Effects of Primers and Taq Polymerase on Randomly Amplified Polymorphic DNA Analysis for Typing Listeria monocytogenes From the Environment of a Shrimp Processing Plant

Ninety-nine randomly selected isolates of Listeria monocytogenes from several processing environment locations, in a shrimp processing plant, obtained during a 5-month sampling period were subjected to randomly amplified polymorphic DNA (RAPD) analysis with the use of four primers. Preliminary studies indicated that the number of DNA bands and their intensity differed greatly with respect to the commercial source of the Taq polymerase used with individual isolates. Eighteen composite RAPD types were discerned with the use of the four primers. Among these 18 composite RAPD types, type 1 comprised 14 indistinguishable isolates, and type 9 comprised 49 indistinguishable isolates. These results indicate that the shrimp processing plant was dominated by these 2 RAPD types that comprised 63.6% of the 99 randomly selected isolates.     

Genetic variability among isolates of Listeria monocytogenes from food products,clinical samples and processing environments,estimated by RAPD typing

RAPD analysis with four primers was used to examine the genetic relationship among 432 strains of Listeria monocytogenes isolated from clinical and veterinarian cases of listeriosis, dairy, vegetable, meat- and fish-based food items, environmental samples and samples collected from one transport terminal, one poultry-processing company and four Atlantic salmon-processing plants. The purpose of the study was to determine whether clinical isolates belonged to a specific genetic group, whether links could be made between food groups and clinical cases and whether specific genetic groups were associated with specific food products or processing units. There was great genetic variability among the isolates, which produced a total of 141 RAPD composites based on the RAPD analysis with four primers. The RAPD composites divided in two major clusters and clinical isolates were evenly distributed in both of them. None of the isolates from food products had the same RAPD composite as isolates from human patients, thus, no particular food commodity could be linked to clinical cases. Each food-processing environment was contaminated with more than one RAPD composite and the genetic variability found within each company was, in most cases, of approximately the same magnitude as the variability found when considering all the samples. In each plant, one or a few types persisted over time, indicating the presence of an established in-house flora. Our results indicate that most of the analysed cases of listeriosis were sporadic and, further, that these cases cannot be traced to a few specific food sources. We also found that no particular RAPD composite was better suited for survival in specific food types or food-processing environments, indicating that although differences may be found in virulence properties of individual strains, all L. monocytogenes must be treated as potentially harmful.     

Incidence and Enumeration of Vibrio parahaemolyticus in Shellfish from Two Retail Sources and the Genetic Diversity of Isolates as Determined by RAPD-PCR Analysis

A total of 83 shellfish samples from two local retail sources (A and B) yielded 38 samples positive for the presence of Vibrio parahaemolyticus based on 3 tube MPN enrichments and isolation from thiosulfate-citrate-bile salts-sucrose agar (TCBS) and biochemical tests. The 38 positive samples yielded 133 biochemically presumptive isolates of V. parahaemolyticus. Among these 133 presumptive isolates, 104 were confirmed by the polymerase chain reaction (PCR), which yielded more reliable identification results than the biochemical tests. The 38 biochemically presumptive samples yielded 29 samples that were confirmed by PCR to be positive for the presence of V. parahaemolyticus. RAPD analysis with three random primers was performed to examine the genetic diversity of 64 strains among the PCR confirmed V. parahaemolyticus isolates from both retail sources. 52 of 56 composite RAPD types consisted of single strains, indicating that most of the V. parahaemolyticus isolates were genetically quite heterogeneous. No strains representing the same RAPD type occurred in both retail outlets, implying that contamination of the shellfish by V. parahaemolyticus from the 2 retail sources was from different environmental locals and shellfish harvesting areas. Eight genomic clusters were generated at the 25% similarity level in a dendrogram based on RAPD profiles. With few exception, isolates with close genetic relationships grouping into an individual cluster tended to be derived from the same retail source.     

Genetic Variability Among Isolates of Plesiomonas shigelloides from Fish, Human Clinical Sources and Fresh Water, Determined by RAPD Typing

Plesiomonas shigelloides has been a suspected pathogen for the past 40 years. Random amplified polymorphic DNA (RAPD) analysis with two random primers was used to examine the genetic diversity among 26 strains of P. shigelloides: 10 from fresh water, 6 from fish, and 10 from human clinical sources. There was notable genetic variability among most of the isolates, and none of the isolates had the same composite RAPD profile. Our results indicate that most of the isolates from the same source grouped together and that the isolates from fish had a closer linkage to the human clinical isolates than did the freshwater isolates, suggesting that fish may be the more serious source for potential risk of infection. We also found that certain human clinical isolates had almost the same RAPD profiles as certain of the isolates from freshwater and fish, indicating that P. shigelloides from both sea food and freshwater should be considered potential pathogens.     

Diversity of Listeria monocytogenes isolates from cold-smoked salmon produced in different smokehouses as assessed by Random Amplified Polymorphic DNA analyses

One hundred and forty-eight Listeria monocytogenes isolates originating from vacuum packed cold-smoked salmon produced in 10 different Danish smokehouses were compared by Random Amplified Polymorphic DNA (RAPD) profiling. A total of 16 different reproducible RAPD profiles were obtained using a standardised RAPD analysis by four primers separately. The grouping of the 148 strains was exactly the same for the four primers used. For a sub-set of 20 strains typed by Pulsed Field Gel Electrophoresis (PFGE), only one strain was allocated into a different group as compared to the grouping by RAPD typing. Different RAPD types dominated in products from different smokehouses. Some identical RAPD types were isolated in several smokehouses. In each of four smokehouses, one particular RAPD type could be repeatedly isolated from products. Each smokehouse/product carried its own specific RAPD type and this may indicate a possible persistence of closely related strains of L. monocytogenes in smokehouses.     

Application of Random Amplified Polymorphic DNA (RAPD) and Pulsed-Field Gel Electrophoresis (PFGE) Analysis to Listeria monocytogenes: A Review of Methodology and Results

Random amplified polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) analyses have been found to be powerful molecular methods for differentiating isolates of a given bacterial species. When applied to Listeria monocytogenes, both methods have been found highly effective in tracking isolates involved in food borne outbreaks of listeriosis and in identifying routes of contamination in food processing plants. Among the two methods, PFGE is considered somewhat superior in discriminatory power. However, the use of two or more independent random primers with RAPD is considered to result in a level of discrimination equal to that of PFGE. When results from both methods are combined, a maximum level of discrimination that exceeds that obtained with both methods independently can be achieved. Individually, both methods far exceed the discriminatory power of serotyping and phage typing of L. monocytogenes strains in that serotypes 1/2a, 1/2b, and 4b, represent over 90% of all human isolates, and phage typing at times has allowed typing of no more than about 50% of isolates. In addition, both RAPD and PFGE on occasion have been found to be superior to ribotyping, multilocus enzyme electrophoresis, and restriction enzyme analysis of L. monocytogenes isolates.     

Differentiation of Australian wine isolates of Oenococcus oeni using random amplified polymorphic DNA (RAPD)

Intraspecific variation of Oenococcus oeni , the preferred lactic acid bacteria species for inducing malolactic fermentation in wine, was studied using the randomly amplified polymorphic DNA (RAPD) strain fingerprinting technique. Ten of fifteen isolates of O. oeni from Australian wineries situated in different wine regions could be distinguished by the RAPD technique. Strains of O. oeni which originated from the same winery were either indistinguishable or closely related to each other. Six different commercially available O. oeni strains could be differentiated with the four RAPD primers used and their genetic similarity determined. Analysis of O. oeni present in wines from a single source of fruit (Cabernet Sauvignon, vintage 2002) that underwent spontaneous malolactic fermentation revealed wide genetic variation amongst the isolates. Each fermentor contained several different O. oeni strains, which were present throughout alcoholic and malolactic fermentation. These data highlight the sensitivity of RAPDs when suitable primers are applied to O. oeni of unknown genetic origin, thus enabling O. oeni strains with desirable sensory and fermentation properties to be genetically analysed.     

Detection, Enumeration, and RAPD Analysis of Listeria monocytogenes Isolates in Fish Derived fromRetail Outlets in WesternMassachusetts

Fish were sampled over a 24-month period from two major supermarket retail outlets in Hadley, Massachusetts, USA, designated A and B, for the incidence of Listeria monocytogenes and numbers of the organism present per 100 g of tissue. Fifteen species of fish were represented. Seventy-four samples out of a total of 320 were confirmed by PCR as yielding L. monocytogenes. From retail source A, a total of 171 samples yielded 59 (34.5%) that were positive for the presence of L. monocytogenes. In contrast, from retail source B, a total of 149 samples yielded 15 (10.0%) that were positive. Only six samples (3.5%) from retail source A had MPN counts of L. monocytogenes in the range of 100 to 1,000 per 1,000 g. Only two samples (1.3%) from retail source B had counts of L. monocytogenes from 100 to 1,000 per 100 g. A total of 221 strains of L. monocytogenes were derived from the MPN cultures, 164 from retail source A, and 57 from retail source B. All 221 strains were subjected to RAPD analysis using three random primers. Primer LMPB1 yielded 21 RAPD profiles, primer LMPB4 yielded 19 profiles, and primer HLWL74 yielded 26 profiles. A total of 55 composite profiles were identified by combining the profiles derived from the three primers. Source A yielded 50 composite RAPD profiles, whereas source B yielded only ten composite profiles. In addition, 27 of the 55 composite profiles were derived from individual isolates and RAPD types 11 and 18 included 49 and 27 isolates respectively. Fish from retail source A clearly harbored far more RAPD types than did source B. The results clearly indicated that two major retail sources in close geographic proximity can vary considerably with respect to the incidence and numbers of L. monocytogenes present on the fish tissue. It was not possible to determine whether the processors furnishing fish to retail outlet A or the supermarket itself was responsible for the notably higher incidence and numbers of L. monocytogenes on fish from retail source A compared to fish from retail source B.     

Characterisation of ropy slime-producing Lactobacillus sakei using repetitive element sequence-based PCR

Eighteen previously characterised Lactobacillus sakei strains exhibiting varying slime production capabilities in vacuum-packaged meat products were analysed using repetitive element sequence-based PCR (rep-PCR). The single primers BOXA1R and RW3A and the primer pair REP1R-Dt and REP2R-Dt were evaluated for their applicability in L. sakei genotyping. The five different patterns produced by RW3A were the least useful, with the discriminatory power equal to ribotyping. BOXA1R and REP–primer pair both produced six different banding patterns and the combination of these results yielded seven different rep-types. Rep-PCR was concluded to have approximately the same discriminatory power as randomly amplified polymorphic DNA (RAPD) analysis, but was inferior to pulsed-field gel electrophoresis (PFGE). However, if the results of rep-PCR and RAPD were combined, the discrimination was comparable to PFGE, with the exception that within Ribogroup I non-slime-producing strains were indistinguishable from weak slime producers. It was concluded that the combination of the two PCR-based typing techniques, rep-PCR and RAPD, would be a valuable tool in large scale contamination studies at meat processing plants, since results can be obtained rapidly with fewer isolates needing further analysis by PFGE.     

Random amplification of polymorphic DNA typing of Listeria monocytogenes isolated from meat

To investigate the epidemiological characteristics of Listeria monocytogenes isolated from imported or domestic meats, L. monocytogenes was isolated and identified through biochemical and serological tests, and epidemiological analysis of the isolates was carried out through the random amplification of polymorphic DNA (RAPD) method. Fifty-four isolates were identified as L. monocytogenes through biochemical tests, of which 36 (67%) were confirmed as serotype 1, and 18 (33%) were serotype 4, through the microagglutination test. In the molecular epidemiological analysis using RAPD method, the isolates could be classified into 10, 6 and 6 types using three random primers, PB1, PB4, and HLWL74, respectively. Forty composite profiles were identified by a combination of the three primers. RAPD analysis demonstrated the relationships between the isolates from beef from Korea and the USA, pork from Korea and Denmark. These results suggested that RAPD could be a useful typing tool for the epidemiological study of L. monocytogenes and other bacteria.     

Identification of Campania Citrus Limon L. by Random Amplified Polymorphic DNA Markers

Genotypes of 10 lemon (Citrus limon L.) cultivars of the Campania region (Southern Italy) have been studied by using Random Amplified Polymorphic DNA (RAPD) markers with 44 arbitrary 10-mer primers. Some of the studied cultivars (Sorrento, Procida, Amalfi, and Gloria d'Amalfi) have been successfully distinguished by their band patterns using five out of the 44 selected primers, confirming that RAPD technology provides a useful tool to identify specific cultivars.     

Prevalence and genetic diversity of Enterobacter sakazakii in ingredients of infant foods

Various food samples in Korea were examined for the presence of Enterobacter sakazakii. Dried shrimp had the highest contamination rate among the examined dried fish products. E. sakazakii isolates were confirmed using an API 20E kit and a polymerase chain reaction (PCR) targeting the rDNA operons. The isolates were subtyped by pulsed-field gel electrophoresis (PFGE) using XbaI to elucidate the genetic diversity of the organisms. Ten pulsotypes were identified using PFGE and 22 types were identified from the random amplified polymorphism DNA (RAPD) assay. An antibiotic resistance test was performed by disk diffusion assay using eight antibiotics: nalidixic acid, ciprofloxacin, chloramphenicol, ampicillin, tetracycline, gentamicin, kanamycin, and cephalothin. Most of the E. sakazakii isolates were resistant to ampicillin or cephalothin but susceptible to the other antibiotics. The analysis of E. sakazakii isolates using PFGE, RAPD, and the antibiotic resistance test identified 18 composite types from 113 isolates, suggesting diverse sources of contamination.     

Random amplified polymorphic DNA typing applied to the study of cross-contamination by Listeria monocytogenes in processed food products

The presence of Listeria spp. was investigated in 369 samples of cooked meat products and 52 of smoked salmon. Incidences of 17.6% for cooked meat and 38.5% for smoked salmon samples were found. All Listeria monocytogenes isolates (34 from meat products and 16 from smoked salmon) were typed serologically and by random amplified polymorphic DNA (RAPD) typing using primers HLWL74 (5'-ACGTATCTGC-3'), HLWL85 (5'-ACAACTGCTC-3'), and OMP-01 (5'-GTI'GGTGGCT-3'). Strains from cooked meat products were characterized and compared in relation to their origin. The detection of identical strains in products of different type and brand packed on the same date suggested cross-contamination, probably during the slicing process. All L monocytogenes isolates from smoked salmon were indistinguishable by serotyping and RAPD, suggesting that this strain was highly disseminated and adapted to the treatment used for the preservation of this food. RAPD subtypes were analyzed using GelCompar version 4.1 software and the unweighted pair method using arithmetic averages, and six groups with at least 78% similarity were established. Serotyping and RAPD results were in concordance, although RAPD showed a higher discriminatory power with L. monocytogenes isolates from meat products. RAPD is an easy method that could be useful to detect cross-contamination occurring during postprocessing manipulations.     

Investigation of Listeria monocytogenes contamination pattern in local Chinese food market and the tracing of two clinical isolates by RAPD analysis

This study was undertaken to investigate the contamination pattern of Listeria monocytogenes in local Chinese food markets and to trace two clinical isolates. Random amplification polymorphic DNA (RAPD) was developed to track the source of L. monocytogenes in ready-to-eat (RTE) food products and from clinical origin. Three random primers, PB1, PB4 and HLWL74, were used to subtype all the L. monocytogenes strains isolated from RTE food products, fresh food products, environmental sewages in the markets and two clinical meningitis patients. It was shown that all the 49 isolates could be classified into 5, 4 and 4 types using these three random primers, PB1, PB4, and HLWL74, respectively. Twenty-seven composite profiles were identified by a combination of the three primers. The same composite profiles of L. monocytogenes could be found both in the fresh food products, environmental sewages and RTE food products, suggesting that the L. monocytogenes in the RTE food products may come from those in the fresh food products or sewage in the same market. The composite profiles of the two clinical isolates were the same as those of strains isolated from RTE food products, indicating that the disease might have resulted from the consumption of the RTE food products contaminated with L. monocytogenes. The results show that RAPD could be a powerful tool for the investigation of contamination pattern of L. monocytogenes in Chinese food markets and also for tracking the source of L. monocytogenes in clinical patients.     

Development of a multiple primer RAPD assay as a tool for phylogenetic analysis in Listeria spp. strains isolated from milkproduct associated epidemics, sporadic cases of listeriosis and dairy environments

A total of 82 Listeria strains comprising four species were examined by amplification with a multiple primer random amplified polymorphic DNA (RAPD) assay. It was the objective of the study to set up a procedure suitable for analysis of the relationships among strains from milkproduct-associated epidemics, strains from sporadic cases of listeriosis and field strains from dairy products and dairy environments. In a preliminary study, 205 primers, each 10 bp long, were screened for suitability as primers and 44 primers showing reliable and reproducible RAPD patterns at a defined reaction condition were selected. The 82 strains were assigned to 54 RAPD groups positioned in 13 major clusters. Strains isolated during milk product-associated epidemics were found to belong to a single cluster I. Human isolates from sporadic cases of listeriosis predominantly were assigned to four separate clusters. It was found that strains of clinical origin were mainly assigned to other clusters than strains of non-clinical origin.     

Sodium chloride enhances adherence and aggregation and strain variation influences invasiveness of Listeria monocytogenes strains

Some subtypes of Listeria monocytogenes can persist in the food-processing industry, but the reasons for such persistence are not known. In the present study, 10 strains of L. monocytogenes representing known persistent randomly amplified polymorphic DNA (RAPD) types from fish processing plants were compared to eight strains of different RAPD type and origin (clinical, food, and animal). All 18 strains of L. monocytogenes had similar growth patterns at different temperatures (5 or 37 degrees C) or different salinities (0.5 or 5% NaCl), and all strains formed a thin layer of adhered cells on a plastic surface when cultured in tryptone soya broth (TSB) with a total of 1% glucose. Many ready-to-eat foods, such as cold-smoked fish, contain NaCl at concentrations of 2 to 5%, and NaCl is present in the processing environment. Adding NaCl to TSB changed the adhesion patterns of all strains, and all adhered better when NaCl was added. Also, the addition of NaCl caused a marked aggregation of 13 of the strains; however, 5 of the 18 strains did not aggregate in the presence of up to 5% NaCl. The aggregates stuck to the plastic surface, and this occurred in all but one of the persistent RAPD types. Four strains represented one particular RAPD type that has been isolated as a persistent RAPD type in several fish processing plants for up to 10 years. Because this RAPD type often can contaminate fish products, it is important to address its potential virulence. The 18 strains differed markedly in their ability to invade Caco-2 cells, and the four strains representing the universal persistent RAPD type were the least invasive (10(2) to 10(3) CFU/ml), whereas other strains invaded Caco-2 cells at levels of 10(4) to 10(5) CFU/ml. Five of the 18 strains belonged to the genetic lineage 1 and were the most invasive. Although the most commonly isolated persistent RAPD type was low invasive, it is important to understand why moderate salinity facilitates aggregation and biofilm formation, for this understanding can be beneficial in developing procedures to reduce processing plant contamination.     

Genetic procedures for identification of enterotoxigenic strains of Staphylococcus aureus from three food poisoning outbreaks

Three food poisoning restaurant outbreaks due to Staphylococcus aureus, occurring during June-October 2002 in the Principality of Asturias (PA), Spain, provided the basis for investigating some aspects of the molecular epidemiology of this organism. The methods applied to identify strains and lineages included multiplex-polymerase chain reaction (PCR) to detect nine enterotoxin (se) genes, and three DNA fingerprinting procedures: pulsed-field gel electrophoresis (PFGE) with SmaI, randomly amplified polymorphic DNA (RAPD) with two selected primers, and plasmid restriction analysis with HindIII. Thirty-two isolates were differentiated into three non-se and 12 se strains, which were outbreak-specific, except for one that was represented in two of the outbreaks. In outbreak 1, the 16 food isolates analyzed had sec, seg and sei genes and generated a distinctive DNA fingerprint, being assigned to a single strain. This strain could be categorized as endemic in the PA and associated to manually handled dairy products and nasal carriers. In outbreak 2, the four food isolates analyzed fell into three strains, each one displaying a different se-gene profile (sea, sec and seg-seh-sei) and a distinctive DNA fingerprint. In outbreak 3, the five food isolates tested fell into four seg-sei strains generating identical RAPD but different PFGE and plasmid profiles, and one sea strain also collected from two nasal carriers. This last strain had also been found in manually handled vegetables in outbreak 2, and it belongs to a not very frequently found sea lineage in the PA. Multiplex-PCR to detect se genes together with the three applied DNA fingerprint typing procedures proved therefore to be useful tools in subclassifying S. aureus for epidemiological purposes.     

Listeria monocytogenes in pork slaughtering and cutting plants. Use of RAPD, PFGE and PCR-REA for tracing and molecular epidemiology

In order to determine the origin of pork cuts contamination by Listeria monocytogenes, 287 isolates, collected from five French pork slaughtering and cutting plants, from live pigs to pork cuts, were characterised using three molecular typing methods: random amplification of polymorphic DNA (RAPD) carried out with five different primers, genomic macrorestriction using ApaI with pulsed-field gel electrophoresis (PFGE) and a PCR-restriction enzyme analysis (PCR-REA) based on the polymorphism existing within the inlA and inlB genes. Results obtained from RAPD and PFGE were closely related and distinguished respectively 17 RAPD types (r1-r17) and 17 PFGE types (a1-a17) among the 287 isolates, whereas the PCR-REA analysis only yielded two profiles (p1 and p2). Considering the combined results obtained with the three molecular typing methods, 19 Listeria monocytogenes genotypes (1-19) were distinguished. Serotyping led at least four serotypes being distinguished: 1/2a, 3a, 1/2c and 3c. The application of genotyping identified the predominance of a Listeria monocytogenes strain of type (1) and other very closely related ones (5, 9, 10, 12, 13, 14, 16 and 19) which were present on pork as well as in the environment within the five investigated plants. This study also pointed out the presence of these closely related Listeria monocytogenes strains over a 1-year period in the environments of two plants, even after cleaning and disinfection procedures. This highlights the possibility for some Listeria monocytogenes strains to persist in pork processing environments and raises the problem of the efficiency of cleaning and disinfection procedures used in pork slaughterhouses, chilling and cutting rooms.     

随机扩增多态性法分析西藏牦牛奶酪中乳酸菌的遗传多样性

目的：利用随机扩增多态性（randomly amplified polymorphic DNA,RAPD）法对西藏地区牦牛奶酪中27 株乳酸菌基因型进行同源性分析。方法：利用5 个随机引物对Mg2+浓度、dNTP用量、退火温度、模版用量/引物用量（ng/pmol）4 个条件做单因素梯度试验,建立最佳反应条件,筛选最佳引物,然后对27 株乳酸菌和4 株乳酸菌标准菌株进行随机扩增,用NTsys 2.10e软件对扩增条带进行聚类和遗传相似性系数分析,分析结果与16S rRNA测序得到的菌种鉴定结果进行对比。结果：31 株菌遗传相似系数在0.72～1.00之间,当相似性系数在0.82时,菌株被分成了8 组,菌株按照不同种属聚类,聚类结果同16S rRNA测序结果基本一致,同时成功将Lactobacillus casei和Lactobacillus paracasei两个亚种区分开。结论：RAPD技术可以较好地应用于西藏地区牦牛奶酪中乳酸菌亲缘性关系分析。     

Distribution of Penicillium commune isolates in cheese dairies mapped using secondary metabolite profiles, morphotypes, RAPD and AFLP fingerprinting

In an 8-year study of the diversity and distribution of Penicillium commune contaminants in two different cheese dairies, swab and air samples were taken from the production plants, the processing environment and contaminated cheeses. A total of 321 Penicillium commune isolates were characterized using morphotypes (colony morphology and colours) and secondary metabolite profiles. Based on production of secondary metabolites the P. commune isolates were classified into 6 groups. The genetic diversity of the P. commune isolates was assessed using randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP). For a sub-set of 272 P. commune isolates RAPD analysis generated 33 RAPD groups whereas AFLP profiling revealed 55 AFLP groups. This study conclusively showed that the discriminatory power of AFLP was high compared to RAPD and that AFLP fingerprinting matched morphotyping. P. commune isolates with identical profiles using all four typing techniques were interpreted as closely related isolates with a common origin and the distribution of these isolates in the processing environment indicated possible contamination points in the cheese dairies. The coating process and unpacking of cheeses with growth of P. commune seemed to cause the contamination problems. Several identical P. commune isolates remained present in the processing environment for more than 7 years in both dairies.