Use of automated ribotyping of Austrian Listeria monocytogenes isolates to support epidemiological typing

Evaluation of repetitive-PCR and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid strain typing of Bacillus coagulans

In order to establish rapid and accurate typing method for Bacillus coagulans strains which is important for controlling in some canned foods and tea-based beverages manufacturing because of the high-heat resistance of the spores and high tolerance of the vegetative cells to catechins and chemicals, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and repetitive-PCR (rep-PCR) were evaluated. For this purpose, 28 strains of B. coagulans obtained from various culture collections were tested. DNA sequence analyses of the genes encoding 16S rRNA and DNA gyrase classified the test strains into two and three groups, respectively, regardless of their phenotypes. Both MALDI-TOF MS and rep-PCR methods classified the test strains in great detail. Strains classified in each group showed similar phenotypes, such as carbohydrate utilization determined using API 50CH. In particular, the respective two pairs of strains which showed the same metabolic characteristic were classified into the same group by both MALDI-TOF MS and rep-PCR methods separating from the other strains. On the other hand, the other strains which have the different profiles of carbohydrate utilization were separated into different groups by these methods. These results suggested that the combination of MALDI-TOF MS and rep-PCR analyses was advantageous for the rapid and detailed typing of bacterial strains in respect to both phenotype and genotype.

Cheese-related listeriosis outbreak, Portugal, March 2009 to February 2012

In Portugal, listeriosis has been notifiable since April 2014, but there is no active surveillance programme for the disease. A retrospective study involving 25 national hospitals led to the detection of an outbreak that occurred between March 2009 and February 2012. The amount of time between the start of the outbreak and its detection was 16 months. Of the 30 cases of listeriosis reported, 27 were in the Lisbon and Vale do Tejo region. Two cases were maternal/neonatal infections and one resulted in fetal loss. The mean age of the non-maternal/neonatal cases was 59 years (standard deviation: 17); 13 cases were more than 65 years old. The case fatality rate was 36.7%. All cases were caused by molecular serogroup IVb isolates indistinguishable by pulsed-field gel electrophoresis and ribotype profiles. Collaborative investigations with the national health and food safety authorities identified cheese as the probable source of infection, traced to a processing plant. The magnitude of this outbreak, the first reported food-borne listeriosis outbreak in Portugal, highlights the importance of having an effective listeriosis surveillance system in place for early detection and resolution of outbreaks, as well as the need for a process for the prompt submission of Listeria monocytogenes isolates for routine laboratory typing.

Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillus insolitus comb. nov., Psychrobacillus psychrotolerans comb. nov. and Psychrobacillus psychrodurans comb. nov

The taxonomic status of three Bacillus species, Bacillus insolitus, B. psychrodurans and B. psychrotolerans was reexamined using a polyphasic approach. In our analysis, these three Bacillus species formed a cluster separate from other members of Bacillus rRNA group 2 [5] and from Bacillus sensu stricto. These three species shared high 16S rRNA gene sequence similarities between them (97.8-99.7%) and showed closest sequence similarity (95.3-96.3%) to Paenisporosarcina quisquiliarum gen. nov., sp. nov. [18]. Sequence similarities with other related genera ranged between 90.9% and 94.5%. Phylogenetic coherence of the three species was supported by phenotypic characteristics, such as growth at low temperatures, negative oxidation and assimilation of many carbohydrates, MK8 as the major isoprenoid quinine and broadly similar polar lipid profiles. All three species had a similar peptidoglycan type of the variation A4β and similar genomic G+C contents (35.7-36.6 mol% [1]). Genomic relatedness among them was shown to be less than 70% and justified their separate species status [1]. These three species could be differentiated from each other and from related taxa on the basis of phenotypic, including chemotaxonomic, characteristics and ribotype patterns. On the basis of our analysis, we propose a new genus Psychrobacillus gen. nov. and to transfer B. insolitus, B. psychrodurans and B. psychrotolerans to the new genus as Psychrobacillus insolitus comb. nov. (type species of the genus; type strain W16B(T)=DSM 5(T)), P. psychrodurans comb. nov. (type strain 68E3(T)=DSM 11713(T)) and P. psychrotolerans comb. nov. (type strain 3H1(T)=DSM 11706(T)).

Characterization of the first oral vagococcus isolate from a root-filled tooth with periradicular lesions

Strain Endo-EH was isolated from a root-filled tooth associated with periradicular lesions. After subculturing on Columbia blood agar, phenotypic and genomic characterizations using different biochemical test systems, automated ribotyping, MALDI-TOF mass spectronomy, antibiotic susceptibility testing, and 16S rRNA gene sequence analysis were applied for further analysis. Phenotypic characterization identified this strain as Vagococcus fluvialis. Riboprint pattern analysis and 16S rRNA sequencing clearly separated it from relevant genera such as Enterococcus and Tetragenococcus and also from other Vagococcus species. This taxon is a new entry to the list of more than 200 microbial species detected in infected root canal systems.

Monitoring hygiene on- and at-line is critical for controlling Listeria monocytogenes during produce processing

The prevalence of Listeria monocytogenes in different types of produce and on processing plant environments was investigated over a 4-year period in a large produce processing plant in Poland. Prevalence of L. monocytogenes was 46% in frozen vegetables and 41.3% in swab samples taken from the plant environment. Survival studies using artificial inocula demonstrated that the number of Listeria in frozen produce stored for 100 days did not significantly decrease in relation to the initial contamination level. A subset of 129 L. monocytogenes isolates originating from produce and the plant environment were typed by pulsed-field gel electrophoresis. Seventy-six of these isolates were retyped by ribo- and serotyping. Thirteen pulsotypes and 18 ribotypes were distinguished. Persistent Listeria isolates were found even when cleansing and sanitization was applied on a daily basis. Nine (69.2%) of 13 pulsotypes were recovered during a period of more than 2 years. L. monocytogenes of the same pulsotype was isolated from broccoli sampled directly before and after blanching, thus suggesting that blanching at 92 to 95 degrees C for 4 to 8 min did not result in a Listeria-free product, most likely due to massive recontamination. This finding is of importance since blanching is the only critical control point in produce processing. Cross-contamination between the two lines was demonstrated through isolating L. monocytogenes strains indistinguishable by pulsed-field gel electrophoresis from contaminated gloves and floor surfaces.

Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain NS11T) was isolated from a lichen-colonized rock surface. On the basis of 16S rRNA gene sequence similarity, strain NS11T was shown to belong to the Betaproteobacteria, and was most closely related to Herminiimonas arsenicoxydans ULPAs1T (98.8%), Herminiimonas aquatilis CCUG 36956T (98.0%) and Herminiimonas fonticola S-94T (98.0%). Major whole-cell fatty acids were C16:0, C17:0 cyclo and C16:1omega7c. Strain NS11T also contained high proportions of C10:0 3-OH and C18:1omega7c. This pattern is typical for members of the genus Herminiimonas. The results of DNA-DNA hybridization experiments and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS11T from the three recognized Herminiimonas species. It is therefore concluded that strain NS11T represents a novel species of the genus Herminiimonas, for which the name Herminiimonas saxobsidens sp. nov. is proposed. The type strain is NS11T (=DSM 18748T=CCM 7436T).

Prevalence of Listeria monocytogenes in fresh and fermented Italian sausages and ribotyping of contaminating strains

Listeria monocytogenes has been detected in fresh as well as dry and semidry fermented sausages, rendering preparation and consumption of these products as a potential risk to human health. The aims of this study were (1) to evaluate the L. monocytogenes prevalence in 288 fresh and 237 fermented sausages produced in northern Italy; (2) to quantify the average pathogen Most Probable Number (MPN) per g of sausage; (3) to evaluate the sausage strain genetic diversity by automated PvuII ribotyping; and (4) to predict the pathogenicity lineage of these isolates determining their DuPont Identification Library Codes (DUP-IDs) by EcoRI ribotyping. The overall prevalence of L. monocytogenes in the sampled sausages was 28.2%. The percentage of L. monocytogenes positive fresh sausages was significantly higher than that of fermented sausages (i.e. 38.9 vs 15.2%), which had a pathogen load always lower than 10 MPN/g. In contrast, 16.1% of fresh sausages were contaminated by 10 to 100 MPN/g and 20.5% had more than 100 MPN/g. PvuII successfully discriminated sausage isolates with a Simpson's numerical index of discrimination of 0.637. A total of 12 and 9 different PvuII ribogroups were identified among 47 fresh and 24 fermented randomly selected sausage strains, respectively. Six of those ribogroups were shared between strains contaminating both kinds of sausages. According to the evaluation of the strain DUP-IDs, the majority of the isolates investigated in this study were part of the type II L. monocytogenes pathogenicity lineage, but type I lineage strains were identified among fermented sausage isolates. In conclusion, L. monocytogenes prevalence in Italian sausages was estimated to be around 28.2%. However, 84.2% of the samples were contaminated by less than 100 MPN of L. monocytogenes per g and the majority of L. monocytogenes contaminating strains would be classified in the type II pathogenicity lineage, including serotypes 1/2a, 1/2c and 3a.

Application of automated ribotyping to support the evaluation of Listeria monocytogenes sources in a Taleggio cheese producing plant

In March 2005, Listeria monocytogenes was detected on the rinds of Taleggio cheeses produced in an Italian plant. To identify the pathogen source, 154 rinds of cheeses that had been manually and automatically salinated and 52 environmental swabs collected from salting equipment, ripening cloths, and ripening boxes were tested for L. monocytogenes. Twenty-seven strains isolated from cheese samples and 16 strains isolated from environmental samples were genotyped by EcoRI and PvuII automated ribotyping. The microbiological results revealed a significant incidence of contamination of cheeses that were automatically salinated and contamination on the salting equipment, ripening cloths, and boxes. All cheese and environmental strains had the same EcoRI and PvuII ribotyping profiles, designated 153-204-S5 and 153-210-S-2, respectively. The only exception were three Taleggio strains, isolated from the same lot of product, that had EcoRI and PvuII ribotyping profiles designated 153-289-S6 and 153-214-S-5, respectively. Strains with EcoRI profile 153-204-S5 were classified as DUP-ID 1045 and serotype 1/2a, whereas strains with EcoRI profile 153-289-S6 were classified as DUP-ID 1034 and serotype 1/2b. The microbiological and molecular typing data collected in this study suggest that the source of the L. monocytogenes contamination in the Taleggio plant under study was the automated salting equipment. The isolate DUP-IDs were used to trace the introduction of potentially dangerous strains, such as those characterized as DUP-ID 1034, in the processing plant.

Characterization of ‘Pseudomonas azelaica’ DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym

Polyphasic characterization of strain DSM 9128, described as 'Pseudomonas azelaica' by Janota-Bassalik et al. [Acta Microbiol Pol B 3, 143-153 (1971)], and four biochemically similar isolates was performed with the aim of validly publishing the name 'Pseudomonas azelaica'. Based on 16S rRNA gene sequence analysis, DNA-DNA hybridization, fatty acid patterns and extensive biochemical testing, it was concluded that DSM 9128, two further strains and the type strains of Pseudomonas nitroreducens and Pseudomonas multiresinivorans form a highly related cluster. However, DNA-DNA binding did not conclusively resolve whether these strains should be regarded as members of one species. Based on results gained with the above-mentioned methods, two other isolates were assigned to the species Pseudomonas citronellolis, a species very close to P. nitroreducens. Based on genetic and biochemical similarities, it is suggested that Pseudomonas multiresinivorans should be considered as a later heterotypic synonym of Pseudomonas nitroreducens. The species descriptions of P. nitroreducens and P. citronellolis are emended.

Isolation and characterization of a Geobacillus thermoleovorans strain from an ultra-deep South African gold mine

A thermophilic facultative bacterial isolate was recovered from 3.2km depth in a gold mine in South Africa. This isolate, designated GE-7, was cultivated from pH 8.0, 50 degrees C water from a dripping fracture near the top of an exploration tunnel. GE-7 grows optimally at 65 degrees C and pH 6.5 on a wide range of carbon substrates including cellobiose, hydrocarbons and lactate. In addition to O(2), GE-7 also utilizes nitrate as an electron acceptor. GE-7 is a long rod-shaped bacterium (4-6microm longx0.5microm wide) with terminal endospores and flagella. Phylogenetic analysis of GE-7 16S rDNA sequence revealed high sequence similarity with G. thermoleovorans DSM 5366(T) (99.6%), however, certain phenotypic characteristics of GE-7 were distinct from this and other previously described strains of G. thermoleovorans.

Taxonomic characterization of members of the genus Corallococcus: molecular divergence versus phenotypic coherency

Corallococcus coralloides DSM 2259(T), Corallococcus exiguus DSM 14696(T), Corallococcus macrosporus DSM 14697(T) and more than 35 strains identified as members of Corallococcus on the basis of morphology were subjected to partial sequences analysis of three housekeeping genes (lepA, fusA and rpoB), complementing a recent phylogenetic analysis based on genes coding for 16S rRNA and gyrB. Phylogenetic analysis of each gene, generated by maximum likelihood and two different additive treeing algorithms, resulted in the separate position of C. macrosporus DSM 14697(T) and a few Corallococcus strains that were more closely related to Myxococcus xanthus than to the other members of Corallococcus. The latter strains formed three clearly separate clusters by 16S rRNA gene phylogeny. This relationship, however, was only partially recovered by the other gene trees. Group 1, embracing the type strains of C. coralloides and C. exiguus, only emerged as a coherent cluster in the 16S rRNA gene tree. In all other gene trees this cluster embraced organisms of cluster 3, which either formed coherent subclusters (gyrB, lepA) or which appeared polyphyletic (fusA, rpoB). Group 2 organisms consistently constituted a monophyletic cluster, though their branching within the gene trees differed. A concatenated tree, based on the analysis of about 5400 nucleotides of all five partial genes was most similar to the 16S rRNA gene tree. In order to determine whether the individual clusters that emerged by 16S rRNA gene analysis (>99.1% intracluster similarities) show phenetic properties that would allow their description as new species, a few strains of each group were subjected to the analysis of whole cell fatty acid and physiological properties. Riboprint patterns were generated for some members of group 1. While the DNA-DNA reassociation values and riboprint patterns confirmed the genomic heterogeneity of members of cluster 1, none of the other properties investigated were sufficiently discriminative to allow the formal description of strain clusters as new species.

Exiguobacterium mexicanum sp. nov. and Exiguobacterium artemiae sp. nov., isolated from the brine shrimp Artemia franciscana

Two Gram-positive strains isolated from cysts of the brine shrimp Artemia franciscana were subjected to a polyphasic taxonomic analysis. Based on 16S rRNA gene sequence comparison and composition of isoprenoid quinones, peptidoglycan and fatty acids, these organisms are members of the genus Exiguobacterium. Both strains showed 95.9% 16S rRNA gene sequence similarity to one another. The 16S rRNA gene sequences of strain 8N(T) and 9AN(T) were 97.5% and 98.9% similar to those of Exiguobacterium aurantiacum DSM 6208(T) and Exiguobacterium undae DSM 14481(T), respectively. Based on differences in chemotaxonomic and physiological characteristics, results of DNA-DNA hybridization and automated riboprinting, two novel species of the genus Exiguobacterium are proposed, Exiguobacterium mexicanum sp. nov. (type strain 8N(T)=DSM 16483(T)=CIP 108859(T)) and Exiguobacterium artemiae sp. nov. (type strain 9AN(T)=DSM 16484(T)=CIP 108858(T)).

Occurrence and ribotypes of Listeria monocytogenes in Gorgonzola cheeses

In this study 1656 Gorgonzola cheeses, collected from October 2003 to April 2004 in the same industrial plant located in Lombardia (Italy), were analysed in order to evaluate their level of contamination with Listeria monocytogenes after packaging, as well as at the end of the shelf life. A subset of Gorgonzola isolates was submitted to automated EcoRI ribotyping to evaluate their DUP-IDs (DuPont identification library code) and their level of genetic diversity. The isolate ribotyping profiles were included in an on-line database named PathogenTracker database. The strain DUP-IDs and the similarities between Gorgonzola isolates and PathogenTracker human sporadic strains allowed to evaluate the potential virulence of Gorgonzola-associated strains. The L. monocytogenes detection rates observed in the cheese samples monitored after packaging and at the end of the shelf life were 2.1% and 4.8%, respectively. Seventy percent of the strains genotyped were classified in the same ribotype, labelled as 204 S5, indicating that L. monocytogenes population associated to Gorgonzola cheese shows a low level of genetic diversity. Ninety percent of the strains were classified in DUP-IDs belonging to the II pathogenicity lineage identified for L. monocytogenes. That lineage includes serotype 1/2a, 1/2c and 3c strains, associated to the 35% of the human sporadic isolates described in the literature as causing listeriosis. Moreover, 16.7% of Gorgonzola isolates showed a similarity >or=99% with PathogenTracker human sporadic strains. The results of this study showed that the incidence of L. monocytogenes in Gorgonzola cheeses commercialised by the plant tested was lower than that observed in other Italian blue-veined cheeses by other authors. However, it increased during cheese storage and it become double at the end of the cheese shelf life, ranging from 30 to 60 days after packaging.

Description of four novel species of Xenorhabdus, family Enterobacteriaceae: Xenorhabdus budapestensis sp. nov., Xenorhabdus ehlersii sp. nov., Xenorhabdus innexi sp. nov., and Xenorhabdus szentirmaii sp. nov

The taxonomic affiliation was determined for four Xenorhabdus strains isolated from four Steinernema hosts from different countries. As compared to the five validly described Xenorhabdus species, i.e., X. nematophila, X. japonica, X. beddingii, X. bovienii and X. poinarii, these isolates represented novel species on the basis of 16S rRNA gene sequences and riboprint patterns, as well as by physiological and metabolic properties. They were named Xenorhabdus budapestensis sp. nov., type strain DSM 16342T, isolated from Steinernema bicornutam; Xenorhabdus ehlersii sp. nov., type strain DSM 16337T, isolated from Steinernema serratum; Xenorhabdus innexi sp. nov., type strain DSM 16336T isolated from Steinernema scapterisci; and Xenorhabdus szentirmaii sp. nov., type strain DSM 16338T, isolated from Steinernema rarum.

Gordonia nitida Yoon et al. 2000 is a later synonym of Gordonia alkanivorans Kummer et al. 1999

The name of the species Gordonia nitida is validly published but its type strain DSM 44499T shares high similarity based on 16S rRNA gene sequences with Gordonia alkanivorans DSM 44369T and Gordonia westfalica DSM 44215T. These three species obviously build up a distinct cluster within the genus Gordonia. In the present paper, data from the literature concerning the three Gordonia species were reviewed and the genetic similarity of G. nitida DSM 44499T and G. alkanivorans DSM 44369T was further investigated by DNA–DNA-hybridization experiments, revealing approximately 80 % DNA–DNA relatedness. Even though the two type strains could be differentiated by automated ribotyping, it is proposed that, according to the rules of priority, G. nitida is a later synonym of G. alkanivorans.

Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species

To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5' end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of > or =98.7% similarity for a "distinct species," a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMerieux, Marcy I'Etoile, France) and VITEK 2 (bioMerieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants.

Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment

Two marine, Gram-negative, aerobic, halophilic strains, designated KMM 3657T and KMM 3840T, were isolated and found to be phylogenetically closely related to each other, showing 96·6 % 16S rRNA gene sequence similarity. Both strains are members of the genus Marinobacter in the γ-Proteobacteria (94·7–98·0 % 16S rRNA gene sequence similarity). Strain KMM 3657T and Marinobacter lipolyticus SM19T were closely related, with 98·0 % sequence similarity. The novel strains shared generic physiological and chemotaxonomic properties with Marinobacter species, but differed in their temperature range for growth, inability to grow in 20 % NaCl and at >43 °C, metabolic properties and fatty acid composition. On the basis of phenotypic and phylogenetic analysis data, it is proposed that the strains represent two novel species, Marinobacter bryozoorum sp. nov., with the type strain KMM 3840T (=50-11T=DSM 15401T), and Marinobacter sediminum sp. nov., with the type strain KMM 3657T (=R65T=DSM 15400T).

Methods for the isolation and identification of Listeria spp. and Listeria monocytogenes: a review

Listeria monocytogenes is an important food-borne pathogen and is widely tested for in food, environmental and clinical samples. Identification traditionally involved culture methods based on selective enrichment and plating followed by the characterization of Listeria spp. based on colony morphology, sugar fermentation and haemolytic properties. These methods are the gold standard; but they are lengthy and may not be suitable for testing of foods with short shelf lives. As a result more rapid tests were developed based on antibodies (ELISA) or molecular techniques (PCR or DNA hybridization). While these tests possess equal sensitivity, they are rapid and allow testing to be completed within 48 h. More recently, molecular methods were developed that target RNA rather than DNA, such as RT-PCR, real time PCR or nucleic acid based sequence amplification (NASBA). These tests not only provide a measure of cell viability but they can also be used for quantitative analysis. In addition, a variety of tests are available for sub-species characterization, which are particularly useful in epidemiological investigations. Early typing methods differentiated isolates based on phenotypic markers, such as multilocus enzyme electrophoresis, phage typing and serotyping. These phenotypic typing methods are being replaced by molecular tests, which reflect genetic relationships between isolates and are more accurate. These new methods are currently mainly used in research but their considerable potential for routine testing in the future cannot be overlooked.

Automated ribotyping, a rapid typing method for analysis of Erysipelothrix spp. strains

Automated ribotyping classified 70 Erysipelothrix species strains, previously classified into 14 RAPD patterns and into 63 PFGE patterns, into 27 ribogroups. Twenty-three strains of the 70 analyzed and classified into 13 ribogroups were previously classified into six ribotypes by the traditional ribotyping method. Moreover, automated ribotyping differentiated seven strains that were not differentiated by PFGE. Therefore, automated ribotyping was more sensitive than RAPD and traditional ribotyping, and it might be a useful method for a rapid screening in epidemiological study of strains of this genus, and more accurate results can be obtained when this method is used together with PFGE.

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

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

Identifying and subtyping species of dangerous pathogens by automated ribotyping

An investigation of dangerous bacterial pathogens was conducted to determine the usefulness of automated rRNA operon ribotyping (RiboPrinter system) to identify species. A total of 26 isolates comprising Bacillus anthracis, Brucella spp., Burkholderia mallei, Francisella tularensis, and Yersinia pestis were tested using restriction endonucleases EcoRI, PstI, PvuII and AseI. The main problem was that the system's database-relying on EcoRI as restriction enzyme-does not contain the essential dangerous pathogens. B. anthracis was misidentified as B. cereus and Y. pestis as Y. pseudotuberculosis. Two isolates of F. tularensis ssp. holarctica were falsely identified as Vibrio cholerae. This study underscores that riboprint patterns generated with a single restriction enzyme are not always unique for each of the species tested. Using more than one enzyme, the RiboPrinter proved to be a valuable primary typing method. Databases of commercially available systems for the identification of bacteria should include the most important dangerous pathogens.

Listeria monocytogenes isolates from invasive infections: variation of sero- and genotypes during an 11-year period in Finland

Listeria monocytogenes strains that were isolated from 314 human listeriosis cases in Finland during an 11-year period were analyzed by O:H serotyping and pulsed-field gel electrophoresis (PFGE). Serotyping divided the isolates into five serotypes, the most common being 1/2a (53%) and 4b (27%). During the study period, the number of cases caused by serotype 1/2a increased from 22% in 1990 to 67% in 2001, and those caused by serotype 4b decreased from 61 to 27%, respectively. PFGE with restriction enzyme AscI divided the strains into 81 PFGE genotypes; among strains of serotypes 1/2a and 4b, 49 and 18 PFGE types were seen, respectively. PFGE type 1 (serotype 1/2a) was the most prevalent single type (37 strains). Together with six other, closely related PFGE types, PFGE type 1 formed a group of 71 strains, representing 23% of all 314 strains. Strains of PFGE type 1 have also been isolated from cold smoked fish, suggesting a source of human infections caused by this type. Moreover, PFGE type 24 (serotype 1/2c) was significantly associated with gender: 5% of 180 male subjects but none of 132 female subjects (P = 0.012). An electronic database library was created from the PFGE profiles to make possible the prompt detection of new emerging profiles and the tracing of potential infection clusters in the future.

High-throughput epidemiologic typing in clinical microbiology

Mapping, and ultimately preventing, the dissemination of infectious agents is an important topic in public health. Newly developed molecular-microbiological methods have contributed significantly to recent advances in the efficient tracking of the nosocomial and environmental spread of microbial pathogens. Not only has the application of novel technologies led to improved understanding of microbial epidemiology, but the concepts of population structure and dynamics of many of the medically significant microorganisms have advanced significantly also. Currently, genetic identification of microbes is also within the reach of clinical microbiology laboratory professionals including those without specialized technology research interests. This review summarizes the possibilities for high-throughput molecular-microbiological typing in adequately equipped medical microbiology laboratories from both clinical and fundamental research perspectives. First, the development and application of methods for large-scale comparative typing of serially isolated microbial strains are discussed. The outcome of studies employing these methods allows for long-term epidemiologic surveillance of infectious diseases. Second, recent methods enable an almost nucleotide-by-nucleotide genetic comparison of smaller numbers of strains, thereby facilitating the identification of the genetic basis of, for instance, medically relevant microbiological traits. Whereas the first approach provides insights into the dynamic spread of infectious agents, the second provides insights into intragenomic dynamics and genetic functionality. The current state of technology is summarized, and future perspectives are sketched.

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

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

Incidence of fecal carriage of Listeria monocytogenes in three healthy volunteers: a one-year prospective stool survey

The aim of this study was to establish the incidence of fecal carriage of Listeria monocytogenes in healthy adults. A total of 868 stool specimens from three healthy volunteers (1 male and 2 females; ages 44, 39, and 60 years) were collected between 1 October 2000 and 30 September 2001. Culture was performed using Fraser broth and Palcam selective agar plates. Polymerase chain reaction (PCR) was performed using Probelia Listeria monocytogenes (BioRad, France). Overall, Listeria monocytogenes was detected in 31 of the 868 (3.57%) stool specimens using PCR. Sixteen of the 31 positive results were single events, i.e., samples collected from the same patient the day before and the day after the positive result were both negative. Positive results on two consecutive days were found four times, on three consecutive days one time, and on four consecutive days one time. Listeria monocytogenes was cultured from 10 of 868 (1.15%) stool specimens. These culture-positive samples, all positive by PCR as well, accounted for five independent episodes. Using automated ribotyping on up to 40 single colonies per stool specimen, 9 of 10 culture-positive samples yielded more than one strain. There was no obvious seasonal clustering of positive results. None of the documented episodes of Listeria monocytogenes carriage, all of which involved serotypes 1/2a and 1/2b, coincided with overt illness. The results of PCR indicate an incidence of five to nine exposures to Listeria monocytogenes per person per year. On average, the incidence of culture-confirmed fecal carriage in healthy adults is two episodes of Listeria monocytogenes carriage per person per year. Fecal shedding was of short duration (maximum 4 days), which argues against the appropriateness of routine stool screening in dairy workers as a tool for prevention of listeriosis.

Genetic homogeneity among Listeria monocytogenes strains from infected patients and meat products from two geographic locations determined by phenotyping, ribotyping and PCR analysis of virulence genes

Thirty Listeria monocytogenes isolates from human patients and foods originated from two different geographic locations without any epidemiological relations were analyzed for their genotypic and phenotypic virulence gene expressions and genetic relatedness. All strains contained virulence genes, inlA, inlB, actA, hlyA, plcA and plcB, with expected product size in PCR assay except for the actA gene. Some strains produced actA gene product of 268 and others 385 bp. Phenotypically, all were hemolytic but showed variable expressions of phospholipase activity. Ribotyping classified isolates into 12 different groups based on the similarity to DuPont Identification numbers (DID), which consisted primarily of clinical or food isolates or both. Cluster analysis also indicated possible existence of clones of L. monocytogenes that are found in food or human hosts or are evenly distributed between these two. Two isolates (F1 from food and CHL1250 from patient) had unique ribotype patterns that were not previously reported in the RiboPrinter database. This study indicates distribution of diverse L. monocytogenes strains in clinical and food environments. The isolates showed 92-99% genetic homogeneity, in spite of their origins from two different geographic locations and environments.

Comparison of an automated ribotyping system to restriction endonuclease analysis and pulsed-field gel electrophoresis for differentiating vancomycin-resistant Enterococcus faecium isolates

The RiboPrinter Microbial Characterization System was compared with pulsed-field gel electrophoresis (PFGE), restriction endonuclease analysis (REA), and epidemiological data for typing 45 vancomycin-resistant Enterococcus faecium (VRE) isolates. In 21 clinically related isolates, 90 to 100% were similar by PFGE and REA, but only 57% were similar by the RiboPrinter. In another eight clinically related isolates, three isolates similar by PFGE and REA were all unique by the RiboPrinter. In contrast, in 16 clinically unrelated isolates, the predominant RiboPrinter ribotype represented 50% of the strains, while the largest PFGE and REA clones represented less than 19% of the strains. These data suggest that the RiboPrinter is not reliable for VRE investigation.

Catheter-related bacteremia due to Kocuria kristinae in a patient with ovarian cancer

We report on the first case of a catheter-related recurrent bacteremia caused by Kocuria kristinae, a gram-positive microorganism belonging to the family Micrococcaceae, in a 51-year-old woman with ovarian cancer. This unusual pathogen may cause opportunistic infections in patients with severe underlying diseases.

Automated ribotyping and random amplified polymorphic DNA analysis for molecular typing of Salmonella enteritidis and Salmonella typhimurium strains isolated in Italy

AIMS

The ability of automated ribotyping and random amplified polymorphic DNA (RAPD) analysis to differentiate Salmonella enteritidis and Salmonella typhimurium isolates in relation to their origin was evaluated.

METHODS AND RESULTS

The restriction enzymes EcoRI, PvuII and PstI, and the random primers OPB17 and P1254, were tested for ribotyping and RAPD analysis, respectively. Seventeen subtypes were identified among the isolates of the two pathogenic Salmonella serovars using the RiboPrinter, and 25 subtypes using RAPD.

CONCLUSIONS

The greatest degree of genetic diversity was observed among Salm. typhimurium isolates using both automated ribotyping (Simpson's index of discrimination 0878) and RAPD (Simpson's index of discrimination 0886).

SIGNIFICANCE AND IMPACT OF THE STUDY

According to the results of this research, automated ribotyping and RAPD are two useful genotyping techniques for identifying unique and common subtypes associated with a specific source and location, and provide powerful tools for epidemiological investigations.

Automated ribotyping using different enzymes to improve discrimination of Listeria monocytogenes isolates, with a particular focus on serotype 4b strains

To develop improved automated subtyping approaches for Listeria monocytogenes, we characterized the discriminatory power of different restriction enzymes for ribotyping. When 15 different restriction enzymes were used for automated ribotyping of 16 selected L. monocytogenes isolates, the restriction enzymes EcoRI, PvuII, and XhoI showed high discriminatory ability (Simpson's index of discrimination > 0.900) and produced complete and reproducible restriction cut patterns. These three enzymes were thus evaluated for their ability to differentiate among isolates representing the two major serotype 4b epidemic clones, those having ribotype reference pattern DUP-1038 (51 isolates) and those having pattern DUP-1042 (20 isolates). Among these isolates, PvuII provided the highest discrimination for a single enzyme (nine different subtypes; index of discrimination = 0.518). A combination of PvuII and XhoI showed the highest discriminatory ability (index of discrimination = 0.590) for these isolates. A group of 44 DUP-1038 isolates and a group of 12 DUP-1042 isolates were identical to each other even when the combined data for all three enzymes were used. We conclude that automated ribotyping using different enzymes allows improved discrimination of L. monocytogenes isolates, including epidemic serotype 4b strains. We furthermore confirm that most of the isolates representing the genotypes linked to the two major epidemic L. monocytogenes clonal groups form two genetically homogeneous groups.

Molecular epidemiologic features and antimicrobial susceptibility profiles of various ribotypes of Pseudomonas aeruginosa isolated from humans and ruminants

OBJECTIVES

To assess automated ribotyping for characterization of Pseudomonas aeruginosa isolates and to identify their type prevalence and geographic distribution.

SAMPLE POPULATION

39 human and 56 ruminant P aeruginosa isolates.

PROCEDURES

Isolates were identified by use of bacteriologic techniques and automated Pvull-based ribotyping. Susceptibility to antimicrobials was tested in vitro. Data were analyzed for index of discrimination; prevalence ratio; geographic distribution of ribotypes found only in humans, only in cows, or only in goats (single-host ribotypes); and geographic distribution of ribotypes found in humans and ruminants (multihost ribotypes).

RESULTS

All isolates were typeable (45 ribotypes, 35 single-host ribotypes). Ribotyping index of discrimination was 0.976. More isolates (45.3%) than expected yielded multihost ribotypes (22% of all ribotypes). Although 8.6% of single-host ribotypes were found in 4 or more isolates, 60% of multihost ribotypes were found in 4 or more isolates. Ninety percent of multihost ribotypes were isolated from different geographic areas, whereas 3.0% of single-host ribotypes were isolated from different geographic areas. All ruminant isolates were susceptible to gentamicin and polymyxin B. In contrast, antibiogram profiles differed for human isolates from different geographic areas. Susceptibility to antimicrobials differentiated 6 isolates not distinguished by ribotyping.

CONCLUSIONS AND CLINICAL RELEVANCE

Automated ribotyping with Pvull discriminated more isolates than in vitro antimicrobial susceptibility. In combination, both tests provided more information than either test alone. Given the greater prevalence and geographic distribution of multihost ribotypes, immunocompromised humans and lactating ruminants may have a greater risk for disease if exposed to multihost P aeruginosa ribotypes, compared with single-host ribotypes.

Binary typing of Staphylococcus aureus strains through reversed hybridization using digoxigenin-universal linkage system-labeled bacterial genomic DNA

A novel binary typing (BT) procedure, based on reversed hybridization of digoxigenin-universal linkage system-labeled bacterial DNA to strip-immobilized probes, is presented. Chromogenic detection of hybrids was performed. Staphylococcus aureus isolates (n = 20) were analyzed to establish the feasibility of BT. A technically simple and fast procedure has been developed for application in routine microbiology laboratories.

Molecular surveillance of European quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping

Nosocomial isolates of Pseudomonas aeruginosa and Acinetobacter spp. exhibit high rates of resistance to antibiotics and are often multidrug resistant. In a previous study (D. Milatovic, A. Fluit, S. Brisse, J. Verhoef, and F. J. Schmitz, Antimicrob. Agents Chemother. 44:1102-1107, 2000), isolates of these species that were resistant to sitafloxacin, a new advanced-generation fluoroquinolone with a high potency and a broad spectrum of antimicrobial activity, were found in high proportion in 23 European hospitals. Here, we investigate the clonal diversity of the 155 P. aeruginosa and 145 Acinetobacter spp. sitafloxacin-resistant isolates from that study by automated ribotyping. Numerous ribogroups (sets of isolates with indistinguishable ribotypes) were found among isolates of P. aeruginosa (n = 34) and Acinetobacter spp. (n = 16), but the majority of the isolates belonged to a limited number of major ribogroups. Sitafloxacin-resistant isolates (MICs > 2 mg/liter, used as a provisional breakpoint) showed increased concomitant resistance to piperacillin, piperacillin-tazobactam, ceftriaxone, ceftazidime, amikacin, gentamicin, and imipenem. The major ribogroups were repeatedly found in isolates from several European hospitals; these isolates showed higher levels of resistance to gentamicin and imipenem, and some of them appeared to correspond to previously described multidrug-resistant international clones of P. aeruginosa (serotype O:12) and Acinetobacter baumannii (clones I and II). Automated ribotyping, when used in combination with more discriminatory typing methods, may be a convenient library typing system for monitoring future epidemiological dynamics of geographically widespread multidrug-resistant bacterial clones.

Cultivatable microbial biodiversity: gnawing at the Gordian knot

Rapid and inexpensive sorting of bacterial isolates may be achieved using Fourier transform infrared spectroscopy (FT-IR), a method that has hitherto been applied to identification and classification. The comprehensive characterization of environmental samples requires the isolation of large numbers of isolates using different growth media and growth conditions. In such cases, sorting the isolates is critical before isolates are subjected to more detailed studies. Using FT-IR, isolates are grown under standardized conditions, and 100 strains can be tested within less than 8 h. Chemotaxonomic and molecular characterization of members of clusters emerging from FT-IR analysis either at a level of spectral distance values below 20-30 (analysis of region 600-800 cm(-1), average linkage algorithm) or at spectral heterogeneity values below 75 (regions 1,200-900, 3,000-2,798 and 901-698, scaling to first region, Ward's algorithm) reveals great similarities in fatty acids and 16S rDNA sequences. As judged from riboprinting analyses and fatty acid analyses, FT-IR analysis is able to unravel intraspecific subclustering. The example used in this study of 100 isolates from a mat system, Lake Fryxell, Dry Valleys, Antarctica, selected from a larger number of isolates, picked mainly on the basis of colony pigmentation and form, reveals the utility of the method for identifying the number of putative species quickly. The method described is able to select strains rapidly that represent clusters at the specific and intraspecific level for subsequent characterization.

Distinguishing species of the Burkholderia cepacia complex and Burkholderia gladioli by automated ribotyping

Several species belonging to the genus Burkholderia are clinically relevant, opportunistic pathogens that inhabit major environmental reservoirs. Consequently, the availability of means for adequate identification and epidemiological characterization of individual environmental or clinical isolates is mandatory. In the present communication we describe the use of the Riboprinter microbial characterization system (Qualicon, Warwick, United Kingdom) for automated ribotyping of 104 strains of Burkholderia species from diverse sources, including several publicly accessible collections. The main outcome of this analysis was that all strains were typeable and that strains of Burkholderia gladioli and of each species of the B. cepacia complex, including B. multivorans, B. stabilis, and B. vietnamiensis, were effectively discriminated. Furthermore, different ribotypes were discerned within each species. Ribotyping results were in general agreement with strain classification based on restriction fragment analysis of 16S ribosomal amplicons, but the resolution of ribotyping was much higher. This enabled automated molecular typing below the species level. Cluster analysis of the patterns obtained by ribotyping (riboprints) showed that within B. gladioli, B. multivorans, and B. cepacia genomovar VI, the different riboprints identified always clustered together. Riboprints of B. cepacia genomovars I and III, B. stabilis, and B. vietnamiensis did not show distinct clustering but rather exhibited the formation of loose assemblages within which several smaller, genomovar-specific clusters were delineated. Therefore, ribotyping proved useful for genomovar identification. Analysis of serial isolates from individual patients demonstrated that infection with a single ribotype had occurred, despite minor genetic differences that were detected by pulsed-field gel electrophoresis of DNA macrorestriction fragments. The automated approach allows very rapid and reliable identification and epidemiological characterization of strains and generates an easily manageable database suited for expansion with information on additional bacterial isolates.