Rapid identification of Yersinia enterocolitica in blood by the 5' nuclease PCR assay

In situ and in vitro evaluation of two antiseptics for blood bank based on chlorhexidine gluconate/isopropyl alcohol and povidone-iodine

BACKGROUND

Poor disinfection is the main cause of blood contamination, so its elimination is key to limiting the entry of bacteria into the collection system. With the advancement of antiseptic technology, antiseptics with sterile, disposable applicators are now available.

AIM

To evaluate in situ two antiseptics (with and without applicators) for blood banks and to demonstrate in vitro antiseptic activity on bacterial biofilms of importance in transfusion medicine.

METHODS

Antiseptic A (2% sterile solution of chlorhexidine gluconate/70% isopropyl alcohol provided with applicator) and bulk antiseptic B (10% povidone-iodine) were evaluated. The deferred blood donor arms were subjected to disinfection with antiseptics A and B and the contralateral arms were cultured to determine the baseline bacterial load (control). Antiseptic activity was assessed by ANOVA and logaritmic reduction values (LRV) and percentage reduction values (PRV) were calculated. Finally, the in vitro activity of antiseptic A was analyzed by confocal laser scanning microscopy (CLSM) on biofilm models.

RESULTS

Prior to disinfection tests, commensal and clinically important bacteria were identified; antiseptic A showed post-disinfection bacterial growth rates of zero compared to controls (p < 0.0001). The frequency of bacterial growth with antiseptic B was 74%. A significant difference was identified between both antiseptics, where antiseptic A showed higher activity (p < 0.5468). LRV and PRV were 0.6-2.5/100% and 0.3-1.7/66.7-99.7% for antiseptics A and B, respectively. Through CLSM, disinfectant A (without applicator) showed lower in vitro antiseptic activity on the tested biofilms at the exposure times recommended by the manufacturer.

CONCLUSIONS

Sterile solution of chlorhexidine gluconate/isopropyl alcohol with applicator showed advantages disinfection in deferred blood donors over povidone-iodine.

Enteropathogenic Yersinia with Public Health Relevance Found in Dogs and Cats in Finland

Yersiniosis is a common zoonotic enteric disease among humans, which has been linked to pigs and contaminated food, especially pork. The epidemiology of yersiniosis is still obscure, and studies on yersiniosis in pets are very scarce. In this study, we performed pheno- and genotypic characterisation of 50 Yersinia strains isolated from pets in Finland between 2012 and 2023. Y. enterocolitica 4/O:3/ST135, the most common type in human yersiniosis, was also the most common type (68%) found in clinical faecal samples in our study. Also, human pathogenic Y. enterocolitica 2/O:9/ST139 and Y. pseudotuberculosis O:1/ST9 and O:1/ST42 strains carrying all essential pathogenic genes were identified. Three Y. enterocolitica 4/O:3/ST9 strains were multi-drug-resistant and two of them were highly related, showing one allelic difference (AD) with core genome multi-locus sequence typing. Non-pathogenic, genotypically highly diverse Y. enterocolitica 1A strains, showing more than 1000 ADs and missing the essential virulence genes, were also recognised in dogs and cats. Our study demonstrates that pets can excrete human pathogenic Yersinia in their faeces and may serve as an infection source for human yersiniosis, especially in families with small children in close contact with their pets.

Nanolitre real-time PCR detection of bacterial, parasitic, and viral agents from patients with diarrhoea in Nunavut, Canada

Background

Little is known about the microbiology of diarrhoeal disease in Canada's Arctic regions. There are a number of limitations of conventional microbiology testing techniques for diarrhoeal pathogens, and these may be further compromised in the Arctic, given the often long distances for specimen transport.

Objective

To develop a novel multiple-target nanolitre real-time reverse transcriptase (RT)-PCR platform to simultaneously test diarrhoeal specimens collected from residents of the Qikiqtani (Baffin Island) Region of Nunavut, Canada, for a wide range of bacterial, parasitic and viral agents.

Study design/methods

Diarrhoeal stool samples submitted for bacterial culture to Qikiqtani General Hospital in Nunavut over an 18-month period were tested with a multiple-target nanolitre real-time PCR panel for major diarrhoeal pathogens including 8 bacterial, 6 viral and 2 parasitic targets.

Results

Among 86 stool specimens tested by PCR, a total of 50 pathogens were detected with 1 or more pathogens found in 40 (46.5%) stool specimens. The organisms detected comprised 17 Cryptosporidium spp., 5 Clostridium difficile with toxin B, 6 Campylobacter spp., 6 Salmonella spp., 4 astroviruses, 3 noroviruses, 1 rotavirus, 1 Shigella spp. and 1 Giardia spp. The frequency of detection by PCR and bacterial culture was similar for Salmonella spp., but discrepant for Campylobacter spp., as Campylobacter was detected by culture from only 1/86 specimens. Similarly, Cryptosporidium spp. was detected in multiple samples by PCR but was not detected by microscopy or enzyme immunoassay.

Conclusions

Cryptosporidium spp., Campylobacter spp. and Clostridium difficile may be relatively common but possibly under-recognised pathogens in this region. Further study is needed to determine the regional epidemiology and clinical significance of these organisms. This method appears to be a useful tool for gastrointestinal pathogen research and may also be helpful for clinical diagnostics and outbreak investigation in remote regions where the yield of routine testing may be compromised.

Impact of antibiotic treatments on the expression of the R plasmid tra genes and on the host innate immune activity during pRAS1 bearing Aeromonas hydrophila infection in zebrafish (Danio rerio)

BACKGROUND

The transfer of R plasmids between bacteria has been well studied under laboratory conditions and the transfer frequency has been found to vary between plasmids and under various physical conditions. For the first time, we here study the expression of the selected plasmid mobility genes traD, virB11 and virD4 in the 45 kb IncU plasmid, pRAS1, conferring resistance to tetracycline, trimethoprim and sulphonamide, using an in vivo zebrafish infection- treatment model.

RESULTS

Three days after oral infection of adult zebrafish with Aeromonas hydrophila harboring pRAS1, elevated expression of pro-inflammatory cytokine (TNF α, IL-1β and IL-8) and complement C3 genes in the intestine coincided with disease symptoms. Tetracycline, trimethoprim and an ineffective concentration of flumequine given 48 h prior to sampling, strongly increased expression of plasmid mobility genes, whereas an effective dosage of flumequine resulted in lower levels of mRNA copies of these genes relative to placebo treatment. Following effective treatment with flumequine, and ineffective treatments with a low concentration of flumequine, with trimethoprim or with sulphonamide, the intestinal expression of immune genes was strongly induced compared to placebo treated control fish.

CONCLUSIONS

Treatment of zebrafish infected with an antibiotic resistant (TcR, TmR, SuR) A. hydrophila with ineffective concentrations of flumequine or the ineffective antimicrobials tetracycline and trimethoprim strongly induced expression of genes mediating conjugative transfer of the R-plasmid pRAS1. Simultaneously, there was a strong induction of selected inflammatory and immune response genes, which was again evident in fish subjected to ineffective treatment protocols. Our findings point to the essential role of therapeutic practices in escalation or control of antibiotic resistance transfer, and suggest that antibiotic substances, even in sub-inhibitory concentrations, may stimulate innate defenses against bacterial infections.

Yersinia enterocolitica and Yersinia pseudotuberculosis Detection in Foods

Yersinia enterocolitica and Y. pseudotuberculosis which can cause yersiniosis in humans and animals are thought to be significant food-borne pathogens and be important as hygiene indicator in food safety. The pathogenic Y. enterocolitica serotypes/biotypes are O:3/4 and 3 variant VP negative, O:5, 27/2, O:8/1b, and O:9/2, have been reported worldwide. Y. pseudotuberculosis is distributed less widely than Y. enterocolitica. Isolation methods usually involve selective and recovery enrichment of the food sample followed by plating onto selective media, confirmation of typical colonies and testing for virulence properties of isolated strains. Recently, DNA-based methods, such as PCR assays, have been developed to detect pathogenic Y. enterocolitica and Y. pseudotuberculosis in foods more rapidly, and sensitivity than can be achieved by conventional culture methods. This paper reviews commercially available conventional and PCR-based procedures for the detection of pathogenic Yersinia in food. These methods are effective as the isolation and detection methods to target pathogenic Y. enterocolitica and Y. pseudotuberculosis in foods.

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.

Rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique

A real-time PCR assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. Current real-time PCR technologies cannot accomplish this task due to severe limitations in multiplexing ability. To this end, we developed a new assay system which supports very high degrees of multiplexing. We developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelting temperature (T(m)) signature approach to bacterial species identification. Sloppy molecular beacons were exceptionally versatile, and they were able to generate specific T(m) values for DNA sequences that differed by as little as one nucleotide to as many as 23 polymorphisms. Combining the T(m) values generated by several probe-target hybrids resulted in T(m) signatures that served as highly accurate sequence identifiers. Using this method, PCR assays with as few as six sloppy molecular beacons targeting bacterial 16S rRNA gene segments could reproducibly classify 119 different sequence types of pathogenic and commensal bacteria, representing 64 genera, into 111 T(m) signature types. Blinded studies using the assay to identify the bacteria present in 270 patient-derived clinical cultures including 106 patient blood cultures showed a 95 to 97% concordance with conventional methods. Importantly, no bacteria were misidentified; rather, the few species that could not be identified were classified as "indeterminate," resulting in an assay specificity of 100%. This approach enables highly multiplexed target detection using a simple PCR format that can transform infectious disease diagnostics and improve patient outcomes.

Prevalence of infectious pathogens in Crohn's disease

The importance of infectious pathogens in Crohn's disease (CD) is still under debate. Therefore, we examined a panel of potential viral and bacterial pathogens in a large series of CD patients and controls. Archival tissue from 76 patients, 56 with CD and 20 control patients, with normal colon mucosa (n=10) and non-steroid anti-inflammatory drug (NSAID)-induced colitis (n=10) were examined using PCR-based detection methods for human cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1, 2 (HSV1,2), adenovirus (AD), varicella-zoster virus (VZV), human herpes virus 6 (HHV6), human herpes virus 8 (HHV8), Mycobacterium tuberculosis complex (Mtbc), atypical mycobacteria (nM/MG1), including Mycobacterium avium (subspecies paratuberculosis, MAP), Stenotrophomonas maltophilia (Sm), and Yersinia enterocolitica (Ye). In CD patients, positive PCR results were achieved in 19 cases (34%). Sm was most frequent in 10 of 56 cases (17.9%) followed by EBV (6/56, 10.7%), nM/MG1 (4/56, 7.1%), including MAP, HHV6, and CMV (2/56, 3.6%), and finally Mtbc and AD (1/56, 1.8%). The control patients showed positive PCR results in 12 patients (12/20, 60%), nine of them with only weak signals, suggesting a persistent infection. In addition, we compared typical pathomorphological features of CD patients with the PCR results and found a significant correlation between EBV infection and mural abscesses (P=0.014). Our data demonstrate that several potential pathogens can be detected in a sizeable fraction of specimens from patients with CD, but also in control patients, suggesting that the analyzed infectious pathogens may be associated with the disease, but do not represent an obligatory cause.

Quantitative PCR monitoring of antibiotic resistance genes and bacterial pathogens in three European artificial groundwater recharge systems

Aquifer recharge presents advantages for integrated water management in the anthropic cycle, namely, advanced treatment of reclaimed water and additional dilution of pollutants due to mixing with natural groundwater. Nevertheless, this practice represents a health and environmental hazard because of the presence of pathogenic microorganisms and chemical contaminants. To assess the quality of water extracted from recharged aquifers, the groundwater recharge systems in Torreele, Belgium, Sabadell, Spain, and Nardò, Italy, were investigated for fecal-contamination indicators, bacterial pathogens, and antibiotic resistance genes over the period of 1 year. Real-time quantitative PCR assays for Helicobacter pylori, Yersinia enterocolitica, and Mycobacterium avium subsp. paratuberculosis, human pathogens with long-time survival capacity in water, and for the resistance genes ermB, mecA, blaSHV-5, ampC, tetO, and vanA were adapted or developed for water samples differing in pollutant content. The resistance genes and pathogen concentrations were determined at five or six sampling points for each recharge system. In drinking and irrigation water, none of the pathogens were detected. tetO and ermB were found frequently in reclaimed water from Sabadell and Nardò. mecA was detected only once in reclaimed water from Sabadell. The three aquifer recharge systems demonstrated different capacities for removal of fecal contaminators and antibiotic resistance genes. Ultrafiltration and reverse osmosis in the Torreele plant proved to be very efficient barriers for the elimination of both contaminant types, whereas aquifer passage followed by UV treatment and chlorination at Sabadell and the fractured and permeable aquifer at Nardò posed only partial barriers for bacterial contaminants.

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.

Development of an internal control for evaluation and standardization of a quantitative PCR assay for detection of Helicobacter pylori in drinking water

Due to metabolic and morphological changes that can prevent Helicobacter pylori cells in water from growing on conventional media, an H. pylori-specific TaqMan quantitative PCR (qPCR) assay was developed that uses a 6-carboxyfluorescein-labeled probe (A. E. McDaniels, L. Wymer, C. Rankin, and R. Haugland, Water Res. 39:4808-4816, 2005). However, proper internal controls are needed to provide an accurate estimate of low numbers of H. pylori in drinking water. In this study, the 135-bp amplicon described by McDaniels et al. was modified at the probe binding region, using PCR mutagenesis. The fragment was incorporated into a single-copy plasmid to serve as a PCR-positive control and cloned into Escherichia coli to serve as a matrix spike. It was shown to have a detection limit of five copies, using a VIC dye-labeled probe. A DNA extraction kit was optimized that allowed sampling of an entire liter of water. Water samples spiked with the recombinant E. coli cells were shown to behave like H. pylori cells in the qPCR assay. The recombinant E. coli cells were optimized to be used at 10 cells/liter of water, where they were shown not to compete with 5 to 3,000 cells of H. pylori in a duplex qPCR assay. Four treated drinking water samples spiked with H. pylori (100 cells) demonstrated similar cycle threshold values if the chlorine disinfectant was first neutralized by sodium thiosulfate.

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.

Applications of real-time PCR in the screening of platelet concentrates for bacterial contamination

Although there have been major improvements over the past few decades in detection methods for blood-borne infectious agents, platelet concentrates are still responsible for most cases of transfusion-transmitted bacterial infections. To date, real-time PCR is an indispensable tool in diagnostic laboratories to detect pathogens in a variety of biological samples. In this article, the applications of this powerful technique in the screening of platelet concentrates for bacterial contamination are discussed. Next to pathogen-specific (real-time) PCR assays, particular attention is directed to the recently developed 16S rDNA real-time PCR. This assay has been proven as a convenient way to detect bacterial contamination of platelet concentrates. The assay is sensitive and enables rapid detection of low initial numbers of bacteria in platelet concentrates. The short turnaround time of this assay allows high-throughput screening and reduction of the risk of transfusion of bacterially contaminated units. As with every method, real-time PCR has its advantages and disadvantages. These and especially limitations inherent to generation of false-positive or -negative results are emphasized. The universal nature of detection of the assay may be suitable for generalized bacterial screening of other blood components, such as red blood cells and plasma. Therefore, it is necessary to adapt and optimize detection in red blood cells and plasma with real-time PCR. Further sophistication, miniaturization and standardization of extraction and amplification methods should improve the total performance and robustness of the assay. Hence, real-time PCR is an attractive method in development as a more rapid screening test than currently used culture methods to detect bacterial contamination in blood components.

Correlation between Yersinia enterocolitica and type I collagen reactivity in patients with arthropathies

We investigated the association with Yersinia infection in patients with arthropathies in our region. To assess the reactivity to articular antigens, the correlation of anti-Yersinia with anti-type I and type II collagen antibodies was studied. Sera from 124 patients with musculoskeletal symptoms, and 47 synovial fluids (SF) from patients with rheumatoid arthritis (RA), spondyloarthopathies (SpA) or osteoarthritis (OA) were examined. Immunoglobulins against Yersinia enterocolitica, type I and type II collagens were determined by enzyme-linked immunosorbent assay. Immunoglobulin (Ig) A to Yersinia lipopolysaccharide (LPS) was present in 13/124 sera (10%) and 3/47 SF (6%). By Western blot, IgA to Yersinia outer proteins (Yops) was found in 14/124 sera (11%) and 2/47 SF (4%). Yersinia DNA from SF was not amplified by polymerase chain reaction. We found a significant correlation with anti-collagen type I but not type II antibodies. These results suggest different reactivity to articular collagen in patients with Yersinia antibodies.

Sensitive quantitative detection of commensal bacteria by rRNA-targeted reverse transcription-PCR

A sensitive rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) method was developed for exact and sensitive enumeration of subdominant bacterial populations. Using group- or species-specific primers for 16S or 23S rRNA, analytical curves were constructed for Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, Clostridium perfringens, and Pseudomonas aeruginosa, and the threshold cycle value was found to be linear up to an RNA amount of 10(-3) cell per RT-PCR. The number of bacteria in culture was determined by RT-qPCR, and the results correlated well with the CFU count over the range from 10(0) to 10(5) CFU. The bacterial counts obtained by RT-qPCR were the same as the CFU counts irrespective of the growth phase in vitro, except for C. perfringens during starvation periods; the viable cell counts obtained by using a combination of 4',6-diamidino-2-phenylindole (DAPI) staining and SYTO9-propidium iodide double staining were in good agreement with the RT-qPCR counts rather than with the CFU counts. The RT-qPCR method could detect endogenous Enterobacteriaceae and P. aeruginosa in feces of hospitalized patients (n = 38) at a level of 10(3) cells per g of feces, and for enumeration of S. aureus or P. aeruginosa spiked into human peripheral blood, the lower detection limit for RT-qPCR quantification of the bacteria was 2 cells per ml of blood, suggesting that this method was equivalent to the conventional culture method. As only 5 h was needed for RT-qPCR quantification, we suggest that rRNA-targeted RT-qPCR assays provide a sensitive and convenient system for quantification of commensal bacteria and for examining their possible invasion of a host.

Quantitative analysis of Staphylococcus aureus in skimmed milk powder by real-time PCR

A large-scale outbreak of food poisoning caused by consumption of skimmed milk powder contaminated with staphylococcal enterotoxin A (SEA) occurred in Japan. No viable Staphylococcus aureus was detected in the skimmed milk powder, however, sea and nuc genes of S. aureus were detected in it by PCR. The number of S. aureus in skimmed milk powder was estimated by quantitative real-time PCR.

Rapid and quantitative detection of blood Serratia marcescens by a real-time PCR assay: its clinical application and evaluation in a mouse infection model

Large-scale nosocomial outbreaks of Serratia marcescens septicaemia in Japan have had a fatality rate of 20-60% within 48 h. As a countermeasure, a real-time PCR assay was constructed for the rapid diagnosis of S. marcescens septicaemia. This assay indeed detected S. marcescens in clinical blood specimens (at ca. 10(2)CFU ml(-1)), at a frequency of 0.5% in suspected cases of septicaemia. In mice, the assay provided estimates of blood S. marcescens levels at various infectious stages: namely, 10(7) to 10(8)CFU ml(-1) at a fatal stage (resulting in 100% death), 10(4)-10(5)CFU ml(-1) at a moderately fatal stage (resulting in 50% or more death), and <10(3)CFU ml(-1) at a mild stage (resulting in 100% survival), consistent with actual CFU measurements. Blood bacterial levels could be an important clinical marker that reflects the severity of septicaemia. The simultaneous detection of S. marcescens and the carbapenem resistance gene was also demonstrated.

High-throughput qualitative multiplex 5' nuclease assay using post-only PCR analysis

Homogenous fluorescence PCR assays offer distinct advantages for qualitative testing and are gaining immense popularity in fields like diagnostic microbiology. To meet the demand of high-volume laboratories, we developed a protocol for qualitative multiplex 5' nuclease assays using post-only PCR analysis. This novel approach overcomes throughput problems encountered with the established methods for TaqMan detection on the ABI PRISM 7700 Sequence Detection system and permits off-site TaqMan PCR, which can be analyzed several days after the reactions are completed. We have validated this novel protocol using an assay for the identification of Bordetella pertussis against real-time and plate-read analysis methods and have shown that our proposed protocol produces no difference in qualitative calls.

Bacterial contamination of blood components

Blood for transfusion is a potential source of infection by a variety of known and unknown transmissible agents. Over the last 20 years, astounding reductions in the risk of viral infection via allogeneic blood have been achieved. As a result of this success, bacterial contamination of blood products has emerged as the greatest residual source of transfusion-transmitted disease. This paper summarizes the current status of detection, prevention, and elimination of bacteria in blood products for transfusion.

In vitro alterations of intestinal bacterial microbiota in fecal samples during storage

The human gastrointestinal tract harbors an extremely diverse and complex microbial ecosystem. Most of the existent data about the enteric microflora have been generated using stool samples, but the collection and storage of fecal samples are often problematic. The influence of the storage of stool samples on the bacterial diversity and the degradation of bacterial DNA was analysed in this study. Stool samples from 5 healthy volunteers were exposed to different storage temperatures and durations. The bacterial diversity and the amount of intact bacterial DNA were analysed by single-stranded conformation polymorphism analysis (SSCP) and real-time polymerase chain reaction (PCR), both using a 16S rDNA approach. Additionally, biopsy specimens were taken from 3 of the 5 individuals to compare fecal and mucosal flora. The bacterial diversity of the fecal flora and the total number of bacteria were significantly reduced after 8 and 24 hours at both room temperature and 4 degrees C. The mucosa-associated bacterial microflora showed substantial differences compared with the fecal flora. The observed alterations of fecal flora during storage point to the difficulty of the molecular analysis of the bacterial diversity and the enumeration of bacterial cells in fecal samples.

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.

Detection by 5'-nuclease PCR of Shiga-toxin producing Escherichia coli O26, O55, O91, O103, O111, O113, O145 and O157:H7, associated with the world's most frequent clinical cases

This paper describes 5'-nuclease PCR assays for detecting eight O-serogroups, H7 flagellar antigen and stx genes from the Shiga toxin-producing Escherichia coli (STEC) associated with the world's most frequent clinical cases. A single set of primers was used to detect the genes stx1 and stx2 in the same reaction by 5'-nuclease PCR. Serotyping by 5'-nuclease PCR of STEC was based on the selection of primers and probes targeting the O-antigen gene clusters of E. coli O26, O55, O91, O111, O113, O157, the eae gene of E. coli O103, the O-island 29 of E. coli O145, and the flagellar H7 antigen gene. Results obtained on a collection of 190 strains indicate that the 5'-nuclease PCR assays used here could serve as a basis for rapid specific stx, O and H7 typing of these major pathogenic serogroups of E. coli. This work provides sensitive and specific tests for the rapid, reliable detection of the main pathogenic E. coli O-serogroups of major public health concern.

Quantification of intestinal bacterial populations by real-time PCR with a universal primer set and minor groove binder probes: a global approach to the enteric flora

The composition of the human intestinal flora is important for the health status of the host. The global composition and the presence of specific pathogens are relevant to the effects of the flora. Therefore, accurate quantification of all major bacterial populations of the enteric flora is needed. A TaqMan real-time PCR-based method for the quantification of 20 dominant bacterial species and groups of the intestinal flora has been established on the basis of 16S ribosomal DNA taxonomy. A PCR with conserved primers was used for all reactions. In each real-time PCR, a universal probe for quantification of total bacteria and a specific probe for the species in question were included. PCR with conserved primers and the universal probe for total bacteria allowed relative and absolute quantification. Minor groove binder probes increased the sensitivity of the assays 10- to 100-fold. The method was evaluated by cross-reaction experiments and quantification of bacteria in complex clinical samples from healthy patients. A sensitivity of 10(1) to 10(3) bacterial cells per sample was achieved. No significant cross-reaction was observed. The real-time PCR assays presented may facilitate understanding of the intestinal bacterial flora through a normalized global estimation of the major contributing species.

A strategy based on 5' nuclease multiplex PCR to detect enterotoxin genes sea to sej of Staphylococcus aureus

We describe the development of a strategy based on 5' nuclease multiplex PCR for the rapid detection of nine enterotoxin genes (sea, seb, sec, sed, see, seg, seh, sei, sej) of Staphylococcus aureus. The genotyping scheme consists in identifying these nine enterotoxin genes by three 5' nuclease Triplex-PCR assays. The strategy was evaluated using a collection of S. aureus reference strains previously examined with conventional PCR assays, and by testing previously characterized food S. aureus field strains. The 5' nuclease Triplex-PCR assays correctly detected the se genes in all the reference strains. In tests with field strains there was generally excellent agreement with the results obtained by conventional PCR, except for some strains harbouring variant se genes. The detection limits of the Triplex-PCR assays evaluated using fivefold dilution of recombinant plasmids for each se gene ranged from 16 to 2000 copies of target se genes in the PCR tube. The 5' nuclease Triplex-PCR assays developed are fast and specific, and provide a useful diagnostic tool for the detection and genotyping of se genes. The development of this method is an improvement that should facilitate epidemiological investigations of staphylococcal food poisoning outbreaks.

Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools

A duplex real-time SYBR Green LightCycler PCR (LC-PCR) assay with DNA extraction using the QIAamp DNA Stool Mini kit was evaluated with regard to detection of 8 of 17 species of food- or waterborne pathogens in five stool specimens in 2 h or less. The protocol used the same LC-PCR with 20 pairs of specific primers. The products formed were identified based on a melting point temperature (T(m)) curve analysis. The 17 species of food- or waterborne pathogens examined were enteroinvasive Escherichia coli, enteropathogenic E. coli, enterohemorrhagic E. coli, enterotoxigenic E. coli, enteroaggregative E. coli, Salmonella spp., Shigella spp., Yersinia enterocolitica, Yersinia pseudotuberculosis, Campylobacter jejuni, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, Aeromonas spp., Staphylococcus aureus, Clostridium perfringens, and Bacillus cereus. No interference with the LC-PCR assay was observed when stool specimens were artificially inoculated with each bacterial species. The detection levels were approximately 10(5) food- or waterborne pathogenic bacteria per g of stool. The protocol for processing stool specimens for less than 10(4) food- or waterborne pathogenic bacteria per g of stool requires an overnight enrichment step to achieve adequate sensitivity. However, the rapid amplification and reliable detection of specific genes of greater than 10(5) food- or waterborne pathogenic bacteria per g in samples should facilitate the diagnosis and management of food- or waterborne outbreaks.

Development of a 5'-nuclease PCR assay for detecting Shiga toxin-producing Escherichia coli O145 based on the identification of an 'O-island 29' homologue

AIMS

A DNA sequence, from Escherichia coli STEC O145, homologous to O-island 29 from STEC O157 is described, together with a real-time PCR assay for detecting it.

METHODS AND RESULTS

PCR and sequencing were used to identify the 'O-island 29' homologous DNA sequence from STEC O145 (strain VTH34). The sequence divergence between the STEC O145 and O157 'O-island 29' allowed a STEC O145 5'-nuclease PCR assay to be developed.

CONCLUSIONS

The characterization of a novel locus in STEC O145 has allowed a specific O145 serogroup 5'-nuclease PCR assay to be designed.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings increase the number of serogroup PCR assays available as alternatives to classical O-serotyping of E. coli.

Low occurrence of pathogenic Yersinia enterocolitica in clinical, food, and environmental samples: a methodological problem

While Yersinia enterocolitica is an important pathogen, which can cause yersiniosis in humans and animals, its epidemiology remains obscure. The pig is the major reservoir of pathogenic Y. enterocolitica of bioserotype 4/O:3, the most common type found in humans. Y. enterocolitica is thought to be a significant food-borne pathogen, although pathogenic isolates have seldom been recovered from foods. The low isolation rate of this pathogenic bacterium in natural samples, including clinical, food, and environmental samples, may be due to the limited sensitivity of culture methods. During the last decade, numerous DNA-based methods, such as PCR and colony hybridization assays, have been designed to detect pathogenic Y. enterocolitica in natural samples more rapidly and with better sensitivity than can be achieved by culture methods. In addition, the occurrence of pathogenic Y. enterocolitica in natural samples is clearly higher with PCR than with culture methods. The methods available for detection of pathogenic Y. enterocolitica in natural samples are reviewed in this article.

Bacterial contamination of blood products: factors, options, and insights

Transfusion of bacterially contaminated blood products remains an overlooked problem. However, the risk of receiving a bacterially contaminated unit is greater than the combined risk of HIV-1/2, HCV, HBV, and HTLV I/II [American Association of Blood Banks Bulletin, no. 294, 1996]. Topics covered in this article include: the current incidence, clinical presentation and outcome, effective methods of detection, and ways to reduce bacterial contamination of blood products. There is no one existing strategy that can completely eliminate the risk of bacterial contamination. It is inevitable that partial solutions or combinations of methods will be implemented in the near future.

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.

Detection of pathogenic Yersinia enterocolitica by a rapid and sensitive duplex PCR assay

A duplex PCR assay targeting the ail and 16S rRNA genes of Yersinia enterocolitica was developed to specifically identify pathogenic Y. enterocolitica from pure culture. Validation of the assay was performed with 215 clinical Yersinia strains and 40 strains of other bacterial species. Within an assay time of 4 h, this assay offers a very specific, reliable, and inexpensive alternative to the conventional phenotypic assays used in clinical laboratories to identify pathogenic Y. enterocolitica.

Application of polymerase chain reaction (PCR) and TaqMan PCR techniques to the detection and identification of Rhodococcus coprophilus in faecal samples

Rhodococcus coprophilus, a natural inhabitant of herbivore faeces, has been suggested as a good indicator of animal (as opposed to human) faecal contamination of aquatic environments. However, conventional detection methods limit its use for this as they require up to 21 days to obtain a result. In this paper an optimised method for extracting R. coprophilus DNA from faecal samples is described. PCR and 5'-nuclease (TaqMan) PCR methods were developed to allow the detection and enumeration of R. coprophilus in faecal samples within 2-3 days. Both PCR methods targeted the 16S rRNA gene, producing an amplicon of 443 bp which was specific for R. coprophilus. Sixty cells were required to produce an amplification product by conventional PCR, while as little as one cell was required for the TaqMan PCR method. The latter approach gave a linear quantitative response over at least four log units with both bacterial cells and DNA. Successful amplification by PCR was achieved using DNA extracted from cow, sheep, horse and deer faeces but was negative for samples from humans, pig, possum, duck and rabbit. These PCR methods enhance the feasibility of using R. coprophilus to distinguish faecal pollution of farmed herbivores from human pollution.

Transfusion-related bacterial sepsis

Transfusion-associated bacterial sepsis is a persistent problem in transfusion medicine, posing a greater threat than the combined risks of receiving a blood product contaminated with HIV-1 or 2, hepatitis C virus (HCV), hepatitis B virus (HBV), and human T-cell lymphtrophic virus (HTVL) -I or -II. This article provides a brief overview of the current incidence, clinical presentation, associated blood products and organisms, and the most feasible and effective methods available to reduce the potential risk of transfusion-associated sepsis. Because bacterial contamination of blood products is the most frequent cause of transfusion-transmitted infectious disease, and as no single existing strategy can completely eliminate its risk, it is important that clinical suspicion be high, and any partial solutions additively be implemented.

Multiplex PCR for detection of Enterobacteriaceae in blood

BACKGROUND

Rapid and sensitive methods are needed to detect the small numbers of bacteria that may sometimes contaminate units of blood during collection. A multiplex 5'-nuclease TaqMan PCR assay (PE Applied Biosystems) was used to detect several bacterial species that may contaminate blood.

STUDY DESIGN AND METHODS

Oligonucleotide primers were made for regions of the 16S rRNA gene conserved in four different bacterial species: Yersinia enterocolitica and Serratia, Klebsiella, and Enterobacter species. Two probes were designed: SL-1 detected Serratia, Klebsiella, and Enterobacter species, and YE-3 detected Y. enterocolitica.

RESULTS

When TaqMan PCR was performed with chromosomal DNA isolated from pure cultures of Serratia liquefaciens, Klebsiella oxytoca, Klebsiella pneumoniae, Enterobacter cloacae, and Enterobacter agglomerans, the limit of detection with probe SL-1 was 1 to 2 CFUs. For S. marcescens, the sensitivity was 8 CFUs. The limit of detection for Y. enterocolitica with probe YE-3 was 2 CFUs. When total chromosomal DNA was extracted from whole-blood samples spiked with different numbers of Y. enterocolitica, S. liquefaciens, E. cloacae, or K. pneumoniae bacteria, the TaqMan PCR detected 12 to 16 organisms in 1 mL of blood.

CONCLUSION

The 5'-nuclease TaqMan PCR assay takes only 3 hours to perform and has the potential to detect very small numbers of bacteria.

Rapid duplex PCR assay for the detection of pathogenic Yersinia enterocolitica strains

For the detection of pathogenic Yersinia enterocolitica strains, a duplex PCR has been developed based on differences observed between the fingerprint profiles of pathogenic and non-pathogenic strains. The profiles were obtained by using a primer derived from the Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences. From the sequence of one pathogen-specific amplified fragment, a discriminative primer has been designed bridging the sequence of the highly conserved core region and 3' end of the ERIC element. In combination with three other primers, all located within the detected open reading frame that resembled the sequence of the bipA gene, this primer was applied in a duplex PCR assay to simultaneously detect Y. enterocolitica and to discriminate between pathogenic and non-pathogenic strains. The same primer combinations were used in an on line rapid cycling real-time PCR assay. The used SYBR Green I format allowed for the easy translation of the PCR conditions and confirmation of the resulting amplicons. The time of analysis was reduced to approximately 60 min.

Quantification of Candida albicans actin mRNA by the LightCycler system as a means of assessing viability in a model of cutaneous candidiasis

The LightCycler system (two-step reverse transcription-PCR-fluorescent hybridization [LC RT-PCR-FH]) was used to quantify Candida albicans actin mRNA as a means of assessing its viability in a reconstituted skin model of cutaneous candidiasis following the application of an antimycotic. A 192-bp ACT exon fragment was ligated into the pCR2.1 plasmid vector, and dilutions of the cloned insert (pACT; 4.092 kb) were used as the standard reference template. The LC RT-PCR-FH system could detect 1 fg of pACT, equivalent to 2.2 copies of the plasmid. The ACT exon-based PCR primers and FH probes were C. albicans specific, and electrophoretic analysis of the LC RT-PCR-FH assay product showed a 174-bp band in agarose gel. The number of copies of C. albicans ACT mRNA per milligram of tissue decreased with increasing amounts of amorolfine applied to a C. albicans-infected skin model, showing a reduction in viability. Detection and quantification of ACT mRNA in tissue by the LC RT-PCR-FH assay corresponded with cultural isolation of C. albicans from samples. The ACT mRNA-targeted LC RT-PCR-FH assay represents a sensitive, specific, rapid, and quantitative means of assessing the viability of C. albicans in infected tissue. This method may also be useful in evaluating the therapeutic efficacies of antifungal drugs in the treatment of various forms of candidiasis and other fungal diseases.

Fluorogenic PCR-based quantitative detection of a murine pathogen, Helicobacter hepaticus

Helicobacter hepaticus infection in mice is being used as an animal model for elucidating the pathogenesis of gastrointestinal and biliary diseases in humans. H. hepaticus, which forms a spreading film on selective agar, is not amenable to routine quantitative counts of organisms in tissues using a CFU method. In this study, a fluorogenic PCR-based assay was developed to quantitatively detect H. hepaticus in mouse ceca and feces using the ABI Prism 7700 sequence detection system. A pair of primers and a probe for this assay were generated from the H. hepaticus cdtB gene (encoding subunit B of the H. hepaticus cytolethal distending toxin). Using this assay, the sensitivity for detection of H. hepaticus chromosomal DNA prepared from pure culture was 20 fg, which is equivalent to approximately 14 copies of the H. hepaticus genome based on an estimated genome size of approximately 1.3 Mb determined by pulsed-field gel electrophoresis. H. hepaticus present in feces and cecal samples from H. hepaticus-infected mice was readily quantified. The selected PCR primers and probe did not generate fluorescent signals from eight other helicobacters (H. canis, H. cineadi, H. felis, H. mustelae, H. nemestrinae, H. pullorum, H. pylori, and H. rodentium). A fluorescent signal was detected from 20 ng of H. bilis DNA but with much lower sensitivity (10(6)-fold) than from H. hepaticus DNA. Therefore, this assay can be used with high sensitivity and specificity to quantify H. hepaticus in experimentally infected mouse models as well as in naturally infected mice.

Evaluation of an automated culture system for detecting bacterial contamination of platelets: an analysis with 15 contaminating organisms

BACKGROUND

Approximately 1 in 2000 platelet components are bacterially contaminated. The time to detection of 15 seeded organisms in platelets recovered from an automated culture system was studied.

STUDY DESIGN AND METHODS

Isolates of Bacillus cereus, Bacillus subtilis, Candida albicans, Clostridium perfringens, Corynebacterium species, Enterobacter cloacae, Escherichia coli, Klebsiella oxytoca, Propionibacterium acnes, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Serratia marcescens, Streptococcus pyogenes, and Streptococcus viridans were inoculated into Day 2 apheresis platelet components to obtain a final concentration of approximately 10 and 100 CFU per mL (2 units/organism). Each bag was sampled 10 times (20 mL/sample). Four mL of each sample was inoculated into standard aerobic and anaerobic bottles and into aerobic and anaerobic bottles containing charcoal; 2 mL was inoculated into pediatric aerobic bottles (so as to maintain a 1:10 ratio of sample to media) and 1 mL into thioglycollate broth.

RESULTS

With the exception of P. acnes, all organisms were detected in a mean of 9.2 to 25.6 hours. A range of 10 serial dilutions in inoculating concentrations was associated with an overall 10.1-percent difference in detection time. A mean of 74.4 and 86.2 hours (100 and 10 CFU/mL inocula, respectively) was required for the detection of P. acnes in anaerobic bottles.

CONCLUSION

Bacteria thought to be clinically significant platelet contaminants can be detected in 9.2 to 25.6 hours when the starting concentration is approximately 10 to 100 CFU per mL. P. acnes required considerably longer incubation times for detection (in either aerobic or anaerobic bottles). However, P. acnes is of questionable clinical significance. Such a detection system could be used in either a blood collection center or a transfusion service to screen platelet concentrates for bacterial contamination. Such testing (with sterile sampling performed so as to maintain a closed-bag system) would be expected to save lives and might allow an extension of platelet storage.