Identification of novel eubacteria from spent mushroom compost (SMC) waste by DNA sequence typing: ecological considerations of disposal on agricultural land

A small study was undertaken to examine the microbiological characteristics of spent mushroom compost (SMC), which is the major waste by-product of the mushroom industry and which is regularly disposed off by application to agricultural land. The primary aim of this study was to examine SMC for the presence of faecal bacterial pathogens, including Campylobacter spp., Salmonella spp. and Listeria monocytogenes. Secondly it was desirable to quantify bacterial and fungal populations within SMC, and also qualitatively identify the diversity of bacterial populations within SMC, through employment of rDNA PCR and direct sequencing techniques on the culturable microflora. Conventional microbiological analyses of SMC material (n=30) from six commercial operations in both Northern Ireland and the Republic of Ireland, failed to detect Salmonella spp, Listeria spp. or Campylobacter spp. in any of the SMC material examined. Total aerobic plate counts gave a mean count of log10 7.01 colony forming units (cfu) per gram SMC material (range: log10 6.53-7.52 cfu/g). Fungal counts gave a mean count of log(10) 4.57 cfu per gram SMC material (range: log10 3.93-4.98 cfu/g). From a total of greater than 50 colony picks, a total of 12 bacterial morphotypes were identified and were further examined by employment of partial 16S rRNA gene amplification and sequencing techniques, yielding several genera and species, including Bacillus licheniformis, Bacillus subtilis, Klebsiella/Enterobacter sp. Microbacterium sp. Paenibacillus lentimorbus, Pseudomonas mevalonii, Sphingobacterium multivorum and Stenotrophomonas sp. This is the first preliminary report on the microbial diversity of SMC waste and demonstrates the presence of several species that have not been previously described in SMC, in addition to two potentially novel species within the genera Microbacterium and Stenotrophomonas. It is thereby important to examine the ecological microbe-microbe and plant-microbe interactions that are occurring between the native bacterial soil flora and those added annually (theoretically estimated at approximately 10(18) cells) through the application of SMC. Such studies would be beneficial in helping to ascertain the ecological consequences involved in the disposal of SMC waste on agricultural land.

Structural analysis and genetic variation of the 16S-23S rDNA internal spacer region from Micrococcus luteus strains

AIMS

To clone and sequence the 16S-23S ribosomal DNA (rDNA) internal spacer region (ISR) from Micrococcus luteus.

METHODS AND RESULTS

The primer pair for 16S-23S rDNA ISR amplified a fragment of about 850 bp in length for two strains, JCM3347 and JCM3348 and a fragment of about 790 bp for a strain, ATCC9341. After sequencing the ISRs were identified by the comparison of the ISRs and the flanking regions of ISR.

CONCLUSIONS

Although the sequence difference of the ISR occurred at only one position between the two JCM strains, the highly variable length (440 and 370 bp) and sequence similarity (about 40%) were demonstrated between the ISRs of the two JCM strains and a ATCC strain.

SIGNIFICANCE AND IMPACT OF THE STUDY

A CCTCCT sequence was first detected at the 3'-end of the 16S rDNA of the three strains. Moreover, highly similar sequence to the 21-bp region containing a putative rRNA processing site was observed in the ISR of the three strains. Interestingly, no intercistronic tRNAs were demonstrated in the ISRs from the three strains.

Purulent rhinitis and otitis caused by Pseudomonas aeruginosa in sheep showered with contaminated 'shower wash'

Three crossbred lowland ewes developed a severe purulent rhinitis and another three ewes developed a severe purulent otitis externa/media after being showered with a wash that had been used 24 to 48 hours before on a separate group of Cheviot ewes with lesions of dermatitis. Pseudomonas aeruginosa was isolated in pure growth from the aural and nasal abscesses and also from the dermatitis lesions. Extended antibiotic susceptibility testing and the random amplification of polymorphic DNA indicated that a single clonal type was associated with the rhinitis and otitis and with the dermatitis, providing strong evidence of an epidemiological link between the lesions of dermatitis and the aural and nasal abscesses through the use of the contaminated 'shower wash'.

Novel employment of lactate dehydrogenase release from porcine aortic endothelial cells (PAEC) as a quantitative marker of cytotoxic activity in thermophilic Campylobacter spp. from human faecal isolates, poultry and environmental sources

The aim of this study was to employ a novel cytotoxicity assay based on primary porcine aortic endothelial cells in combination with a lactate dehydrogenase release assay to quantitatively determine differences in cytotoxin production between Campylobacter jejuni, C. coli, C. lari and urease-positive thermophilic campylobacters (UPTC), isolated from human faeces, animals and environmental sources. Campylobacter isolates totalling 34 and comprising of C. jejuni (n = 24) C. coli (n = 5) and UPTC (n = 4) and C. lari (n = 1) were analysed. The cytotoxic response ranged from 32.15 to 64.47% and 33.08 to 59.41%, for C. jejuni from chicken and human isolates, respectively and there was no statistically significant difference (P > 0.05) in cytotoxic response between C. jejuni isolated from humans and chicken isolates (50.78% versus 50.55% cytotoxicity, respectively). However, there was a difference in response between C. jejuni and C. coli isolated from chickens (50.78% versus 33.22% cytotoxicity, respectively). The greatest cytotoxic response was obtained with the UPTC group of organisms examined (n = 4 isolates) (mean cytotoxic response = 57.11% cytotoxicity. Employment of this cytotoxin assay may help identify virulent strains in poultry that could potentially proceed to cause clinical problems for humans and thus intervention measures targeted at the reduction or elimination of such specific strains, may be sought.

Mycobacterium celatum pulmonary infection

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Development of a Gram-negative selective agar (GNSA) for the detection of Gram-negative microflora in sputa in patients with cystic fibrosis

AIMS

To develop a selective agar medium to help detect and quantify Gram-negative flora in the sputum of patients with cystic fibrosis (CF).

METHODS AND RESULTS

A novel Gram-negative Selective Agar (GNSA) medium was developed consisting of tryptone soya broth (30 g), bacteriological agar no.1 (10 g), yeast extract (5 g), crystal violet (2 mg), nisin (48 mg), novobiocin (5 mg), cycloheximide (100 mg), amphotericin (2 mg) and double distilled water (1 l), for the selective culture of all Gram-negative flora from the sputum of patients with CF. GNSA was able to support the proliferation of all 34 Gram-negative organisms examined, including 23 species most commonly associated with CF, but was unable to support the growth of the 12 Gram-positive or seven fungal organisms examined. Sensitivity studies demonstrated that the GNSA medium was able to detect not less than 1.50 x 102 CFU ml-1 sputum Pseudomonas aeruginosa, 2.38 x 102 CFU ml-1 sputum Burkholderia cepacia genomovar IIIb and 6.70 x 103 CFU ml-1 sputum Stenotrophomonas maltophilia. A comparison of the microbial flora detected in the sputa of 12 adult CF patients by employment of routine bacteriological agar media and GNSA, demonstrated that GNSA was able to detect all Gram-negative organisms cultured by routine media, but had the advantage of detecting Alcaligenes xylosoxidans in two CF patients, whom had no previous history of Gram-negative infection.

CONCLUSIONS

GNSA was unable to support the proliferation of any Gram-positive organism or yeast/fungi, but was successful in supporting the growth of all Gram-negative organisms challenged.

SIGNIFICANCE AND IMPACT OF THE STUDY

Employment of this medium coupled with semi-automated technology may aid in helping to efficiently determine Gram-negative loading of respiratory secretions, particularly in response to antibiotic intervention.

Studies on the genomic heterogeneity of Micrococcus luteus strains by macro-restriction analysis using pulsed-field gel electrophoresis

Macro-restriction analysis by means of double digestion using DraI and VspI demonstrated that they cleaved the genomic DNAs from Micrococcus luteus JCM1464(T), JCM3347, and JCM3348 into four to five fragments in a distinguishable manner by pulsed-field gel electrophoresis (PFGE). Separate digestion with DraI and VspI cleaved the genomic DNA from M. luteus ATCC9341 into a relatively limited number of restriction fragments (six pieces). SspI and XbaI cleaved the genomic DNA from each of the four strains into restriction fragments in a distinctly different and distinguishable manner.Thus, PFGE profiles after digestion with these four restriction enzymes that recognize six specific base sequences demonstrated the heterogeneity at the whole genomic DNA level among the four strains of M. luteus. The size of the genomic DNA of M. luteus ATCC9341 was estimated to be approximately 2.3 Mb by the summing the lengths of the restriction fragments generated by each three restriction enzymes (DraI, SspI, and VspI) and averaging the results.

Comparison of three techniques for estimating the forage intake of lactating dairy cows on pasture

Quantifying DMI is necessary for estimation of nutrient consumption by ruminants, but it is inherently difficult on grazed pastures and even more so when supplements are fed. Our objectives were to compare three methods of estimating forage DMI (inference from animal performance, evaluation from fecal output using a pulse-dose marker, and estimation from herbage disappearance methods) and to identify the most useful approach or combination of approaches for estimating pasture intake by lactating dairy cows. During three continuous 28-d periods in the winter season, Holstein cows (Bos taurus; n = 32) grazed a cool-season grass or a cool-season grass-clover mixture at two stocking rates (SR; 5 vs. 2.5 cows/ha) and were fed two rates of concentrate supplementation (CS; 1 kg of concentrate [as-fed] per 2.5 or 3.5 kg of milk produced). Animal response data used in computations for the animal performance method were obtained from the latter 14 d of each period. For the pulse-dose marker method, chromium-mordanted fiber was used. Pasture sampling to determine herbage disappearance was done weekly throughout the study. Forage DMI estimated by the animal performance method was different among periods (P < 0.001; 6.5, 6.4, and 9.6 kg/d for Periods 1, 2, and 3, respectively), between SR (P < 0.001; 8.7 [low SR] vs. 6.3 kg/d [high SR]) and between CS (P < 0.01; 8.4 [low CS] vs. 6.6 kg/d [high CS]). The period and SR effect seemed to be related to forage mass. The pulse-dose marker method generally provided greater estimates of forage DMI (as much as 11.0 kg/d more than the animal performance method) and was not correlated with the other methods. Estimates of forage DMI by the herbage disappearance method were correlated with the animal performance method. The difference between estimates from these two methods, ranging from -4.7 to 5.4 kg/d, were much lower than their difference from pulse-dose marker estimates. The results of this study suggest that, when appropriate for the research objectives, the animal performance or herbage disappearance methods may be useful and less costly alternatives to using the pulse-dose method.

Prevalence of bacterial faecal pathogens in separated and unseparated stored pig slurry

AIMS

To examine the prevalence and diversity of bacterial faecal pathogens in unseparated slurry, separated solids and liquid fractions from a commercial pig farm.

METHODS

A total of 43 stored slurry specimens originating from a fattening house over the period February-April 2002 were analysed, consisting of unseparated (n = 14) slurry, separated solids (n = 16) and separated liquid (n = 13). Specimens were examined for the presence of five bacterial pathogens including Salmonella spp., Shigella spp., Campylobacter spp., Escherichia coli O157 and Yersinia enterocolitica. Selective enrichment and plating methods were employed for detection of Salmonella spp. and Campylobacter spp. and conventional selective plating techniques for the remaining genera. Antibiogram profiles to 12 antibiotic agents were obtained for all Salmonella isolates obtained.

RESULTS

Salmonella spp. were identified in all components of the slurry specimens, whereas Campylobacter spp. was only recovered from the unseparated and separated liquid fractions. In both cases, the separated liquid fraction had the highest prevalence of pathogens and the separated solid fraction had the lowest prevalence. None of the slurry specimens examined were positive for E. coli O157:H7, Shigella spp. or Y. enterocolitica. Twenty-nine isolates of Salmonella were recovered from the slurry specimens, comprising seven serovars, of which Salmonella manhattan was the most prevalent, accounting for over half [15 of 29 (51.7%)] of all Salmonella isolates. Salmonella anatum, Salm. derby, Salm. give, Salm. heidelberg, Salm. simi and Salm. stanley serovars were also recovered. All Salmonella isolates were sensitive to ampicillin, augmentin (amoxicillin/clavulanic acid), chloramphenicol, ciprofloxacin, gentamicin, kanamycin and trimethoprim, but has variable resistance to tetracycline (100%), sulphonamides (84.6%), furazolidone (38.5%), nalidixic acid (15.4%) and streptomycin (15.4%). The majority (57.7%) of isolates displayed antibiotic resistance to at least two antibiotic agents, followed by 34.6% of isolates being resistant to three agents and the remainder (7.7%) being resistant to four antibiotics.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrated a marked reduction in the prevalence of Campylobacter and Salmonella in the solids component of separated pig slurry. The adoption of control processes such as aeration of slurry prior to its spread onto agricultural land and newer approaches to pathogen reduction should be investigated, to reduce the transmission of pathogens from pig slurry to the environment.

Flow changes in the aorta associated with the deployment of a AAA stent graft

The purpose of this study was to investigate the hemodynamic implications of a proximal shift in the aortic bifurcation that results from abdominal aortic aneurysm (AAA) stent graft deployment. A flow model was constructed in which an anatomically accurate model of the aorta was subjected to physiologic pulsatile flow. The model included the celiac, superior mesenteric, left and right renal arteries. The aortic bifurcation, leading to the right and left iliac arteries was included, as well as the lumbar curvature. Flow simulations were performed under resting and mild exercise conditions with and without a Cordis AAA stent graft deployed. Flow patterns were visualized with dye injection and recorded onto video. The flow rates through the iliac and renal arteries were continuously monitored using ultrasonic flowmeters. Flow visualization revealed that flow disturbances at the level of the renal arteries were slightly increased with the deployment of the stent graft. The orientation of the endolegs within the aorta had no perceptible effect on these disturbances. Under mild exercise conditions, very little flow disturbance was observed. In conclusion, there are slight changes in flow disturbance near the renal arteries due to stent graft deployment, but these changes would not be expected to have significant clinical implications.

Pasture forages, supplementation rate, and stocking rate effects on dairy cow performance

Objectives were to evaluate effects of forage species, stocking rate, and supplementation rate on performance and physiology of grazing lactating Holstein cows under intensive rotational stocking management during summer. Eight treatments were arranged in a 2 x 2 x 2 factorial design. Animals (n = 62) grazed pastures of Tifton 85 bermudagrass or Florigraze rhizoma peanut, a tropical legume. Low and high stocking rates were 7.5 and 10.0 cows/ha for bermudagrass and 5.0 and 7.5 cows/ha for rhizoma peanut. Within each forage-stocking rate combination, cows were fed supplement at 0.33 or 0.5 kg of supplement (as-fed basis)/kg daily milk production. Cows grazing rhizoma peanut pastures produced more milk (16.9 vs. 15.4 kg/d) but had higher rectal temperatures (39.4 vs. 39.1 degrees C). Milk production per cow was improved at the higher stocking rate for bermudagrass but was reduced at the higher stocking rate for peanuts. Increasing supplementation rate boosted plasma glucose, milk production, and milk protein percent. Increased supplementation rate had a greater positive impact on milk production of cows grazing bermudagrass compared to rhizoma peanut (21.9 vs. 10.6% increase) due to a lower substitution of grain for forage intake. Organic matter intakes of forage, supplement, and total diet were greatest by cows grazing rhizoma peanut pastures and averaged 12.4, 6.1, and 18.5 kg/d compared to 9.2, 5.4, and 14.6 kg/d for cows grazing bermudagrass. Despite lower individual feed intake and performance, production per unit land area was 29% greater (112 vs. 90 kg of milk/ha per d) for cows grazing bermudagrass due to the greater stocking rate possible with that forage. Only cows supplemented at the high rate and kept at the high stocking rate on bermudagrass maintained body weight. Cows on other treatments lost body weight. Tifton 85 bermudagrass appears to be an excellent summer forage for dairy cows grazing in the southeastern U.S. given its nutritive value characteristics and high yields. Optimum stocking rate may be as high as 10 cows/ha during times of peak growth of forage for low-to-moderately producing cows fed supplement. Furthermore, the positive milk production response to additional supplement when cows grazed Tifton 85 pastures (0.8 kg/kg of supplement), indicates the value of providing supplement to cows grazing this moderate quality forage.

Comparison of media for optimal recovery of Candida albicans and Candida glabrata from blood culture

BACKGROUND

Candida spp., mainly Candida albicans, are frequently responsible for complications in immunocompromised patients. There are limited data comparing recovery efficiency using simple non-selective basal broth media.

AIM

To compare several commercially available basal growth media to determine the medium that gave highest yeast proliferation.

METHOD

Eight commercially available non-selective basal broth culture media were evaluated for optimum recovery of clinical C. albicans and C. glabrata. They included nutrient broth (NB), nutrient broth no. 2 (NB2), Todd-Hewitt (TH) broth, tryptone soya broth (TSB), tryptone soya broth supplemented with yeast extract (0.5% w/v [TSBYE]), brain heart infusion broth supplemented with yeast extract (0.5% w/v [BHIYE]), salt meat broth (SMB) and 0.1% [w/v] peptone saline (PS). Differences in cell density were evaluated by spectrophotometrical analysis.

RESULTS

TSBYE>BHIYE>TSB>TH>NB2>NB>SMB>PS for the optimum proliferation of cells in vitro. Either TSBYE or BHIYE broth may be employed as suitable basal broth media for growth of C. albicans and C. glabrata. NB should be considered the least suitable medium for routine use when others are available.

CONCLUSION

These data may be of value to laboratories setting up simple blood culture systems to detect Candida spp., particularly in developing and underdeveloped countries.

Employment of broad-range 16S rRNA PCR to detect aetiological agents of infection from clinical specimens in patients with acute meningitis--rapid separation of 16S rRNA PCR amplicons without the need for cloning

AIMS

The aim of this study was to develop a polyacrylamide gel electrophoresis (PAGE) method for the rapid separation of 16S rRNA PCR amplicons from aetiological agents of acute meningitis.

METHODS AND RESULTS

Blood samples from 40 patients with suspected acute meningococcal meningitis were examined for the presence of causal agents, including Neisseria meningitidis employing two methods: (i) broad-range 16S rRNA PCR in conjunction with PAGE and automated sequencing and (ii) species-specific PCR employing ABI TaqMan technology for N. meningitidis. Analysis of clinical specimens employing 16S rRNA PCR yielded 33/40 (82.5%) positive for the presence of bacterial DNA. Species-specific PCR yielded 30/40 (75%) clinical specimens positive for N. meningitidis. Prior to separation by PAGE, only 6/33 (18.2%) amplicons were able to be identified by sequence analysis, the remaining amplicons (n=27) did not yield an identification due to the presence of mixed 16S rRNA PCR amplicons. Following separation, amplicons were re-amplified and sequenced, yielding 24/27 (88.9%) positive for N. meningitidis and three specimens positive for Acinetobacter sp., Staphylococcus aureus and Streptococcus pneumoniae. One specimen was positive for both N. meningitidis and Streptococcus spp. and another specimen was positive for N. meningitidis and Pseudomonas sp., by broad-range PCR. Seven clinical specimens were negative for N. meningitidis and other eubacteria using both detection techniques.

CONCLUSIONS

Clinical specimens including blood and cerebrospinal fluid from patients with suspected acute bacterial meningitis, may become contaminated with commensal skin flora, resulting in difficulties in downstream sequencing of pathogen plus contaminant DNA. This study allows for the rapid separation of amplified pathogen from contaminant DNA.

SIGNIFICANCE AND IMPACT OF STUDY

This study demonstrated the usefulness of the rapid separation of multiple 16S rRNA PCR amplicons using a combination of PAGE and automated sequencing, without the need of cloning. Adoption of this technique is therefore proposed when trying to rapidly identify pathogens in clinical specimens employing broad-range 16S rRNA PCR.

A comparison of pulmonary exacerbations with single and multiple organisms in patients with cystic fibrosis and chronic Burkholderia cepacia infection

STUDY OBJECTIVES

To compare pulmonary exacerbations with single and multiple organisms in patients with chronic Burkholderia cepacia infection.

DESIGN

Data was collected over a 23-month period and for each of the patients two episodes of pulmonary exacerbation were identified, one with B. cepacia isolated as the sole respiratory pathogen and the other with one or more coinfecting organisms grown from the sputum culture.

SETTING

Regional tertiary referral center for Respiratory Medicine and Adult Cystic Fibrosis Center for Northern Ireland, Belfast City Hospital.

PATIENTS

Adult (over 16 years) CF patients with chronic (more than 4 years) B. cepacia complex infection who attended the Belfast City Hospital between January 1997 and November 1998.

MEASUREMENTS

Forced expiratory volume in 1s, forced vital capacity, forced expiratory flow rate 25-75, C-reactive protein, leucocyte count and body mass index were measured before and after two weeks of treatment and analysed for any differences in change between the two episodes.

RESULTS

All variables in both groups improved following treatment except for body mass index, which remained unchanged. No significant differences between the measurements were identified on comparison of single (monomicrobial) and multiple (polymicrobial) isolate episodes.

CONCLUSION

Patients with chronic B. cepacia infection who develop a pulmonary exacerbation improve, as reflected by clinical and biochemical markers, following IV antibiotic treatment. Pulmonary exacerbations with multiple organisms are no more severe than those where only B. cepacia is isolated.

Biohazards and ecotoxicological considerations of landspreading of spent compost wastes

Spent mushroom compost (SMC) is a major waste of the mushroom industry with low economic value. SMC arises after mushroom production in phase II compost (pIIC), predominantly comprising straw and chicken litter as principal raw ingredients. The majority of SMC waste is disposed off by application to agricultural land. It is an attractive proposition for utilising SMC as soil inorganic fertiliser supplementation. However, there is limited data available as to the consequences of this method of disposal either in terms of microbiological loading of food-borne pathogens and those of concern to mushroom industry itself. The resulting imbalance of the natural flora of the agricultural land has not been properly audited. This study aims to initially examine SMC for prevalence of faecal bacterial pathogens including Campylobacter spp., Salmonella spp. and Listeria monocytogenes that may arise from chicken litter. At another level, it aims to ascertain the pathogenic bacteria (Pseudomonas syringae, pv phaseolicola or tolasii) and fungal populations (Trichoderma, Verticillium species) originating mainly from the straw component of the SMC, which are of concern to the mushroom industry. Lastly, the study would also qualitatively identify the diversity of bacterial populations within SMC. This was largely accomplished through employment of rDNA, PCR and direct sequencing strategies on the culturable microflora. However, for specific mushroom pathogens, nucleic acids (DNA or RNA) were directly extracted from composts before subjecting to sequence analysis. In accordance with the current legislation (ABP 02/02, Animal By Products wastes disposal EC No. 1774/2002), it is imperative to regulate the farm wastes carrying residues from animal sources including SMC before they are regarded safe for land spreading operations. The ecological microbe-microbe and plant-microbe interactions that potentially occur between the native bacterial soil flora and those added annually (approximately 10(18) cells) needs to be reviewed with caution. The above study highlights the ecological consequences involved in the disposal of SMC wastes on agricultural land and its implications for plant, animal and human health.

flaA-like sequences containing internal termination codons (TAG) in urease-positive thermophilic Campylobacter isolated in Japan

AIMS

To demonstrate two flaA-like sequences containing two internal termination codons (TAG) in two Japanese strains of urease-positive thermophilic Campylobacter (UPTC).

METHODS AND RESULTS

A primer pair of A1 and A2, which ought to generate a product of approx. 1700 bp of the flaA gene for Campylobacter jejuni, was used to amplify products of approx. 1450 bp for two Japanese strains of UPTC, CF89-12 and CF89-14. After molecular cloning and sequencing, the nucleotide sequences of the amplicons from the two strains were found to be 1461 bp in length and to have nucleotide sequence differences in relation to each other at four nucleotide positions, respectively.

CONCLUSIONS

Nucleotide and amino acid sequence alignment and homology analysis demonstrated that the polymerase chain reaction (PCR) amplicons from the two Japanese strains have approx. 83% nucleotide and 80% amino acid sequence homology to the possible open reading frame of the flaA gene of UPTC NCTC 12892.

SIGNIFICANCE AND IMPACT OF THE STUDY

Surprisingly, both PCR amplicons from the Japanese UPTC have two internal termination codons (TAG) at nucleotide positions from 775 to 777 and 817 to 819, respectively.

Molecular diversity of Campylobacter coli and C. jejuni isolated from pigs at slaughter by flaA-RFLP analysis and ribotyping

A population of porcine isolates of Camplobacter jejuni (n = 11) and C. coli (n = 17) were examined for genotypic relatedness employing ribotyping, as well as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the flagellin (fla)A gene locus. PCR was employed to amplify a 533 bp fragment from the flaA gene, including the previously described short variable region (SVR), employing the novel primers, A2 and Al and successfully generated this amplicon for all wild-type strains examined (n = 28) of both C. jejuni and C. coli, as well as with both type strains, i.e. C. jejuni NCTC 11351 and C. coli NCTC 11366. Individual genotypes were assigned to each isolate typed employing the four typing methods (flaA-RFLP(Hae) III, flaA-RFLP(Pst) I ribotyping(Hae) III and ribotyping(Pst) I) and were assigned an arbitrary genotype code in ascending alphabetical order in comparison with a database of established genotypes for each of the methods employed. This study showed that several flaA-RFLP and ribopatterns existed within C. jejuni and C. coli, and demonstrated a heterogeneous diversity of strains occurring in the pigs examined. Ribotyping of strains with 16S and 23S rRNA with Pst I and Hae III digested chromosomal DNA allowed subdivision of strains into nine and eight groups, respectively. RFLP analyses with Pst I and Hae III digests probed with the flaA gene probe allowed subdivision of strains into eight and eleven subtypes, respectively. Employment of RFLP with the flaA nucleic acid probe and Hae III digests produced the greatest amount of variation of any genotyping scheme employed. Although there was a high degree of variability demonstrated by both typing methods, most isolates ( > 60%) clustered into four main genotypes, i.e. genotypes A-D. FlaA-PCR-RFLP typing demonstrated that the majority of isolates, 67.9 and 60.7%, were included in these four main genotypes for Pst I and Hae III restriction digests, respectively, although there was a high prevalence (7/11; 63.6%) of fla(Hae) III genotype A occurring within the C. jejuni isolates. Likewise, ribotyping studies demonstrated that most isolates were clustered into these four main genotypes, accounting for 81.5 and 60.7% of isolates for Pst I and Hae III restriction digests, respectively. This may indicate that the clonal population of campylobacters within this pig population is largely composed of persistent and dominant types, with a smaller number of hypervariable subtypes. Such data may useful in determining epidemiological routes of transmission of campylobacters from animal to animal, as well as helping to identify virulence determinants in persistent subtype populations.

Comparison of API20C with molecular identification of Candida spp isolated from bloodstream infections

A study was carried out to compare the API20C technology with polymerase chain reaction amplification and direct sequencing of the short internal transcribed spacer region 2 (ITS2) for the identification of 58 isolates of invasive candida species obtained from patients with bloodstream infections over the seven year period 1994 to 2000. Overall, there was only one disagreement between the phenotypic and genotypic identification, where the API scheme identified the isolate as C albicans but the molecular method identified it as C dubliniensis. This study demonstrated that the API20C method is useful in the identification of Candida spp isolated from blood culture and that molecular methods do not enhance identifications made using the API20C scheme. However, for correct reporting of C dubliniensis, an emerging bloodborne pathogen, it is recommended that all isolates identified as C albicans by the API20C scheme are further examined phenotypically and/or genotypically.