Ribotyping of Pseudomonas aeruginosa: discriminatory power and usefulness as a tool for epidemiological studies

Molecular epidemiology of Pseudomonas aeruginosa isolated from lower respiratory tract of ICU patients

Lower respiratory tract infections (LRTIs) caused by Pseudomonas aeruginosa are the most common infection among hospitalized patients, associated with increased levels of morbidity, mortality and attributable health care costs. Increased resistant Pseudomonas worldwide has been quite meaningful to patients, especially in intensive care unit (ICUs). Different species of Pseudomonas exhibit different genetic profile and varied drug resistance. The present study determines the molecular epidemiology through DNA fingerprinting method and drug resistance of P. aeruginosa isolated from patients with LTRIs admitted in ICU. A total of 79 P. aeruginosa isolated from patients with LRTIs admitted in ICU were characterized by Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD) and Repetitive Extrapalindromic PCR (REP-PCR). Antibiotic resistance was determined by minimum inhibitory concentration (MIC) assay while MDR genes, viz, blaTEM, blaOXA, blaVIM, blaCTX-M-15 were detected by polymerase chain reaction (PCR). Of the 137 Pseudomonas sp isolated from ICU patients, 57.7% of the isolates were reported to be P. aeruginosa. The overall prevalence of P. aeruginosa among the all included patients was 34.5%. The RAPD analysis yielded 45 different patterns with 72 clusters with 57% to 100% similarity level. The RFLP analysis yielded 8 different patterns with 14 clusters with 76% to 100% similarity level. The REP PCR analysis yielded 37 different patterns with 65 clusters with 56% to 100% similarity level. There was no correlation among the different DNA patterns observed between the three different methods. Predominant of the isolates (46.8%) were resistant to amikacin. Of the 79 isolates, 60.8% were positive for blaTEM gene and 39.2% were positive for blaOXA gene. P. aeruginosa was predominantly isolated from patients with LRTIs admitted in ICU. The difference in the similarity level observed between the three DNA fingerprinting methods indicates that there is high inter-strain variability. The high genetic variability and resistance patterns indicates that we should continuously monitor the trend in the prevalence and antibiotic resistance of P. aeruginosa especially in patients with LRTIs admitted in ICU.

Phenotypic and molecular characterization of nosocomial K. pneumoniae isolates by ribotyping

PURPOSE

To characterize clinical isolates of Klebsiella pneumoniae by phenotypic and genotypic methods.

MATERIAL/METHODS

Over a 12-month period, 52 isolates of K. pneumoniae were isolated. Of these 52 isolates, 7 were isolated over a period of 21 days from a suspected outbreak in the Neonatal Intensive Care Unit (NICU) and 45 from sporadic cases occurring in different wards of hospital were analysed.

RESULTS

The prevalence of K. pneumoniae isolates was 4% (52/1295). Quinolones, aztreonam and amikacin showed the greatest efficacy showing >85% sensitivity. Of the 52 isolates of K. pneumoniae, 8 (15.4%) isolates were positive for ESBL-production. Among the ESBL-producing K. pneumoniae, two out of 8 (25%) and 6 out of 8 (75%) were positive for (bla)SHV and (bla)CTX-M genes respectively. Ribotyping identified 30 distinct ribogroups among 52 isolates evaluated. Seven NICU outbreak isolates were divided into 2 ribotypes, as many as 6 belonged to one ribotype while one isolate which was isolated a week later was of a different ribotype, indicating the termination of the outbreak in the NICU. The outbreak in the NICU thus, was shown to have been caused by a single clone.

CONCLUSIONS

A high discriminatory power, ease of interpretation coupled with excellent reproducibility and stability make ribotyping a very useful technique for investigating the molecular epidemiology of nosocomial infections caused by K. pneumoniae. A regular surveillance of hospital associated infections including monitoring antibiotic sensitivity pattern of K. pneumoniae, ESBL-production and molecular characterization is mandatory to control the spread of multidrug-resistant and ESBL-producing K. pneumoniae and for epidemiological purposes especially in outbreak situations.

Four genotyping schemes for phylogenetic analysis of Pseudomonas aeruginosa: comparison of their congruence with multi-locus sequence typing

Several molecular typing schemes have been proposed to differentiate among isolates and clonal groups, and hence establish epidemiological or phylogenetic links. It has been widely accepted that multi-locus sequence typing (MLST) is the gold standard for phylogenetic typing/long-term epidemiological surveillance, but other recently described methods may be easier to carry out, especially in settings with limited access to DNA sequencing. Comparing the performance of such techniques to MLST is therefore of relevance. A study was therefore carried out with a collection of P. aeruginosa strains (n = 133) typed by four typing schemes: MLST, multiple-locus variable number tandem repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE) and the commercial DiversiLab microbial typing system (DL). The aim of this study was to compare the results of each typing method with MLST. The Simpson's indices of diversity were 0.989, 0.980, 0.961 and 0.906 respectively for PFGE, MLVA, DL and MLST. The congruence between techniques was measured by the adjusted Wallace index (W): this coefficient indicates the probability that a pair of isolates which is assigned to the same type by one typing method is also typed as identical by the other. In this context, the congruence between techniques was recorded as follow: MLVA-type to predict MLST-type (93%), PFGE to MLST (92%), DL to MLST (64.2%), PFGE to MLVA (63.5%) and PFGE to DL (61.7%). Conversely, for all above combinations, prediction was very poor. The congruence was increased at the clonal complex (CC) level. MLST is regarded the gold standard for phylogenetic classification of bacteria, but is rather laborious to carry out in many settings. Our data suggest that MLVA can predict the MLST-type with high accuracy, and even higher when studying the clonal complex level. Of the studied three techniques MLVA was therefore the best surrogate method to predict MLST.

Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus

Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed.

[Various typing methods of Pseudomonas aeruginosa strains isolated from cystic fibrosis patients]

Typing methods are essential to understand the epidemiology of bacterial infections. Strain typing is important for the detection of sources or routes of infections, identification between endemic and epidemic strains and prevention of transmission between patients. Some Pseudomonas aeruginosa cystic-fibrosis strains could not be typed with conventional typing methods. Due to the diverse phenotypic nature of P. aeruginosa, phenotyping methods are not discriminatory enough to identify strains belonging to the same genotype. Thus, molecular typing methods are required. These methods should be applied when data from phenotypic typing analysis becomes ambiguous, such as in cystic fibrosis. Molecular typing methods, developed over the past decade, are highly discriminatory in capacity and reproducibility. However, they are more likely applied in specialized laboratories since they are expensive and increase the workload. A reliable and low-cost typing system is required for better defining the epidemiology of this pathogen and designing more rational policies of infection control. Comparison between typing methods will pinpoint the limits and effectiveness of each method and will improve in turn the choice of a nonspecialized laboratory in terms of simplicity, time and cost.

Population genetic analysis of Pseudomonas aeruginosa using multilocus sequence typing

To study the population genetic structure of Pseudomonas aeruginosa, we developed a multilocus sequence typing scheme. The sequences of internal fragments of seven housekeeping genes were obtained for 34 P. aeruginosa isolates from patients hospitalized in five different European cities. Twenty-six different allelic profiles were identified. The mean allelic diversity was 0.854 (range: 0.606-0.978), which was about six times greater than the results obtained with the multilocus enzyme electrophoresis method. Linkage disequilibrium was measured with the index of association. An index of 1.95+/-0.24 was calculated when all the strains were considered. This index was 1.76+/-0.27 when only one strain per sequence type was considered. Both results were different from 0, indicating linkage among loci, which means that the population structure of our set of P. aeruginosa isolates is clonal. The clonal structure of the population was also suggested by the congruence of the topology of the different trees obtained from the seven housekeeping genes. These results are in contrast to previous studies, finding a non clonal population structure. Since a small number of isolates was analyzed in this study, there might be a bias of selection which includes the possibility that they belong to widely disseminated epidemic clones. Another possibility is that recombination did not occurred homogeneously throughout the genome of P. aeruginosa, so that part of it has a clonal structure, while the remaining part of the genome is more frequently subject to recombination.

PCR identification and automated ribotyping of Pseudomonas aeruginosa clinical isolates from intensive care patients

Nosocomial isolates of Pseudomonas aeruginosa exhibit high rates of resistance to antibiotics, and are often multidrug resistant. P. aeruginosa clinical isolates (n = 56) were obtained from ICU patients in a hospital in Pakistan over a 3-y period. Antimicrobial susceptibility of the 56 P. aeruginosa clinical isolates was investigated using 7 antibiotics and the resistance rates were as follows: aztreonam (68% resistant), ceftazidime (67%), imipenem (66%), ofloxacin (59%), amikacin (56%), gentamicin (44%), and piperacillin-tazobactam (27%) (p < 0.01). In addition, 55% of the P. aeruginosa clinical isolates were resistant to 4 or more antibiotics. Imipenem-resistant strains were frequently associated with ceftazidime, ofloxacin, aztreonam, and more strikingly, amikacin resistance (p < 0.05). PCR (using P. aeruginosa-specific primers VIC1 + VIC2 and P1 + P2, respectively) was highly specific and sensitive, and was positive for all 56 P. aeruginosa isolates tested. Automated ribotyping was used to investigate the clonal diversity of the 56 P. aeruginosa isolates. Automated ribotyping indicated that the clinical isolates were clonally related and could be clustered into 4 major ribogroups based on their similarity index, with ribogroup II being the dominant one. The P. aeruginosa isolates in ribogroup II were correlated with their antibiotic resistance pattern and, interestingly, there seemed to be a gradual acquisition of multiple antibiotic resistance associated with the isolates within this group over time. The ribotyping data, together with the antibiotic resistance profile, provide valuable molecular epidemiology information for the control of hospital-acquired P. aeruginosa infections.

A single phylogenetic analysis of Bacillus thuringiensis strains and bacilli species inferred from 16S rRNA gene restriction fragment length polymorphism is congruent with two independent phylogenetic analyses

AIMS

To assess the congruence between two earlier independent phylogenetic studies on Bacillus thuringiensis strains and on Bacillus-related species and the single, all-encompassing, phylogenetic tree presented here inferred from the combination of the two earlier datasets.

METHODS AND RESULTS

A dendrogram was constructed using a combination of the data from our previous studies on 16S rRNA gene fingerprinting of 86 B. thuringiensis strains and of 77 species of Bacillus and related taxa. It revealed that all B. thuringiensis strains were clustered together in four distinct groups at a DNA similarity rate of 93%, except two serovars, bolivia and finitimus. Four bacilli species, Paenibacillus alvei, P. azotofixans, B. lentus and B. licheniformis, share a DNA similarity rate of 92% with Bt Group IV.

CONCLUSIONS

Most, but not all, B. thuringiensis strains could be grouped together based on the DNA similarity rate. They were also very close to some other bacilli species.

SIGNIFICANCE AND IMPACT OF THE STUDY

The combined phylogenetic study presented here, inferred from 16S rRNA gene restriction fragment length polymorphism, is congruent with two earlier independent phylogenetic studies, one on B. thuringiensis and the other on bacilli species.

Pseudo-outbreak of Pseudomonas aeruginosa and Serratia marcescens related to bronchoscopes

OBJECTIVE

To investigate an apparent outbreak involving simultaneous isolation of Pseudomonas aeruginosa and Serratia marcescens from bronchoalveolar lavage (BAL) samples.

DESIGN

Retrospective and prospective cohort studies using chart review, environmental sampling, and ribotyping of all available isolates. Cleaning and disinfection procedures for the bronchoscopes were also evaluated.

SETTING

A 380-bed private hospital in São Paulo, Brazil

PATIENTS

Forty-one patients who underwent bronchoscopic procedures between December 1994 and October 1996 and from whom P. aeruginosa and S. marcescens were concomitantly isolated. Bronchoscopes and related items were microbiologically assessed.

RESULTS

P. aeruginosa and S. marcescens were simultaneously isolated from BAL samples 12.6% of the time (41 of 324) during the epidemic period versus 1.8% of the time (1 of 54) in the pre-epidemic period (P = .035). Ribotyping revealed two strains of P. aeruginosa and one of S. marcescens that were isolated from BAL samples of patients with no signs of respiratory tract infection, suggesting a pseudo-outbreak. Evaluation of bronchoscope disinfection revealed that inappropriate methods were being used. Implementation of simple control measures resulted in a significant decrease in simultaneous isolation of these species.

CONCLUSION

Prevention of pseudo-outbreaks requires meticulous use of preventive measures for infection-prone medical procedures.

An outbreak of multidrug-resistant Pseudomonas aeruginosa associated with increased risk of patient death in an intensive care unit

OBJECTIVE

To investigate an outbreak of multidrug-resistant Pseudomonas aeruginosa in an intensive care unit (ICU).

DESIGN

Epidemiologic investigation, environmental assessment, and ambidirectional cohort study.

SETTING

A secondary-care university hospital with a 10-bed ICU.

PATIENTS

All patients admitted to the ICU receiving ventilator treatment from December 1, 1999, to September 1, 2000.

RESULTS

An outbreak in an ICU with multidrug-resistant isolates of P aeruginosa belonging to one amplified fragment-length polymorphism (AFLP)-defined genetic cluster was identified, characterized, and cleared. Molecular typing of bacterial isolates with AFLP made it possible to identify the outbreak and make rational decisions during the outbreak period. The outbreak included 19 patients during the study period. Infection with bacterial isolates belonging to the AFLP cluster was associated with reduced survival (odds ratio, 5.26; 95% confidence interval, 1.14 to 24.26). Enhanced barrier and hygiene precautions, cohorting of patients, and altered antibiotic policy were not sufficient to eliminate the outbreak. At the end of the study period (in July), there was a change in the outbreak pattern from long (December to June) to short (July) incubation times before colonization and from primarily tracheal colonization (December to June) to primarily gastric or enteral July) colonization. In this period, the bacterium was also isolated from water taps.

CONCLUSION

Complete elimination of the outbreak was achieved after weekly pasteurization of the water taps of the ICU and use of sterile water as a solvent in the gastric tubes.

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.

Specific and rapid identification of multiple-antibiotic resistant Pseudomonas aeruginosa clones isolated in an intensive care unit

Seventeen multiple-antibiotic-resistant Pseudomonas aeruginosa isolates were collected from two patients hospitalized in the same intensive care unit. They showed a parallel acquisition of resistance to antibiotics and they were, therefore, thought to have a common clonal origin. These strains were typed by biotyping, serotyping, plasmid profile, three different PCR-based techniques, and macrorestriction analysis to determine their relationship. Only the use of PCR techniques and macrorestriction analysis allowed an accurate identification of the clones and revealed that each patient was infected by A unique multidrug-resistant strain. Therefore, there was no cross-infection or reinfection with a new strain.

Enzyme polymorphism in Pseudomonas aeruginosa strains recovered from cystic fibrosis patients in France

Each of 314 strains of Pseudomonas aeruginosa recovered from 87 French cystic fibrosis (CF) patients was typed by multilocus enzyme electrophoresis to investigate the genetic diversity, the relatedness and the molecular epidemiology of strains isolated from cases of chronic pulmonary colonization. Comparison of allele profiles at 18 enzyme loci identified 17 electrophoretic types (ETs). Of the 314 isolates, 290 (92%) were either ET1 (n = 127) or ET2 (n = 163), which differed only at the shikimate dehydrogenase (SKD) locus. The mean genetic diversity (H) was 0.138. These results suggest that there is cross-colonization between patients and/or that two predominant groups of strains are able to colonize French CF patients. Sequential isolates collected from 18 patients during a period of 12-28 months were analysed to assess genomic variability and its relationship to clinical outcome. Six patients were colonized by a stable strain. For the others, double infections or changes in colonization over time were observed. No relationships were detected between the clinical outcome and the persistence of stable isolates, the emergence of transient superinfecting variants, the presence of multiple ETs or the shift of ET during the monitoring.

Frequency and molecular diversity of Pseudomonas aeruginosa upon admission and during hospitalization: a prospective epidemiologic study

OBJECTIVE: To assess the molecular epidemiology and risk factors for Pseudomonas aeruginosa colonization and infection in hospitalized patients. METHODS: In a 1000-bed university hospital, newly admitted patients were assessed prospectively for colonization and infection with P. aeruginosa. Anal swabs were obtained upon admission and at discharge. Ribotyping was used for the typing of isolates. Epidemiologic and clinical data were recorded prospectively. Independent risk factors were assessed using multivariate analysis. RESULTS: The recovery rate of patients with P. aeruginosa from anal specimens on admission was 6.7% (42/628). Infection due to P. aeruginosa was observed in 20 of 628 (3.2%) patients, of whom 10 (1.6%) were already infected on admission. Independent risk factors for colonization/infection on admission were age, indwelling urinary catheter, the presence of wound and seropositivity for HIV. Independent risk factors for nosocomial infection were anal colonization on admission, alcoholism, indwelling urinary catheter and antibiotic treatment during hospitalization. Ribotyping revealed that 27 patients were colonized or infected with a unique ribotype, whereas 24 shared one or more ribotypes with other patients. Analysis of epidemiologic and molecular typing data revealed that transmission from patients to patients or from patients to environment was documented on only three occasions. CONCLUSIONS: A great many P. aeruginosa strains were isolated from patients and the environment, and most environmental strains were different from those recovered in patients, suggesting a low rate of hospital acquisition of P. aeruginosa from the environment. The main risk factors for hospital-acquired infection were detectable colonization on admission, antibiotic treatment and urinary catheter.

Computerized restriction endonuclease analysis compared with O-serotype and phage type in the epidemiologic fingerprinting of Pseudomonas aeruginosa strains

OBJECTIVE: To assess restriction endonuclease analysis (REA) of chromosomal DNA using SalI enzyme, low-concentration (0.4%) agarose gels and digitalized data management of the REA patterns obtained for the typing of clinical Pseudomonas aeruginosa isolates. METHODS: A group of 67 clinical unrelated isolates from 10 Spanish hospitals was used to study the discriminatory power, reproducibility and typeability of REA typing. RESULTS: A SalI REA pattern consisted of a variety (1--10) of restriction bands in the range between 12.2 and 48.5 kb and an unresolvable smear of low-molecular-weight bands. Forty different SalI REA patterns with an index of discrimination of 0.979 were obtained. Low typeability (91.04%) was the major limitation of REA typing. Analysis of blinded subcultures of eight Pseudomonas aeruginosa strains showed the reproducibility of REA typing to be 87.5%. Combined phenotypic typing (O-serotyping and phage typing) performed on the same group of strains showed comparable discrimination but much lower reproducibility. Isolates selected from five clusters of nosocomial infections in hospitals in the UK were typed by REA typing, and the results show high agreement when compared with conventional phenotypic typing methods in distinguishing between strains. CONCLUSIONS: These data underline the usefulness of REA typing enhanced with digitalized data management for the epidemiologic subtyping of clinical Pseudomonas aeruginosa isolates.

Multiresistant Pseudomonas aeruginosa serogroup O:11 outbreak in an intensive care unit

OBJECTIVE: To determine whether 15 multiresistant Pseudomonas aeruginosa isolates from an intensive care unit (ICU) outbreak were related, were endemic, and belonged to the O:12 European clone. METHODS: Forty-six P. aeruginosa isolates from a large hospital were investigated with respect to their antibiotic resistance profiles, serogroups, bacteriocin types and DNA fingerprints obtained by pulsed-field gel electrophoresis (PFGE) of genomic DNA digested with Xbal. RESULTS: Fourteen of the ICU outbreak isolates were indeed identical with respect to their serogroup, O:11, pyocin type, 10/a, and PFGE type, A. Clone A was endemic and dominant throughout the hospital, even though, within the ICU, it underwent phenotypic alterations, such as loss of cell wall lipopolysaccharide side-chains, or acquisition of ceftazidime and imipenem resistance. Bacteriocin typing was more discriminatory than serotyping, but PFGE could differentiate further among phenotypically identical strains. It also allowed the tracking of an O:6 strain, as it was becoming gradually more resistant and undergoing a bacteriocin-type conversion while remaining genotypically unaltered. CONCLUSIONS: Using three typing methods, a nosocomial multiresistant strain distinct from the previously described dominant European O:12 clone was characterized, and the ability of PFGE to identify clonal isolates even when these appear phenotypically distinct was demonstrated.

Arbitrary primed PCR fingerprinting and serotyping of clinical Pseudomonas aeruginosa strains

Arbitrary primed PCR (AP-PCR) analysis was compared with serotyping as a means of high-resolution typing of Pseudomonas aeruginosa. Seventy-four isolates from 3 different hospitals and 18 reference strains were studied. Serotyping provided good index of discrimination, although eleven isolates could not be serotyped. Genomic DNA was amplified with a single 10 nucleotide primer (sequence 5'-AGG GGT CTT G-3'). The strains were genetically diverse and 61 different AP-PCR profiles of 2-7 bands between 0.3 and 2.4 kb were obtained. AP-PCR profiles were not consistently associated with serotypes, but they clearly subtyped strains of the same serotype. Numerical analysis of AP-PCR patterns defined 7 groups at the 55% similarity level, and identified predominant strains in each hospital. The results show that AP-PCR analysis provides a simple and practical approach to typing P. aeruginosa that is more discriminatory than traditional serotyping scheme. We suggest that maximum discrimination can be achieved by a combination of both methods.

Genetic diversity of rRNA operons of unrelated Streptococcus agalactiae strains isolated from cerebrospinal fluid of neonates suffering from meningitis

The genetic diversity of a collection of 54 unrelated Streptococcus agalactiae strains isolated from the cerebrospinal fluid of neonates and of 60 unrelated carrier strains was evaluated by investigating the restriction fragment length polymorphism of the rRNA gene region. Three restriction enzymes were selected for use: PstI, HindIII, and CfoI. Clustering analysis revealed two phylogenetic groups of strains with 40% divergence. Group I contained two clusters, A and B, and group II contained three clusters, C, D, and E. Strains of serotype Ia were mostly distributed in cluster A, and strains of serotype Ib were mostly distributed in cluster E. Serotype III isolates did not cluster. Nevertheless, 37 of 39 isolates belonging to cluster B were serotype III. With HindIII, two rRNA gene banding patterns characterized 38 of the 39 strains of cluster B, which represents a high-virulence group. In addition, two rRNA gene banding patterns with each enzyme and/or a pair of CfoI fragments of 905 and 990 bp identified 81% of the invasive strains. On account of the genetic homogeneity of the cerebrospinal fluid strains, ribotyping is a powerful typing method for investigation of nosocomial or epidemic invasive infections only when all three enzymes are used or when PstI and HindIII or PstI and CfoI are combined with serotyping (index of discrimination, > 0.95).

Quantitative Antibiogram as a Typing Method for the Prospective Epidemiological Surveillance and Control of MRSA Comparison with Molecular Typing

Objective:

Evaluation of the quantitative antibiogram as an epidemiological tool for the prospective typing of methicillin-resistantStaphylococcus aureus(MRSA), and comparison with ribotyping.

Methods:

The method is based on the multivariate analysis of inhibition zone diameters of antibiotics in disk diffusion tests. Five antibiotics were used (erythromycin, clindamycin, cotrimoxazole, gentamicin, and ciprofloxacin). Ribotyping was performed using seven restriction enzymes (EcoRV,HindIII,KpnI,PstI,EcoRI,SfuI, andBamHI).

Setting:

1,000-bed tertiary university medical center.

Results:

During a 1-year period, 31 patients were found to be infected or colonized with MRSA. Cluster analysis of antibiogram data showed nine distinct antibiotypes. Four antibiotypes were isolated from multiple patients (2, 4, 7, and 13, respectively). Five additional antibiotypes were isolated from the remaining five patients. When analyzed with respect to the epidemiological data, the method was found to be equivalent to ribotyping.

Among 206 staff members who were screened, six were carriers of MRSA. Both typing methods identified concordant of MRSA types in staff members and in the patients under their care.

Conclusions:

The quantitative antibiogram was found to be equivalent to ribotyping as an epidemiological tool for typing of MRSA in our setting. Thus, this simple, rapid, and readily available method appears to be suitable for the prospective surveillance and control of MRSA for hospitals that do not have molecular typing facilities and in which MRSA isolates are not uniformly resistant or susceptible to the antibiotics tested.

Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics

Most of the bacterial species are still unknown. Consequently, our knowledge about bacterial ecology is poor and expectations about specialized species with novel enzymatic functions or new products are high. Thus, bacterial identification is a growing field of interest within microbiology. In this review, suitability of developments for identification based on miniaturized biochemical and physiological investigations of bacteria are evaluated. Special emphasis is given to chemotaxonomic methods such as analysis of quinone system, fatty acid profiles, polar lipid patterns, polyamine patterns, whole cell sugars, peptidoglycan diaminoacids, as well as analytical fingerprinting methods and cellular protein patterning. 16S rDNA sequencing introduced to investigate the phylogenetic relationships of bacteria, nucleic acids hybridization techniques and G + C content determination are discussed as well as restriction fragment length polymorphism (RFLP), macrorestriction analysis and random amplified polymorphic DNA (RAPD). The importance of the different approaches in classification and identification of bacteria according to phylogenetic relationships are demonstrated on selected examples.

Comparative evaluation of an automated ribotyping system versus pulsed-field gel electrophoresis for epidemiological typing of clinical isolates of Escherichia coli and Pseudomonas aeruginosa from patients with recurrent gram-negative bacteremia

Ribotyping and macrorestriction analysis of chromosomal DNA using pulsed-field gel electrophoresis (PFGE) are among the more useful molecular epidemiologic typing methods. Because these techniques are labor intensive, automation of one or more steps may allow clinical laboratories to apply molecular typing methods. We compared the recently developed automated ribotyping system, the RiboPrinter Microbial Characterization System (DuPont), with PFGE as a means of typing clinical isolates of E. coli and P. aeruginosa. A total of 22 E. coli and 24 P. aeruginosa were typed by both PFGE and the RiboPrinter. When compared with PFGE typing of E. coli and P. aeruginosa, the RiboPrinter was less sensitive in identifying different strains, particularly among the isolates of P. aeruginosa. The RiboPrinter was completely automated and allowed up to 32 isolates to be typed within an 8-hour period. The pattern of results obtained in this study suggests that a heirarchical approach to molecular typing using the RiboPrinter Microbial Characterization System plus PFGE might be feasible. The RiboPrinter Microbial Characterization System promises to be a very useful addition to the expanding molecular typing armamentarium.

Pseudomonas aeruginosa ribotyping: stability and interpretation of ribosomal operon restriction patterns

Fifty-one Pseudomonas aeruginosa isolates were differentiated into 21 types by ribotyping. Several enzyme combinations, including the best ones proposed in literature, were utilized and the highest discrimination was reached by individual digestion with PvuII, HindII, and EcoRI or BamHI. Clinical isolates from outbreaks were clonally related as identified by this molecular approach. Restriction rDNA profiles were composed of strong and weak bands. Using 6 micrograms DNA we were able to demonstrate that PvuII, HindIII, and BamHI weak bands were reproducible. These weak bands should be considered not only to accomplish the highest discrimination but also to correctly assign isolate clonality. Conversely, we found that EcoRI weak bands were not reproducible and, therefore, are not recommended for ribotype analysis. Finally, profiles differing in one single band actually represented isolates of different genotype, as confirmed by further analysis using other molecular methods. In this report on P. Aeruginosa ribotyping of clinical isolates, criteria for band pattern interpretation are established.

Ribotyping of Pseudomonas aeruginosa isolates from patients and water springs and genome fingerprinting of variants concerning mucoidy

Thirty-one strains of Pseudomonas aeruginosa, isolated from water springs, clinical isolates (some of which were from cystic fibrosis (CF) patients), and two type cultures, were characterized by ribotyping. After restriction of chromosomal DNA of the different isolates with EcoRI and hybridization of Southern transfer blots with 2-acetylaminofluorene labelled Escherichia coli 16S + 23S rRNA probe, eleven different ribopatterns were obtained, representing variations of a dominant profile. This largely predominant pattern included both type cultures, all six isolates from water springs, 33% of the nine CF isolates and 43% of fourteen other clinical isolates most of them from nosocomial infections. When the genomic macrorestriction fingerprints of three mucoid CF isolates, with Asel, Drai or BfrI were compared with those of their spontaneous variants, concerning mucoidy, no differences were detected.

Pulsed-field gel electrophoresis as an epidemiological tool for clonal identification of Aeromonas hydrophila

Pulsed-field gel electrophoresis (PFGE) was used to characterize Aeromonas hydrophila strains isolated from a cluster of hospital-acquired infections that occurred over approximately 1 month in a French hospital. Five isolates from patients and 10 isolates from the water supply were characterized by biotyping and antibiotic susceptibility patterns and compared with 10 epidemiologically unrelated strains isolated from patients and rivers, by PFGE of digests of chromosomal DNA. Five environmental and four clinical isolates belonged to the same biotype and antibiotic susceptibility pattern type. The endonucleases XbaI, SpeI and SwaI gave satisfactory profiles whereas DraI did not. The profiles were stable, reproducible and discriminatory. The 10 epidemiologically unrelated strains exhibited 10 different patterns after digestion with XbaI, the least expensive, suitable endonuclease. PFGE is a rapid and discriminatory technique for the typing of Aeromonas hydrophila where a common origin of infection is suspected.

Discriminatory power and usefulness of pulsed-field gel electrophoresis in epidemiological studies of Pseudomonas aeruginosa

We assessed the discriminatory power of pulsed-field gel electrophoresis (PFGE) for the analysis of DNA restriction fragment length polymorphism (RFLP) in Pseudomonas aeruginosa. We determined DraI PFGE-RFLP of DNA of unrelated clinical and environmental strains, and clinical strains isolated from two intensive care units of the Besançon University Hospital. The typeability and reproducibility was 100%. The discriminatory index was 0.998, and the DNA patterns were stable in vitro and in vivo. There was a very low correlation between PFGE-RFLP and traditional typing methods. The typeability, reproducibility, the high discriminatory power and the stability of PFGE-RFLP make this a valuable method to be used in conjunction with serotyping. Further standardization and quantitative interpretation are possible and should lead to this technique becoming a library typing system.

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

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

Use of pulsed-field gel electrophoresis as an epidemiologic tool during an outbreak of Pseudomonas aeruginosa lung infections in an intensive care unit

OBJECTIVE

A retrospective study was performed to evaluate the use of DNA polymorphism analysis by pulsed-field gel electrophoresis (PFGE) in assessing the rate of exogenous contamination during an outbreak of Pseudomonas aeruginosa lung infections in an intensive care unit ICU. Another goal was to determine the risk factors, involved in the outbreak.

DESIGN

Rectal swabs and tracheal secretions were cultured from all patients upon admission and thereafter once a week throughout their stay in the ICU. Resistance patterns were determined in all P. aeruginosa isolates. We determined the serotypes, pyocin types, plasmid profiles and total DNA macrorestriction patterns for isolates. The restriction fragment length polymorphism (RFLP) of Dra I total DNA digest was studied by PFGE. A retrospective case-control study was performed to determine the risk factors for P. aeruginosa bronchopulmonary colonization.

SETTING

The study was carried out in the medical ICU of Besancon University Hospital (France).

RESULTS

The typability, stability and reproducibility of phenotypic markers were not completely satisfactory. Only the RFLP profile satisfied all the criteria for a good typing technique. In four of the 17 patients, P. aeruginosa strains with the same DNA pattern were found. Among the previously reported risk factors for hospital-acquired bronchopulmonary infections, only invasive procedures were determined by multivariate analysis to be significant in our study group. The oropharynx and the bronchial tract are the most likely endogenous sources.

CONCLUSION

PFGE-RFLP is a valuable tool for the epidemiologic study of P. aeruginosa. This typing method revealed that exogenous contamination is not always the major source of P. aeruginosa lung infections in mechanically ventilated patients in ICUs.

Genetic diversity of Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis revealed by restriction fragment length polymorphism of the rRNA gene region

The restriction fragment length polymorphism patterns of rDNAs from Pseudomonas aeruginosa strains isolated from the respiratory tracts of patients suffering from cystic fibrosis were obtained to evaluate the genetic polymorphism of this population of strains. Eighty-seven P. aeruginosa strains isolated from 87 patients from diverse areas of France and the ATCC 10145 strain were examined. Four restriction enzymes were used: BamHI, ClaI, EcoRI, and PstI. Forty-nine strains (56%) were in the three most frequent ribotypes (ribotypes R1 to R3). In addition, hierarchical clustering analysis of the data showed that 71 of the 88 strains (81%) clustered at a distance of less than one-third of the greatest distance observed in the total population. This indicates that clinical isolates implicated in the pathology of cystic fibrosis present a low degree of heterogeneity of rRNA operons, in contrast to the heterogeneity of strains of P. aeruginosa isolated from patients with various other pathologies. This relative homogeneity of rRNA genes was observed independently of the clinical status of the patient and the colony morphology.

Identity of streptococcal blood isolates and oral isolates from two patients with infective endocarditis

The purpose of this study was to isolate streptococcal strains from the oral cavities of streptococcal endocarditis patients and compare these strains biochemically and genetically with the corresponding streptococcal blood isolates. Total identity was observed between the blood and oral cavity isolates from the two patients studied.

Comparison of ribotyping and pulsed-field gel electrophoresis for molecular typing of Acinetobacter isolates

Seventy-three isolates of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex, including 26 isolates from 10 hospital outbreaks, were typed by ribotyping with EcoRI and ClaI and by pulsed-field gel electrophoresis (PFGE) of genomic DNA after digestion with ApaI. Ribotyping with EcoRI distinguished 31 ribopatterns. Digestion with ClaI generated another eight ribotypes. PFGE, in contrast, identified 49 distinct patterns with seven variants. Both methods detected all outbreak-related isolates. By ribotyping, nine epidemiologically unrelated strains could not be differentiated from outbreak strains, in contrast to only one isolate not identified by PFGE. Thus, PFGE was more discriminating than ribotyping. However, ribotyping is known to generate banding patterns specific to each DNA group in the A. calcoaceticus-A. baumannii complex that may be used for taxonomic identification of the strains. PFGE was shown to lack this property. Both methods are therefore useful for strain differentiation in epidemiological studies of Acinetobacter isolates.

Discriminatory power of three DNA-based typing techniques for Pseudomonas aeruginosa

We assessed the capacity of three DNA typing techniques to discriminate between 81 geographically, temporally, and epidemiologically unrelated strains of Pseudomonas aeruginosa. The methods, representing powerful tools for hospital molecular epidemiology, included hybridization of restricted chromosomal DNA with toxA and genes coding for rRNA (rDNA) used as probes and macrorestriction analysis of SpeI-digested DNA by pulsed-field gel electrophoresis. The probe typing techniques were able to classify all strains into a limited number of types, and the discriminatory powers were 97.7 and 95.6% for toxA and rDNA typing, respectively. Strains that were indistinguishable on the basis of both toxA and rDNA types defined 12 probe type homology groups. Of these, one contained five strains, three contained three strains each, and eight groups were represented by two strains each. Strains in 10 of the homology groups had the same O serotype. SpeI macrorestriction patterns discriminated between all strains with at least four band differences, which corresponded to a similarity level of 85%. Fifteen pairs of strains were similar at a level of > 75% and differed by only four to seven bands. Of these pairs, 11 belonged to the same probe type homology group, indicating their clonal relatedness. We conclude that macrorestriction analysis of P. aeruginosa with SpeI provides the best means of discrimination between epidemiologically unrelated strains. However, DNA probe typing with either toxA or rDNA reveals information on the strain population structure and evolutionary relationships.

Restriction fragment length polymorphism of rRNA genes for molecular typing of members of the family Legionellaceae

Typing of Legionella pneumophila remains important in the investigation of outbreaks of Legionnaires' disease and in the control of organisms contaminating hospital water. We found that the discriminatory power of a nonradioactive ribotyping method could be improved by combining results obtained with four restriction enzymes (HindIII, NciI, ClaI, and PstI). Fifty-eight clinical and environmental L. pneumophila strains including geographically unrelated as well as epidemiologically connected isolates were investigated. Epidemiologically related strains had the same ribotypes independent of the combinations of enzymes used. Some strains belonging to the same serogroup were assigned to different ribotypes, and some ribotypes contained members of different serogroups, indicating, as others have found, that serogroup and genotype are not always related. The discriminatory power of the method was estimated by calculating an index of discrimination (ID) for individual enzymes and combinations thereof. The combined result with all four enzymes was highly discriminatory (ID = 0.97), but results for three enzymes also yielded ID values acceptable for epidemiological purposes. In addition, the testing of 27 type strains and 6 clinical isolates representing Legionella species other than L. pneumophila indicated that ribotyping might be of value for species identification within this genus, as previously suggested.

Ribotyping on small-sized spirochetes isolated from subgingival plaque

In the present study DNA restriction patterns and corresponding ribotypes of 17 subgingival small-sized spirochetes (1:2:1 and 2:4:2 isolates), 2 Treponema socranskii strains and two Treponema denticola strains were examined. Purified chromosomal DNA was digested by BamHI, HindIII, PstI and ClaI. The DNA fragments were separated in a horizontal slab of 0.7% agarose containing ethidium bromide and transferred by nylon membranes. Hybridization was carried out with digoxigenin-labelled copy DNA of 16S and 23S ribosomal RNA from Escherichia coli. Depending on the restriction endonuclease used, up to 4 distinct bands were observed for the 2:4:2 isolates and the T. denticola strains. For each of the endonucleases used, identical band patterns were always observed for this group of isolates, and these patterns differed persistently from the T. denticola strains. For the 1:2:1 strains, up to 11 distinct bands were observed after digestion with HindIII, whereas a maximum of 6 bands were observed when PstI or ClaI was used. By using ClaI, the examined 1:2:1 isolates were separated into 8 groups, whereas PstI and HindIII separated these isolates into 5 groups. The ribotyping showed that the tested 1:2:1 spirochetes were more heterogeneous than the 2:4:2 spirochetes examined.

Molecular characterization and antibiotic susceptibility of Vibrio cholerae non-O1

A collection of 64 clinical and environmental Vibrio cholerae non-O1 strains isolated in Asia and Peru were characterized by molecular methods and antibiotic susceptibility testing. All strains were resistant to at least 1 and 80% were resistant to two or more antibiotics. Several strains showed multiple antibiotic resistance (> or = three antibiotics). Plasmids most often of low molecular weight were found in 21/64 (33%) strains. The presence of plasmids did not correlate with antibiotic resistance or influence ribotype patterns. In colony hybridization studies 63/64 (98%) V. cholerae non-O1 strains were cholera toxin negative, whereas only strains recovered from patients were heat-stable enterotoxin positive. Forty-seven Bgl I ribotypes were observed. No correlation was shown between ribotype and toxin gene status. Ribotype similarity was compared by cluster analysis and two main groups of 13 and 34 ribotypes was found. Ribotyping is apparently a useful epidemiological tool in investigations of V. cholerae non-O1 infections.

Application of ribotyping for differentiating Vibrio cholerae non-O1 isolated from shrimp farms in Thailand

A collection of 143 Vibrio cholerae non-O1 strains isolated from shrimp farms in Thailand were characterized and grouped by ribotyping. Sixty-four ribotypes were distinguished following digestion of chromosomal DNA with the restriction enzyme BglI, and the reproducibility of the method was 100%. There was no correlation between specific ribotype distributions and the locations of the shrimp farms. Ribotype similarity was examined by cluster analysis, and two main groups with 10 and 54 ribotypes, respectively, were found. Correlation between ribotype and O-antigen expression was shown to exist among those isolates tested. Ribotyping appears to be a suitable method for differentiating environmental V. cholerae non-O1 strains, and comparison of ribotype patterns showed a high degree of genetic divergence within V. cholerae non-O1.

rRNA gene restriction patterns of Streptococcus pyogenes: epidemiological applications and relation to serotypes

The use of rRNA gene restriction fragment length polymorphism analysis (ribotyping) to subtype Streptococcus pyogenes strains was investigated. Sixty-eight S. pyogenes strains, including 17 reference strains and 51 isolates from blood, acute or chronic pharyngitis, and food-borne outbreaks, were characterized by determination of both their rDNA restriction fragment length polymorphism profiles and their serotypes (T and M). Total DNA was cleaved with five selected restriction enzymes and then probed with a digoxigenin-labeled stretch of 1,063 bp hybridizing with 16S rRNA genes. Fifteen and nine distinct patterns were generated with SacI and XhoI, respectively, and five patterns were generated with each of the three additional restriction enzymes. With the combination SacI-XhoI, a total of 21 distinct ribotypes were obtained among the 68 isolates. This number was not increased by the results obtained with the other restriction enzymes. All strains tested were typeable. All isolates from each food-borne outbreak belonged to the same ribotype, and all isolates (pre- and posttreatment) from each child with chronic pharyngitis also belonged to the same ribotype, suggesting antibiotic treatment failures. A discriminatory index was calculated for the 47 isolates which were epidemiologically unrelated, using the Hunter-Gaston formula. This index reached 0.955 when the combination SacI-XhoI was used, showing the good discriminatory power of this typing method. Therefore, ribotyping proved to be a molecular method of interest to subtype S. pyogenes. Moreover, there was some correlation between ribotyping and serotyping, as several ribotypes were related to a unique distinct M serotype.

Discrimination of Mycobacterium avium-Mycobacterium intracellulare strains by genomic DNA fingerprinting with a 16S rRNA gene probe

Ribotyping was investigated as a means of distinguishing ten different serotyped reference strains and seven epidemiologically unrelated isolates of Mycobacterium avium-Mycobacterium intracellulare using a labelled 16S rDNA probe. Thirteen restriction enzymes were screened towards an accurate discrimination of strains. Two selected restriction enzymes (SacI and ClaI) enabled us to classify the 17 strains into ten ribotypes with an index of discrimination of 0.897. Typeability and reproducibility of the method reached 100%. The patterns obtained exhibited polymorphism of RE fragments within and outside the 16S rRNA gene and may be useful for epidemiological studies.

Quantitative antibiogram typing using inhibition zone diameters compared with ribotyping for epidemiological typing of methicillin-resistant Staphylococcus aureus

Antibiogram typing of methicillin-resistant Staphylococcus aureus with selected antibiotics was evaluated as a primary epidemiological typing tool and compared with ribotyping. Antibiograms were derived with the Kirby-Bauer disk diffusion method by using erythromycin, clindamycin, cotrimoxazole, gentamicin, and ciprofloxacin. For typing, antibiogram data were analyzed by similarity analysis of disk zone diameters (quantitative antibiogram typing). One hundred seventy-two isolates were typed. Reproducibility reached 98% for the quantitative antibiogram and 100% for ribotyping. With three selected restriction enzymes (EcoRV, HindIII, and KpnI), 40 epidemiologically unrelated isolates could be classified into 21 ribotypes, whereas quantitative antibiogram typing classified these isolates into 19 groups. To evaluate the discriminatory power of the methods, we calculated an index of discrimination from data obtained with these 40 isolates. This index takes into consideration both the number of types defined by the typing method and their relative frequencies. With both ribotyping and quantitative antibiogram typing, high discrimination indices (0.972 and 0.954, respectively) were obtained. When epidemiological links between patients (ward, period of hospitalization, and contacts between staff and patients) were compared with the results of ribotyping or the quantitative antibiogram typing method, it appeared that both methods were able to discriminate epidemiological clusters, with only a few discrepancies. In conclusion, quantitative antibiogram typing, although not necessarily based on genomic markers, is a simple method which enables a reliable workup of methicillin-resistant S. aureus epidemic when sophisticated molecular typing methods are not available.

Use of ribotyping in epidemiological surveillance of nosocomial outbreaks

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

Pseudomonas aeruginosa serotype O12 outbreak studied by arbitrary primer PCR

A total of 16 colonizing and infecting ofloxacin-resistant Pseudomonas aeruginosa strains and two strains isolated from ventilation equipment fluids, all with similar colonial morphologies and with minor but distinct susceptibility differences, were suspected of belonging to a single outbreak and were studied by arbitrary primer (AP) PCR. Thirteen nonrelated strains were included to evaluate the discriminatory capacity of the technique. AP PCR fingerprinting was compared with serotyping, phage typing, and antibiotic susceptibility testing. AP PCR was performed independently with three different primers. The different AP PCR typing systems yielded almost identical patterns for the epidemic strains and enabled us to differentiate most of the nonrelated strains from each other and from the outbreak strains. The combination of AP PCR typing and the phenotyping techniques that we used enabled us to conclude that an outbreak was occurring. In general, the typeability of AP PCR was greater than those of phage typing and serotyping, while the discriminatory powers of the three methods were comparable.

Ribotyping for differentiating Flavobacterium meningosepticum isolates from clinical and environmental sources

On the basis of DNA-DNA hybridization data, two main genomic relatedness groups (I and II) have been reported for a geographically varied collection of 52 strains of Flavobacterium meningosepticum. Herein, we have shown that genomic group II can be further divided into four subgroups (II:1 to II:4). To examine the taxonomic relevance of the ribosomal patterns of the 52 F. meningosepticum strains, the patterns were compared with existing DNA-DNA hybridization data with restriction enzymes PstI and HindIII. Ribotyping of the 52 F. meningosepticum strains showed banding patterns that could identify them correctly to one of the five genomic groups or subgroups. To assess the value of ribotyping for the interpretation of epidemiological data, the discriminatory power of the method was investigated for the 52 F. meningosepticum strains. With one to four restriction enzymes (PstI, HindIII, ClaI, EcoRI), a discriminatory index of 0.95 to 0.97 was found. The value of ribotyping in an epidemiological setting was assessed for three clinical isolates of F. meningosepticum from an outbreak of meningitis and bacteremia in the neonatal intensive care unit, Rigshospitalet, Copenhagen, Denmark. The three clinical isolates were shown to belong to the same ribotype, characteristic of genomic subgroup II:1. This ribotyping method will prove to be a useful tool for epidemiological studies concerning F. meningosepticum in the future.