT results varied substantially between centers (<0.2%-3.2%). Tracings from false-positive cultures lacked an exponential increase of the signal during incubation. Most of these false-positives were due to malfunctioning cells in various BacT/ALERT incubation units.

CONCLUSION

Careful assessment of individual tracings of samples with positive signals helps to identify malfunctioning incubation units. Their early shutdown or replacement minimizes the high rate of unrectifiable product rejects attributed to false-positive alarms and avoids unnecessary concern of doctors and patients after conversion to a reconfigured BacT/ALERT assay.

Two novel real-time reverse transcriptase PCR assays for rapid detection of bacterial contamination in platelet concentrates

The incidence of platelet bacterial contamination is approximately 1 per 2,000 units and has been acknowledged as the most frequent infectious risk from transfusion. In preliminary studies, the sterility of platelet concentrates (PCs) was tested with an automated bacterial blood culturing system and molecular genetic assays. Two real-time reverse transcriptase PCR (RT-PCR) assays performed in a LightCycler instrument were developed and compared regarding specificity and sensitivity by the use of different templates to detect the majority of the clinically important bacterial species in platelets. Primers and probes specific for the conserved regions of the eubacterial 23S rRNA gene or the groEL gene (encoding the 60-kDa heat shock protein Hsp60) were designed. During the development of the 23S rRNA RT-PCR, problems caused by the contamination of reagents with bacterial DNA were noted. Treatment with 8-methoxypsoralen and UV irradiation reduced the level of contaminating DNA. The sensitivity of the assays was greatly influenced by the enzyme system which was used. With rTth DNA polymerase in a one-enzyme system, we detected 500 CFU of Escherichia coli or Staphylococcus epidermidis/ml. With a two-enzyme system consisting of Moloney murine leukemia virus RT and Taq DNA polymerase, we detected 16 CFU/ml. With groEL mRNA as the target of RT-PCR under optimized conditions, we detected 125 CFU of E. coli/ml, and no problems with false-positive results caused by reagent contamination or a cross-reaction with human nucleic acids were found. Furthermore, the use of mRNA as an indicator of viability was demonstrated. Here we report the application of novel real-time RT-PCR assays for the detection of bacterial contamination of PCs that are appropriate for transfusion services.

Effect of comprehensive validation of the template isolation procedure on the reliability of bacteraemia detection by a 16S rRNA gene PCR

The influence of the DNA extraction method on the sensitivity and specificity of bacteraemia detection by a 16S rRNA gene PCR assay was investigated. The detection limit of the assay was 5 fg with purified DNA from Escherichia coli or Staphylococcus aureus, corresponding to one bacterial cell. However, with spiked blood samples, the detection limits were 10(4) and 10(6) CFU/mL, respectively. The sensitivity of the S. aureus assay was improved to the level of the E. coli test with the addition of proteinase K to the commercial DNA extraction kit protocol. Ten (16.6%) of 60 amplification reactions were positive with templates isolated from sterile blood, while PCR reagent controls were negative, thereby indicating contamination during the DNA extraction process. Blood samples were spiked with serial dilutions of E. coli and S. aureus cells, and six PCR results were obtained from three extractions for each blood sample. A classification threshold system was devised, based on the number of positive reactions for each sample. Samples were deemed positive if at least four positive reactions were recorded, making it possible to avoid false-positive results caused by contamination. These results indicate that a comprehensive validation procedure covering all aspects of the assay, including DNA extraction, can improve considerably the validity of PCR assays for bacteraemia, and is a prerequisite for the meaningful detection of bacteraemia by PCR in the clinical setting.

Risk and prevention of transfusion-related sepsis

PURPOSE OF REVIEW

Transfusion-related sepsis is both the oldest recognized and most common transfusion-associated infectious risk. Despite an increased awareness and recognition of this problem, particularly with room-temperature stored platelets, strategies to prevent or reduce the occurrence of this problem have proved daunting.

RECENT FINDINGS

With the recent FDA approval of culture methods for platelet bacterial testing and the promulgation of accreditation standards by the College of American Pathologists and American Association of Blood Banks to limit and detect platelet bacterial contamination, it is anticipated that the frequency of this problem will now begin to diminish.

SUMMARY

As methods to reduce and/or inactivate pathogens emerge, it is hoped that transfusion-related sepsis will essentially disappear.

DNase pretreatment of master mix reagents improves the validity of universal 16S rRNA gene PCR results

DNase I pretreatment of 16S rRNA gene PCR reagents was tested. The DNase I requirement for the elimination of false-positive results varied between 0.1 and 70 IU per master mix depending on the applied Taq polymerase. PCR sensitivity was mostly maintained when 0.1 IU of DNase I was used.

Electrochemiluminescent detection of bacteria in blood components

Transfusion-transmitted bacterial infections cause significant patient morbidity and mortality. This study aimed to improve the sensitivity of a nucleic acid-based electrochemiluminescence (ECL) assay for pretransfusion bacterial testing of cellular blood components. The approach is dependent on the detection of bacterial 16S ribosomal RNA (rRNA). The modifications studied included the use of a chaotrope-based lysis buffer with high-energy mechanical cell disruption by RiboLysis, increased ruthenium (Ru2+) labelling per 16S rRNA molecule and concomitant use of fluorescent nucleic acid dyes (CyQUANT, Syto 17 red and Syto 61 red). The methodological changes made did lead to more effective bacterial cell disruption and enhanced ECL signal generation. Nevertheless, assay sensitivity was only slightly improved at approximately 10(4)-10(5) colony forming units per mL (CFU mL(-1)) and the results were highly inconsistent. The method is still not sensitive to the required 10(2) CFU mL(-1) and remains impractical for routine use in blood centres.