Restriction fragment length polymorphisms in rRNA operons for subtyping Shigella sonnei

Diversity of Variable Number Tandem Repeat Loci in Shigella Species Isolated from Pediatric Patients

Multilocus variable number tandem repeat (VNTR) analysis (MLVA) is a new typing method with several advantages compared to other methods. Dissemination of Shigella is highly significant in developing countries. Whilst Shigella is becoming increasingly important as an etiologic agent of pediatric shigellosis in Iran, little is known about the genetic diversity of the local strains. Therefore, the aim of this study was to describe the genetic diversity of Shigella species isolated from pediatric patients in Tehran, Iran. A total of 53 Shigella isolates were obtained from 1070 patients with diarrhea (less than 12 years of age). All isolates were identified by routine biochemical and serological tests. The confirmed Shigella isolates were further serogrouped (by the slide agglutination) using slide agglutination method. MLVA assay with the seven loci resolved 53 Shigella isolates into 36 different genotypes. Almost all the isolates were classified into five clonal complexes. Furthermore, our MLVA assay could effectively distinguish the four Shigella species. This study has provided valuable insights into the genetic heterogeneity of Shigella species in Tehran, Iran. Our findings can be helpful for further epidemiological surveillance of Shigella species in this country in the future.

Multilocus variable-number tandem-repeat analysis for genotyping of Shigella sonnei strains isolated from pediatric patients

AIM

The aims of this study were to characterize Iranian Shigella sonnei strains isolated from pediatric cases and evaluate the utility of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) for genotyping of local S. sonnei strains.

BACKGROUND

S.  sonnei has become the dominant species in certain parts of Iran. Although PFGE is still a gold standard for genotyping and source tracking of food-borne pathogens, it is laborious, expensive, time-consuming, and often difficult to interpret. However, MLVA is a PCR-based method, which is rapid, relatively inexpensive and easy to perform.

PATIENTS AND METHODS

A total of 47 S. sonnei isolates were obtained from sporadic cases of pediatric shigellosis in Tehran, Iran, during the years 2002-2003 (n=10) and 2008-2010 (n=37). The patients suffered from acute diarrhea and had evidence of more than three episodes of watery, loose, or bloody stools per day. A MLVA scheme based on 7 VNTR loci was established to assess the diversity of 47 S. sonnei isolates.

RESULTS

Based on the results, it was clear that the S. sonnei isolates were heterogeneous. Overall, 47 S. sonnei isolates were discriminated into 21 different genotypes. Analysis of the MLVA profiles using a minimum spanning tree (MST) algorithm showed the usefulness of the MLVA assay in discriminating S. sonnei isolates collected over different time periods. However, no correlation was found between the MLVA genotypes and age, gender or clinical symptoms of the patients.

CONCLUSION

It is assumed that our S. sonnei isolates are derived from a limited number of clones that undergo minor genetic changes in the course of time. The present study has provided some valuable insights into the genetic relatedness of S. sonnei in Tehran, Iran.

Increased isolation and characterization of Shigella sonnei obtained from hospitalized children in Tehran, Iran

Shigella flexneri has been the most frequent cause of shigellosis in children in Iran. To evaluate the changes in frequency of serogroups, 302 Shigella species were isolated in 2003 from hospitalized children, aged less than 12 years, with acute diarrhoea in Tehran, Iran. The number of collected S. sonnei, S. flexneri, S. boydii, and S. dysenteriae isolates was 178 (58.9%), 110 (37.4%), 10 (3.3%), and 4 (1.3%) respectively. Most (94%) S. sonnei isolates were resistant to co-trimoxazole. They were, however, relatively or completely sensitive to 15 commonly-used antibiotics. The extracted plasmids showed 12 different profiles with two closely-related patterns constituting 70% of the total isolates. Ribotyping, using PvuII, HindIII or SalI restriction enzymes, generated a single pattern for all S. sonnei isolates. Data suggest that S. sonnei has become the predominant serogroup in children in the hospitals of Tehran.

Antibiotic resistance and genetic diversity of Shigella sonnei isolated from patients with diarrhoea between 1999 and 2003 in Bangladesh

Shigella sonnei is a significant cause of diarrhoeal infection in both developing and industrialized countries. From 1999 to 2003, 445 strains of Shigella sonnei were isolated from patients admitted to the diarrhoea treatment centre of the International Center for Diarrhoeal Disease Research, Bangladesh. More than 60% of the isolates were resistant to nalidixic acid, 89% to sulfamethoxazole-trimethoprim and 9.5% to ampicillin. In addition, 4% of strains were resistant to multiple antibiotics (AmpR TetR SxtR StrR) and 4.2% of strains were sensitive to all antibiotics tested. None of the strains were positive for the set1 gene, whereas 46% were positive for the sen gene. Forty-six per cent of the strains (stored at -70 degrees C) harboured the 120 MDa invasive plasmid and representative strains produced keratoconjunctivitis in the guinea pig eye. In addition, three plasmids of approximately 5, 1.8 and 1.4 MDa were found to be present in more than 90% of the strains. A self-transmissible, middle-ranged plasmid (35-80 MDa) carrying the multiple antibiotic resistance gene was found in some strains. PFGE analysis of the strains identified five unique types with many subtypes, which were characterized into four unique types by ribotyping analysis. It can be concluded that endemic strains of Shigella sonnei isolated from patients in Bangladesh are diverse in their genetic pattern.

Comparative study of three different DNA fingerprint techniques for molecular typing of Shigella flexneri strains isolated in Romania

In this study, 97 epidemiologically unrelated Shigella flexneri strains isolated during 1994 (69 isolates) and 1997 (28 isolates) were characterised by ribotyping, enterobacterial repetitive intergenic consensus sequence-based PCR typing, and pulsed-field gel electrophoresis. Number of strains belonging to each of the six serotypes is selected equal to their distribution in Romania. The isolates comprise 24 ribotypes based on combination of two restriction patterns obtained with HindlII and PstI, respectively, 7 enterobacterial repetitive intergenic consensus (ERIC)-PCR types, and 92 XbaI pulsed-field gel electrophoresis (PFGE) patterns grouped in 31 pulsotypes at Dice coefficients of 85% similarity. We find no significant difference in the distribution of isolates collected during the two periods. Macrorestriction analysis by PFGE offers maximal discrimination. There seems to be little genetic variability among circulating S. flexneri strains of serotype 2a, suggesting that even a combination of several molecular techniques, including PFGE, could not easily differentiate an outbreak strain from temporally associated independent isolates.

Application of a geographic information system to the tracking and control of an outbreak of shigellosis

A personal computer-based commercial geographic information system (GIS) was applied to an outbreak of Shigella sonnei infection at Fort Bragg, North Carolina. We used a database consisting of demographic, temporal, and home-address information for all recognized cases of S. sonnei that occurred among health care beneficiaries from 23 May 1997 through 14 August 1997. We imported this database into the GIS, which contained a digitized basemap of the local community. Through simultaneous examination of temporal and spatial distribution of the 59 identified cases of S. sonnei, a focus of infection in a single housing area was identified. Targeted education among residents of the neighborhood in which there was intense transmission was associated with prompt extinction of the epidemic. A GIS offers an efficient and practical way to directly visualize the dynamics of transmission of infectious diseases in the setting of a community outbreak.

Study of the relatedness of isolates of Shigella flexneri and Shigella sonnei obtained in 1986 and 1987 and in 1994 and 1995 from Hong Kong

We used pulsed-field gel electrophoresis (PFGE) to study the genetic relatedness of 235 isolates of Shigella flexneri and Shigella sonnei collected in Hong Kong (97 isolates from 1986 and 1987 and 138 isolates from 1994 and 1995). Altogether, 13 gels were run with bacteriophage lambda ladder DNA (Pharmacia) as an external reference in every sixth lane, standardized reagents and methods, and isolates randomized for species and years. For quantitative illustration of the relationships within a large body of isolates, computer-generated dendrograms were used to determine the number of isolates in pulsotypes at Dice coefficients of similarity of 75% (PT75) and 50% (PT50). For S. flexneri, there was a significant difference in the distribution of isolates collected during the two periods in both PT75 and PT50, with 68% of isolates collected in 1994 and 1995 sharing a coefficient of similarity of >/=68%. For S. sonnei, a significant difference was observed in PT50 only. We also used Upholt's formula for an approximation of the fraction of nucleotide difference between isolates and Molecular Evolutionary Genetics Analysis to determine relative genetic distances. For both species, the relative genetic distances between isolates of the earlier collection period were significantly greater (P < 0.0001), i. e., they were further apart and therefore more diverse than those of the later period. We conclude that it is possible for a typical clinical laboratory to analyze a large amount of PFGE information on Shigella isolates obtained under controlled conditions. Such data analysis should enhance surveillance capabilities and give indications of further work to be done on various aspects of bacterial pathogenicity of the species.

Combined use of ribotyping, PFGE typing and IS431 typing in the discrimination of nosocomial strains of methicillin-resistant Staphylococcus aureus

We have previously reported the phenotypic characterization of methicillin-resistant Staphylococcus aureus (MRSA) clinical strains isolated in Malaya University Hospital in the period 1987 to 1989 using antibiogram, coagulase typing, plasmid profiles, and phage typing. Here, we report the analysis of the same strains with three genotyping methods; ribotyping, pulsed-field gel electrophoresis (PFGE) typing, and IS431 typing (a restriction enzyme fragment length polymorphism analysis using an IS431 probe). Ribotyping could discriminate 46 clinical MRSA strains into 5 ribotypes, PFGE typing into 22 types, and IS431 typing into 15 types. Since the differences of the three genotyping patterns from strain to strain were quite independent from one another, the combined use of the three genotyping methods could discriminate 46 strains into 39 genotypes. Thus, the powerful discriminatory ability of the combination was demonstrated.

WHO-sponsored international collaborative study to evaluate methods for subtyping Listeria monocytogenes: restriction fragment length polymorphism (RFLP) analysis using ribotyping and Southern hybridization with two probes derived from L. monocytogenes chromosome

Seven laboratories participated in a WHO-sponsored international collaborative study, to evaluate methods for subtyping Listeria monocytogenes, by performing restriction fragment length polymorph sm (RFLP) analysis-based subtyping of an international study set of 80 strains of L. monocytogenes that included 22 epidemiologically related groups. The RFLP analysis was done by Southern hybridization with one of two types of probes found in multiple copies on the chromosome of L. monocytogenes. Six laboratories performed ribotyping. These laboratories used EcoRI enzyme to restrict the L. monocytogenes DNA and ribosomal RNA or DNA as the probe for Southern hybridizations. The seventh laboratory used Ncil to restrict the DNA, and two probes, one randomly cloned and the other containing repeat sequences cloned from L. monocytogenes DNA. The overall discriminating power of ribotyping, as estimated by calculation of Simpson's index of diversity, ranged from 0.83 to 0.88 for the six laboratories. The discriminating power of the combination of two probes used by Laboratory 7 was 0.91. Ribotyping and the cloned probes used by Laboratory 7 discriminated poorly between serotype 4b strains. Neither method identified three atypical strains (identified by other subtyping methods) included in three apparently epidemiologically related groups. Ribotyping did not discriminate between strains of serotypes 4b and 4b(X) in one epidemiologically related group of strains; one cloned probe used by Laboratory 7 discriminated between these strains. Intra-laboratory reproducibilities for the seven laboratories ranged from 80.0 to 100%. as determined by their abilities to correctly identify 11 pairs of duplicate strains included in the study set. Inter-laboratory reproducibilities were generally very good considering that no attempt was made to standardize protocols used by the participants.

Usefulness of ribotyping in a molecular epidemiology study of shigellosis

Ribotyping performed with six restriction endonucleases was used to study the molecular epidemiology of shigellosis in Asturias, Spain. The series included Shigella sonnei from 34 sporadic cases, 3 outbreaks and 3 reference strains, and S. Flexneri from sporadic cases and 1 reference strain. The S. sonnei strains were grouped into 5 ribotypes with Sal I, 4 with Hind III and Pvu II, 3 with Bgl II and EcoR I and 2 with Hinc II (Discriminatory Index (DI) between 0.54 and 0.14); the S. flexneri into 5 ribotypes with Sal I, Hinc II and Hind III, and 4 with the other enzymes (DI = 0.71 - 0.63). The combination of results for 2 or more enzymes facilitated and additional discrimination, the highest values in S. sonnei were for the 6 enzymes (16 types, DI = 0.91) and in S. flexneri for some combinations of 3 or more enzymes (7 types, DI = 0.81). Ribotypes with the 6 enzymes defined 16 clonal lines in S. sonnei and 7 in S. flexneri, which showed a different degree of genetic heterogeneity, and all the lines of each species falling into a different cluster. No line appeared as clearly endemic in the bowels of Asturian people.

Ribotyping to differentiate Fusobacterium necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme isolated from bovine ruminal contents and liver abscesses

Differences in biological activities (hemagglutination, hemolytic, leukotoxic, and virulence) and ribotypes between the two subspecies of Fusobacterium necrophorum of bovine ruminal and liver abscess origins were investigated. Hemagglutination activity was present in all hepatic, but only some ruminal, strains of Fusobacterium necrophorum subsp. necrophorum. Ruminal F. necrophorum subsp. necrophorum had low leukotoxin titers yet was virulent in mice. Fusobacterium necrophorum subsp. funduliforme of hepatic or ruminal origin had no hemagglutination activity, had low hemolytic and leukotoxic activities, and was less virulent to mice. For ribotyping, chromosomal DNAs of 10 F. necrophorum subsp. necrophorum and 11 F. necrophorum subsp. funduliforme isolates were digested with restriction endonucleases (EcoRI, EcoRV, SalI, PstI, and HaeIII) and examined by restriction fragment length polymorphisms after hybridizing with a digoxigenin-labeled cDNA probe transcribed from a mixture of 16 and 23S rRNAs from Escherichia coli. The most discriminating restriction endonuclease enzyme for ribotyping was EcoRI. The presence or absence of two distinct bands of 2.6 and 4.3 kb differentiated the two subspecies. Regardless of the origin, only F. necrophorum subsp. necrophorum, a virulent subspecies, had a ca. 2.6-kb band, whereas F. necrophorum subsp. funduliforme, a less virulent subspecies, had a ca. 4.3-kb band. Ribotyping appears to be a useful technique to genetically differentiate the two subspecies of F. necrophorum.

Subtyping of Shigella sonnei for tracing nosocomial transmission

Nosocomial transfer of Shigella spp. occurred between two patients sharing the patient room and toilet in a ward for internal medicine. Both patients had travelled abroad shortly before the onset of illness. Based on the epidemiology of Shigella sonnei strains imported into Finland, nosocomial infection was strongly suspected. The isolates of S. sonnei were subtyped using ribotyping, plasmid analysis and antibiotic resistance patterns. The greatest discrimination between the strains was achieved by ribotyping. The results of the typing scheme confirmed the nosocomial transmission of S. sonnei. The outbreak did not spread further within the ward. The importance of isolation of a patient with diarrhoea in a hospital setting is emphasized.

Analysis of clonal relationships among isolates of Shigella sonnei by different molecular typing methods

Shigella sonnei is a major cause of diarrheal disease in developed as well as in developing countries. Epidemiologic studies of this organism have been limited by the lack of a simple and effective method for comparing strains. In this study, we have compared different molecular typing methods, i.e., plasmid profile analysis, restriction endonuclease analysis of plasmids, rRNA gene restriction analysis (ribotyping), pulsed-field gel electrophoresis (PFGE), and enterobacterial repetitive intergenic consensus (ERIC) sequence-based PCR (ERIC-PCR) for typing 20 clinical isolates of S. sonnei collected from six incidents of infection. PFGE and ERIC-PCR fingerprintings had the highest discriminatory power for discrimination of epidemiologically related isolates from epidemiologically unrelated strains of S. sonnei, and both gave seven distinct strain types among these isolates and the type strain of the species. Plasmid study and ribotyping produced only six and typing techniques demonstrated two distinct patterns, respectively, among these strains. All of these molecular an identical fingerprint for eight temporally related sporadic isolates. It is possible that these temporally related isolates belonged to a single bacterial clone and circulated obscurely through the community. Our results indicate that the ERIC-PCR technique represents a rapid and simple means for typing S. sonnei with a level of discrimination equivalent to that of PFGE but greater than those of plasmid profile analysis, restriction endonuclease analysis of plasmids, and ribotyping.

Detection of genomic heterogeneity in Streptococcus suis isolates by DNA restriction fragment length polymorphisms of rRNA genes (ribotyping)

Whole-cell chromosomal digests of 54 isolates of Streptococcus suis encompassing all known serotypes from a geographically varied collection were examined by PstI restriction fragment length polymorphisms and then hybridized with a digoxigenin-11-dUTP-labeled cDNA probe transcribed from a mixture of 16S and 23S rRNAs from Escherichia coli MRE600. The hybridization patterns showed genetic heterogeneity within and between S. suis serotypes. Most isolates (87%) representing 28 serotypes contained a common band at approximately 1.8 kb. However, 13% of the isolates representing seven serotypes lacked the 1.8-kb band, indicating that the species as currently defined is diverse. Nonetheless, the 1.8-kb band may be a useful genotypic marker for identification of most S. suis isolates. We tested the ability of this technique to discriminate between virulent and avirulent S. suis type 2 isolates. A virulent strain of S. suis type 2 could be distinguished from avirulent strains by the presence of specific bands. No correlation was obvious between band pattern and hemolysin production.

Shigella sonnei strains isolated from U.S. summer students in Guadalajara, Mexico, from 1986 to 1992

Plasmid DNA analysis and antibiotic susceptibilities were used to study strains of Shigella sonnei isolated from U.S. travelers to Guadalajara, Mexico, over a period of seven years (1986 to 1992). One hundred sixty-one isolates were analyzed. By the use of cluster analysis, eight different plasmid profiles were identified during this interval. At any point in time, three to seven different plasmid profiles were present in this population. The introduction of strains that carried a new plasmid with a molecular mass of 5.1 MDa was coincidental with an increase in isolation of S. sonnei in 1988. This new plasmid was present in 87.5% of the isolates that were resistant to chloramphenicol. Shigellosis in Guadalajara follows a pattern of hyperendemic transmission with transient peaks of high-frequency isolation of S. sonnei. This pattern results from the concurrent presence of a heterogeneous group of strains as opposed to the widespread transmission of one or a few clones.

Use of ribotyping in epidemiological surveillance of nosocomial outbreaks

Over the past few years, genotypic methods based on the study of bacterial DNA polymorphism have shown high discriminatory power for strain differentiation and superiority over most phenotypic methods commonly available in the clinical microbiology laboratory. Some of the methods used, however, required either a high level of technology and sophisticated equipment (e.g., pulsed-field gel electrophoresis) or species-specific reagents of restricted availability (randomly cloned DNA probes or gene-specific probes). Because ribotyping uses a universal probe (rRNA) and is a rather simple technology, particularly since the advent of nonradioactive labelling systems, it has been widely used for strain differentiation of most bacterial species involved in nosocomial outbreaks. In vitro and in vivo stability of the markers studied has been demonstrated. Although there may be limitation to this approach, ribotyping was found to be highly discriminative, particularly for typing members of the family Enterobacteriaceae, Pseudomonas cepacia, and Xanthomonas maltophilia. In many cases, it has improved the understanding of the mechanism of nosocomial acquisition of organisms by allowing a distinction between endogenous and exogenous infections. Among exogenous infections, it has distinguished between individual and epidemic strains, thus differentiating cross-infection from independent acquisition.

Genetic variability and molecular typing of Shigella sonnei strains isolated in Canada

Restriction fragment length polymorphisms (RFLPs) of genomic DNAs from 49 clinical isolates of Shigella sonnei were analyzed by using a modified restriction endonuclease analysis procedure to investigate the genetic variability of this species. After cleavage with the restriction enzyme HaeIII or RsaI, DNA samples were electrophoresed in polyacrylamide gels and the RFLP patterns were visualized by silver staining. The results showed that among 20 strains associated with sporadic cases of infection in three Canadian provinces, 15 distinct RFLP patterns were revealed by HaeIII digestion and 12 distinct patterns were revealed by RsaI digestion. In contrast, the RFLP patterns of individual isolates within six groups of epidemiologically related isolates were identical to each other but distinct from those of unrelated isolates, and these patterns could be used to determine the genetic relationships between isolates associated with separate outbreaks of shigellosis. Our results indicate that the modified restriction endonuclease analysis technique represents a rapid, reproducible, and highly discriminatory method for the molecular typing of this species.

Acquisition of Pseudomonas cepacia at summer camps for patients with cystic fibrosis. Summer Camp Study Group

To assess the risk of acquisition of Pseudomonas cepacia by person-to-person transmission at cystic fibrosis summer camps, we conducted in 1990 a study at three camps attended by patients with cystic fibrosis who had P. cepacia infection and patients without P. cepacia infection but who were considered susceptible to infection. We obtained sputum or throat cultures from campers on their arrival at, weekly during, at the end of, and 14 to 30 days after camp. We compared the incidence of sputum conversion of patients at camp with that of patients outside camp by culturing specimens from noncamper control subjects with cystic fibrosis who were known not to be infected < or = 2 weeks before and 4 to 6 weeks after camp. We also determined the risk factors for P. cepacia acquisition by determining the relative risk of acquisition between campers who were exposed versus campers who were not exposed to campers known to be infected or to potential environmental sources of P. cepacia at camp. The ribotype of P. cepacia isolates from campers with sputum conversion was compared with that of isolates from other campers and from an environmental source. The cumulative incidence of sputum conversion during the study period was 6.1% (11/181) among campers compared with no incidence (0/92) among noncampers (p = 0.02, Fisher Exact Test). The incidence of sputum conversion at camp varied according to the prevalence of campers with known infection (p < 0.001, chi-square test for trend). The rate of sputum conversion was higher in the camp with longer duration (relative risk = 12.0; 95% confidence interval = 2.7 to 53.5). Ribotyping showed that P. cepacia isolates from all 11 campers with sputum conversion were identical or similar (1 to 2 band difference) to isolates of other P. cepacia-infected campers including co-converters. These results suggest that P. cepacia can be acquired by patients with cystic fibrosis who are attending summer camp for such patients, possibly through person-to-person transmission, and that the risk increases with the prevalence of P. cepacia-infected campers and the duration of camp.

Sequence variation in Shigella sonnei (Sonnei), a pathogenic clone of Escherichia coli, over four continents and 41 years

The genetic variation within a bacterial clone (known as Shigella sonnei but in effect a clone of Escherichia coli) was examined by studying 46 clinical isolates that were epidemiologically unassociated and isolated from patients in different countries over a period of 41 years (1950 to 1991). Restriction fragment length polymorphism and DNA sequencing of two housekeeping genes, mglB and gnd, in 10 strains revealed only one nucleotide substitution in the mglB gene in one strain. Ribotyping of 31 strains recovered from five countries over the 41 years proved more sensitive, detecting eight polymorphic sites with worldwide change in frequency of alleles at one site over the period studied.

Software tools and databases for bacterial systematics and their dissemination via global networks

The dynamic expansion of the taxonomic knowledge base is fundamental to further developments in biotechnology and sustainable conservation strategies. The vast array of software tools for numerical taxonomy and probabilistic identification, in conjunction with automated systems for data generation are allowing the construction of large computerised strain databases. New techniques available for the generation of chemical and molecular data, associated with new software tools for data analysis, are leading to a quantum leap in bacterial systematics. The easy exchange of data through an interactive and highly distributed global computer network, such as the Internet, is facilitating the dissemination of taxonomic data. Relevant information for comparative sequence analysis, ribotyping, protein and DNA electrophoretic pattern analysis is available on-line through computerised networks. Several software packages are available for the analysis of molecular data. Nomenclatural and taxonomic 'Authority Files' are available from different sources together with strain specific information. The increasing availability of public domain software, is leading to the establishment and integration of public domain databases all over the world, and promoting co-operative research projects on a scale never seen before.

Epidemiologic application of a standardized ribotype scheme for Vibrio cholerae O1

A standardized scheme of 27 different BglI ribotypes and subtypes of Vibrio cholerae O1 strains is proposed on the basis of data from 214 human and environmental strains isolated in 35 countries and 14 U.S. states over the past 60 years. The ribotype patterns obtained are reproducible and stable over time. Seven different but very similar ribotypes (1a to 1g) were observed among 16 strains of the classical biotype. Twenty ribotypes and subtypes were identified among 198 V. cholerae O1 strains of the El Tor biotype. Six different patterns were found among the strains causing the current seventh pandemic. Strains of ribotype 8 originated only in central African countries, while those of ribotype 3 originated mainly in Asia and the Pacific Islands. The most widely distributed strains were those of ribotype 6, which was subdivided into three very similar but still distinguishable subtypes. The present Latin American epidemic is caused by strains of ribotype 5. Strains of this ribotype were isolated from several other geographic locations but can be differentiated from the Latin American strains by other molecular methods. Strains associated with two documented environmental reservoirs exhibited three distinct ribotype patterns; those isolated from patients who ate food from the U.S. Gulf waters were all of ribotype 2, while the strains related to the northeast Australian rivers were of ribotypes 9 and 10. Nontoxigenic V. cholerae O1 strains originating in Latin America and the U.S. Gulf Coast did not form a specific cluster of ribotypes. Ribotyping in combination with other well-defined methods can assist in epidemiologic investigations, helping to trace the movement of strains and to identify their geographic origins.

Evaluation of the molecular epidemiology of an outbreak of multiply resistant Shigella sonnei in a day-care center by using pulsed-field gel electrophoresis and plasmid DNA analysis

Outbreaks of diarrhea in child day-care centers (DCC) are common. This study was undertaken to evaluate the molecular epidemiology of an outbreak of diarrhea due to Shigella sonnei. This outbreak involved 25 of 52 (48%) DCC children and 14 of 132 (11%) teachers and household contacts. S. sonnei isolates from nine children and five contacts were characterized by antimicrobial susceptibility, plasmid content, plasmid DNA restriction fragment pattern, and pulsed-field gel electrophoresis (PFGE) of total genomic DNA; 33 isolates from Houston, Tex., Chicago, Ill., and Mexico City, Mexico, also were studied. All outbreak isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole and shared five to six plasmids ranging from 3.3 to 70 MDa. A total of 8 of 12 temporally associated nonoutbreak Houston isolates had plasmid profiles and restriction fragment patterns similar to those of the outbreak strain, despite possessing different antibiotic susceptibility patterns. PFGE demonstrated identical DNA patterns among outbreak isolates and similar or identical patterns among temporally associated sporadic Houston isolates with plasmid profiles similar to that of the outbreak strain. All other nonoutbreak strains from Houston, Chicago, and Mexico had plasmid profiles, restriction fragment patterns, and PFGE patterns different from those of the outbreak strain. DCC outbreak isolates could be distinguished from most sporadic isolates by antimicrobial susceptibility testing, but plasmid analysis and PFGE could not differentiate common-source isolates from sporadic isolates in the same location during the same time period, indicating that isolates present in the community were genetically similar to those producing outbreaks in the DCC.

Molecular typing of Pseudomonas pseudomallei: restriction fragment length polymorphisms of rRNA genes

The aim of this study was to develop a typing scheme for Pseudomonas pseudomallei by comparison of patterns of restriction fragment length polymorphisms in rRNA genes (ribotyping). BamHI restriction digests of 100 isolates from various animal (34), human (58), and environmental (6) sources, including six reference strains, were hybridized to Escherichia coli 16S and 23S rRNAs. A chemiluminescent labelling and detection system was used to visualize bands. On the basis of patterns, the strains were classified into 22 different groups, with the largest containing 29 isolates. While most of the ribotypes were not exclusive to a particular source, some ribotypes were restricted to a particular geographic area or to either a human or a particular animal species. Application of the typing scheme to isolates of four independent outbreaks among animals showed that certain ribotypes predominated. The study demonstrated ribotyping to be a useful tool in epidemiological investigations of melioidosis.

rRNA gene restriction patterns and biotypes of Shigella sonnei

Shigella sonnei is a major agent of diarrhoeal disease in developed as well as in developing countries. Several phenotypic methods to define strain differences have been applied to this species of Shigella including, more recently, analysis of extrachromosomal and chromosomal DNA. In this study, 432 endemic and epidemic strains isolated between 1975 and 1991 in Italy, France and Switzerland were submitted to rRNA gene restriction pattern analysis, after digestion of whole-cell DNA by Hinc II, and to concomitant biotyping. Thirteen ribotypes, H1 to H13, and five biotypes, a, d, e, f, g, were detected. Ninety-five percent of the sporadic strains were assigned to ribotypes H1 to H4, which could be subtyped, except for H4, in different biotypes. Strains from each of seven different outbreaks had indistinguishable ribotype-biotype patterns. In contrast, 65 strains, isolated in Sicily in 1980 over an extended period of apparently epidemic increase of isolations and which had previously been considered to be a single bacterial clone on the basis of resistance pattern and phage type, were found to belong to two different and scarcely related ribotypes. Ribotyping and biochemical subtyping appear to be a useful epidemiological tool in studies on the circulation and distribution of strains of S. sonnei.

Molecular epidemiology of Shigella infections in Israel

The DNAs of Shigella sonnei or Shigella dysenteriae type 1 strains isolated in outbreaks of shigellosis or in sporadic cases were analysed by restriction fragment length polymorphism (RFLP). Southern blots of the DNAs of 36 S. sonnei isolates digested by 8 restriction enzymes were hybridized with an Escherichia coli rRNA probe. The S. sonnei strains were unexpectedly diverse in their RFLP. Antibiotypes of the same isolates showed clusters of strains corresponding to the various outbreaks. On the other hand, RFLP analysis suggested concomitant multiple sources of infection rather than a common source and thereby introduced a new insight in the epidemiology of shigellosis. RFLP was also used to trace S. dysenteriae type 1 transmission in a recent cluster of clinical cases. Although antibiotic resistance patterns indicated the presence of more than one strain, RFLP analysis showed that the six isolates were identical clones and suggested the loss of an R episome after one person-to-person passage.

Differentiation of Shigella flexneri strains by rRNA gene restriction patterns

We studied the restriction endonuclease cleavage patterns of rRNA genes (ribotypes) of 72 clinical isolates of Shigella flexneri representing eight serotypes to determine whether ribotyping could be used to distinguish S. flexneri strains and to compare the discriminating ability of the method with that of serotyping. By using a cloned Escherichia coli rRNA operon as the probe, Southern blot hybridization of restriction endonuclease-digested total DNA was carried out. Ribotyping of the isolates with each of the five restriction endonucleases BamHI, EcoRI, HindIII, PstI, and SalI generated reproducible restriction patterns. However, HindIII produced the optimum digestion pattern of the rRNA genes and was more useful than the other enzymes used in differentiating strains. Analysis of the 72 isolates showed 11 different HindIII cleavage patterns of their rRNA genes. Four of these HindIII-generated ribotypes could be further differentiated into two to four subribotypes by using PstI. The results indicate that ribotyping has an application for differentiation of S. flexneri strains and can complement serotyping. Definition of strains in terms of both serotype and ribotype may be of greater use in epidemiological studies.