[Contribution of molecular biology to typing: Methodological over view.]

Molecular biology yielded universal typing methods. However, different methods have different applications. Multilocus enzyme electrophoresis allows precise population genetics studies. Random amplification is useful for quickly comparing a few strains. Pulse field gel electrophoresis, which is more discriminating than ribotyping, is indicated for the study of epidemics which do not last more than a few months. Ribotyping, which gives most stable types, is indicated for tracing clones world-wide and for many years. Automatization of key experimental steps and computer-aided interpretation are essential for an objective comparison of many strains. Databases of molecular typing patterns are in completion.

Community-wide outbreak of Escherichia coli O157:H7 associated with consumption of frozen beef burgers

On 24-25 October 2005 a cluster of five haemolytic uraemic syndrome (HUS) cases was reported in southwest France. An investigation was undertaken to identify the outbreak source and implement control measures. Cases were defined as individuals with HUS or diarrhoea with isolation of Escherichia coli O157:H7 in stools or a positive antibody response to E. coli O157 lipopolysaccharide, resident in southwest France with symptom onset after 19 September 2005. Sixty-nine identified patients had symptom onset between 5 October and 3 November 2005, including 17 cases of HUS. One brand of frozen beef burgers produced on 22 August 2005 was consumed by all patients in the week before symptom onset. E. coli O157:H7 strains from patients, patients' burgers and the manufacturing plant were genetically related. This is the largest community-wide outbreak of E. coli O157:H7 in France to date and the first associated with consumption of contaminated frozen beef burgers.

Clonal relationship among Vibrio cholerae O1 El Tor strains causing the largest cholera epidemic in Kenya in the late 1990s

Eighty Vibrio cholerae O1 strains selected to represent the 1998-to-1999 history of the largest cholera epidemic in Kenya were characterized by ribotyping, antimicrobial susceptibility, and random amplified polymorphic DNA patterns. Except for 19 strains from 4 local outbreaks in North Eastern Province along the Somalia border, the other 61 strains from 25 outbreaks occurring in districts scattered around the country were all ribotype B27 and resistant to chloramphenicol, spectinomycin, streptomycin, sulfamethoxazole, and trimethoprim. The 61 strains showed similar and specific amplified DNA patterns. These findings indicate that the predominant strains that caused the Kenyan epidemic had a clonal origin and suggest that ribotype B27 strains, which first appeared in West Africa in 1994, have had a rapid spread to eastern Africa.

O148 Shiga toxin-producing Escherichia coli outbreak: microbiological investigation as a useful complement to epidemiological investigation

An outbreak of Shiga toxin-producing Escherichia coli (STEC) O148 infection occurred among wedding attendees in France in June 2002. A retrospective cohort study was performed and ten cases were identified, including two adults with haemolytic uraemic syndrome (HUS). The analytical study revealed that > 80% of affected individuals had eaten lightly roasted mutton and poultry pâté, but only the consumption of pâté tended to be associated with illness (relative risk 3.4; 95% CI 0.8-14.4). Left-overs (cooked mutton and raw offal) and processed foods (pâté) from the same batches as served at the party were sampled. Human, food and environmental samples were examined for the Shiga toxin (stx) gene and virulence traits by PCR. Stx-positive samples were cultured for STEC. HUS cases were tested for serum antibodies against 26 major STEC serogroups. An STEC O26 strain (stx1, eae, ehxA) was isolated from one case with diarrhoea, and an STEC O148 strain (stx2c) from one case of HUS. Serum antibodies against O26 were not detected in either of these patients; antibodies against O148 were not tested. Three STEC strains were isolated from the mutton and the offal (stx2c, O148), and two from the pâté (stx2c, O-X and O-Y). The isolates from the mutton were indistinguishable from the human stx2c isolate, whereas the pâté isolates differed. Although four different STEC strains were identified in patients and foods, the results of molecular subtyping, in conjunction with analysis of food consumption patterns, strongly suggested that this outbreak was caused by mutton contaminated with STEC O148.

Escherichia coli O157 outbreak associated with fresh unpasteurized goats' cheese

A family cluster of three cases of Escherichia coli O157 infection was identified in France. Two cases developed haemolytic-uraemic syndrome. The source was fresh unpasteurized goats' cheese, produced by an independent producer. Three E. coli O157 strains, isolated from one HUS case and faeces of one cow and one goat, were indistinguishable by toxin type and PFGE pattern.

Case management of a multidrug-resistant Shigella dysenteriae serotype 1 outbreak in a crisis context in Sierra Leone, 1999-2000

From December 1999 to the end of February 2000, 4218 cases of dysentery were reported in Kenema district, southeastern Sierra Leone, by a Médecins Sans Frontières team operating in this region. Shigella dysenteriae serotype 1 was isolated from the early cases. The overall attack rate was 7.5% but higher among children under 5 years (11.2%) compared to the rest of the population (6.8%) (RR = 1.6; 95% CI 1.5-1.8). The case fatality ratio was 3.1%, and higher for children under 5 years (6.1% vs. 2.1%) (RR = 2.9; 95% CI 2.1-4.1). A case management strategy based on stratification of affected cases was chosen in this resource-poor setting. Patients considered at higher risk of death were treated with a 5 day ciprofloxacin regimen in isolation centres. Five hundred and eighty-three cases were treated with a case fatality ratio of 0.9%. Patients who did not have signs of severity when seen by health workers were given hygiene advice and oral rehydration salts. This strategy was effective in this complex emergency.

Outbreak of Pseudomonas putida bacteraemia in a neonatal intensive care unit

During the period of 9-27 March 2001, Pseudomonas putida strains were recovered from 10 neonates hospitalized in the neonatal intensive care unit of Farhat Hached Hospital, Sousse (Tunisia). Seven neonates developed bacteraemia, and three had an umbilical catheter-related infection (without bacteraemia). A total of 18 isolates were cultured from blood (N = 11) and catheters (N = 7). These isolates were identified as P. putida by routine biochemical methods (API 20 NE, bioMérieux, Lyon, France). Restriction endonuclease DNA profiles were determined by pulsed-field gel electrophoresis using two endonucleases XbaI and SpeI. They yielded the same patterns showing that the outbreak was caused by a single clone of P. putida. Although the antiseptic solutions used to clean the umbilicus were implicated circumstantially as probable sources, they were not sampled and so this could not be confirmed.

Two outbreaks of Salmonella enteritidis phage type 8 linked to the consumption of Cantal cheese made with raw milk, France, 2001

Salmonelloses are one are the main causes of foodborne infections in industrialised countries. In France, the incidence of human salmonellosis recorded by the National Reference Centre for Salmonella and Shigella (CNRSS) in 2001 was 21 cases per 100,000 inhabitants, and Salmonella serotype Enteritidis represented 39% of cases (1). This article reports the investigation results of two community outbreaks of salmonellosis that occurred simultaneously in the south west of France, and which were linked to the consumption of cheese made from raw milk.

Corynebacterium macginleyi isolation from conjunctival swab in Italy

Corynebacterium macginleyi was isolated from conjunctival swabs of a farmer suffering from purulent conjunctivitis. This species has only recently been reported in Switzerland and Germany to be exclusively isolated from ocular surfaces. This represents the first isolation of C. macginleyi in Italy indicating that its circulation is not geographically limited.

A molecular and phenotypic study of Vibrio cholerae in Iran

Vibrio cholerae is again the subject of attention on account of the current increase in the world-wide incidence of cholera. In this study, 200 clinical isolates of V. cholerae serotypes O1 and non-O1, non-O139, were collected from different provinces in Iran. The isolates were subjected to biochemical analysis, antibiogram, PCR of toxin genes, plasmid profile, ribotyping and pulsed-field gel electrophoresis (PFGE). The analysis of plasmid content showed that 33-96% of V. cholerae isolated from different provinces carry a large plasmid. PCR analysis of V. cholerae O1 showed that the genes encoding cholera toxin (ctx), toxin co-regulated pilus (tcp), accessory cholera enterotoxin (ace) and zonula occludens toxin (zot) were present in 55-97% of isolates in different provinces. Restriction fragment length polymorphism (RFLP) of BglI-digested DNA probed with five oligonucleotides revealed three different ribotype patterns in isolates of V. cholerae O1. The ribotype pattern B21 of V. cholerae O1 El Tor was found to be the predominant pattern in the isolates studied. V. cholerae non-O1, non-O139 isolates showed a single ribotype pattern. PFGE analysis also showed 10 different patterns amongst the isolates, 9 of which were in V. cholerae O1. Overall, the analysis of polymorphism of ribotypes and PFGE patterns of the isolates showed that the provinces in Iran were affected by a limited number of clones of V. cholerae O1 and non-O1, non-O139 strains.

Legionella gresilensis sp. nov. and Legionella beliardensis sp. nov., isolated from water in France

Novel Legionella-like isolates, strains Montbéliard A1T and Gréoux 11 D13T, isolated from two different French water sources, were studied taxonomically and phylogenetically. Morphological and biochemical characterization revealed that they were Gram-negative, aerobic, non-spore-forming bacilli with a cut-glass appearance that grew only on L-cysteine-supplemented buffered charcoal yeast extract agar. Phenotypic characterization using fatty acid and ubiquinone profiles and SDS-PAGE analysis confirmed that they were closely related, but distinct from, other species of the genus Legionella, since serotyping could not relate them to any existing serogroup. Genotypic profiles generated by randomly amplified polymorphic DNA and 16S-23S rDNA spacer region PCR analyses were unique for each of these isolates. DNA-DNA relatedness values of strains Montbéliard A1T and Gréoux 11 D13T to each other and to other Legionella type strains were less than 25%. Phylogenetic affiliation of these organisms obtained by 16S rDNA sequence comparisons confirmed that they were distinct from any other known Legionella species. All the above results confirm that these strains constitute two novel species for which the names Legionella gresilensis sp. nov. (type strain Gréoux 11 D13T = ATCC 700509T = CIP 106631T) and Legionella beliardensis sp. nov. (type strain Montbéliard A1T = ATCC 700512T = CIP 106632T) are proposed.

Minced beef and human salmonellosis: review of the investigation of three outbreaks in France

The synthesis of investigations of three salmonellosis outbreaks which occured in France between 1998 and 2000 confirms the role of the consumption of minced beef and highlights the importance of prevention measures.

Clonal relationships among Shigella serotypes suggested by cryptic flagellin gene polymorphism

The presence of cryptic fliC alleles in the genomes of 120 strains representative of the four Shigella species was investigated. One fragment was obtained by PCR amplification of fliC, with a size varying from 1.2 to 3.2 kbp, depending on the species or serotype. After digestion with endonuclease HhaI, the number of fragments in patterns varied from three to nine, with sizes of between 115 and 1,020 bp. Patterns sharing most of their bands were grouped to constitute an F type. A total of 17 different F types were obtained from all strains included in this study. A unique pattern was observed for each the following serotypes: Shigella dysenteriae 1, 2, 8, and 10 and S. boydii 7, 13, 15, 16, and 17. On the contrary, S. dysenteriae serotype 13 and S. sonnei biotype e were each subdivided into two different F types. S. flexneri serotypes 3a and X could be distinguished from the cluster containing S. flexneri serotypes 1 to 5 and Y. S. flexneri serotype 6 clustered with S. boydii serotypes 1, 2, 3, 4, 6, 8, 10, 11, 14, and 18 and S. dysenteriae serotypes 4, 5, 6, 7, 9, 11, and 12. Two other clusters were outlined: one comprising S. dysenteriae serotypes 3, 12, 13 (strain CDC598-77), 14, and 15 and the other one joining S. boydii serotypes 5 and 9. None of the 17 fliC patterns was found in the fliC HhaI pattern database previously described for Escherichia coli. Overall, this work supports the hypothesis that Shigella evolved from different ancestral strains of E. coli. Moreover, the method outlined here is a promising tool for the identification of some clinically important Shigella strains as well as for confirmation of atypical isolates as Shigella spp.

Molecular and phenotypic characterization of potentially new Shigella dysenteriae serotype

From September 1997 to November 1998, the French National Center for Salmonella and Shigella received 22 Shigella isolates recovered from 22 different patients suffering from dysentery. None of these isolates reacted with any of the antisera used to identify established Shigella serotypes, but all of them agglutinated in the presence of antisera to a previously described potentially new Shigella dysenteriae serotype (represented by strain 96-204) primarily isolated from stool cultures of imported diarrheal cases in Japan. All French isolates, as well as strain 96-204, showed biochemical reactions typical of S. dysenteriae and gave positive results in a PCR assay for detection of the plasmid ipaH gene coding for invasiveness. No Shiga toxin gene was detected by PCR. These isolates were indistinguishable by molecular analysis of ribosomal DNA (ribotyping) and seemed to be related to S. dysenteriae serotypes 3 and 12. However, further characterization by restriction of the amplified O-antigen gene cluster clearly distinguished this new serotype from all other Shigella or Escherichia coli serotypes.

Computer identification of Shigella species by rRNA gene restriction patterns

We describe a MluI ribotyping scheme for Shigella which approaches correlation with serotyping. One hundred and seventeen reference strains and previously serotyped clinical isolates representing the 57 Shigella serotypes and biotypes were included in this study. A total of 51 distinct ribotypes were obtained and a database was built with them. The number of bands composing each ribotype varied from 9 to 15. The fragments ranged in size from 1.6 to 18.8 kbp. One hundred and eleven clinical isolates were successfully identified in a double blind study with standard biochemical/serologic methods, by automatic comparison of their ribotypes with our database using the software Taxotron.

Investigation of concurrent outbreaks of gastroenteritis and typhoid fever following a party on a floating restaurant, France, March 1998

A retrospective cohort study was carried out to investigate concurrent outbreaks of gastroenteritis and typhoid fever that occurred among guests of a supper on a floating restaurant in France in March 1998. A total of 133 guests (attack rate = 90%) reported gastroenteritis within 12 days of the supper. Twenty-seven guests developed typhoid fever (attack rate = 18%) of whom 15 were confirmed by stool or blood culture. All patients with typhoid fever had had an initial gastroenteritis. The results suggest that the same food items served during the supper, chicken and rice, were the vehicles of both gastroenteritis and typhoid fever, but the authors could not determine the specific source of infection. Initial gastroenteritis has been described as a clinical manifestation of typhoid fever but whether or not these two syndromes (gastroenteritis and typhoid fever) were due to the same etiology remains unclear in this outbreak.

Classification of Brucella strains isolated from marine mammals using DNA-DNA hybridization and ribotyping

DNA-DNA hybridization showed that the Brucella strains recently isolated from marine mammals belong to the monospecific genus Brucella (more than 77% DNA relatedness). Ribotyping (HindIII rDNA restriction patterns) showed that they may represent a separate subgroup (marine type) specifically associated with marine mammals.

Identification of Escherichia coli O-serogroups by restriction of the amplified O-antigen gene cluster (rfb-RFLP)

The precise serotyping of clinical Escherichia coli isolates is a crucial step for diagnostic and epidemiological purposes. Epidemiological knowledge associated with serotyping is so important that no alternative method may be considered if it does not correlate with serotyping. Unfortunately, E. coli are difficult to serotype. Genes specifically involved in O-antigen synthesis are clustered in E. coli, Shigella and Salmonella. Published oligonucleotide sequences complementary to JUMPstart and the gnd gene (the conserved flanking sequences upstream and downstream of O-antigen gene clusters, respectively) were used to amplify the O-antigen gene cluster of representative strains of 148 E. coli O-serogroups. A unique amplified fragment was observed for each serogroup (size ranging from 1.7 to 20 kbp). Clearly identifiable and reproducible O-patterns were obtained for the great majority of O-serogroups after MboII digestion of amplified products. The number of bands composing each pattern varied from five to 25. A database was built with the patterns obtained. A total of 147 O-patterns were obtained. Thirteen O-serogroups were subdivided into different O-patterns. However, each of 13 other O-patterns was shared by two or more O-serogroups. 0-serogroups of clinical isolates were deduced accurately from O-patterns in all cases, even for some rough or nonagglutinating isolates. The restriction method (rfb-RFLP) may prove to be better than serotyping since 100% of strains are typable, which is not the case with serotyping.

Identification of Escherichia coli flagellar types by restriction of the amplified fliC gene

A total of 182 strains of Escherichia coli (133 reference strains, 22 clinical strains, nine nonmotile strains and 18 strains derived from K-12) were characterized by HhaI restriction of the amplified flagellin gene (fliC). The amplified fliC product was a single band between 0.9 and 2.6 kbp. With the collection of reference strains which represented 48 flagellar types (H-types), a total of 62 patterns (F-types) were observed after HhaI restriction. A single F-type was associated with each of 39 H-types and more than one F-type was associated with the other nine H-types. Antigenically related H-types 12 and 45 gave a single F-type. The determination of HhaI-fliC F-types could allow deduction of all H-types and subdivision of some of these. Application of this identification system to 22 E. coli clinical isolates yielded nine F-patterns and the deduced H-types were confirmed by serotyping in all cases. Nine nonmotile strains were studied and their F-types were also identified. The proposed determination of fliC restriction patterns should be helpful for epidemiological studies.

Streptococcus infantarius sp. nov., Streptococcus infantarius subsp. infantarius subsp. nov. and Streptococcus infantarius subsp. coli subsp. nov., isolated from humans and food

Eighteen strains isolated from human specimens or from food products were characterized as atypical variants of mannitol-negative Streptococcus bovis. They were tested for extended biochemical criteria, ribotyping and DNA-DNA hybridization in order to define their taxonomic status. These strains were demonstrated to constitute a DNA relatedness group that includes strains of DNA group 4 of Farrow et al. (1984). Comparative analysis of 16S rRNA sequences demonstrated that these strains represent a new species which belongs to the Streptococcus bovis/Streptococcus equinus complex and which has been provisionally named S. infantarius by Bouvet et al. (1997). Biotyping and ribotyping allowed differentiation of these strains from the aesculin-positive strains of S. bovis belonging to the previously described biotypes I, II.1 and II.2. The results of the ribotyping and hybridization assays demonstrated the presence of two different DNA subgroups within the 18 strains. On the basis of these data, the names S. infantarius subsp. infantarius (aesculin-negative for five strains out of seven, including the type strain HDP 90056T = NCDO 599T) and S. infantarius subsp. coli (aesculin-positive, reference strain HDP 90248 = NCDO 2620) are proposed as the names for these two subspecies within the S. infantarius species.

Outbreak of typhoid fever on the French Riviera

A case-control study was conducted to establish the source of a community outbreak of typhoid fever in Utelle, France, a village located in the Alpes-Maritimes district of the French Riviera. Thirteen confirmed cases of typhoid fever and 41 confirmed community controls were included in the study. Cases and controls did not differ regarding ingestion of water. Multivariate logistic regression analysis identified consumption of pork meats during a village festival as the only statistically significant risk factor for typhoid fever after adjusting for age and sex (odds ratio, 76.0; 95% confidence interval, 3.5-1660). Assessment of food-handling procedures at the inn where the food had been prepared showed that the refrigeration and cooking facilities were inadequate to maintain a proper sanitary environment during the preparation of a meal for 350 people. Although the exact cause of the epidemic could not be confirmed, food contaminated by a chronic typhi carrier is the most plausible hypothesis.

Haemolytic uraemic syndrome and Shiga toxin-producing Escherichia coli infection in children in France. The Société de Néphrologie Pédiatrique

We conducted a study to determine the incidence of haemolytic uraemic syndrome (HUS) in children in France and to assess the role of Shiga-toxin-producing Escherichia coli (STEC) infection in the aetiology of HUS. In collaboration with the Société de Néphrologie Pédiatrique we undertook a retrospective review of all cases of HUS hospitalized from January 1993 to March 1995 and a 1-year prospective study (April 1995-March 1996) of epidemiological and microbiological features of cases of HUS. The polymerase chain reaction (PCR) procedure was used to detect stx, eae, e-hlyA genes directly from case stool samples. Serum samples from cases were examined for antibodies to lipopolysaccharide (LPS) of 26 major STEC serogroups. Two hundred and eighty-six cases were reported. The average incidence per year was 0.7/10(5) children < 15 years and 1.8/10(5) children < 5 years. During the prospective study, 122/130 cases were examined for evidence of STEC infection using PCR and/or serological assays and 105 (86%) had evidence of STEC infection. Serum antibodies to E. coli O157 LPS were detected in 79 (67%) cases tested. In conclusion, this study showed that STEC infection is an important cause of HUS in children in France, with a high proportion related to the O157 serogroup.

A community--wide outbreak of Salmonella enterica serotype Typhimurium infection associated with eating a raw milk soft cheese in France

In 1997, a community-wide outbreak of Salmonella enterica serotype Typhimurium (S. typhimurium) infection occurred in France. The investigation included case searching and a case-control study. A case was defined as a resident of the Jura district with fever or diarrhoea between 12 May and 8 July 1997, from whom S. typhimurium was isolated in stool or blood. One hundred and thirteen cases were identified. Thirty-three (83 %) of 40 cases but only 23 (55 %) of 42 community controls, matched for age and area of residence, reported eating Morbier cheese (Odds ratio: 6.5; 95 % Confidence Interval: 1.4-28.8). Morbier cheese samples taken from the refrigerators of two case-patients and one symptom-free neighbour cultured positive for S. typhimurium of the same phage type as the human isolates. The analysis of distribution channels incriminated one batch from a single processing plant. These findings show that an unpasteurized soft cheese is an effective vehicle of S. typhimurium transmission.

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.

Identification of Shigella serotypes by restriction of amplified O-antigen gene cluster

Due to the scarcity of distinctive biochemical reactions for differentiation of Shigella-Escherichia coli, antigenic analysis has long been used for identification and typing of Shigella isolates. Nevertheless, several intra- and interspecific cross-reactions have been reported to disturb serotyping assays. Shigella serotyping is also occasionally affected by the transition from the smooth (S) form to the rough (R) form. Thus, there is a need for the development of novel robust and discriminating methods for Shigella identification and typing. Characteristically, all genes specifically involved in O-antigen synthesis are clustered in E. coli, Shigella, and Salmonella. Published oligonucleotide sequences complementary to JUMPstart and gene gnd, the conserved flanking sequences upstream and downstream of O-antigen gene clusters, were used to amplify the O-antigen gene cluster of representative strains of each Shigella serotype. A unique, amplified fragment was generally observed for each serotype (size ranging from 6 kbp to 17 kbp). Clearly identifiable and reproducible patterns were obtained for each serotype after MboII digestion of the products, except for S. boydii 12 which showed two distinct patterns, and S. flexneri serotypes 1 to 5 and X and Y which showed a single pattern. A database was built with the Taxotron package allowing automated identification of clinical Shigella isolates to all known serotypes.

Molecular characterization of the genera Proteus, Morganella, and Providencia by ribotyping

The so-called Proteus-Providencia group is constituted at present by three genera and 10 species. Several of the recognized species are common opportunistic pathogens for humans and animals. Different methods based on the study of phenotypic characters have been used in the past with variable levels of efficiency for typing some species for epidemiological purposes. We have determined the rRNA gene restriction patterns (ribotypes) for the type strains of the 10 different species of the genera Proteus, Morganella, and Providencia. Visual inspection of EcoRV- and HincII-digested DNA from the type strains showed remarkably different patterns for both enzymes, but EcoRV provided better differentiation. Both endonucleases were retained to study a large number of wild and collection strains belonging to the different species. Clinical isolates of Proteus mirabilis, Proteus penneri, Morganella morganii, and Providencia heimbachae showed patterns identical or very similar to those of the respective type strains, so that groups of related patterns (ribogroups) were found to correspond to the diverse species. On the contrary, distinct ribogroups were detected within Providencia alcalifaciens (two ribogroups with both enzymes), Providencia rettgeri (four ribogroups with EcoRV and five with HincII), Providencia stuartii (two ribogroups with EcoRV), Providencia rustigianii (two ribogroups with HincII), and Proteus vulgaris (two ribogroups with both enzymes). The pattern shown by the ancient P. vulgaris type strain NCTC 4175 differed considerably from both P. vulgaris ribogroups as well as from the newly proposed type strain ATCC 29905 and from any other strain in this study, thus confirming its atypical nature. Minor differences were frequently observed among patterns of strains belonging to the same ribogroup. These differences were assumed to define ribotypes within each ribogroup. No correlation was observed between ribogroups or ribotypes and biogroups of P. vulgaris, P. alcalifaciens, P. stuartii, and P. rettgeri. Since, not only different species showed different rRNA gene restriction patterns, but also different ribogroups and ribotypes have been found in the majority of the species, ribotyping would be a sensitive method for molecular characterization of clinical isolates belonging to the genera Proteus, Morganella, and Providencia.

Multidrug-resistant human and animal Salmonella typhimurium isolates in France belong predominantly to a DT104 clone with the chromosome- and integron-encoded beta-lactamase PSE-1

Epidemiologic relationships were investigated in 187 ampicillin-resistant Salmonella typhimurium strains (86 human, 101 animal) from >2000 strains isolated in 1994. Of 23 resistance patterns, the most frequent (ampicillin [Am], chloramphenicol [Cm], tetracycline [Tc], streptomycin and spectinomycin [Sm], and sulfonamides [Su]) was found in 69.5% of human and 64.8% of animal isolates. Four beta-lactamase genes were identified, blaTEM (24%), blaPSE-1 (78%), and blaSHV and oxa-2 (each <3%). blaPSE-1 and the integrase gene, intI1, but not blaTEM, blaSHV or oxa-2, were chromosomeborne and found almost exclusively in the AmCmTcSmSu strains. In these, polymerase chain reaction mapping revealed two distinct integrons carrying blaPSE-1 or aadA2. Lysotypes, plasmid profiles, and restriction fragment length polymorphisms (IS200) were determined for 50 representative isolates and for 3 DT104 strains from the United Kingdom (UK). The phage type of the PSE-1-producing AmCmTcSmSu strains was 12 atypic, indistinguishable from that of the DT104 strains. The combined data indicate that the same multiresistant clone has spread through human and animal ecosystems in the UK and France.

DNA relatedness among the pathovars of Pseudomonas syringae and description of Pseudomonas tremae sp. nov. and Pseudomonas cannabina sp. nov. (ex Sutic and Dowson 1959)

A total of 48 pathovars of Pseudomonas syringae and eight related species were studied by DNA-DNA hybridization (S1 nuclease method) and ribotyping. The existence of nine discrete genomospecies was indicated. Genomospecies 1 corresponded to P. syringae sensu stricto and included P. syringae pathovars syringae, aptata, lapsa, papulans, pisi, atrofaciens, aceris, panici, dysoxyli and japonica. Genomospecies 2 included P. syringae pathovars phaseolicola, ulmi, mori, lachrymans, sesami, tabaci, morsprunorum, glycinea, ciccaronei, eriobotryae, mellea, aesculi, hibisci, myricae, photiniae and dendropanacis and nomenspecies Pseudomonas savastanoi, Pseudomonas ficuserectae, Pseudomonas meliae and Pseudomonas amygdali, which are thus synonymous. P. amygdali is the earliest valid name for this genomospecies. Genomospecies 3 included P. syringae pathovars tomato, persicae, antirrhini, maculicola, viburni, berberidis, apii, delphinii, passiflorae, philadelphi, ribicola and primulae. We recommend strain CFBP 2212 of P. syringae pv. tomato to serve as the type strain. Genomospecies 4 included 'Pseudomonas coronafaciens' and P. syringae pathovars porri, garcae, striafaciens, atropurpurea, oryzae and zizaniae and corresponds to 'P. coronafaciens'. Genomospecies 5 included P. syringae pv. tremae and corresponds to Pseudomonas tremae sp. nov. Genomospecies 6 included Pseudomonas viridiflava and the presently misidentified pathotype strains of P. syringae pv. ribicola and P. syringae pv. primulae and thus corresponds to P. viridiflava. Genomospecies 7 included P. syringae pv. tagetis and P. syringae pv. helianthi. We recommend strain CFBP 1694 of P. syringae pv. tagetis to serve as a reference strain. Genomospecies 8 included P. syringae pv. these and Pseudomonas avellanae and thus corresponds to P. avellanae. Genomospecies 9 included P. syringae pv. cannabina and corresponds to Pseudomonas cannabina sp. nov. Ribotyping (SmaI and HincII endonucleases) could separate seven of the nine genomospecies. The unnamed genomospecies 3 and 7 will be named when phenotypic data are available for identification. Two species are described, P. tremae sp. nov. and P. cannabina sp. nov. Other species will be named when phenotypic data are available for identification.

Legionella taurinensis sp. nov., a new species antigenically similar to Legionella spiritensis

A group of 42 Legionella-like organisms reacting specifically with Legionella spiritensis serogroup 1 antisera were collected throughout Europe by the Centre National de Référence (French National Reference Centre) for Legionella. This group of isolates differed somewhat from L. spiritensis in terms of biochemical reactions, ubiquinone content and protein profile. The latter two analyses revealed that one of these L. spiritensis-like isolates, Turin I no. 1T, was highly related, but not identical to any of the red autofluorescent species of Legionella. In fact, this strain was the first of these particular isolates recognized to emit a red autofluorescence when exposed to UV light. Profile analysis of randomly amplified polymorphic DNA established that the red autofluorescent L. spiritensis-like isolates constituted a homogeneous group distinct from Legionella rubrilucens and Legionella erythra. DNA-DNA hybridization studies involving the use of S1 nuclease confirmed that the indicated group of isolates are a new species of Legionella, for which the name Legionella taurinensis is proposed with strain Turin I no. 1T (deposited as ATCC 700508T) as the type strain.

Pseudomonas aeruginosa endophthalmitis caused by contamination of the internal fluid pathways of a phacoemulsifier

PURPOSE

To report 4 cases of Pseudomonas aeruginosa endophthalmitis caused by internal contamination of the internal pathways of a phacoemulsifier.

SETTING

Ophthalmology Center, Perpignan, France.

METHODS

Four clinical cases of postoperative endophthalmitis occurred after phacoemulsification. An investigation was necessary to prove the cause of the bacteriological contamination.

RESULTS

Serotyping and ribotyping of the Pseudomonas aeruginosa strains obtained from the vitreous samples and from the phacoemulsifier showed that all these strains were identical and that the initial site of the contamination was the phacoemulsifier.

CONCLUSIONS

The profession should be cognizant of this cause of endophthalmitis, although its occurrence is rare. Cataract surgeons should test samples from the collection bags of their phacoemulsifiers to ensure there is no bacteriological contamination.

Molecular characterization of Vibrio cholerae O1 strains isolated in Romania

A collection of 89 Vibrio cholerae O1 strains, isolated in Romania between 1977 and 1994, and 6 strains from the Republic of Moldavia, was characterized by ribotyping, toxin gene restriction pattern (toxinogenotype) and distribution of cholera toxin gene (ctx), accessory toxin gene (ace) and zonula occludens toxin gene (zot). After Bg/I endonuclease restriction of chromosomal DNA, a total of 18 ribotypes and 21 toxinogenotypes were distinguished. Deletions in the core region of the toxin gene cassette were found in 20% of strains; however, with the exception of one strain, all the isolates contained the ctx gene. Used in association, the three methods of molecular typing provided an accurate characterization of V. cholerae O1 isolates.

Fingerprinting of Flavobacterium psychrophilum isolates by ribotyping and plasmid profiling

Flavobacterium psychrophilum is the agent of cold-water disease and rainbow trout fry syndrome in salmonid fish worldwide. Ribosomal RNA gene restriction patterns (ribotypes) and plasmid profiles were determined on a collection of 85 strains isolated from different countries and fish species. Several ribotypes were obtained by using the restriction endonucleases Hinc II and Pvu II. Computer analysis of the ribotypes revealed that some of them were clearly associated with the fish species from which the strains were isolated, whereas no correlation with the geographical origin was found. Most of the strains harboured at least one plasmid and several different plasmid profiles were observed, even among strains sharing the same ribotype. These methods, used alone or in combination with other typing techniques, can be considered powerful tools for the epidemiological tracing of F. psychrophilum infections.

Comparison of 14 PCR systems for the detection and subtyping of stx genes in Shiga-toxin-producing Escherichia coli

The specificity of 14 polymerase chain reaction (PCR) systems designed for the detection and subtyping of stx genes was tested on a set of Escherichia coli strains with known sequences of stx genes. Systems designed for the detection of genes of the stx1 type did not detect any variant genes of the stx2 type and conversely, no stx2 type-specific systems detected stx1 variant genes. Among five stx2 type-specific systems, none detected the stx2ev gene, and two detected the stx2e gene. Among systems designed for screening genes of the both stx1 and stx2 types with a single primer pair, only one system (the Lin system) was able to detect stx genes in all studied strains. Shiga-toxin-producing E. coli frequently carry more than one stx variant gene. Coamplification of stx genes present in the same strain was demonstrated by restriction of PCR products with endonucleases generating fragments of variant-specific size. The amplification product obtained by the Lin system restricted by Hincll yielded fragments of different size for stx1, stx2, stx2c, stx2e and stx2ev. Thus it was possible to identify different genes carried in a single strain with a simple two-step PCR/endonuclease restriction protocol.

Computer identification of Escherichia coli rRNA gene restriction patterns

A total of 191 strains of Escherichia coli comprising 164 serovar reference strains and 28 clinical strains were characterized by rRNA gene restriction patterns (ribotypes) generated after cleavage of total DNA with MluI, ClaI or HindIII restriction endonucleases and hybridization of fragments with acetylaminofluorene-labelled 16 + 23S rRNA. A wide diversity of ribotypes was observed with endonucleases MluI (104 patterns), ClaI (90 patterns) and HindIII (98 patterns). When MluI was used, 85% of patterns (11 to 15 fragments) shared five fragments 17.09, 3.94, 3.06, 2.23 and 1.76 kb in size. When these fragments were used as internal standards, the percent errors in fragment length determination was half of that obtained with an external standard. Two fragment size databases of MluI and ClaI ribotypes were built. Automatic identification was obtained after setting the percent fragment size variation tolerance (error) at 5%. MluI ribotyping is recommended as a primary epidemiological marker. Strains with similar MluI ribotype should then be submitted to ClaI ribotyping. Ribotyping with HindIII can only be the third choice, since the patterns were often uncertain due to the frequent occurrence of faint bands. Most of the studied serovars gave discrete patterns and these data provide the basis for a molecular typing system for E. coli which could possibly substitute for serotyping when the latter is not available.

Phenotypic and genotypic characterization of Vibrio cholerae isolates from a recent cholera outbreak in Senegal: comparison with isolates from Guinea-Bissau

A total of 127 strains of Vibrio cholerae (117 V. cholerae O1 and 10 nonagglutinating strains) isolated from a recent cholera outbreak in Senegal and four strains isolated in Guinea-Bissau (during the survey of a cholera epidemic that occurred 10 months before the Senegalese one) were analyzed. Strains were characterized by conventional methods (biochemical and serologic identification, susceptibility to antimicrobial agents), polymerase chain reaction for genes encoding cholera toxin (CtxA), zonula occludens toxin (Zot), and accessory cholera enterotoxin (Ace), and by ribotyping. Conventional methods showed that all strains of V. cholerae O1 belonged to serotype Ogawa, biotype El Tor and were resistant to the vibriostatic agent O129 (2,4-diamino 6,7-diisopropylpteridine phosphate), cotrimoxazole, and chloramphenicol; all strains were sensitive to tetracycline, a drug that has been extensively used in cholera therapy. Most of these V. cholerae O1 (112 strains from Senegal and four strains from Guinea-Bissau) had an intact core region (virulence cassette) and amplified a 564-basepair (bp) fragment of ctxA, a 1083-bp fragment of zot, and a 314-bp fragment of ace. Ribotyping of V. cholerae O1 strains after Bgl I restriction of total DNA revealed that ribotype B5a, which is the predominant ribotype of this seventh pandemic of cholera, was not isolated. Instead, a new ribotype was identified and designated B27 in our data bank. Since O1 isolates from Guinea-Bissau and Senegal have the same biotype, serotype, and ribotype and as the Guinea-Bissau outbreak that preceded the one in Senegal, this emerging ribotype probably came from Guinea-Bissau. Nonagglutinating strains exhibited no resistance to the O129 agent and to the tested antibiotics, they were all negative for virulence cassette, except for one strain with the ctxA and zot genes isolated from a patient with diarrhea, and there was a great variability of ribotypes among these strains. There was no difference between environmental O1 strains isolated from water and strains isolated from patients with cholera, suggesting that fecally contaminated water is an important reservoir for infection.

Isolation of a new variant of Vibrio cholerae O1: V. cholerae O1 ribotype B27 toxinogenotype TB31 during the last cholera epidemic in Senegal

A total of 205 Vibrio cholerae O1 isolates from recent cholera epidemic in Senegal were analyzed by conventional methods, polymerase chain reaction (PCR) for genes encoding cholera toxin (ctx A), zonula occludens toxin (zot) and accessory cholera enterotoxin (ace), ribotyping and toxinogenotyping. Ribotyping after Bg1 I digestion of total DNA revealed that ribotype B5a, the predominant ribotype of the seventh pandemic in Africa and Asia, was not isolated. A new ribotype designated B27 in our database is predominant and was associated with a new toxinogenotype designated TB31.

Universal ribotyping method using a chemically labelled oligonucleotide probe mixture

Some of the present problems in ribotyping are associated with a lack of uniform reactivity of probes when bacterial DNAs are of phylogenetically diverse origins. To overcome these problems, a set of five oligonucleotides (referred to as OligoMix5) was selected to react with conserved sequences located near both extremities of rrs (16S rRNA gene) and near both extremities and the middle of rrl (23S rRNA gene). DNA samples from 13 bacterial species selected to represent various phylogenetic branches within the Eubacteria were cleaved by a restriction endonuclease and electrophoresed in 0.8% agarose, and the fragments were vacuum-transferred to nylon membranes and hybridized with digoxigenin-labelled OligoMix5, plasmid DNA from pKK3535 (cloned rrn operon from Escherichia coli) or pBA2 (cloned rrs from Bacillus subtilis), or acetylamino-fluorene-labelled E. coli 16 + 23S rRNA. The results showed OligoMix5 to visualize patterns in DNA from phylogenetically diverse bacteria with comparable intensity. Banding patterns (not band intensity) obtained with OligoMix5 were identical with those obtained with 16 + 23S rRNA or plasmid pKK3535 for each strain studied and represented complete ribotypes. For DNA from Gram-positive bacteria, complete ribotypes were observed after prolonged enzymatic detection of bands when probes were either E. coli 16 + 23S rRNA or pKK3535. Patterns given by plasmid pBA2 were subsets of the complete ribotypes for 9/13 strains. Each oligonucleotide of the OligoMix5 set was used as a probe to determine its contribution to the complete ribotype. The five oligonucleotide probes, used individually, visualized one to four patterns per DNA sample. Use of DNA from Xenorhabdus sp. CIP 105189 cleaved by EcoRI is suggested to control the quality of the oligonucleotide probes composing OligoMix5. Probe OligoMix5 was found to be an essential tool for ribotyping phylogenetically diverse eubacteria.

Molecular epidemiology of Vibrio cholerae O1 isolates from Colombia

A total of 173 Vibrio cholerae O1 isolates from the recent cholera epidemic in Colombia was analysed by the polymerase chain reaction (PCR) for the genes encoding the A subunit of cholera toxin (ctxA) and the zonula occludens toxin (zot), and by ribotyping. All isolates were positive for ctx A and zot, which was confirmed by hybridisation. Ribotyping with restriction endonuclease Bg/I digestion of total DNA revealed three ribotypes: B5a comprising 165 (96.4%) isolates, and two new designated ribotypes B20 and B21a in six (3.5%) isolates and two (1.1%) isolates, respectively. These findings have significant public health implications.

[Identification and typing of hospital strains of Acinetobacter calcoaceticus-Acinetobacter baumanni complex]

A collection of 95 strains of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex, isolated between 1991 and 1993 in the Prague Burn Center (BC), was studied. Ninety-one strains were isolated from 43 patients: 50 of them from burnt sites, 22 from endotracheal tube, 13 from urine, 3 from blood and 3 from venous catheter, and 4 strains were isolated from the hospital environment and the nursing staff. The strains were classified by restriction endonuclease fingerprinting of total DNA, plasmid profile analysis, ribotyping, comparison of antibiograms, biotyping and according to epidemiological data, into 31 relatedness groups each of them including 1 to 29 strains, likely to be isolates of the same strain. None of the methods used enabled to distinguish all groups. The importance of the polyphasic approach is emphasized since three multiresistant strains, isolated almost simultaneously in the BC, needed at least two methods to be distinguished (e.g. ribotyping and biotyping). Twenty-eight representative strains of different groups were identified by ribotyping: 18 of them were allocated to genomospecies 2 (A. baumannii), 5 to genomospecies 3 and 5 to genomospecies 13 sensu Tjernberg and Ursing. Only A. baumannii was found to spread among patients. Strains of two multiresistant groups persisted in the BC throughout the period studied and strains of one of these groups were responsible for an outbreak in the autumn of 1993. The methods mentioned above were used to describe 12 multiresistant strains isolated in three hospital wards in other localities. When ribotyped these strains were identified as A. baumannii. The strains of the same origin were identical in their typing profiles while the strains of different origins were easy to differentiate using any of the above methods; nevertheless, 2 of these groups were almost identical to 2 groups of multiresistant strains isolated in the BC.

Cluster of cases of haemolytic uraemic syndrome due to unpasteurised cheese

A cluster of four patients (1 girl, 3 boys) from a French village (2,000 inhabitants) had acute haemolytic uraemic syndrome (HUS) between March 1992 and May 1993. All had prodromes with fever and diarrhoea, then acute renal failure, anaemia, schistocytosis and thrombocytopenia. Peritoneal dialysis was carried out in three children (duration 3-12 days). The verotoxin VT2 gene was identified by polymerase chain reaction in the stools of two children. Some days prior to the diarrhoea, all children had eaten a cheese made with unpasteurised mixed cows' and goats' milk from the same farm. A case control study showed that the occurrence of HUS was linked to the consumption of this milk product (P = 0.006). The VT 2 gene was isolated from the cheese and from the stools of goats and cows from the farm, but not from the stools of farm employees.

Outbreak of Salmonella dublin infection in France, November - December 1995

On 20 December 1995, the National Network of Public Health (Reseau National de Sante Publique - RNSP) was notified by the Salmonella and Shigella National Reference Centre (Centre National de Reference - CNR) that a greater than expected number of human i

Large outbreak of Salmonella enterica serotype paratyphi B infection caused by a goats' milk cheese, France, 1993: a case finding and epidemiological study

OBJECTIVE

To assess the magnitude of a nationwide outbreak of infection with Salmonella enterica serotype paratyphi B and identify the vehicle and source of infection.

DESIGN

A case finding study of S paratyphi B infection between 15 August and 30 November 1993; a pair matched case-control study; an environmental investigation at a processing plant that produced a raw goats' milk cheese incriminated in the outbreak; phage typing and genotyping of food and human S paratyphi B isolates.

SETTING

France, 15 August to 30 November 1993.

SUBJECTS

273 patients with S paratyphi B infection; 59 pairs of cases and controls matched for age, sex, and city of residence.

MAIN OUTCOME MEASURES

Numbers of cases and incidence rates by region of residence and age; matched odds ratios for dairy food preferences.

RESULTS

Among the 273 cases there was one death; 203 (78%) strains belonged to phage type 1 var 3. The incidence of infection was greatest in the region where goats' milk cheese is commonly produced. Comparison of cases and controls showed a 12-fold greater risk of illness (95% confidence interval 1.6 to 92.3) from eating brand A unpasteurised goats' milk cheese. S paratyphi B isolates of phage type 1 var 3 were recovered from cheese A, goats' milk at the plant processing cheese A, and goats' milk supplied to the plant by a single farm. Genotypic IS 200 typing of food and human 1 var 3 phage type isolates showed a common IS 200 pattern.

CONCLUSION

This outbreak emphasises the potential health hazards of widely distributed unpasteurised milk products in France and the need for their close bacterial monitoring.