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PubMed1995

Molecular analysis of Salmonella enteritidis by pulsed-field gel electrophoresis and ribotyping.

A total of 61 isolates of Salmonella enteritidis were analyzed by the techniques of pulsed-field gel electrophoresis (PFGE) and ribotyping. Twenty-three of the isolates were from Zurich, Switzerland, and 38 isolates were from the University Hospital, Kuala Lumpur, Malaysia. Five of the Malaysian isolates were hospital-related outbreak strains and were shown to be indistinguishable by PFGE analysis following digestion with three different restriction endonucleases, XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3'). The PFGE pattern of an isolate from a suspected carrier staff nurse was found to be identical to those of the hospital outbreak isolates. These isolates were also indistinguishable by ribotyping with SmaI and SphI. The same single PFGE pattern was also detected in 29 of 32 sporadic isolates of S. enteritidis. Four closely related ribotypes were detected among these 29 isolates. Similarly, outbreak-related strains from Switzerland showed close genetic identity by PFGE and ribotyping. Strains obtained from poultry showed more variations in their PFGE patterns and ribotypes, although the patterns were still closely related. In addition, SphI ribotypes A and D among the Swiss strains correlated with phage types 4 and 8, respectively. No correlation of phage types with PFGE pattern was noted. Both PFGE and ribotyping indicate that the S. enteritidis strains circulating in Malaysia and Switzerland are very similar and may be clonally related. Comparison of the PFGE patterns with the ribotypes for 23 Swiss and 16 Malaysian isolates showed that there was a 69% concordance in the grouping of isolates. We conclude that the close genetic similarity observed between epidemiologically unrelated and outbreak-related isolates of S. enteritidis suggests that both PFGE and ribotyping are of limited value in the epidemiological analysis of these particular isolates, possibly because of the highly clonal nature of pathogenic strains of S. enteritidis.

Animals↗
PubMed2004

Diversity of Listeria monocytogenes isolates of human and food origin studied by serotyping, automated ribotyping and pulsed-field gel electrophoresis.

Automated ribotyping, pulsed-field gel electrophoresis (PFGE) and serotyping were evaluated for the epidemiological study of isolates of Listeria monocytogenes collected in Finland in 1997-1999 from human blood (n = 116) and the food industry (n = 72). The isolates divided into six serotypes, 23 EcoRI ribotypes, 54 AscI PFGE types, and 57 final subtypes if all results were combined. The discrimination index of ribotyping was lower (0.873) than that of PFGE (0.946). Two final subtypes dominated among human isolates, and identical subtypes were also found among food industry isolates. All PFGE types were serotype-specific, whereas two ribotypes included isolates of two serotypes. Isolates of serotype 3a, involved in an outbreak in Finland in 1999, matched one of these ribotypes, which also included some food industry isolates of serotype 1/2a. Ribotyping with EcoRI would not have been sufficient to define the outbreak in Finland caused by serotype 3a isolates. Although ribotyping is applicable as the first method in outbreak situations, human and food isolates with identical ribotypes should be investigated further by PFGE.

Animals↗
PubMed2005

Identification of coagulase-negative staphylococci other than Staphylococcus epidermidis by automated ribotyping.

As routine identification of coagulase-negative staphylococci is problematic, the performance of automated ribotyping was evaluated for identification of coagulase-negative staphylococci other than Staphylococcus epidermidis. In total, 177 isolates were tested, comprising 149 isolates from blood samples, 15 isolates that were not identified by internal transcribed spacer (ITS)-PCR in a previous study, and 13 reference strains. The identification results were compared with those obtained by the API 20 Staph system, with standard phenotypic and molecular methods as reference. Most (n = 166; 93.8%) isolates were identified correctly by automated ribotyping. For 61 isolates, API 20 Staph and ribotyping were in agreement, but for 105 isolates, ribotyping provided correct identification and API 20 Staph did not. Four isolates not identified by automated ribotyping were recognised correctly by API 20 Staph. The remaining seven isolates could not be identified by either of the two methods. Automated ribotyping was able to distinguish Staphylococcus capitis reliably from Staphylococcus caprae. The results demonstrate the value of automated ribotyping for identification of coagulase-negative Staphylococcus (CoNS) isolates from human sources and may help to clarify the clinical relevance of CoNS species. In addition, automated ribotyping was able to detect polymorphisms that may be useful for epidemiological purposes within S. capitis, Staphylococcus hominis, Staphylococcus haemolyticus, Staphylococcus simulans, S. caprae, Staphylococcus warneri, Staphylococcus lugdunensis, Staphylococcus schleiferi, Staphylococcus sciuri, Staphylococcus pasteuri and Staphylococcus xylosus.

Phenotype↗
PubMed2026

Ribotyping for Accurate Identification of Infectious Bacteria in Animal-Derived Foods and Laboratory Samples: Implications for Human Health.

Ribotyping is a molecular typing approach based on ribosomal RNA (rRNA) gene sequences for the identification and characterization of bacterial strains. This review aims to evaluate the effectiveness of ribotyping in the identification of infectious bacteria in animal-derived foods and veterinary samples. A narrative literature review was conducted using major scientific databases, including PubMed, Scopus, Google Scholar, and Web of Science, covering studies published to 2025. Relevant articles were selected based on their focus on ribotyping methodologies (e.g., RFLP-, PCR-, and automated ribotyping) and their applications in food safety, veterinary microbiology, and zoonotic disease investigations. The findings indicate that ribotyping has been widely applied for epidemiological investigations, source tracking, and characterization of foodborne and zoonotic pathogens. These approaches have contributed to understanding bacterial diversity and monitoring antibiotic resistance patterns in animal populations and related food products. However, compared with high-resolution molecular techniques such as whole genome sequencing (WGS), ribotyping demonstrates lower discriminatory power and limited resolution for fine-scale epidemiological analysis. Despite these limitations, ribotyping remains a useful, accessible, and cost-effective tool in certain laboratory and surveillance settings, particularly where advanced genomic technologies are not readily available. Overall, integrating ribotyping with newer genomic approaches can enhance the monitoring and control of infectious bacteria, thereby supporting animal health, food safety, and public health outcomes.

animal-derived foods↗
PubMed2003

Typing of Listeria monocytogenes isolates originating from the food processing industry with automated ribotyping and pulsed-field gel electrophoresis.

A total of 486 Listeria monocytogenes isolates originating from 17 Finnish food processing plants (representing meat, poultry, fish, and dairy production) were collected and typed by automated ribotyping using EcoRI as the restriction enzyme. The isolates were divided into 16 different ribotypes (RTs). Some of these isolates (121), representing all EcoRI types and 16 food plants, were subjected to ribotyping with the PvuII enzyme, to pulsed-field gel electrophoresis (PFGE) typing with AscI and SmaI restriction enzymes, and to serotyping with O-antigen antisera. Nineteen ribotypes were generated with PvuII, 42 macrorestriction patterns were generated with AscI and 24 with SmaI, and three serotypes were generated with antisera. When the results were combined, the overall number of RTs was 23, and that of the PFGE types was 46. Thus, the overall discrimination power of PFGE was higher (discrimination index [DI] 0.966) than that of ribotyping (DI 0.906). The most common serotype (90.1% of the isolates) was 1/2, and isolates of serotype 4 (3.3%) were rare. There was no connection between food sectors and RTs or PFGE types, but PFGE indicated the single plants (78.3% of the types) better than ribotyping (56.5%). On the basis of its automation and on the availability of identification databases, automated ribotyping had some advantages over PFGE. Overall, automated ribotyping can be considered a practical and rapid tool when Listeria contamination is suspected and when screening a large number of isolates is necessary, e.g., when tracing contamination sources. However, in cases of outbreaks, the identical patterns must be confirmed by PFGE, which is a more discriminatory method.

Animals↗
PubMed1999

Traditional ribotyping shows a higher discrimination than the automated RiboPrinter system in typing Vibrio cholerae O1.

Sixteen clinical Vibrio cholerae O1 strains from four different countries were selected for comparison by traditional ribotyping and an automated RiboPrinter system for identification and discrimination purposes. Automated ribotyping, which routinely uses the restriction enzyme EcoRI for typing all bacterial species, produced only five different ribotypes compared with 10 different EcoRI ribotypes obtained by the traditional method. Traditional and automated ribotyping using the restriction enzyme BglI, which is recommended for the ribotyping of V. cholerae, produced 10 and seven different ribotypes, respectively. The lower discrimination shown by the RiboPrinter system was caused mainly by an inability to differentiate closely located fragments due to a lower resolution and electrophoresis conditions, a parameter which cannot be changed in the automated system. The RiboPrinter system includes a database for bacterial identification. However, none of the V. cholerae O1 strains studied showed EcoRI ribotype patterns which matched any of the patterns included in the database. In conclusion, the existing RiboPrinter system is not adequate for taxonomic identification and classification of V. cholerae O1.

Automation↗
PubMed1992

Molecular epidemiology of group B streptococcal infections: use of restriction endonuclease analysis of chromosomal DNA and DNA restriction fragment length polymorphisms of ribosomal RNA genes (ribotyping).

Epidemiologic investigation of group B streptococcal (GBS) infections has been limited by the lack of a discriminatory typing system. Therefore, the use of restriction endonuclease analysis of chromosomal DNA (REAC) and DNA restriction fragment length polymorphisms of rRNA genes (ribotyping) to subtype molecularly GBS isolates associated with human invasive disease was investigated. Chromosomal DNA of selected GBS isolates was initially digested with 24 different restriction enzymes. HhaI gave the best discrimination of hybridization banding patterns (ribotypes) and was used with all study isolates. Ribotyping and REAC differentiated among isolates of the same and different serotypes. Nine ribotype patterns were noted among the 76 isolates studied, including 4 among serotype Ia/c and 4 additional ribotypes among serotype III isolates. Epidemiologically related isolates (e.g., mother-infant or twin-twin pairs) had identical REAC and ribotype patterns. Epidemiologically unrelated isolates with the same ribotype usually had different REAC patterns, suggesting that REAC may be a more sensitive technique for strain differentiation. REAC and ribotyping were reproducible and proved to be successful molecular epidemiologic methods for subtyping GBS.

Adult↗
PubMed1997

Detection of identical ribotypes of Porphyromonas gingivalis in patients residing in the United States, Sudan, Romania and Norway.

Porphyromonas gingivalis has been isolated from periodontitis lesions in subjects from many geographical locations. The purpose of this investigation was to determine whether similar ribotypes of P. gingivalis could be detected among strains isolated in different countries. A total of 198 isolates of P. gingivalis were obtained from 52 periodontitis patients in Boston (130 isolates), Bergen, Norway (17 isolates), Khartoum, Sudan (26 isolates), and Bucharest, Romania (25 isolates). DNA was isolated from each strain, cut separately by the restriction endonucleases KpnI and PstI. The resulting preparations were subjected to electrophoresis in a 0.8% agarose gel using a Tris-acetate EDTA buffer. Uncut lambda and a 1000-bp fragment of 16S rRNA were included as internal standards in each lane. In addition, a HindIII digest of lambda was present in a separate lane in each run. The DNA fragments were transferred to a nylon membrane by downward capillary transfer. 16S rRNA bands were detected using a 1000-kb digoxigenin-labelled probe generated by a polymerase chain reaction. At the same time, a digoxigenin-labelled probe to lambda was employed to detect the internal and molecular weight standards. The bands were detected using antibody to digoxigenin conjugated to alkaline phosphatase and chemiluminescence. The positions of the bands relative to the internal standards were determined and normalized to correct for run-to-run variations, and the molecular weight of each band was determined by comparison with standards within each gel. The resulting data for the 2 enzymes were combined and subjected to cluster analysis using an average unweighted linkage sort. In some instances, isolates that appeared to be of identical ribotype using one endonuclease gave different ribotypes using the other. Strains of P. gingivalis within a subject were usually identical, except for 3 patients who harbored 2 different ribotypes/individual. All subsequent analyses employed a single ribotype strain for each subject. A total of 32 ribotypes were observed for isolates from distant countries. A total of 11.5% of the patients had isolates exhibiting the same ribotype: ribotype 7a. Identical ribotypes of P. gingivalis can be recovered from subgingival plaque samples of periodontitis patients in different countries.

Bacterial Typing Techniques↗
PubMed1995

Application of ribotyping for differentiating Vibrio cholerae non-O1 isolated from shrimp farms in Thailand.

A collection of 143 Vibrio cholerae non-O1 strains isolated from shrimp farms in Thailand were characterized and grouped by ribotyping. Sixty-four ribotypes were distinguished following digestion of chromosomal DNA with the restriction enzyme BglI, and the reproducibility of the method was 100%. There was no correlation between specific ribotype distributions and the locations of the shrimp farms. Ribotype similarity was examined by cluster analysis, and two main groups with 10 and 54 ribotypes, respectively, were found. Correlation between ribotype and O-antigen expression was shown to exist among those isolates tested. Ribotyping appears to be a suitable method for differentiating environmental V. cholerae non-O1 strains, and comparison of ribotype patterns showed a high degree of genetic divergence within V. cholerae non-O1.

Animals↗
PubMed1997

Comparison of ribotyping and randomly amplified polymorphic DNA PCR for characterization of Vibrio vulnificus.

A total of 85 isolates of Vibrio vulnificus were characterized by ribotyping with a probe complementary to 16S and 23S rRNA of Escherichia coli and by randomly amplified polymorphic DNA-PCR (RAPD-PCR) with a 10-mer oligonucleotide primer. The RAPD-PCR results were scanned, and the images were analyzed with a computer program. Ribotype membranes were evaluated visually. Both the ribotyping and the RAPD-PCR results showed that the collection of strains was genetically very heterogeneous. Ribotyping enabled us to differentiate U.S. and Danish strains and V. vulnificus biotypes 1 and 2, while the RAPD-PCR technique was not able to correlate isolates with sources or to differentiate the two biotypes, suggesting that ribotyping is useful for typing V. vulnificus strains whereas RAPD-PCR profiles may subdivide ribotypes. Two Danish clinical biotype 2 strains isolated from fishermen who contracted the infection cleaning eels belonged to the same ribotype as three eel strains (biotype 2), providing further evidence that V. vulnificus biotype 2 is an opportunistic pathogen for humans. One isolate (biotype 2) from Danish coastal waters also showed the same ribotype as the eel strains. This is, to our knowledge, the first time the isolation of V. vulnificus biotype 2 from coastal waters has been described.

Animals↗
PubMed1999

Role of genomic rearrangements in producing new ribotypes of Salmonella typhi.

Salmonella typhi is the only species of Salmonella which grows exclusively in humans, in whom it causes enteric typhoid fever. Strains of S. typhi show very little variation in electrophoretic types, restriction fragment length polymorphisms, cell envelope proteins, and intervening sequences, but the same strains are very heterogeneous for ribotypes which are detected with the restriction endonuclease PstI. In addition, the genome of S. typhi has been proven to undergo genomic rearrangement due to homologous recombination between the seven copies of rrn genes. The relationship between ribotype heterogeneity and genomic rearrangement was investigated. Strains of S. typhi which belong to 23 different genome types were analyzed by ribotyping. A limited number of ribotypes were found within the same genome type group; e. g., most strains of genome type 3 belonged to only two different ribotypes, which result from recombination between rrnH and rrnG operons. Different genome type groups normally have different ribotypes. The size and identity of the PstI fragment containing each of the seven different rrn operons from S. typhi Ty2 were determined, and from these data, one can infer how genomic rearrangement forms new ribotypes. It is postulated that genomic rearrangement, rather than mutation, is largely responsible for producing the ribotype heterogeneity in S. typhi.

Bacterial Typing Techniques↗
PubMed1993

Ribotype analysis of Pseudomonas pseudomallei isolates.

No epidemiological typing system to differentiate among Pseudomonas pseudomallei isolates has been available. Ribotype analysis was developed and used to examine 74 clinical and 10 environmental isolates of P. pseudomallei from Thailand. Six P. pseudomallei ribotypes were identified from restriction fragment polymorphisms of EcoRI chromosomal digests. The predominant ribotype, A, was found in 59 of the isolates examined. By using patterns from hybridizations with SalI, HindIII, and PstI restriction digests, isolates of ribotype A were subdivided into a further five subtypes, giving a total of 10 differentiable P. pseudomallei types. In 23 of 34 melioidosis patients studied, multiple P. pseudomallei isolates were present. In all but one of these patients, a single ribotype of the organism was present. Isolation of two different ribotypes of P. pseudomallei from one patient, one each in sputum and urine, suggests that superinfection may have occurred. The ribotype was shown to be conserved during the course of antibiotic treatments in seven patients studied, although the antibiotic sensitivity patterns in the isolates from these patients varied. The prevalence of subtype A1 in clinical and environmental specimens suggests that this strain may be predominant in this geographical location. These results demonstrate the usefulness of the ribotyping method for epidemiological studies of P. pseudomallei.

Bacterial Typing Techniques↗
PubMed2000

Evaluation of the discriminatory powers of the Dienes test and ribotyping as typing methods for Proteus mirabilis.

A total of 63 clinical isolates of Proteus mirabilis collected over a 19-month period were typed by the Dienes test and ribotyping. Ribotyping was performed using the fully automated RiboPrinter Microbial Characterization System (Qualicon, Wilmington, Del.). Isolates that were indistinguishable by the Dienes test and/or ribotyping were characterized further by pulsed-field gel electrophoresis (PFGE). Most of the isolates represented unique strains as judged by the Dienes test and ribotyping. Forty isolates represented 40 different ribotypes and Dienes types. The remaining 23 isolates were grouped into 13 Dienes types, 12 ribotypes, and 14 PFGE types. The index of discrimination was 0.980 for the Dienes test, 0.979 for ribotyping, and 0.992 for PFGE. Both the Dienes test and ribotyping are useful methods for identifying individual strains of P. mirabilis. The Dienes test is simple, inexpensive, and easy to perform. It can be performed in virtually any laboratory and should be used in the initial epidemiologic characterization of P. mirabilis isolates.

Automation↗
PubMed2005

Ribotyping of Lactobacillus casei group strains isolated from dairy products.

A series of lactobacilli isolated from dairy products were characterized using biotyping and ribotyping with EcoRI and HindIII restriction enzymes. Biotyping assigned 14 strains as Lactobacillus casei, 6 strains as Lactobacillus paracasei subsp. paracasei and 12 as Lactobacillus rhamnosus. The obtained ribotype patterns separated all analyzed strains into two clearly distinguished groups corresponding to L. rhamnosus and L. casei/L. paracasei subsp. paracasei. The HindIII ribotypes of individual strains representing these two groups were visually very similar. In contrast, EcoRI ribotyping revealed high intraspecies variability. All ribotypes of L. casei and L. paracasei subsp. paracasei dairy strains were very close and some strains even shared identical ribotype profiles. The type strains L. casei CCM 7088T (= ATCC 393T) and Lactobacillus zeae CCM 7069T revealing similar ribopatterns formed a separate subcluster using both restriction enzymes. In contrast, the ribotype profile of L. casei CCM 7089 (= ATCC 334) was very close to ribopatterns obtained from the dairy strains. These results support synonymy of L. casei and L. paracasei species revealed by other studies as well as reclassification of the type strain L. casei CCM 7088T as L. zeae and designation of L. casei CCM 7089 as the neotype strain.

Dairy Products↗
PubMed2003

Deer diet affects ribotype diversity of Escherichia coli for bacterial source tracking.

Ribotyping is one of a number of genotypic methods for bacterial source tracking. This method requires a host origin database of one bacterial species be established in order to identify environmental isolates. Researchers establishing these databases have observed considerable ribotype diversity within a specific bacterial species. One source of this diversity may be diet. We determined the effect of diet on ribotype diversity for Escherichia coli in penned and wild deer (Odocoileus virginianus) in a 13-ha forested watershed. A total of 298 E. coli isolates was obtained, 100 from penned deer, 100 from wild deer, and 98 from the stream in the watershed to which all deer had access. The wild deer had significantly more ribotypes (35) than the penned deer (11 ribotypes, p = 0.05). This result suggests that diet affected ribotype diversity, and that a host origin database for bacterial source tracking should contain bacterial isolates from wild rather than from captive animals. Also, 42 of 98 (42.9%) environmental isolates matched penned and wild deer ribotypes. If bacterial source tracking determines that fecal contamination is predominantly from wildlife, then it may be unnecessary to monitor these watersheds because control over wildlife is difficult.

Animals↗
PubMed2000

Epidemiologic typing of Escherichia coli using RAPD analysis, ribotyping and serotyping.

OBJECTIVE: To compare random amplified polymorphic DNA (RAPD) analysis and ribotyping with serotyping for epidemiologic typing of Escherichia coli. METHODS: Thirty-two epidemiologically unrelated strains, nine cerebrospinal fluid isolates with the O7K1 serotype from nine patients, and nine sets of epidemiologically related E. coli isolates from nine patients were typed by RAPD analysis, ribotyping and serotyping. RESULTS: Among the 32 epidemiologically unrelated E. coli isolates, 29 types were distinguished by RAPD analysis, 25 by ribotyping and 27 by serotyping. Indistinguishable patterns were obtained by RAPD analysis and ribotyping within the collection of nine cerebrospinal fluid isolates. For the epidemiologically related isolates, intrapatient variation was only found by RAPD analysis among the isolates of one set and by ribotyping among the isolates of two sets. No interpatient variation was observed between three sets of isolates. With serotyping, the epidemiologically related isolates yielded similar typing relationships to those obtained by RAPD analysis and ribotyping. CONCLUSIONS: RAPD analysis had the highest discriminatory capacity for typing E. coli isolates. RAPD analysis, ribotyping and serotyping can all be used for assessment of strain relationships.

Adult↗
PubMed2006

Ribotype diversity of Listeria monocytogenes isolates from two salmon processing plants in Norway.

The purpose of this study was to use automated ribotyping procedure to track Listeria monocytogenes transmission in the cold smoked fish production chain and to characterize L. monocytogenes subtypes associated with the salmon processing industry. A total of 104 isolates, which had previously been obtained from a raw fish slaughter and processing plant (plant B) and an adjacent, downstream, salmon smoking operation (plant A), were characterized. These isolates had been obtained through a longitudinal study on Listeria presence, which covered a 31-week period, in both plants. Isolates had been obtained from samples taken from different machinery used throughout the production process. In addition, six isolates obtained from products produced in plant A two years after the initial study were included, so that a total of 110 isolates were characterized. Automated ribotyping was performed using both the restriction enzymes EcoRI and PvuII to increase the discriminatory power. The 110 L. monocytogenes isolates could be divided into 11 EcoRI ribotypes; PvuII ribotype data yielded multiple subtypes within 7 EcoRI ribotypes for a total of 21 subtypes based on both EcoRI and PvuII ribotyping. A total of three EcoRI ribotypes (DUP-1023C, DUP-1045B, and DUP-1053E) were isolated at multiple sampling times from both plants. In addition, one subtype (DUP-1053B) was isolated at multiple sampling times in only plant A, the salmon smoking operation. These data not only support that L. monocytogenes can persist throughout the salmon production system, but also showed that L. monocytogenes may be transmitted between slaughter and smoking operations or may be unique to smoking operations. While the majority of subtypes isolated have been rarely or never linked to human listeriosis cases, some subtypes have previously caused human listeriosis outbreaks and cases. Molecular subtyping thus is critical to identify L. monocytogenes transmission and niches in order to allow design and implementation of control strategies at the appropriate stage of production and in order to reduce the prevalence of L. monocytogenes linked to human disease.

Animals↗
PubMed2001

Comparison of toxinotyping and PCR ribotyping of Clostridium difficile strains and description of novel toxinotypes.

Toxinotyping and PCR ribotyping are two methods that have been used to type Clostridium difficile isolates. Toxinotyping is based on PCR-RFLP analysis of a 19 kb region encompassing the C. difficile pathogenicity locus. PCR ribotyping is based on comparison of patterns of PCR products of the 16S-23S rRNA intergenic spacer region. Representative strains (101) from a C. difficile PCR ribotype library and 22 strains from previously described toxinotypes were analysed to compare ribotyping with toxinotyping. Within this panel of strains all 11 toxinotypes (0-X) described previously and an additional 5 novel toxinotypes (XI-XV) were observed. PCR ribotyping and toxinotyping correlated well and usually all strains within a given ribotype had similar changes in toxin genes. The new toxinotype XI comprises strains that did not express toxins TcdA or TcdB at detectable levels, but contained part of the tcdA gene. Strains of toxinotype XII exhibit changes only in the 5' end of the tcdB gene. Toxinotype XIV is composed of strains that have a large insertion at the beginning of the tcdA gene. A total of 25 of the 89 tested PCR ribotypes of C. difficile contained variant strains. It was estimated that they represent 7.7% of the total number of strains in the Anaerobe Reference Unit collection.

Bacterial Toxins↗