Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis

Genome fingerprinting by pulsed-field gel electrophoresis of isolates of Burkholderia pseudomallei from patients with melioidosis in Thailand

A total of 95 isolates of Burkholderia pseudomallei from 53 sporadic cases in Thailand were examined by pulsed-field gel electrophoresis. Digestion of genomic DNA of all isolates by NcoI generated a macrorestriction pattern similar to that of B. pseudomallei which cannot assimilate L-arabinose. Analysis using restriction enzymes SpeI and AvrII demonstrated greater sensitivity than NcoI digestion in the differentiation of B. pseudomallei and could be used for epidemiological groupings. Four cluster groups were evident among 37 isolates tested and the majority of isolates within each cluster displayed more than 65% similarity. Furthermore, multiple isolates from 18 and 35 patients with single and recurrent episodes of melioidosis, respectively, were examined. All patients with a single episode yielded genetically identical isolates and four of 35 patients with recurrent episodes were infected with strains of different genotypic patterns from the primary isolate(s). Hence, most repeated episodes of infection in melioidosis are as a result of the original infecting strains.

Epidemic typhoid in vietnam: molecular typing of multiple-antibiotic-resistant Salmonella enterica serotype typhi from four outbreaks

Multidrug-resistant Salmonella enterica serotype Typhi isolates from four outbreaks of typhoid fever in southern Vietnam between 1993 and 1997 were compared. Pulsed-field gel electrophoresis, bacteriophage and plasmid typing, and antibiotic susceptibilities showed that independent outbreaks of multidrug-resistant typhoid fever in southern Vietnam are caused by single bacterial strains. However, different outbreaks do not derive from the clonal expansion of a single multidrug-resistant serotype Typhi strain.

Molecular methods for the epidemiological typing of Salmonella enterica serotype Typhi from Hong Kong and Vietnam

A total of 217 and 73 strains of Salmonella enterica serotype Typhi isolated from 1985 to 1997 in Hong Kong and in 2 months of 1989 and 1990 in Vietnam, respectively, were studied. These isolates were typed by plasmid profile analysis, plasmid fingerprinting, ribotyping with PstI, and total DNA fingerprinting with NarI. There appeared to be no major outbreak of typhoid fever in Hong Kong during the study period since there was considerable heterogeneity among the isolates. Isolates from Hong Kong were different from those from Vietnam. Thirty-seven percent of Vietnamese isolates belonged to two predominant clones, with the rest being heterogeneous in nature. Total DNA fingerprinting supplemented with ribotyping could be a reliable and rapid method for epidemiological typing of S. enterica serotype Typhi.

Characterization of extended-spectrum beta-lactamase-producing Salmonella typhimurium by phenotypic and genotypic typing methods

During 1994, 10 isolates of extended-spectrum beta-lactamase-producing Salmonella typhimurium were recovered from children transferred to our hospital from two different centers. Two additional isolates were recovered from two nurses from one of these centers. The aim of this study was to determine if there is any relationship between these isolates. The characterization was done by phenotypic and genotypic methods: biotyping, phage typing, antibiotic susceptibility pattern determination, plasmid analysis, ribotyping (by the four endonucleases EcoRI, SmaI, BglII, and PvuII), pulsed-field gel electrophoresis (PFGE) of genome macrorestriction patterns with XbaI, and randomly amplified polymorphic DNA (RAPD) pattern determination (with the three primers 217 d2, B1, and A3). The same biotype, the same serotype, and an identical antibiotype were found. All isolates were resistant to oxyimino-beta-lactams, gentamicin, tobramycin, and sulfamethoxazole-trimethoprim. All isolates showed an indistinguishable pattern by ribotyping and very similar patterns by PFGE and RAPD. The overall results indicated the spread of a closely related strain of S. typhimurium in children and nurses.

Differences in genomic macrorestriction patterns of arabinose-positive (Burkholderia thailandensis) and arabinose-negative Burkholderia pseudomallei

We reported previously two biochemically and antigenically distinct biotypes of Burkholderia pseudomallei. These two distinct biotypes could be distinguished by their ability to assimilate L-arabinose. Some B. pseudomallei isolated from soil samples could utilize this substrate (Ara+), whereas the other soil isolates and all clinical isolates could not (Ara-). Only the Ara isolates were virulent in animals and reacted with monoclonal antibody directed at the surface envelope, most likely the exopolysaccharide component. In the present study, pulsed-field gel electrophoresis was employed for karyotyping of these previously identified B. pseudomallei strains. We demonstrate here that the DNA macrorestriction pattern allows the differentiation between B. pseudomallei, which can assimilate L-arabinose, and the proposed B. thailandensis, which cannot do so. Bacterial strains from 80 melioidosis patients and 33 soil samples were examined by genomic DNA digestion with NcoI. Two major reproducible restriction patterns were observed. All clinical (Ara-) isolates and 9 Ara- soil isolates exhibited macrorestriction pattern I (MPI), while 24 soil isolates (Ara+) from central and northeastern Thailand displayed macrorestriction pattern II (MPII). The study here demonstrated pulsed-field gel electrophoresis to be a useful tool in epidemiological investigation possibly distinguishing virulent B. pseudomallei from avirulent B. thailandensis or even identifying closely related species of Burkholderia.

Molecular typing of multiple-antibiotic-resistant Salmonella enterica serovar Typhi from Vietnam: application to acute and relapse cases of typhoid fever

The rate of multiple-antibiotic resistance is increasing among Salmonella enterica serovar Typhi strains in Southeast Asia. Pulsed-field gel electrophoresis (PFGE) and other typing methods were used to analyze drug-resistant and -susceptible organisms isolated from patients with typhoid fever in several districts in southern Vietnam. Multiple PFGE and phage typing patterns were detected, although individual patients were infected with strains of a single type. The PFGE patterns were stable when the S. enterica serovar Typhi strains were passaged many times in vitro on laboratory medium. Paired S. enterica serovar Typhi isolates recovered from the blood and bone marrow of individual patients exhibited similar PFGE patterns. Typing of S. enterica serovar Typhi isolates from patients with relapses of typhoid indicated that the majority of relapses were caused by the same S. enterica serovar Typhi strain that was isolated during the initial infection. However, some individuals were infected with distinct and presumably newly acquired S. enterica serovar Typhi isolates.

Bacterial fingerprinting by flow cytometry: bacterial species discrimination

BACKGROUND

A flow cytometric measurement (FCM) technique has been developed to size DNA fragments. Individual fragments of a restriction digest of genomic DNA, stained with an intercalating dye, are passed through an ultrasensitive cytometer. The measured fluorescence intensity from each fragment is proportional to the fragment length.

METHODS

The isolation of bacterial genomic DNA and digestion by restriction enzymes were performed inside an agarose plug. Rare cutting enzymes were employed to produce a manageable number of DNA fragments. Electroelution was used to move the DNA fragments from the agarose plug into a solution containing polyamines to protect the DNA from shear-induced breakage. The DNA was stained with the bisintercalating dye thiazole orange homodimer and introduced into our ultrasensitive flow cytometer. A histogram of the fluorescence intensities (fingerprint) was constructed.

RESULTS

Gram-positive Bacillus globigii and gram-negative bacteria Escherichia coli and Erwinia herbicola were distinguished by the fingerprint pattern of restriction fragments of their genomic DNA. DNA sizes determined by FCM are in good agreement with pulsed-field gel electrophoresis (PFGE) analysis. Flow cytometry requires only picogram quantities of purified DNA and takes less than 10 min for data collection and analysis. When the total sample preparation time is included, the analysis times for PFGE and FCM are similar ( approximately 3 days).

CONCLUSIONS

FCM is an attractive technique for the identification of bacterial species. It is more sensitive and potentially much faster than PFGE.

Salmonella enteritidis phage types 1 and 4: pheno- and genotypic epidemiology of recent outbreaks in Finland

In the 1990s, Salmonella enterica subsp. enterica serovar Enteritidis has caused 15 outbreaks in Finland; 12 of them were caused by phage type 1 (PT1) and PT4. Thus far, there has been no clear evidence as to the source of these Salmonella Enteritidis PT1 and PT4 strains, so it was necessary to try to characterize them further. Salmonella Enteritidis PT1 (n = 57) and PT4 (n = 43) isolates from different sources were analyzed by genomic pulsed-field gel electrophoresis (PFGE), plasmid profiling, and antimicrobial resistance testing to investigate the distribution of their subtypes in Finland. It was also hoped that this investigation would help in identifying the sources of the infections, especially the sources of the outbreaks caused by PT1 and PT4 in the 1990s. The results showed that both PFGE and plasmid profiling, but not antimicrobial susceptibility testing, were capable of differentiating isolates of Salmonella Enteritidis PT1 and PT4. By genotypic methods, it was possible to divide both PT1 and PT4 isolates into 12 subtypes. It could also be shown that all PT1 outbreak isolates were identical and, at least with this collection of isolates, that the outbreaks did not originate from the Baltic countries or from Russia, where this phage type predominates. It was also established that the outbreaks caused by PT4 all had different origins. Valuable information for future investigations was gained on the distribution of molecular subtypes of strains that originated from the tourist resorts that are popular among Finns and of strains that were isolated from livestock.

Early detection of typhoid by polymerase chain reaction

BACKGROUND

Typhoid is a common problem in developing countries. Cultivation of bacteria and serology (especially Widal test) give unacceptable levels of false-negative and false-positive results, respectively.

PATIENTS AND METHODS

In this study, a recently introduced polymerase chain reaction-based technique (which has 100% specificity for Salmonella typhi) was compared with blood culture and Widal test during the first week of illness of 82 suspected cases of typhoid.

RESULTS

The respective figures of positivity for PCR, blood culture and Widal test were 71.95%, 34.1%, and 36.5%. A control group of 20 healthy persons gave figures of 0%, 0%, and 33.3%, respectively.

CONCLUSION

We conclude that this PCR-based technique is not only absolutely specific, but also very sensitive and, therefore, much superior to blood culture and Widal test for the early diagnosis of typhoid.

Assessment of strain relatedness among Salmonella serotypes Salinatis, Duisburg, and Sandiego by biotyping, ribotyping, IS200 fingerprinting, and pulsed-field gel electrophoresis

Salinatis (antigenic formula, 4,12:d:eh:enz15) is a rare Salmonella serotype currently designated a triphasic variant of the diphasic serotype Duisburg (1,4,12,27:d:enz15) (underlining indicates that the O antigen is determined by phage lysogenization). Salinatis could also be related to serotype Sandiego (4,[5],12:eh:enz15), from which it might have been derived by loss of H-d flagellin genes. Nineteen Salmonella strains of serotypes Salinatis, Duisburg, and Sandiego were examined by biotyping, PvuII and SmaI ribotyping, IS200 fingerprinting, and pulsed-field gel electrophoretic profiling. Results from these methods, used alone or together, indicate that serotype Salinatis is more likely to be related to serotype Sandiego than to serotype Duisburg. For future lists of serotype names, it is recommended that Salinatis be considered a variant of Sandiego.

Use of pulsed field gel electrophoresis as an epidemiological tool for analysis of sporadic associated strains of Salmonella typhi isolated in Taiwan

In order to characterize the subtypes of Salmonella typhi which cause sporadic disease in Taiwan, 55 isolates of Salm. typhi obtained from unrelated patients of sporadic cases during 1992-96 were subjected to chromosomal DNA digestion and pulsed field gel electrophoresis (PFGE). When DNAs of these 55 Salm. typhi strains were digested with XbaI, 41 PFGE patterns were observed. Strains sharing the same XbaI digestion pattern could not be further discriminated by PFGE analysis using SpeI and NotI as digestion enzymes. Thus, considerable genetic diversity exists among the Salm. typhi isolates. Although strains of the same patterns were mainly isolated during the same time, recirculation of certain infectious strains could be possible. When 12 antibiotics, i.e. ampicillin, trimethoprim/sulfamethoxazole, erythromycin, norfloxacin, tetracycline, sulphonamide, streptomycin, neomycin, chloramphenicol, kanamycin, cefoperazone and gentamycin were used to test the antibiotic susceptibility for these Salmonella isolates, only three antibiogram patterns were obtained and 49 of the 55 Salm. typhi isolates were found to belong to one pattern. Phage typing and plasmid profiles were also poor in discriminating these strains. Thus, PFGE alone may be used as a powerful tool for analysis of sporadic associated Salm. typhi strains.

Genotype analysis of Escherichia coli strains isolated from children and chickens living in close contact

Escherichia coli isolates from rectal swabs from 62 chickens and stools from 42 children living in close contact with chickens on the same farms in Kiambu district, Kenya, were compared for their genetic relatedness. Antibiotic susceptibility profiles broadly categorized isolates from the children and from the chickens into two separate clusters: the majority (144; 85.5%) of the E. coli isolates from children were multidrug resistant, while the majority (216; 87.1%) of the E. coli isolates from chickens were either fully susceptible or resistant only to tetracycline. Sixty- and 100- to 110-MDA plasmids were found to encode the transferable resistance to co-trimoxazole and tetracycline. HindIII restriction endonuclease digestion of the 60- and 100- to 110-MDA plasmids produced four distinct patterns for isolates from children and three distinct patterns for isolates from chickens. XbaI digestion of genomic DNA followed by pulsed-field gel electrophoresis (PFGE) analysis produced 14 distinct clusters. There were six distinct PFGE clusters among the isolates from children, while among the isolates from chickens there were seven distinct clusters. Only one PFGE cluster contained isolates from both children and chickens, with the isolates displaying an approximately 60% coefficient of similarity. This study showed that although several different genotypes of E. coli were isolated from children and chickens from the same farms, the E. coli strains from these two sources were distinct.

Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella typhi and other Salmonella species

A Random Amplified Polymorphic DNA (RAPD) fingerprinting method was developed to differentiate isolates of Salmonella serotype typhi (S. typhi) and other Salmonella isolates. A panel of five primers was used to examine 63 isolates of Salm. typhi, including 56 strains isolated in Taiwan and seven strains obtained abroad. Twenty-one RAPD types were revealed using the RAPD fingerprinting method. An RAPD with primer 6032 yielded a polymorphism in a 350 bp fragment that differentiated the attenuated vaccine strain Salm. typhi Ty21a from the rest of the Salm. typhi strains. Strains of Salm. typhi were divided into five types with primer D14307. Primer D14307 also proved capable of discrimination among 65 other Salmonella isolates representing 42 different serotypes. The bacterial DNA used in this RAPD protocol was obtained using a commercially available DNA extraction kit (GeneReleaser). The DNA of various strains of Salmonella from this simple extraction procedure could be discriminated within a few hours using the RAPD technique.

Multiple analysis of a foodborne outbreak caused by infant formula contaminated by an atypical Salmonella virchow strain

An outbreak of food poisoning involving most autonomous Spanish communities was detected in the first half of 1994. The causative food was infant formula milk contaminated by lactose-fermenting Salmonella virchow. It was not possible to isolate the causative strain from the manufacturer's facilities. During the same period of time, there was a significant increase in lactose-non-fermenting Salmonella virchow strains compared with the same period in previous years. Simultaneously, lactose-non-fermenting strains were recovered from clinical samples from children and from some milk samples that were involved in the outbreak. Therefore, it was speculated that the outbreak might be more extensive than initially thought. The following epidemiological markers were used for typing the Salmonella virchow strains involved in the outbreak: (i) phage typing: (ii) ribotyping, using a set of 20 different endonucleases: and (iii) pulsed-field gel electrophoresis, using three different endonucleases. The most useful markers for this serotype were phage typing and pulsed-field gel electrophoresis, since ribotyping was not able to distinguish all strains tested. The results obtained revealed that the outbreak was caused by at least two strains: one presenting phage type 4-4a and pulsed-field patterns A1 or A2 and L+ or L-, and another presenting phage type 2 and pulsed-field patterns A1 or A2 and L+ or L-. The results indicate that the outbreak was more extensive than initially thought and that the Virchow serotype is very clonal in Spain.

Virulence determinants of uropathogenic Escherichia coli in fecal strains from intestinal infections and healthy individuals

Twenty-five fecal Escherichia coli strains of serogroups O6 and O18 from patients with and without intestinal infections were analyzed for fimbrial adhesins pap, prs and sfa, hemolysin, cytonecrotic factor, colicins, capsules, antibiotic resistances, plasmid content and some plasmid encoded characteristics. A high percentage of strains expressing P fimbriae was found with an even higher percentage in strains isolated from intestinal infections. A correlation was found between colicinogenicity and P fimbriae production. None of the strains produced hemolysin while 28% had cytonecrotic factor type 1 sequences, demonstrating that cytonecrotic factor type 1 is not always associated with hemolysin production and indicating that the examined strains do not harbor a larger pathogenicity island. Plasmids and plasmid associated characteristics were more frequently associated with the O18 serogroup and chromosomal colicin V genes were found independently of plasmids.

Epidemiologic study of Shigella sonnei from sequential outbreaks and sporadic cases using different typing techniques

We noted that eight outbreaks of Shigella sonnei from an unknown source occurred sequentially in Aichi Prefecture, Japan, between October 1992-June 1993. For comparative purposes we analyzed 53 outbreak-related isolates of Shigella sonnei using different subtyping methods and studied the epidemiology of the outbreaks. It appeared from our study that DNA-based techniques such as plasmid typing and pulsed-field gel electrophoresis (PFGE) were more useful tools for subtyping Shigella sonnei than colicin typing and the antimicrobial susceptibility test. Moreover, according to PFGE analysis, four genetically related isolates of Shigella sonnei were responsible for the eight sequential outbreaks. To further investigate the epidemiology of outbreaks, 58 sporadic isolates of Shigella sonnei from overseas travelers with shigellosis during the same period were also examined. We found that some sporadic isolates from travelers in Asia were genetically related to those of the outbreak-related isolates, indicating that genetically related isolates prevailed in Asia during this period, probably because of the extensive movement of people or food.

Molecular analysis of and identification of antibiotic resistance genes in clinical isolates of Salmonella typhi from India

A representative sample of 21 Salmonella typhi strains isolated from cultures of blood from patients at the Christian Medical College and Hospital, Vellore, India, were tested for their susceptibilities to various antimicrobial agents. Eleven of the S. typhi strains possessed resistance to chloramphenicol (256 mg/liter), trimethoprim (64 mg/liter), and amoxicillin (>128 mg/liter), while four of the isolates were resistant to each of these agents except for amoxicillin. Six of the isolates were completely sensitive to all of the antimicrobial agents tested. All the S. typhi isolates were susceptible to cephalosporin agents, gentamicin, amoxicillin plus clavulanic acid, and imipenem. The antibiotic resistance determinants in each S. typhi isolate were encoded by one of four plasmid types. Plasmid-mediated antibiotic resistance genes were identified with specific probes in hybridization experiments; the genes responsible for chloramphenicol, trimethoprim, and ampicillin resistance were chloramphenicol acetyltransferase type I, dihydrofolate reductase type VII, and TEM-1 beta-lactamase, respectively. Pulsed-field gel electrophoresis analysis of XbaI-generated genomic restriction fragments identified a single distinct profile (18 DNA fragments) for all of the resistant isolates. In comparison, six profiles, different from each other and from the resistance profile, were recognized among the sensitive isolates. It appears that a single strain containing a plasmid conferring multidrug-resistance has emerged within the S. typhi bacterial population in Vellore and has been able to adapt to and survive the challenge of antibiotics as they are introduced into clinical medicine.

The use of pulsed-field gel electrophoresis for subdivision of Salmonella typhimurium in an outbreak situation

An institutional outbreak of gastroenteritis provided an opportunity to investigate further the isolates of Salmonella typhimurium by pulsed-field gel electrophoresis (PFGE). Three phage types were identified. Antibiograms identified two types and two distinct patterns were found on PFGE. If phage typing alone is used for epidemiological study of strains, it is possible that an association between strains may be missed.

Utilization of both phenotypic and molecular analyses to investigate an outbreak of multidrug-resistant Salmonella anatum in horses

Phenotypic and molecular techniques, including antimicrobial susceptibility testing, plasmid analysis, and pulsed-field gel electrophoresis (PFGE) were used to characterize 15 isolates of multidrug-resistant (MDR) Salmonella anatum cultured during a 16 mo period from horses and a veterinary clinic environment. The isolates were resistant to multiple antimicrobial agents and could be placed into 4 groups based on their antimicrobial resistance patterns. The isolates contained multiple plasmids ranging in size from 2 to > 100 kb that could be grouped into 3 different plasmid profile patterns; these patterns did not correlate with the antimicrobial resistance groupings. Furthermore, antimicrobial resistance was conjugatively transferable. Digestion of genomic DNA from the 15 isolates with 3 different restriction endonucleases, SfiI, SpeI, and XbaI followed by PFGE revealed a highly conserved restriction endonuclease digestion pattern. In contrast, diverse banding patterns were observed with S. anatum obtained from other sources. These observations suggest that the MDR S. anatum isolates represent a common outbreak strain even though they possess different, albeit similar, antibiograms and plasmid profiles. The study showed that PFGE is a useful epidemiological tool for discriminating between unrelated and outbreak-related strains of S. anatum. In conclusion, epidemiological studies of outbreaks caused by MDR isolates of S. anatum should consist of both genotypic and phenotypic methods of analysis.

Genome size variation among recent human isolates of Salmonella typhi

We performed genome size estimation of 17 recent human isolates of Salmonella typhi from geographically diverse regions using pulsed-field gel electrophoresis (PFGE) after digestion of chromosomal DNA with restriction endonucleases XbaI (5'-TCTAGA-3'), AvrII (5'-CCTAGG-3') and SpeI (5'-ACTAGT-3'), and summation of the sizes of restriction fragments obtained. All 17 isolates had circular chromosomes, and genome sizes differed by as much as 959 kb, ranging from 3,964 to 4,923 kb (mean genome size = 4,528 kb). The data obtained confirm the usefulness of PFGE in studies of bacterial genome size and are in agreement with recent results indicating considerable genetic diversity and genomic plasticity of S. typhi. The variation in genome sizes noted may be relevant to the observed biological properties of this important human pathogen, including its virulence.

Antimicrobial resistance pattern and plasmid profile of Salmonella typhi isolated from an outbreak in Tehran province

The antimicrobial resistance patterns and plasmid profiles of Salmonella typhi isolates from sporadic cases (n = 33) and an outbreak (n = 48) were compared. Of 28 sporadic drug-resistant isolates, 24 (85.7%) were multiply resistant. The predominant antibiotic resistance pattern was TeCmSmSxTAp, which was also the most common pattern of the outbreak isolates. 13 drug-resistant strains isolated before the outbreak (46.4%) were able to transfer the whole resistance pattern or part of it to Escherichia coli K 12 by conjugation. Although 20 of the sporadic strains contained plasmid DNA, transferable R plasmids were only detected in 13 (65%) of them. Among the outbreak strains, the rate of R plasmid transfer was 92.3%, with only the TeCmSmSxTAp pattern transferred. Plasmid profiling and Hind III endonuclease digestion of plasmid DNA identified a 91.2 megadaltons (Mda) plasmid that was recovered from most of the outbreak isolates and from 4 strains collected before the outbreak. This plasmid coded for TeCmSmSxtAp and transferred the pattern of resistance in toto. The results indicate multidrug-resistant S. typhi as a potential cause of infection in the region.

Molecular typing of Salmonella enterica serovar typhi

The efficiencies of different tests for epidemiological markers--phage typing, ribotyping, IS200 typing, and pulsed-field gel electrophoresis (PFGE)--were evaluated for strains from sporadic cases of typhoid fever and a well-defined outbreak. Ribotyping and PFGE proved to be the most discriminating. Both detected two different patterns among outbreak-associated strains.

Pulsed-field gel electrophoresis indicates genotypic heterogeneity among Campylobacter upsaliensis strains

To determine the genomic relatedness among a selection of animal and human Campylobacter upsaliensis isolates, macrorestriction profiles were generated for 20 C. upsaliensis strains, among 7 serogroups, using pulsed-field gel electrophoresis (PFGE). XhoI, SalI and SacII restriction enzyme profiles indicated genomic heterogeneity among strains. Using XhoI and SacII restriction enzyme digestion, genomic similarities between some pairs of strains were Lior serogroup specific. The genomic sizes of these isolates varied from 1.74 to 2.09 Mb. These results demonstrate molecular heterogeneity of this species similar to that found among Helicobacter pylori isolates. Among C. upsaliensis strains, PFGE is highly discriminatory and should prove a useful molecular typing method for epidemiological purposes.

Epidemic typhoid in Chile: analysis by molecular and conventional methods of Salmonella typhi strain diversity in epidemic (1977 and 1981) and nonepidemic (1990) years

From 1977 to 1986, Chile experienced an important typhoid fever epidemic, despite statistics that indicated apparently improving levels of sanitation of drinking water and sewage disposal. The lack of antibiotic resistance among the Salmonella typhi strains isolated during this period, the mild clinical presentation of the disease, and the initially low level of efficacy of the S. typhi Ty21a vaccine in the population exposed to the epidemic suggested that this epidemic might have resulted from the dissemination of S. typhi strains with unique characteristics. To investigate this hypothesis, we used conventional methods (bacteriophage typing and biotyping) and molecular methods (restriction fragment length polymorphism analysis, ribotyping, IS200 typing, and PCR amplification of the fliC-d gene) to study a population of 149 S. typhi isolates during 1977, 1981, and 1990, the years that included periods with low (when the disease was endemic) and high (when the disease was epidemic) morbidities. Our results indicate that these S. typhi isolates in Chile represent a number of highly diverse variants of the clone of S. typhi with a worldwide distribution described by Selander et al. (R. K. Selander, P. Beltran, N.H. Smith, R. Helmuth, F.A. Rubin, D.J. Kopecko, K. Ferris, B.D. Tall, A. Cravioto, and J.M. Musser, Infect. Immun. 58:2262-2275, 1990). For example, we detected 26 PstI and 10 ClaI ribotypes among 47 and 16 S. typhi strains belonging to this clone, respectively. These results suggest that the Chilean epidemic was probably produced by multiple sources of infection because of deficient sanitary conditions. These findings illustrate the usefulness of molecular methods for characterizing the potential causes of the typhoid epidemics and the possible routes of transmission of S. typhi strains in typhoid epidemics.

Molecular analysis of isolates of Salmonella typhi obtained from patients with fatal and nonfatal typhoid fever

Molecular characterization of a total of 52 human isolates of Salmonella typhi from Papua New Guinea was performed by using pulsed-field gel electrophoresis (PFGE) after digestion of chromosomal DNA with three restriction endonucleases, XbaI (5'-TCTAGA-3'), AvrII (5'-CCTAGG-3'), and SpeI (5'-ACTAGT-3'). Of the 52 isolates tested, 11 were obtained from patients with fatal typhoid fever and 41 were obtained from patients with nonfatal disease. The 52 isolates showed limited genetic diversity as evidenced by only three different PFGE patterns detected following digestion with XbaI (patterns X1 to X3; F [coefficient of similarity] = 0.86 to 1.0), four patterns detected following digestion with AvrII (patterns A1 to A4; F =0.78 to 1.0), and two patterns detected following digestion with SpeI (patterns S1 and S2; F = 0.97 to 1.0). Of the 52 isolates, 37 were phage typed, and all belonged to phage type D2. All 11 isolates obtained from patients with fatal typhoid fever were identical (F = 1.0) and possessed the PFGE pattern combination X1S1A1, whereas the 41 isolates from patients with nonfatal typhoid fever had various PFGE pattern combinations, the most common being X2S1A2 (39%), X1S1A1 (24%), and X1S1A2 (15%). Thus, all the isolates from patients with the fatal disease had the X1 and A1 patterns, whereas the majority of the isolates from patients with nonfatal typhoid fever possessed the X2 and A2 patterns. The data suggest that there is an association among strains of S. typhi between genotype, as assessed by PFGE patterns, and the capability to cause fatal illness. Analysis of blood and fecal isolates of S. typhi from the same patient also indicated that some genetic changes occur in vivo during the course of infection.

Evaluation and comparison of molecular techniques for epidemiological typing of Salmonella enterica subsp. enterica serovar dublin

A total of 28 unrelated isolates of the Salmonella enterica subsp. enterica serovar dublin (S. dublin) collected during a 6-year period, as well as four samples of the S. dublin live vaccine strain Bovisaloral and its prototype strain S. dublin 442/039, were investigated by different molecular typing methods for the following reasons: (i) to find the most discriminatory method for the epidemiological typing of isolates belonging to this Salmonella serovar and (ii) to evaluate these methods for their capacity to discriminate among the live vaccine strain Bovisaloral, its prototype strain S. dublin 442/039, and field isolates of the serovar dublin. Five different plasmid profiles were observed; a virulence plasmid of 76 kbp as identified by hybridization with an spvB-spvC gene probe was present in all isolates. The detection of 16S rRNA genes and that of IS200 elements proved to be unsuitable for the epidemiological typing of S. dublin; only one hybridization pattern could be observed with each of these methods. The results obtained from macrorestriction analysis strongly depended on the choice of restriction enzyme. While the enzyme NotI yielded the lowest discriminatory index among all enzymes tested, it was the only enzyme that allowed discrimination between the Bovisaloral vaccine strain and its prototype strain. In contrast to the enzymes XbaI and SpeI, which only differentiated among the S. dublin field isolates, XhoI as well as AvrII also produced restriction fragment patterns of the Bovisaloral strain and of its prototype strain that were not shared by any of the S. dublin field isolates. Macrorestriction analysis proved to be the most discriminatory method not only for the epidemiological typing of S. dublin field isolates but also for the identification of the S. dublin live vaccine strain Bovisaloral.

Molecular analysis of environmental and human isolates of Salmonella typhi

Molecular characterization of a total of 54 isolates of Salmonella typhi from Santiago, Chile, was performed by pulsed-field gel electrophoresis (PFGE) after digestion of chromosomal DNA with three restriction endonucleases: XbaI (5'-TCTAGA-3'), AvrII (5'-CCTAGG-3'), and SpeI (5'-ACTAGT-3'). Thirteen of the 54 isolates were obtained from environmental sources (sewage and river water), and the rest were isolates from clinical cases of typhoid fever. Considerable genetic diversity was detected among the human isolates obtained in 1994, as evidenced by the presence of 14 to 19 different PFGE patterns among 20 human isolates, with F (coefficient of similarity) values ranging from 0.69 to 1.0 (XbaI), 0.61 to 1.0 (AvrII), and 0.70 to 1.0 (SpeI). A total of eight phage types were detected among these 20 isolates, with 50% possessing the E1 or 46 phage type. There was no correlation between PFGE pattern and phage types. Similar diversity was seen among 21 isolates obtained in 1983, with 17 to 19 PFGE patterns detected and F values of 0.56 to 1.0 (XbaI), 0.55 to 1.0 (AvrII), and 0.67 to 1.0 (SpeI). Comparison of these two groups of human isolates obtained 11 years apart indicated that certain molecular types of S. typhi are shared and are able to persist for considerable periods. A similar degree of genetic diversity was also detected among the environmental isolates of S. typhi, for which 10 to 12 different PFGE patterns were detected among the 13 isolates analyzed, with F values ranging from 0.56 to 1.0 (XbaI), 0.52 to 1.0 (AvrII), and 0.69 to 1.0 (SpeI). Certain molecular types present among the environmental isolates of S. typhi were also found among the human isolates from the same time period, providing evidence for the epidemiological link between environmental reservoirs and human infection.

Comparison of PFGE, ribotyping and phage-typing in the epidemiological analysis of Campylobacter jejuni serotype HS2 infections

In this study we have evaluated the ability of three typing methods, pulsed field gel electrophoresis (PFGE), phage-typing and ribotyping, to discriminate not only between strains of differing serotypes but also between strains within a single serotype, heat stable serotype 2 (HS2). Forty-five isolates derived from cases of campylobacter enteritis occurring in the Cardiff area were examined. These included 18, mostly HS2, strains associated with an outbreak. The typing results for these and a further 39 epidemiologically unrelated strains of serotype HS2 were compared. This is the first report documenting the use of PFGE in an epidemiological investigation of Campylobacter jejuni in the UK. The results presented suggest that this technique is the most discriminatory of the three subtyping methods examined.

Genomic cleavage map of Salmonella typhi Ty2

The genomic cleavage map of Salmonella typhi Ty2, 4,780 kb in size, was determined through digestion of the genomic DNA with endonucleases and separation of the fragments by pulsed-field gel electrophoresis. The chromosome has 33, 26, 7, and 35 sites for the enzymes XbaI, BlnI, I-CeuI, and SpeI, respectively. The fragments were arranged around the chromosome through excision of fragments from the gel, redigestion with a second enzyme, and labelling with 32P, and reelectrophoresis and named in alphabetical order. Tn10 transposons inserted in 82 different genes of Salmonella typhimurium were transduced by phage P22 into S. typhi, and the location of Tn10, and thus of the gene, was mapped through the XbaI and BlnI sites of Tn10. All seven I-CeuI sites (in rrl genes for 23S rRNA) were conserved, and the gene order within the I-CeuI fragments resembles that of S. typhimurium LT2, but the order of I-CeuI fragments is rearranged from ABCDEFG in S. typhimurium LT2 to AGCEFDB in S. typhi. In addition, there is a 500-kb inversion which covers the terminus region. Comparisons of lengths of segments between genes showed that S. typhi has segments which differ in size from those in S. typhimurium. The viaB locus, for synthesis of the Vi antigen of S. typhi, was shown to be within a 118-kb loop (a segment of DNA with no homolog in most other Salmonella species) between mel and poxA on the chromosome.

Analysis of Salmonella typhi isolates from Southeast Asia by pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis (PFGE) revealed that multiple genetic variants of Salmonella typhi are simultaneously present in Southeast Asia and are associated with sporadic cases of typhoid fever and occasional outbreaks. Comparative analysis of PFGE patterns also suggested that considerable genetic diversity exists among S. typhi strains and that some PFGE patterns are shared between isolates obtained from Malaysia, Indonesia, and Thailand, implying movement of these strains within these regions of Southeast Asia, where they are endemic.

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.

Comparison of macrorestriction analysis of genomic DNA by pulsed-field gel electrophoresis and ribotyping with conventional methods for differentiation of Escherichia coli 0124 isolates

OBJECTIVE: To evaluate the usefulness of different phenotypic and genotypic markers for epidemiological typing of enteroinvasive Escherichia coli 0124 (EIEC 0124). METHODS: Seven sporadic EIEC 0124 isolates and 22 isolates from two different outbreaks were characterized. Chromosomal deoxyribonucleic acid (DNA) macrorestriction analysis with XbaI resolved by pulsed-field gel electrophoresis (PFGE) and ribotyping with each of the three restriction endonucleases BglII EcoRI, and ClaI were compared with biotyping, antimicrobial susceptibility patterns and plasmid profiles. RESULTS: Biotypes and antimicrobial resistance profiles of the outbreak-associated strains showed considerable variation, thereby limiting the usefulness of such phenotypic markers. Only 57% of the sporadic isolates harbored plasmids. Three different ribotypes based on 5 to 7 bands were recorded among sporadic isolates whereas all outbreak-associated strains showed the same ribotype. BglII appeared to give the best discrimination whereas EcoRI and ClaI provided no additional information. Sporadic EIEC 0124 isolates showed a marked diversity of macrorestriction patterns (similarity coefficient 58 to 93%) and five different patterns were detected. In contrast, the outbreak isolates were closely related (similarity coefficient 90 to 100%). Genomic DNA macrorestriction analysis correlated well with ribotyping, but PFGE was more discriminating. CONCLUSIONS: PFGE is a useful method for epidemiological comparison and differentiation of EIEC 0124 isolates.

Genome fingerprinting of Salmonella typhi by pulsed-field gel electrophoresis for subtyping common phage types

The genomic DNA of 39 strains of Salmonella typhi isolated from local residents and patients who had visited countries in the Asian region was analysed for restriction fragment length polymorphisms (RFLP). Pulsed-field gel electrophoretic (PFGE) analysis of Xba I- and Spe I-generated genomic restriction fragments established 22 PFGE types whereas phage typing differentiated the 39 isolates into 9 distinct phage types. This study showed that PFGE is more discriminatory than phage typing as it is capable of subtyping S. typhi strains of the same phage types. Genetic relatedness among the isolates was determined. Seven major clusters were identified at SABs of > 0.80 and the remaining 13 isolates were distributed into minor clusters which were related at SABs of less than 0.80. In conclusion, PFGE analysis in conjunction with distance matrix analysis served as a useful tool for delineating common S. typhi phage types of diverse origins from different geographical locales and separated in time.

Molecular epidemiologic analysis of Vibrio cholerae O1 isolates by pulsed-field gel electrophoresis

Isolates of Vibrio cholerae O1 El Tor from two well-defined cholera outbreaks in Malaysia were analyzed by using pulsed-field gel electrophoresis (PFGE). Isolates from sporadic cases occurring during the same time period were also studied. Digestion of chromosomal DNA from these isolates of V. cholerae O1 with restriction endonucleases NotI (5'-GCGGCCGC-3') and SfiI (5'-GGCCNNNN-3'), followed by PFGE, produced restriction endonuclease analysis (REA) patterns consisting of 13 to 24 bands (ranging in size from 46 to 398 kbp). Analysis of the REA patterns generated by PFGE after digestion with NotI and SfiI suggested the clonal nature and close genetic identity of the isolates obtained during each of the two outbreaks (Dice coefficient, 0.93 to 1.0). Although they had very similar REA patterns, the two outbreak clones were not identical. Isolates of V. cholerae O1 from sporadic cases, on the other hand, appeared to be much more heterogeneous (five different REA patterns detected in the five isolates tested; Dice coefficient, 0.31 to 0.81) than those obtained during the two outbreaks. We conclude that PFGE of V. cholerae O1 chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for molecular typing of V. cholerae isolates for epidemiological purposes.