Detection of Clostridium botulinum types A, B, E and F in foods by PCR and DNA probe

A PCR procedure was developed for the detection of Clostridium botulinum in foods. PCR products were detected in agarose gels and by Southern hybridization. The sensitivity of PCR was tested in broth cultures and in canned asparagus, dry cured ham and honey. The sensitivity of the method in broth was high (2·1–8·1 cfu ml⁻¹) for types A and B, but rather low (10⁴ cfu ml⁻¹) for types E and F. However, after enrichment at 37°C for 18 h, it was possible to detect Cl. botulinum types A, B, E and F in food samples at initial levels of about 1 cfu 10 g⁻¹ of food. This PCR detection protocol provides a sensitive and relatively rapid technique for the routine detection of Cl. botulinum in foods.     

The magnetic immuno-polymerase chain reaction assay for the detection of Campylobacter in milk and poultry

L. DOCHERTY, M.R. ADAMS, P. PATEL AND J. McFADDEN. 1996. A rapid and sensitive technique, based on the magnetic immuno-polymerase chain reaction assay (MIPA), was developed for the detection of Campylobacter jejuni in milk and chicken products. Target bacteria are captured from the food sample by magnetic particles coated with a specific antibody and the bound bacteria then lysed and subjected to PCR. The MIPA could detect 420 cfu g^-1of chicken after 18 h, 42 cfu g^-1after 24 h, and 4.2 cfu g^-1after 36 h enrichment. For artificially contaminated milk 63 cfu ml^-1could be detected after 18 and 24 h and 6.3 cfu ml^-1after 36 h enrichment.     

Survival of free and alginate-encapsulated Pseudomonas aeruginosa UG2Lr in soil treated with disinfectants

Pseudomonas aeruginosa UG2Lr, a rifampicin-resistant strain possessing the luxAB on a chromosomal Tn5 insert, was inoculated into soil microcosms as either free cells or encapsulated in dry alginate beads. A 100-fold increase in cell number g^-1 dry soil was observed in microcosms inoculated with alginate-encapsulated UG2Lr after 3 weeks incubation at 22°C compared to microcosms inoculated with free cells. After 98 d, microcosms inoculated with free UG2Lr cells contained 10⁴ cfu g^-1 dry soil compared to 10⁷ cfu g^-1 dry soil in microcosms inoculated with alginate-encapsulated UG2Lr cells. The effects of disinfectants on both the free and alginate-encapsulated UG2Lr cells were also examined. 1·0% (w/g dry soil) calcium hypochlorite, formaldehyde and Spectrum Clear Bath, were added to microcosms each week for 4 weeks. Formaldehyde killed both free and alginate-encapsulated UG2Lr cells within 14 d after only two amendments. Calcium hypochlorite reduced free UG2Lr cell numbers 10-fold 2 d after initial application; however, the introduced population recovered and was unaffected by subsequent treatments at 7, 14 and 21 d. Alginate-encapsulated UG2Lr cells were not affected by calcium hypochlorite treatment. Spectrum Clear Bath did not kill either free or alginate-encapsulated UG2Lr cells in soil. Alginate encapsulation improved survival of introduced bacteria in soil except in the presence of formaldehyde. Killing genetically-engineered bacteria in soil may be difficult unless a powerful disinfectant such as formaldehyde is used or the genetically-engineered micro-organism is allowed to become non-viable over time.     

Survival of κ-carrageenan-encapsulated and unencapsulated Pseudomonas aeruginosa UG2Lr cells in forest soil monitored by polymerase chain reaction and spread plating

Abstract A method was developed for direct extraction, purification and amplification of DNA from forest soil. Eighty-two % of the DNA in Pseudomonas aeruginosa UG2Lr introduced into soil was recovered. The detection limit for the strain was approximately 800 cfu g⁻¹ of dry soil based on the polymerase chain reaction (PCR). Survival of κ-carrageenan-encapsulated and unencapsulated UG2Lr was monitored by antibiotic selective and bioluminescence-based nonselective plating and PCR-amplification of a tnsA fragment. After freeze-thaw treatment of soil samples, the unencapsulated UG2Lr declined from an initial population density of 1 × 10⁹ cfu g⁻¹ of dry soil to below the detection threshold of both selective (14 cfu g⁻¹ of dry soil) and nonselective (1 × 10³ cfu g⁻¹ of dry soil) plating. However, presence of nonculturable UG2Lr cells in the soil was revealed by PCR and resuscitation of the bacteria. Population density of the encapsulated UG2Lr increased from 2.7 × 10⁶ to 2.9 × 10⁸ cfu g⁻¹ of dry soil after a 3-week incubation at 22°C and declined to 6.3 × 10⁶ cfu g⁻¹ of dry soil after the freeze-thaw treatment.     

Characterization of glycerol kinase and NAD-independent glycerol-3-phosphate dehydrogenase from Pediococcus pentosaceus N5p

The polymerase chain reaction (PCR) has the potential to detect low levels of the human pathogen Escherichia coli O157 : H7 in bovine faeces. To improve the utility of PCR for this application, several methods for preparing template DNA from bovine faeces, both directly and after non-selective enrichment, were tested. These were boiling, enzyme treatment, enzyme treatment plus phenol-chloroform extraction, and enzyme treatment plus phenol-chloroform extraction plus Geneclean^® purification. Of these, the boiling method was the most consistent and had a sensitivity of approximately 3 cfu g⁻¹ faeces, with an assay time of less than 32 h. The boiling method was also combined with immunomagnetic separation (IMS) to detect E. coli O157 : H7 in less than 8 h, but with a sensitivity of approximately 10³ cfu g⁻¹ faeces. These methods can be used to prepare template for PCR screening of bovine faeces using any appropriate PCR primers.     

Seasonal metabolism of a small, arboreal monitor lizard, Varanus scalaris, in tropical Australia

The field metabolic rates (FMR) and water fluxes of Varanus scalaris were measured during the wet and dry seasons by the doubly-labelled water technique. Seasonal measurements of standard (night-time) metabolism (SMR) and resting (daytime) metabolism (RMR) were made in the laboratory at 18, 24, 30 and 36°C, and maximal oxygen consumption was measured at 36°C on a motorized treadmill. This population was active throughout the year. In the wet season, the mean FMR was 7.8 kJ day⁻¹ (128.0 kJkg⁻¹ day⁻¹; mean mass = 66.4 g, n = 13), and during the dry season the mean was 5.0 kJ day⁻¹ (67.6 kJ kg⁻¹ day⁻¹; mean mass = 77.4 g, n = 17). The mean water flux rates for these animals were 3.6 and 1.2 ml day⁻¹, respectively (60.4 and 16.6 ml kg⁻¹ day⁻¹). The seasonal means of FMR and water flux were significantly different by ANCOVA ( P < 0.0001). Measurements of SMR and RMR were significantly higher in the wet season (ANCOVA: P < 0.0001), but we found no difference in the maximal oxygen consumption between seasons (ANCOVA: P = 0.6). The maximal oxygen consumption of the lizards on the treadmill (2.9 ml min⁻¹= 1.8 ml g⁻¹ h⁻¹), mean mass = 97.4 g, n = 16) was 20 times that of the SMR at the same temperature during the dry season, and 11 times that of the SMR during the wet season. The seasonal differences in FMR were attributable to: changes in SMR (12.2%) and RMR (16.4%); differences in night-time body temperatures (11.3) and daytime body temperatures (16.4%); and activity (broadly defined to include locomotion, digestion, and reproductive costs (43.7%).     

Quantitative detection of meat spoilage bacteria by using the polymerase chain reaction (PCR) and an enzyme linked immunosorbent assay (ELISA)

A quantitative PCR-ELISA for the rapid enumeration of bacteria in refrigerated raw meat has been developed using primers designed from conserved regions in the 16S ribosomal RNA gene (rRNA). Amplified PCR products generated using a digoxigenin-labelled primer were automatically hybridized to a biotinylated probe included in the PCR reaction. The hybridization was performed as part of the PCR programme. The biotin-digoxigenin hybrids were quantified by an enzyme-linked immunosorbent assay (ELISA). Streptavidin bound to the wells of a microtitre plate was used to capture the biotin-digoxigenin-labelled fragments that were detected with a peroxidase anti-digoxigenin conjugate. Subsequent enzymic conversion of substrate gave distinct absorbance differences when assaying meat samples containing bacteria in the range 10²–10⁷ cfu cm⁻². The detection threshold for the PCR-ELISA assay developed in this work is 10² cfu cm⁻².     

DETECTION OF SALMONELLA SPP. CONTAMINATION IN RAW MATERIALS AND COSMETICS/PHARMACEUTICAL PRODUCTS USING THE BAXTM SYSTEM, A PCR-BASED ASSAY

Abstract A system utilizing the polymerase chain reaction (PCR), the BAX ^TM , was compared and validated against standard selective/enrichment assays to detect the presence of Salmonella spp. in artificially contaminated samples of raw materials and cosmetic/pharmaceutical products. After a 24 h incubation in lactose broth or lactose broth with Tween 20, the inoculated samples were analyzed both by the BAX ^TM system and by standard enrichment/selective methods. Standard enrichment assays required 5–7 days to confirm the presence and identification of Salmonella typhimurium , while the BAX ^TM system reduced the detection time to 30 h. The BAX ^TM system allowed a faster quality control evaluation of those raw materials and cosmetic/pharmaceutical formulations that require Salmonella spp. screening.     

Phytoplankton production and growth rate in Lake Tanganyika: evidence of a decline in primary productivity in recent decades

1. This study focused on phytoplankton production in Lake Tanganyika. We provide new estimates of daily and annual primary production, as well as growth rates of phytoplankton, and we compare them with values published in former studies.
2. Chlorophyll- a (chl- a ) in the mixed layer ranged from 5 to 120 mg chl- a  m⁻² and varied significantly between rainy and dry seasons. Particulate organic carbon concentrations were significantly higher in the south basin (with 196 and 166 mg C m⁻³ in the dry and the rainy season, respectively) than in the north basin (112 and 109 mg C m⁻³, respectively).
3. Carbon : phosphorus (C : P) ratios varied according to season. Phosphorus limitation seemed to occur more frequently than nitrogen limitation, especially during the rainy season. Severe P deficiencies were rare.
4. Measured particulate daily primary production ranged from 110 to 1410 mg C m⁻² day⁻¹; seasonal contrasts were well marked in the north basin, but less in the south basin, where primary production peaks occurred also in the rainy season. Estimates of annual primary production, based on daily primary production calculated from chl- a and water transparency, gave values lower than those reported in previous studies. Picophytoplankton accounted on average for 56% of total particulate production in the south basin during the wet season of 2003.
5. Phytoplankton growth rates, calculated from primary production, ranged from 0.055 to 0.282 day⁻¹; these are lower than previously published values for Lake Tanganyika.     

Design and evaluation of malolactic enzyme gene targeted primers for rapid identification and detection of Oenococcus oeni in wine

Rapid identification and detection of Oenococcus oeni was achieved by species-specific PCR. Two primers flanking a 1025 bp region of the O. oeni gene encoding the malolactic enzyme were designed. The expected DNA amplificate was obtained only when purified DNA from O. oeni was used. The identity of PCR product was confirmed by nested PCR and restriction analysis. Within 8 h, 10³ cfu ml⁻¹ of oenococci were detected in fermenting grape must containing 10⁷ yeast cells, whereas the detection limit in wine was 10⁴ cfu ml⁻¹. The rapidity and reliability of the PCR procedure established suggests that the method may be profitably applied in winery laboratories for quality control.     

A combined PCR and selective enrichment method for rapid detection of Listeria monocytogenes

Development of a routine detection assay for Listeria monocytogenes in foods that uses the polymerase chain reaction (PCR) and enrichment cultures was investigated. Oligonucleotide primers were chosen to amplify a 3'region of L. monocytogenes hly A gene spanning a conserved Hin dIII site. PCR detection sensitivity for L. monocytogenes in dilutions of pure enrichment cultures was between 50 and 500 colony forming units. A short enrichment period before PCR amplification allowed detection of the organisms in a range of complex foods contaminated with 10⁴ cfu/g. Detection sensitivity for the assay in the presence of chicken skin and soft cheese was determined at 10–100 cfu/g. Utilization of enrichment cultures and PCR allowed identification of the organism within 24 h or 2 days.     

The use of a surface adhesion immunofluorescent (SAIF) method for the rapid detection of Yersinia enterocolitica serotype O:3 in meat

This study examined the attachment kinetics of Yersinia enterocolitica serotype O:3 to determine the optimum conditions for its isolation from meat enrichment systems using a novel surface adhesion technique. Minced beef was inoculated with Y. enterocolitica at an initial level of 10 cfu g⁻¹ and incubated at 25 °C in an enrichment broth. Yersinia was recovered from enriched samples on polycarbonate membranes by surface adhesion and enumerated using immunofluorescence microscopy. The surface adhesion immunofluorescence technique (SAIF) had a minimum detection limit of approximately 4·0–4·5 log₁₀ cfu ml⁻¹ and provided good correlation between the estimation of the numbers of Yersinia in the enrichment broth derived from plate counts on Yersinia Selective agar (CIN) and those determined by SAIF ( r ² ₌ 0·94; rsd ₌ ± 0·21). A derived regression equation of the SAIF count vs plate counts was used to predict Y. enterocolitica numbers in spiked meat samples stored at 0 °C for up to 20 d. The numbers as predicted by the SAIF method showed good correlation with counts derived by plating techniques ( r ² ₌ 0·78; rsd ₌ ± 0·42). The application of the SAIF technique for the rapid detection of Y. enterocolitica serotype O:3 from meat is discussed.     

Metabolism of 1-naphthyl-N-methyl carbamate (carbaryl) by bacterial isolates from honey bees and the effect of bacterial inoculations on carbaryl tolerance in bees

I.D. SHARMA AND A. NATH. 1996. The bacteria which inhabit the body of foragers of Apis cerana indica F. were evaluated for degradation of carbaryl (1-naphthyl- N -methyl carbamate). Citrobacter sp., Enterobacter aerogenes and an unidentified isolate could utilize carbaryl as sole carbon and energy source. The enrichment cultures of bacteria could degrade carbaryl 0.019–0.082 in nutrient broth and 0.111–7.895 mg μg^-1 bacterial dry wt in basal salts medium of 1 mmol 1^-1 carbaryl. 1-Naphthol was the major product of carbaryl degradation. The dip and injection inoculations of foragers ( Apis cerana indica F. and Apis mellifera L.) with these bacteria resulted in a significant increase in tolerance to carbaryl. The application of mixed culture to bees induced higher tolerance than the individual isolates. This is the first report of the use of bacteria to decontaminate a living system.     

Monitoring the fate of genetically engineered bacteria sprayed on the phylloplane of bush beans and grass

Abstract The fate of a Bacillus amyloliquefaciens with the recombinant plasmid pSB20 sprayed on the phyllosphere of grass, and of a Tn 5 marked Pseudomonas syringae sprayed on the phyllosphere of bush beans was studied in planted soil microcosms. B. amyloliquefaciens showed a decline from 1.5×10⁸ to 3.1×10² cfu g⁻¹ on the phylloplane of grass in the course of the experiment. B. amyloliquefaciens was easy to follow by selective cultivation due to the complete absence of bacterial background growth. Southern blot hybridization of Hin dIII digested genomic DNA showed plasmid restriction patterns identical with pSB20 indicating high plasmid stability. In total DNA extracts from phyllosphere bacteria the recombinant plasmid was detectable by Southern blot hybridization up to 6×10⁴ cfu g⁻¹ (wet weight). Counts of hybridizing colonies showed that P. syringae established on the phyllosphere of bush beans at between 5×10³ and 4×10⁶ cfu g⁻¹ fresh weight. During senescence of the bean plants the strain was no longer detectable by selective cultivation and subsequent colony hybridization. In contrast, Tn5 marked DNA was detected after PCR amplification over the whole period of the experiment.     

Detection ofBurkholderia pseudomallei in rice fields with PCR-based technique

Burkholderia pseudomallei Ara- in rice fields was detected using PCR-based techniques with 16S RNA and flagella gene primer sets. The sensitivity of these PCRs was at least 1 CFU/mL of B. pseudomallei Ara- preincubated into Ashdown's medium for 6 h. B. pseudomallei Ara- DNA from watery soil were more detectable than from dry soil. The distribution of this DNA was mainly found at a depth of 300-600 mm under crop-covered fields, but not detected in the location of soil close to the land surface. The results suggest that PCR based on 16S RNA and flagella gene primer sets can be applied to investigate the presence of B. pseudomallei Ara- in contaminated soil of rice fields.     

Development and use of a multiplex PCR system for the rapid screening of heat labile toxin I, heat stable toxin II and shiga-like toxin I and II genes of Escherichia coli in water

Enterotoxigenic Escherichia coli (ETEC) may produce heat-labile toxin (LT) I and LTII and heat-stable toxin (ST) I and STII, while shiga toxin producing E. coli (STEC) strains, including enterohaemorrhagic E. coli (EHEC), may produce shiga-like toxin (SLT) I and/or SLTII. Both ETEC and STEC are pathogenic to humans, pigs and cattle. As contamination of environmental water by any of these pathogenic E. coli cells is possible, a multiplex polymerase chain reaction (PCR) system for the rapid screening of LTI, STII, and SLTI and SLTII genes of E. coli was developed. The PCR primers used were the SLTI and SLTII genes specific primers developed by the present authors and the LTI and STII genes specific primers reported by other laboratories. The detection specificity of this multiplex PCR system was confirmed by PCR assay of ETEC, STEC and other E. coli cells as well as non- E. coli bacteria. Its detection limit was 10²–10³ cfu each of the target cells per assay. When this multiplex PCR system was used for the rapid screening of LTI, STII ETEC and STEC in water samples such as tap, underground and lake waters, it was found that after the enrichment step, as few as 10⁰ cells 100 ml⁻¹ of the water sample could be detected. Therefore, this PCR system could be used for the rapid monitoring of ETEC and/or STEC cells contaminating water samples.     

Photosynthesis and Optimal Light Microhabitats for a Rare Cactus, Mammillaria gaumeri, in Two Tropical Ecosystems

Mammillaria gaumeri , an endemic cactus from Yucatan, is threatened due to human-mediated habitat fragmentation but knowledge regarding factors that would inform management plans is limited, including information on optimal microhabitats and growth. We studied seasonal patterns of microclimate, net CO₂ uptake and growth of adult individuals during the dry, rainy and northwind (late fall to winter) seasons in separate populations located in a coastal dune and in a dry forest. To provide an assay of primary productivity, we measured the production of new axillary buds (areoles) from the apex. We found that patterns of net CO₂ uptake in the three seasons were consistent with obligate crassulacean acid metabolism. The reduction in soil water potential and the increase in water vapor pressure deficit led to a reduction in 24-h net CO₂ uptake from 18.0 to 1.3 mmol CO₂/m², after 30 d of drought. Dry-weight gain was maximal during the rainy season and there was no growth during the dry season, thus seasonal patterns of net CO₂ uptake and growth for M. gaumeri reflected soil and atmospheric water contents. Annual dry-weight gain increased linearly with plant size and with total daily photosynthetic photon flux density (PPFD) up to 80 percent of ambient. Maximal growth was in exposed microhabitats receiving 60–80 percent of total ambient PPFD. We hypothesize that low-magnitude disturbances, resulting in more exposed microhabitats, might be beneficial for growth and conservation of adult individuals of this rare species.     

The sizes, maturity stages and biomass of mayfly assemblages colonizing disturbed stream bed patches in central Kenya

The sizes, maturity stages and biomass of mayfly species colonizing disturbed patches on the stream bed surface of the Naro Moru River, Kenya, were determined from June 1993 to January 1994. All maturity stages I–VI⁺ were present in the pre-disturbance mayfly assemblages. Colonization of the disturbed patches by mayflies of different maturity stages was continuous, but slow or fast depending on the season and species. The overall post-disturbance maturity structure of the mayflies colonizing the disturbed patches did not demonstrate any distinct pattern. The majority of Caenis nymphs colonizing the patches in wet season II (November–January) were in emerging maturity stage VI⁺, whilst the majority of the individuals of Afronurus and Choroterpes ( Euthraulus ) populations matured from stage I in the wet seasons to stage VI⁺ in the dry season. Furthermore, the majority of the individuals of Baetis ( Nigrobaetis ) sp.1 were maturing to stages IV–VI during the wet seasons. Small-sized mayfly individuals (body length <3.0 mm) of all mayflies colonized the disturbed patches in the majority of numbers. However, although having the highest densities, they contributed a very low biomass compared with the fewer large-sized nymphs. There was no size gradation in the colonization of the disturbed patches, since all sizes were sampled at all times but in differing proportions. Colonization of the patches by mayflies was not size- or maturity stage-specific. Size distribution patterns could be useful in assessing which mayfly size-spectra are more or less susceptible to disturbance in streams.     

Interaction between the effects of bacteria and dry storage on the opening and water relations of cut rose flowers

W.G. VAN DOORN AND K. D'HONT. 1994. Flowering stems of four rose cultivars (Sonia, Madelon, Jacaranda and Frisco) were placed in aqueous suspensions of bacteria at 10⁴ and 10⁸ colony-forming units (cfu) ml^-1 for 24 h at 5C, then stored dry or held in water for 24 h at 8C and subsequently placed in vase-water at 20C. The effects of these treatments on vase-water uptake were similar to the effects on flower opening. In Sonia and Madelon roses flower opening was negatively affected both by 10⁸ cfu ml^-1 of bacteria and by dry storage. No effect was found at 10⁴ cfu ml^-1, but this concentration had a detrimental effect on flower opening when combined with dry storage. Although flower development in Jacaranda roses was not affected by the bacteria treatments it was inhibited by dry storage. This inhibition was progressively greater when the stems had previously been pulse-treated with a larger number of bacteria. Flower opening in Frisco roses was not affected by even the highest concentration of bacteria, nor by the period of dry storage. It is concluded that placing flowers in water containing bacteria (up to 10⁸ cfu ml^-1) may not always have a negative effect on flower development in cut rose flowers but, together with the effects of dry storage, the presence of even a low number of exogenous bacteria (10⁴ cfu ml^-1) inhibits the development in several cultivars. Such bacterial counts are nearly always found in samples of water used for standing roses during distribution to the consumers.     

A quantitative PCR-ELISA for the rapid enumeration of bacteria in refrigerated raw milk

We have developed a quantitative PCR-ELISA for the rapid enumeration of bacteria inrefrigerated raw milk using primers designed from conserved regions in the 16S ribosomal RNAgene (rRNA). The designed primers permitted the amplification of a 147 bp DNA fragment froma wide selection of bacteria which may grow in milk at refrigeration temperatures. Amplified PCRproducts generated using a digoxigenin-labelled primer were heat-denatured before beingquantified by an enzyme-linked immunosorbent assay (ELISA). A biotinylated probe immobilizedonto streptavidin-coated microplates was used to capture the digoxigenin-labelled fragments thatwere detected with a peroxidase anti-digoxigenin conjugate. Subsequent enzymic conversion ofsubstrate gave distinct absorbence differences when assaying milk samples containing bacteria inthe range 10³–10⁷ cfu ml⁻¹. The detection threshold for thePCR-ELISA assay developed in this work is 103 cfu ml⁻¹.