Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates

Phylogenetic relationships within the genus Pseudomonas were examined by comparing partial (about 1000 nucleotides) rpoB gene sequences. A total of 186 strains belonging to 75 species of Pseudomonas sensu stricto and related species were studied. The phylogenetic resolution of the rpoB tree was approximately three times higher than that of the rrs tree. Ribogroups published earlier correlated well with rpoB sequence clusters. The rpoB sequence database generated by this study was used for identification. A total of 89 isolates (79.5%) were identified to a named species, while 16 isolates (14.3%) corresponded to unnamed species, and 7 isolates (6.2%) had uncertain affiliation. rpoB sequencing is now being used for routine identification of Pseudomonas isolates in our laboratory.

Nomenclature and taxonomy of the genus Salmonella

The nomenclature of the genus Salmonella has reached an unsatisfactory state of affairs, with two systems of nomenclature in circulation. One system, proposed in the 1980s by Le Minor and Popoff, has received wide acceptance, although it does not conform to the rules of the Bacteriological Code. The other system, which conforms to the rules of the Bacteriological Code, is being used by an ever-decreasing minority. As a result of a number of recent Requests for an Opinion, the Judicial Commission of the International Committee on the Systematics of Prokaryotes has issued an Opinion (Opinion 80) with the intention that it should solve these discrepancies. However, like all Opinions, it is limited to matters of nomenclature and does not help to interpret the taxonomic consequences. The Judicial Commission has therefore asked experts in the field of nomenclature and taxonomy to write a commentary on the nomenclatural and taxonomic consequences of Opinion 80. The present article explains the nomenclatural consequences of Opinion 80, together with a clear presentation of the taxonomy that results when applying the currently widely accepted interpretation that the genus Salmonella currently includes only two species.

Mediation of arsenic oxidation by Thiomonas sp. in acid-mine drainage (Carnoulès, France)

AIMS

To isolate, identify, and characterize heterotrophic bacteria in acid-mine drainage that mediate oxidation of As(III).

METHODS AND RESULTS

Samples of acid-mine drainage were collected over a period of 14 months. Heterotrophic and non-obligatory acidophilic bacteria in the samples were cultured on a solid medium (pH 7.0-7.2), and three strains were isolated. The three different strains belong to the genus Thiomonas, and have more than 99% homology with the group Ynys1. Culturing in mineral media demonstrated that the isolated strains used thiosulphate as an energy source, and oxidized iron in the presence of thiosulphate. However, none of the strains were able to oxidize arsenic in the presence of thiosulphate, nor could they use iron or arsenic alone as an energy source. In vitro experiments demonstrated that two of the Thiomonas strains were able to oxidize more than 90% of the As(III) present in the acid-mine drainage, whereas no abiotic oxidation of arsenic occurred.

CONCLUSIONS

Two strains of newly identified Thiomonas sp. found in acid-mine drainage are capable of oxidizing arsenic.

SIGNIFICANCE AND IMPACT OF STUDY

These results represent the first reported oxidation of arsenic by Thiomonas sp. Biologically mediated oxidation and subsequent immobilization of arsenic is of great interest for the remediation of contaminated mine sites.

Clostridium orbiscindens sp. nov., a human intestinal bacterium capable of cleaving the flavonoid C-ring

Clostridium orbiscindens sp. nov. is an obligate anaerobe that is capable of cleaving the C-3-C-4 bond of the natural anticarcinogen quercetin. The metabolic products, 3,4-dihydroxyphenylacetic acid and presumably phlorglucinol, are not known to possess anticarcinogen properties. This organism was isolated from human feces. On sheep blood agar plates C. orbiscindens forms minute, irregular, convex, gray or white, shiny, smooth, nonhemolytic colonies. It is beta-hemolytic on rabbit blood agar. The motile peritrichous rods are gram variable. Subpolar spores are common. Cultures are resistant to 80 degrees C for 10 min. Capsules are absent. This asaccharolytic organism does not metabolize esculin, urea, meat, gelatin, casein, or nitrate. The G + C content is 56 to 57 mol%. DNA hybridization experiments did not reveal relatedness to phenotypically similar Clostridium strains. Strain 265 (= ATCC 49531) is the type strain.

Molecular fingerprinting defines a strain of Salmonella enterica serotype Anatum responsible for an international outbreak associated with formula-dried milk

Molecular analyses based on plasmid profile typing and pulsed-field gel electrophoresis have defined a strain of Salmonella enterica serotype Anatum associated with the consumption of a particular brand of formula-dried milk responsible for an outbreak in late 1996/early 1997 involving 15 infants and 2 relatives in the UK, and 2 infants in France. The study has demonstrated the value of laboratory-based surveillance involving identification of the outbreak strain at the molecular level coupled with food microbiology and targeted epidemiological investigations, and has highlighted the importance of rapid communication and subsequent international collaboration through the European Union-funded Salm-Net salmonella surveillance network.

Both sulfate-reducing bacteria and Enterobacteriaceae take part in marine biocorrosion of carbon steel

AIMS

In order to evaluate the part played in biocorrosion by microbial groups other than sulfate-reducing bacteria (SRB), we characterized the phylogenetic diversity of a corrosive marine biofilm attached to a harbour pile structure as well as to carbon steel surfaces (coupons) immersed in seawater for increasing time periods (1 and 8 months). We thus experimentally checked corroding abilities of defined species mixtures.

METHODS AND RESULTS

Microbial community analysis was performed using both traditional cultivation techniques and polymerase chain reaction cloning-sequencing of 16S rRNA genes. Community structure of biofilms developing with time on immersed coupons tended to reach after 8 months, a steady state similar to the one observed on a harbour pile structure. Phylogenetic affiliations of isolates and cloned 16S rRNA genes (rrs) indicated that native biofilms (developing after 1-month immersion) were mainly colonized by gamma-proteobacteria. Among these, Vibrio species were detected in majority with molecular methods while cultivation techniques revealed dominance of Enterobacteriaceae such as Citrobacter, Klebsiella and Proteus species. Conversely, in mature biofilms (8-month immersion and pile structure), SRB, and to a lesser extent, spirochaetes were dominant.

CONCLUSIONS

Corroding activity detection assays confirmed that Enterobacteriaceae (members of the gamma-proteobacteria) were involved in biocorrosion of metallic material in marine conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

In marine biofilms, metal corrosion may be initiated by Enterobacteriaceae.

Molecular epidemiology of diphtheria

Molecular subtyping of Corynebacterium diphtheriae identified significant genetic diversity within the species and led to the identification of a unique clonal group that emerged in Russia in 1990 at the beginning of the current epidemic. Strains of this group belong to a distinct electrophoretic type complex and are of ribotypes D1 and D4. Identification of the group allowed for precise monitoring of the epidemic's progression and for rapid detection of cases imported to other countries. The evolution of this clonal group was monitored, and changes were identified. Molecular analysis revealed that no amino acid substitutions have occurred in the diphtheria toxin gene of the epidemic clone strains, reaffirming the use of the current vaccine as the single most effective preventive measure. Application of molecular subtyping methods and continuous monitoring of the spread of these clones has made it possible to distinguish rapidly between epidemic, endemic, and imported cases, allowing for implementation of timely and adequate preventive measures and providing reassurance that no secondary spread resulted from importations.

Chromosomal DNA fingerprinting analysis using the insertion sequence IS6110 and the repetitive element DR as strain-specific markers for epidemiological study of tuberculosis in French Polynesia

The polymorphism of Mycobacterium tuberculosis strains was evaluated in French Polynesia, an area with a low incidence of tuberculosis and a population which has been geographically stable during recent decades. Nonrepetitive strains isolated from 64 patients during 1991 and 1992 were subjected to DNA restriction fragment length polymorphism (RFLP) analysis, using the insertion sequence IS6110 and the repetitive element DR as probes. Thirty-eight different IS6110 RFLP types were identified. They could be clustered in 11 groups. All the members of each group are identical or differ by one to three bands. All the other strains are gathered in the miscellaneous group. In some cases, transmission of strains with identical RFLP types between patients of the same family or between patients living in the same area was identified. Strains exhibiting similar IS6110 RFLP types also exhibited identical DR RFLP patterns, confirming that strains with similar types were genetically linked. Strains belonging to two different IS6110 clusters exhibited the same DR RFLP type. These data may also indicate a common origin for these strains and evolution to new IS6110 types. The results obtained in this study suggest that not only reactivation of latent tuberculous infections but also active transmissions are still occurring in French Polynesia.

How many foodborne outbreaks of Salmonella infection occurred in France in 1995? Application of the capture-recapture method to three surveillance systems

Despite control measures, foodborne outbreaks of non-typhi Salmonella infection continue to occur in developed countries. The authors aimed to assess the number of foodborne Salmonella outbreaks that occurred in France in 1995 using a capture-recapture approach. Data from three sources--the National Public Health Network (NPHN), the Ministry of Agriculture (MA), which receives mandatory notification, and the National Salmonella and Shigella Reference Center (NRC)-were collected. Matching algorithms permitted identification of matched outbreaks. The total number of outbreaks was estimated by log-linear modeling taking into account source dependencies and the variable catchability. The final estimate was adjusted for the positive predictive value (66%) of the NRC case definition. The dependence between the NPHN and the MA was also evaluated by means of a qualitative survey. A total of 716 foodborne Salmonella outbreaks were reported to the three sources, and 108 matches were identified. The best-fitting model, taking into account a positive dependence between the NPHN and MA sources, gave an estimate of 757 outbreaks. The sensitivity was 15% for the NPHN, 10% for the MA, and 50% for the NRC. In France, routine mandatory reporting of foodborne Salmonella outbreaks is very incomplete, and it is not representative of the serotype and the type of outbreak.

Bacteremia caused by a novel species of Sphingobacterium

A Gram-negative rod was isolated from the blood cultures of an 84-year-old man with foot cellulitis. The bacterium was first identified as Sphingobacterium spiritivorum on the basis of standard assimilation tests. However, sequencing analysis of its 16S rRNA genes and whole genome hybridization studies with other related bacteria showed that this isolate belongs to a so far undescribed species of Sphingobacterium, close to S. mizutae. This bacterium was susceptible to most of the antibiotics tested, including glycopeptides, but was resistant to aminoglycosides and polymyxins. Treatment with amoxicillin-clavulanate cured the infection.

Vibrio ponticus sp. nov., a neighbour of V fluvialis-V. furnissii clade, isolated from gilthead sea bream, mussels and seawater

A new Vibrio species, Vibrio ponticus, is proposed to accommodate four marine bacteria isolated from sea water, mussels and diseased sea bream (Sparus aurata), at the Mediterranean coast of Spain. Strains are Gram negative, slightly halophilic bacteria that require Na+ ion for growth, oxidase and catalase positive, negative for arginine dihydrolase and ornithine decarboxylase but positive for lysine decarboxylase and indole, and utilize beta-hydroxybutyrate as a sole carbon source. Phylogenetic analysis locate these marine bacteria in the vicinity of the V. fluvialis-V. furnissii clade, sharing with these two species 16S rDNA sequence similarities slightly above 97% (97.1 and 97.3%, respectively). DNA-DNA hybridisation values confirm that the four strains form a genospecies and represent a new species in the genus Vibrio. We propose strain 369T (CECT 5869T, DSM 16217T) as the type strain.

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.

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.

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.