Comparison of ribotyping with conventional methods for the type identification of Enterobacter cloacae

Genetic Characterization of the O-Antigen and Development of a Molecular Serotyping Scheme for Enterobacter cloacae

Enterobacter cloacae is a well-characterized opportunistic pathogen that is closely associated with various nosocomial infections. The O-antigen, which is one of the most variable constituents on the cell surface, has been used widely and traditionally for serological classification of many gram-negative bacteria. E. cloacae is divided into 30 serotypes, based on its O-antigen diversity. In this study, by using genomic and comparative-genomic approaches, we analyzed the O-antigen gene clusters of 26 E. cloacae serotypes in depth. We also identified the sero-specific gene for each serotype and developed a multiplex polymerase chain reaction (PCR) method. The sensitivity of the assay was 0.1 ng for genomic DNA and 10³ colony forming units for pure cultures. The assay reliability was evaluated by double-blinded testing with 81 clinical strains. Furthermore, we established a valid, genome-based tool for in silico serotyping of E. cloacae. By screening 431 E. cloacae genomes deposited in GenBank, 304 were classified into current antigenic scheme, and 112 were allocated into 55 putative novel serotypes. Our results represent the first genetic basis of the O-antigen diversity and variation of E. cloacae, providing a rationale for studying the O-antigen associated evolution and pathogenesis of this bacterium. In addition, we extended the current serotyping system for E. cloacae, which is important for detection and epidemiological surveillance purposes for this important pathogen.

Microbial Ecology: Where are we now?

Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages.

Enterobacter cloacae complex: clinical impact and emerging antibiotic resistance

Species of the Enterobacter cloacae complex are widely encountered in nature, but they can act as pathogens. The biochemical and molecular studies on E. cloacae have shown genomic heterogeneity, comprising six species: Enterobacter cloacae, Enterobacter asburiae, Enterobacter hormaechei, Enterobacter kobei, Enterobacter ludwigii and Enterobacter nimipressuralis, E. cloacae and E. hormaechei are the most frequently isolated in human clinical specimens. Phenotypic identification of all species belonging to this taxon is usually difficult and not always reliable; therefore, molecular methods are often used. Although the E. cloacae complex strains are among the most common Enterobacter spp. causing nosocomial bloodstream infections in the last decade, little is known about their virulence-associated properties. By contrast, much has been published on the antibiotic-resistance features of these microorganisms. In fact, they are capable of overproducing AmpC β-lactamases by derepression of a chromosomal gene or by the acquisition of a transferable ampC gene on plasmids conferring the antibiotic resistance. Many other resistance determinants that are able to render ineffective almost all antibiotic families have been recently acquired. Most studies on antimicrobial susceptibility are focused on E. cloacae, E. hormaechei and E. asburiae; these studies reported small variations between the species, and the only significant differences had no discriminating features.

Integrons as tools for epidemiological studies

The integron content of Gram-negative strains implicated in three distinct episodes of suspected cross-infection among inpatients was investigated and compared with ribotyping. In the first episode, ribotyping identified a strain of Acinetobacter, isolated over a 3-month period, responsible for an outbreak associated with the use of mechanical ventilation in the intensive care unit (ICU). The second episode concerned simultaneous isolations of Pseudomonas aeruginosa and Serratia marcescens from 13 bronchoscopy patients. In these two episodes, results obtained by analysis of integron content and ribotyping were in agreement and correctly identified the epidemiologically related strains. In the third episode, isolates of Enterobacter cloacae were collected from patients in the neonatal ICU over a 3-month period. Although several isolates belonged to the same ribotype, cross-infection could not always be confirmed when the integron content was analysed. Integron detection can be considered a useful tool for studying molecular epidemiology in hospital environments, facilitating the quick detection of possible cross-infection cases, especially in critical wards such as the ICU.

Molecular epidemiological typing of Enterobacter cloacae isolates from a neonatal intensive care unit: three-year prospective study

Since 1992, there has been an increase in the incidence of Enterobacter sepsis in the neonatal intensive care unit (NICU) of the authors' hospital. From 1995 to 1997, a prospective molecular epidemiological survey of the colonizing and infecting strains isolated from neonates was conducted. Enterobacter cloacae was the most frequent cause of neonatal sepsis, accounting for 19.2% of all neonatal infections, reaching a peak incidence of 2.2/1000 during 1996. Fifty isolates from the NICU and four epidemiologically unrelated strains were characterized by pulse-field gel electrophoresis (PFGE), ribotyping, enterobacterial repetitive intergenic consensus (ERIC)-PCR and plasmid profiling. PFGE was the most discriminatory technique and identified 13 types (two of them classified into two and three subtypes) compared with ERIC-PCR, plasmid profiling and ribotyping that identified 11, 11 and seven types, respectively. A good correlation was found between all techniques. Five different clones caused 15 cases of sepsis. Clones A and B were prevalent in 1995 and 1996, but they were not isolated in 1997. An outbreak caused by clone G in 1997 was controlled by cohort nursing and hygienic measures, without changing the antibiotic policy. Strains were characterized by their antibiotic resistance pattern and divided into three groups. Group I correlated with PFGE types A, B1 and B2, which hyperproduced Bush type 1 chromosomal beta-lactamase and expressed extended-spectrum ?-lactamases (ESBLs). Group II only hyperproduced Bush type 1 chromosomal beta-lactamase and correlated with PFGE-types D1, D2, D3 and I. Finally, Group III, with inducible beta-lactamases, correlated with the rest of PFGE types. The sudden disappearance of E. cloacae after reinforcement of hygienic measures confirms the importance of patient-to-patient transmission.

Suitability of PCR fingerprinting, infrequent-restriction-site PCR, and pulsed-field gel electrophoresis, combined with computerized gel analysis, in library typing of Salmonella enterica serovar enteritidis

Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate of PCR fingerprinting interassay and intercenter reproducibility was low and was only increased when DNA samples were extracted at the same time and amplified with the same reaction mixtures. Reproducibility of IRS-PCR technique reached 100%, but discrimination was low (D = 0.52). The PFGE procedure showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI, BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4.0 software. Three computer libraries of PFGE DNA profiles were constructed, and their ability to recognize new DNA profiles was analyzed. The results obtained pointed out that the combination of PFGE with computerized analysis could be suitable in long-term epidemiological comparison and surveillance of Salmonella serovar Enteritidis, specially if the prevalence of genetic events that could be responsible for changes in PFGE profiles in this serovar was low.

Molecular epidemiology of a nosocomial outbreak due to Enterobacter cloacae and Enterobacter agglomerans in Campinas, São Paulo, Brazil

A total of 73 isolates (57 Enterobacter cloacae and 16 Enterobacter agglomerans), recovered during an outbreak of bacteremia in the Campinas area, São Paulo, Brazil, were studied. Of these isolates, 61 were from parenteral nutrition solutions, 9 from blood cultures, 2 from a sealed bottle of parenteral nutrition solution, and one was of unknown origin. Of the 57 E. cloacae isolates, 54 were biotype 26, two were biotype 66 and one was non-typable. Of 39 E. cloacae isolates submitted to ribotyping, 87.2% showed the same banding pattern after cleavage with EcoRI and BamHI. No important differences were observed in the antimicrobial susceptibility patterns among E. cloacae isolates exhibiting the same biotype, serotype and ribotype. All E. agglomerans isolates, irrespective of their origin, showed same patterns when cleaved with EcoRI and BamHI. The results of this investigation suggest an intrinsic contamination of parenteral nutrition solutions and incriminate these products as a vehicle of infection in this outbreak.

The discriminatory power of ribo-PCR compared to conventional ribotyping for epidemiological purposes

Molecular typing techniques have become increasingly important for confirmation of epidemiological relationships and delimitation of nosocomial outbreaks. The discriminatory power of the two DNA-based typing methods, conventional ribotyping and ribo-PCR, was assessed to distinguish between selected strains of Acinetobacter calcoaceticus, Enterobacter cloacae, Serratia marcescens and Pseudomonas aeruginosa. Overall, conventional ribotyping was more discriminatory than ribo-PCR.

Phenotyping and genotyping methods applied to investigate the relatedness of Brazilian isolates of Enterobacter cloacae

In order to evaluate the resolving power of several typing methods to identify relatedness among Brazilian strains of Enterobacter cloacae, we selected twenty isolates from different patients on three wards of a University Hospital (Orthopedics, Nephrology, and Hematology). Traditional phenotyping methods applied to isolates included biotyping, antibiotic sensitivity, phage-typing, and O-serotyping. Plasmid profile analysis, ribotyping, and macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) were used as genotyping methods. Sero- and phage-typing were not useful since the majority of isolates could not be subtyped by these methods. Biotyping, antibiogram and plasmid profile permitted us to classify the samples into different groups depending on the method used, and consequently were not reliable. Ribotyping and PFGE were significantly correlated with the clinical epidemiological analysis. PFGE did not type strains containing nonspecific DNase. Ribotyping was the most discriminative method for typing Brazilian isolates of E. cloacae.

Variation in structure and location of VanA glycopeptide resistance elements among enterococci from a single patient

Forty-six VanA glycopeptide-resistant enterococci (GRE) from a single patient were investigated for variation in structure and location of VanA resistance elements. Together with identification to species level and pulsed-field gel electrophoresis, these data divided the GRE into 10 groups and subgroups. Combining data in this manner appears helpful when investigating the epidemiology of GRE.

Molecular epidemiology of an outbreak of Enterobacter cloacae in the neonatal intensive care unit of a provincial hospital in Gauteng, South Africa

An outbreak of Enterobacter cloacae in the neonatal intensive care unit of a provincial hospital in Gauteng, South Africa, resulting in nine deaths was investigated. Macrorestriction analysis using pulsed-field gel electrophoresis revealed that three isolates of E. cloacae from blood cultures of patients, six from environmental sources, and one from the hands of a staff member belonged to the same genotypic cluster.

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.

Study of an outbreak of cefoxitin-resistant Klebsiella pneumoniae in a general hospital

During a 3-month period, six Klebsiella pneumoniae isolates resistant to cefoxitin and penicillin-inhibitor combinations were derived from patients in the intensive care unit of a hospital in Athens, Greece. Enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis provided evidence of the clonal origin of the isolates. Conventional techniques and ribotyping were inadequate in proving that the isolates were related. Resistance was due to a plasmidic class C beta-lactamase.

Comparison of outbreak and nonoutbreak Acinetobacter baumannii strains by genotypic and phenotypic methods

Thirty-one Acinetobacter baumannii strains, comprising 14 strains from 14 outbreaks in different northwestern European cities and 17 sporadic strains, were compared by investigating various properties of the strains including biotype, antibiogram, cell envelope protein electrophoretic profile, ribotype pattern, and the band pattern generated by a novel genomic fingerprinting method, named AFLP, which is based on the selective amplification of restriction fragments. Results showed that 12 strains from unrelated outbreaks were linked together in two clusters according to their similarities by these typing methods, whereas sporadic strains were more heterogeneous. Outbreak strains appeared to be markedly more resistant to antibiotics than nonoutbreak strains. The uniformity of typing characters in two sets of outbreak strains suggests that strains in each cluster have a common clonal origin.

Hospital outbreak of Klebsiella pneumoniae resistant to broad-spectrum cephalosporins and beta-lactam-beta-lactamase inhibitor combinations by hyperproduction of SHV-5 beta-lactamase

An aminoglycoside- and ceftazidime-resistant strain of Klebsiella pneumoniae K2 producing the extended-spectrum beta-lactamase SHV-5 infected or colonized 14 pediatric patients at Guy's Hospital. The patients were mostly neonates recovering from cardiac surgery for congenital defects. The organism was also isolated from a nurse and from the father of one of the children. Four patients had septicemia, and two septicemic neonates with postoperative renal failure died. Aminoglycoside and cephalosporin resistance transferred to Escherichia coli in vitro on a 160-kb plasmid, and a similar resistant E. coli strain was isolated from the stools of one of the affected children. The epidemic organism colonized the bowel and skin and was probably transmitted via staff hands. Five wards were involved because of extensive patient movements. The outbreak was controlled by patient isolation and attention to handwashing. All of the isolates of the outbreak strain were identical by phage typing, ribotyping, plasmid profiling, and biochemical and serological testing, but they varied in their production of SHV-5. Some isolates produced normal amounts of SHV-5 and were susceptible to beta-lactam-beta-lactamase inhibitor combinations. Others, including the single isolate of multiresistant E. coli, produced up to five times as much enzyme as "normal" isolates. This hyperproduction resulted in increased resistance to several penicillins and cephalosporins and to the beta-lactam-beta-lactamase inhibitor combinations amoxicillin-clavulanic acid, ampicillin-sulbactam, piperacillin-tazobactam, and ceftazidime-clavulanic acid. The hyperproduction of SHV-5 by K. pneumoniae and E. coli seen in this outbreak suggests that beta-lactam-beta-lactamase inhibitor combinations may be unreliable for the treatment of organisms producing extended-spectrum beta-lactamases.

Biochemical profiles and serotypes of nosocomial Enterobacter cloacae strains in Northern Norway: biochemical identification problems with commercial test systems

During a period of 2 years, 118 strains of Enterobacter cloacae were collected consecutively in connection with nosocomial infections in Northern Norway; identified by conventional methods and by the API 20E system. The API 20E profile 3305573 predominated and was present in 73 of 118 strains. Among 96 serotyped strains, 73 were serotypable, 20 nontypable and two polyagglutinable. Predominating serotypes were 3 (29 strains), 8 (21 strains) and 23 (nine strains). When the API 20E profiles of the 118 strains were read in the new ATB (automated computer-assisted) 20E data base system, 97 of 118 (82.2%) strains were identified as E. cloacae. The 118 strains were tested in the new ATB Rapid ID 32E and ATB ID 32E (ATB system, bioMérieux, France) systems. Only 69 of 118 (58.5%) strains were identified as E. cloacae in both systems. The ATB Rapid ID 32E identified 97 of 118 strains (82.2%), and the ATB ID 32E only 80 of 118 strains (67.8%). Among 73 serotypable strains, the ATB Rapid ID 32E identified 79.5% as E. cloacae, while the ATB ID 32E identified only 64.4%. Among 40 serotypable strains with API 20E profile 3305573, all 40 were identified as E. cloacae by the ATB Rapid ID 32E, while only 27 (67.5%) by the ATB ID 32E system. Further improvements may increase the value of biochemical identification of E. cloacae in diagnostic work.

Typing of sequential bacterial isolates by pulsed-field gel electrophoresis

We typed 39 sets of multiple bacterial isolates of the same species from patients by pulsed-field gel electrophoresis of genomic DNA (PFGE). Isolates were cultured from different sites or over a 2-week or longer interval. Staphylococcus aureus, Enterococcus faecalis, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Enterobacter cloacae were tested. Excluding E. cloacae, 28 of 32 sets of isolates (87%) demonstrated only identical or highly related PFGE types. Four of the seven sets of E. cloacae showed different types. For species other than E. cloacae, our results suggest that patients are usually colonized and infected with a single strain of these bacterial pathogens. Unlike all of the other tested species, E. cloacae PFGE typing differences suggested the presence of multiple strains causing colonization and infection.

Detection of heat-stable enterotoxin genes among Australian Vibrio cholerae O1 strains

DNA probes derived from the heat-stable enterotoxin gene of Vibrio cholerae non-O1 (stn), and the cholera toxin gene (ctx), were used to screen 199 strains of V. cholerae O1, which were isolated within Australia from 1977-1986. 13 environmental strains isolated from the riverine environment in Southeast Queensland in 1980 and 1981, hybridized with the stn and ctx DNA probes. The concentrated supernatant of 6 of these strains elicited fluid accumulation in the infant mouse assay both before and after heating at 100 degrees C for 5 min. Genetic relationships among the 13 stn+ strains were studied by a comparison of the rRNA-RFLPs (ribotyping) and by Southern blot analysis with a stn gene probe. The results indicate that there is a clonal relationship among the Australian stn+ strains and that there is an environmental reservoir of stn genes among Australian V. cholerae O1 isolates.

Enterobacter cloacae in a neonatal intensive care unit: account of an outbreak and its relationship to use of third generation cephalosporins

After uneventful use of cefotaxime and ceftazidime as first line therapy for three years in our neonatal intensive care unit we isolated cephalosporin-resistant Enterobacter cloacae (CREC) strains which caused clusters of cases or colonization and/or serious neonatal infection. By using two or more typing methods, at least five different strains with similar patterns of antimicrobial sensitivities were identified. The results of a case-control study did not support the notion that the use of third generation cephalosporins was associated with colonization and infection by CREC. The outbreak was brought under control by interrupting the transmission of the epidemic strain D, by measures such as cohort nursing, diligent handwashing before and after procedures, and thorough environmental cleaning as well as by decontamination with glutaraldehyde after dismantling of the blood gas analyser believed to have acted as a persistent reservoir. Our experience highlights the danger of inadequate supervision and maintenance of equipment used for near-patient testing and the need to monitor such equipment not only in terms of its calibration and analytical performance but also microbiologically.

Clinical and bacteriological survey after change in aminoglycoside treatment to control an epidemic of Enterobacter cloacae

The effect of a change in the first line antibiotic treatment in a neonatal unit was studied. A total of 238 neonates (G1), admitted between 1 January and 31 July 1989, and treated with gentamicin, were compared with 398 (G2) admitted between 1 August 1989 and 31 July 1990 who received amikacin, in the combination of ampicillin plus an aminoglycoside. This change was implemented in an attempt to prevent the spread of an epidemic strain of Enterobacter cloacae resistant to third generation cephalosporins and all aminoglycosides, except amikacin. The change in treatment had no effect on the incidence of nosocomial infections [19.7% (G1) vs. 16.3% (G2) RR = 1.21 (0.86-1.70)], but the proportion of patients with nosocomial infections caused by the E. cloacae decreased (6.3% vs. 2.0% RR 3.14 CI 1.35-7.28). Certain trends in the bacterial ecology emerged: E. aerogenes and Enterococci increased in G2. The proportion of gentamicin-resistant strains such as E. cloacae or Staphylococci decreased and there was no increase in aminoglycoside-resistant strains, except in Escherichia coli, in which resistance to amikacin rose from 0 to 3%. This study illustrates the influence of antimicrobial therapy on the species and the resistance of strains isolated in nosocomial infections. It also highlights the need for epidemiologic surveillance, and poses the question of how best to modify antibiotic policy.

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.

Biochemical and Molecular Characterization of Obesumbacterium proteus , a Common Contaminant of Brewing Yeasts

We have evaluated the effectiveness of API 20E, Biolog testing, plasmid profiling, ribotyping, and enteric repetitive intergenic consensus (ERIC)-PCR to characterize, classify, and differentiate nine bacterial isolates of the common brewery contaminant Obesumbacterium proteus. Of the five typing techniques, Biolog testing, plasmid profiling, and ERIC-PCR provided the most differentiation, and API 20E testing and ribotyping were relatively indiscriminate. The molecular biology approach of ERIC-PCR offered the ideal combination of speed, simplicity, and discrimination in this study. Overall, the results are supportive of the view that O. proteus can be subdivided into two biogroups, biogroup 1, which has considerable biochemical and genetic homology to Hafnia alvei , and biogroup 2, which is relatively heterogeneous.

Identification and characterization of Serpulina hyodysenteriae by restriction enzyme analysis and Southern blot analysis

Chromosomal DNA restriction enzyme analysis and Southern blot hybridization were used to characterize Serpulina hyodysenteriae strains. When chromosomal DNAs from selected strains (reference serotypes) of S. hyodysenteriae were digested with the restriction endonuclease Sau3A and hybridized with a 1.1-kb S. hyodysenteriae-specific DNA probe, a common 3-kb band was always detected in S. hyodysenteriae strains but was absent from Serpulina innocens strains. When the chromosomal DNA was digested with the restriction endonuclease Asp 700 and hybridized with two S. hyodysenteriae-specific DNA probes (0.75 and 1.1 kb of DNA), distinct hybridization patterns for each S. hyodysenteriae reference strain and the Australian isolate S. hyodysenteriae 5380 were detected. Neither the 1.1-kb nor the 0.75-kb DNA probe hybridized with Asp 700- or Sau3A-digested S. innocens chromosomal DNA. The presence of the 3-kb Sau3A DNA fragment in S. hyodysenteriae reference strains from diverse geographical locations shows that this fragment is conserved among S. hyodysenteriae strains and can be used as a species-specific marker. Restriction endonuclease analysis and Southern blot hybridization with these well-defined DNA probes are reliable and accurate methods for species-specific and strain-specific identification of S. hyodysenteriae.

Arbitrarily primed PCR, ribotyping, and plasmid pattern analysis applied to investigation of a nosocomial outbreak due to Enterobacter cloacae in a neonatal intensive care unit

In December 1992, Enterobacter cloacae was isolated from the oropharynx and respiratory tract of six ventilated neonates hospitalized in the intensive care unit (ICU) of our hospital. To establish the spread of the outbreak, 41 strains of E. cloacae were analyzed for genotypic markers by three methods: plasmid profile analysis, ribotyping with EcoRI or PvuII endonuclease, and arbitrarily primed (AP) PCR. The tested strains included 12 isolates from the 6 epidemic cases, 4 isolates from the respiratory tract of 4 children hospitalized in other wards during the same period, 13 isolates from 12 children hospitalized in pediatric units before or after the outbreak, and 12 epidemiologically unrelated isolates. Ribotyping and AP PCR demonstrated that each of the last 12 strains exhibited distinct genomic patterns, as did each of the strains isolated from neonates hospitalized before or after the epidemic peak. Conversely, two clones of strains were found among the isolates recovered in December, with concordant results being obtained by the three typing methods: the first clone included seven strains from five ventilated children in the ICU and two children from another ward; another clone was shared by one neonate in the ICU and an infant from another ward. These results indicate that ribotyping and AP PCR-the latter applied, to our knowledge, for the first time to the genotypic analysis of E. cloacae--represent very discriminatory tools for the investigation of nosocomial outbreaks caused by this species.

Biotyping, phage typing, and O-serotyping of clinical isolates of Enterobacter cloacae

The purpose of this study was to make an independent evaluation of the methods of bio-, phage-, and O-serotyping which had been used only in the laboratory of origin, and to assess the extent of possible cross-infection of Enterobacter cloacae in a Danish university hospital. The material consisted of 237 clinical isolates of E. cloacae from the clinical microbiology laboratory at Hvidovre Hospital. The typability of bio-, phage-, and serotyping was 100%, 83%, and 85%, respectively. Reproducibility of serotyping was 90% and of phage typing 96% if two major differences were allowed to differentiate between patterns. O-serotyping had the highest discriminatory power and combination of all typing methods further increased discrimination. Outbreaks of E. cloacae were not evident in clinical departments, but cross-infections from one department to another could not be completely ruled out. We concluded that the combination of bio-, phage- and O-serotyping is sufficiently discriminating and will be satisfactory in the majority of clinical situations.

Enterobacter cloacae cross-colonization in neonates demonstrated by ribotyping

The intestinal colonization by Enterobacter cloacae strains with a derepressed cephalosporinase was studied in a paediatric ward between February 1990 and January 1991. Environmental sampling was performed simultaneously. Fifty-two isolates were recovered from 200 neonates (stool, blood) and 14 strains were isolated from the neonatal environment. An epidemiological study based on the typing of 36 Enterobacter cloacae isolates was carried out using antibiotyping, biotyping and ribotyping methods. The isolates selected were from 21 neonates (24 isolates), the neonatal ward environment (8 isolates) and from other wards (4 isolates). Thirty-two isolates had the same antibiotic resistance pattern, corresponding to a derepressed cephalosporinase and resistance to the following aminoglycosides: kanamycin, gentamicin, tobramycin and netilmicin. No predominant biotyping pattern could be established. Ribotyping done with two endonucleases (EcoRI and BamHI) showed 28 Enterobacter cloacae isolates to have a single pattern. Ribotyping was the most discriminating method used in this study, permitting identification of cross-contamination with Enterobacter cloacae in the paediatric ward.

Epidemic of Pseudomonas cepacia in an adult cystic fibrosis unit: evidence of person-to-person transmission

An epidemic of Pseudomonas cepacia occurred in an adult cystic fibrosis center in the United Kingdom, despite a policy of segregation of infected and noninfected patients within the hospital. Investigation of the outbreak by ribotyping and pulsed-field gel electrophoresis to characterize P. cepacia strain genomes together with inquiry into social contacts between patients revealed evidence of person-to-person transmission outside the hospital environment. Segregation policies aimed at reducing the spread of this infection in the cystic fibrosis community need to encompass patient contacts outside the hospital environment.

Ribotyping of selected isolates of Enterobacter cloacae and clinical data related to biotype, phage type, O-serotype, and ribotype

In order to evaluate if ribotyping of selected isolates of Enterobacter cloacae could further elucidate the epidemiology, we performed ribotyping of 109 isolates indistinguishable by bio-, phage-, and O-serotyping, with inconclusive typing results, or from patients with more than one isolate. Ribotyping provided additional information, and some cases of cross-infection or common source of infection were revealed. Under the supposition that isolates sharing the same ribotype were of the same origin, problems arose with respect to bio-, O-sero, as well as phage typing; in particular a remarkable number of isolates showed differences in phage type. In order to identify possible virulence characteristics of certain types, clinical data were related to bio-, phage-, O-sero-, and ribotype. Biotype 66 was significantly more frequent among blood culture isolates (P = 0.001), but this might have reflected the presence of a certain strain in the environment of the intensive care unit, where patients were more likely to develop bacteraemia; serotype 04 was significantly more frequent among isolates from the urinary tract (P = 0.02), and serotype 013 was more frequent among women (P = 0.05). One ribotype was found only among community-acquired isolates, which might suggest that it is a frequent but less virulent strain.

Cluster of Enterobacter cloacae pseudobacteremias associated with use of an agar slant blood culturing system

From 1 February through 12 October 1990, 27 blood cultures processed at Shiprock Hospital were positive for Enterobacter cloacae; only 3 had been reported in the preceding 12 months. Twenty (74%) of the cultures were obtained from patients without clinical evidence of gram-negative septicemia. The increase in E. cloacae-positive blood cultures was temporally associated with the introduction of a new blood culturing system. To evaluate potential risk factors for an E. cloacae-positive blood culture (case-culture), we conducted a case-control study. Case-cultures were compared with 81 randomly selected cultures that were processed during the epidemic period and that were not positive for E. cloacae (controls). Because several factors suggested the possibility of pseudoinfection, we limited our analysis to the 20 blood cultures that appeared to be contaminants. Blood samples received in the laboratory during the midnight shift (5 of 20 [25%] versus 5 of 81 [6%]; odds ratio, 5.1; 95% confidence intervals, 1.01 to 24.6; P = 0.02) or present in the incubator with other E. cloacae-positive samples (17 of 20 [85%] versus 29 of 81 [36%]; odds ratio, 10.2, 95% confidence interval, 2.6 to 57.3; P < 0.001) were at increased risk for contamination. During mock experiments of the procedures for processing blood samples for culture, several breaks in aseptic technique and leakage from the blood culturing system were observed. Cultures of samples obtained from several environmental sites in the laboratory and the hand washings of two laboratory technicians grew E. cloacae. Plasmid and restriction enzyme analyses of E. cloacae isolates recovered from the patients' blood cultures, the two technicians' hand washings, and environmental sites in the laboratory indicated that all had identical plasmid profiles. Our findings suggest that the breaks in aseptic technique and the environmental contamination that occurred in association with the use of the new blood culturing system resulted in contamination of the blood cultures. This outbreak highlights the importance of routine environmental cleaning, periodic quality control assessments, and adherence to aseptic practices in clinical laboratories, particularly when new methods or equipment are introduced and/or new personnel are hired.

Comparison of serotype, biotype and bacteriocin type with rDNA RFLP patterns for the type identification of Serratia marcescens

Variations in rDNA gene loci in DNA digests of 209 clinical isolates of Serratia marcescens were determined with an Escherichia coli rRNA probe. Forty-one restriction fragment length polymorphism patterns (ribotypes) were identified, based on the size of 4-14 (mean 7.5) hybridization bands. The patterns differed by more than a single band in 98% of pair-wise comparisons. On a subset of 76 isolates, ribotyping proved to be marginally more discriminating than biotyping (discrimination index 0.92 v. 0.89) followed by serotyping (0.87) and bacteriocin typing (0.74). About one-third of isolates belonged to unique ribotypes and only two ribotypes exceeded 5% in frequency (23.0 and 6.4% respectively). A combination of serotype or biotype with ribotyping defined a similar number of strains, although none of the methods alone was sufficiently discriminatory to identify strains. We conclude that due to the accessibility of biotyping and the lack of commercially available antisera for S. marcescens, the biotype and ribotype together provide reliable markers of strain identity.

Endemic cross-infection in an acute medical ward

Urine samples from patients on an acute medical ward were examined each week over a three-month period in order to detect endemic cross colonization or infection. The bed positions for each patient in the ward were recorded continuously and the patients cared for by each different nurse team noted. We found an outbreak of urinary colonization/infection with a strain of Klebsiella K8 in nine patients. Two groups of two patients probably suffered cross colonization/infection with different strains of Escherichia coli. These episodes were not detected by our routine laboratory ward liaison surveillance, but by the weekly samples and molecular typing methods applied to these relatively common strains. This survey demonstrates that cross colonization/infection may occur more widely than is normally detected. The implications of these findings to surveillance audit programmes are discussed.

Relationships among Pseudomonas pseudomallei isolates from patients with recurrent melioidosis

Patients with melioidosis may present with recurrent infections after clinical resolution of their primary illness. Because there has been no satisfactory typing scheme for Pseudomonas pseudomallei, recrudescence could not be distinguished from reinfection. We determined the strain identity of primary and relapse isolates of P. pseudomallei from 25 patients with culture-proven melioidosis to answer whether secondary infections were due to the initial infecting strain or to the acquisition of a new strain. Fifty-four isolates were compared by the patterns of BamHI restriction digests produced after hybridization with a cDNA copy of Escherichia coli rRNA. Twenty-three patients had primary and relapse isolates with identical or highly similar ribotype patterns. The patterns of isolates from two patients were different; the primary and relapse isolates differed by a single fragment for one, and the other had identical primary and first-relapse isolates while the second-relapse isolate was markedly different. The results indicated that recurrent infection probably resulted from endogenous relapse in most of the melioidosis patients studied, although reinfection from an exogenous source was also possible in two cases.

Correlation of typing methods for Acinetobacter isolates from hospital outbreaks

Four methods, namely, biotyping, cell envelope protein electrophoresis, ribotyping, and comparison of antibiograms, were used for strain identification of Acinetobacter isolates from five outbreaks in hospitals. There was good agreement among the methods for the identification of an index strain, but biotyping and the comparison of antibiograms were the least discriminatory.

Application of DNA probes for rRNA and vanA genes to investigation of a nosocomial cluster of vancomycin-resistant enterococci

DNA probes specific for genes encoding rRNA and the glycopeptide resistance gene vanA were used to investigate a cluster of vancomycin-resistant (MICs, > 512 mg/liter) Enterococcus faecalis and Enterococcus faecium isolated from separate patients in a renal unit in a London hospital. When digested with BamHI, 12 of 13 vancomycin-resistant E. faecalis isolates exhibited a common restriction fragment length polymorphism pattern of rRNA genes (ribotype). A vanA probe hybridized with chromosomal DNA in these 12 isolates. The other isolate of vancomycin-resistant E. faecalis had a different ribotype and the vanA gene was located on plasmid DNA. These data suggest that cross-infection with a single strain of vancomycin-resistant E. faecalis occurred in most instances. In contrast, 23 vancomycin-resistant E. faecium isolates showed greater heterogeneity, comprising 8 ribotypes, suggesting that multiple strains were present in the unit. Twenty-one of these 23 isolates harbored a 24-MDa plasmid which hybridized with the vanA probe, implying that interstrain dissemination of a vancomycin resistance plasmid may have occurred among E. faecium isolates in the renal unit.

Epidemiological fingerprinting of Enterobacter cloacae by small-fragment restriction endonuclease analysis and pulsed-field gel electrophoresis of genomic restriction fragments

A cluster of infections caused by Enterobacter cloacae was observed among preterm neonates in a neonatal intensive care unit (NICU) of a pediatric hospital in Osnabrück, Germany. The presence of similar antimicrobial susceptibility patterns among the bacterial isolates prompted an investigation to determine whether a limited spread of a single strain existed. All 12 E. cloacae isolates from the NICU and 50 nonrelated strains were fingerprinted by small-fragment restriction endonuclease analysis (SF-REA) of EcoRI DNA digests. Selected isolates were further characterized by pulsed-field gel electrophoresis (PFGE) of NotI- or XbaI-generated genomic restriction fragments. Epidemiologically unrelated strains were clearly discriminated by both methods. Results achieved by SF-REA and PFGE revealed that of the 12 isolates from the NICU, 11 belonged to the same genotypic cluster. Since all reagents and equipment for both techniques are commercially available, DNA fingerprinting by SF-REA or PFGE is proposed as a useful tool in the microbiology laboratory for investigating the epidemiological relatedness of E. cloacae strains of clinical and environmental origin.

Application of ribotyping for differentiating aeromonads isolated from clinical and environmental sources

We have investigated the usefulness of ribotyping for the differentiation of aeromonads isolated from five patients with gastroenteritis and from the source water, treatment plant, and distribution system of a small public water supply. Aeromonas hydrophila and Aeromonas caviae were isolated from fecal specimens preserved in Cary-Blair transport medium by using blood ampicillin agar or alkaline peptone water (pH 8.4) subcultured to blood ampicillin agar plates. A. hydrophila, Aeromonas sobria, and A. caviae were isolated from duplicate 100-ml water samples by the membrane filter technique by using ampicillin dextrin agar for quantitative determination of growth and alkaline peptone water enrichment for detection of the presence or absence of aeromonads below the detection limit of the membrane filter method. In addition, free chlorine residuals and pH values were determined for all water samples and heterotrophic plate counts and total and fecal coliform analyses were performed on them. Ribotyping patterns of aeromonads recovered from well 1, detention basin, sand filter, softener, and distribution samples were compared with those of the five clinical isolates. All patient strains were unique; however, identical ribotypes of A. hydrophila and A. sobria isolated from multiple sites in the water system indicated colonization of a well, sand filters, and the softener, with the potential for sporadic contamination of distribution water. Plant operational deficiencies were noted and corrected. Ribotyping can effectively differentiate otherwise indistinguishable strains of bacteria, thus providing a powerful tool for investigation of waterborne diseases and bacteriological problems within water treatment plants and distribution systems.

Rapid genotyping shows the absence of cross-contamination in Enterobacter cloacae nosocomial infections

Restriction fragment length polymorphism analysis (RFLP) of total DNA and rDNA regions was used for the epidemiological evaluation of 10 Enterobacter cloacae nosocomial isolates obtained from nine patients in our hospital. Five of these patients were hospitalized during overlapping periods, thus raising the question of cross-contamination. A single biochemical pattern and antibiotic susceptibility profile was observed for all isolates but one. In contrast, based on the results of total DNA and rDNA RFLP patterns, the genetic unrelatedness of the isolates was clearly shown, thus excluding a common source of contamination or patient-to-patient transfer.

Application and assessment of cloacin typing of Enterobacter cloacae

Three methods, O-serotyping, phage typing and susceptibility to bacteriocins, were used to type 357 clinical isolates of Enterobacter cloacae cultured from 219 patients. One hundred and sixty isolates were typed by serology and phage typing. When these two methods were used, primary classification of isolates was based on serology (65.7% typable) and phage typing for further subdivision (94.1% typable). When all the isolates were typed by cloacin susceptibility, 81.5% of them were typable. Maximum discrimination between cultures was achieved when the three methods were used together; no single method was sufficiently discriminatory. There was a close parallel between serotyping and bacteriocin lysis pattern. The latter was easy to perform and the results were achieved within 48 h. By applying this typing system two episodes of cross-infection were identified in a haematology/oncology unit and intensive care unit.

Molecular typing of Neisseria gonorrhoeae by restriction fragment length polymorphisms

OBJECTIVE

To characterise Neisseria gonorrhoeae isolates by restriction fragment length polymorphisms (RFLPs) in ribosomal RNA genes.

DESIGN

Generation of RFLP patterns by HincII restriction of rRNA genes followed by hybridisation with a non-radioactive labelled broad spectrum 16 + 23S rRNA gene probe. This typing method was developed and compared with MAb based serotyping.

SPECIMENS

Forty three randomly collected isolates from Bangkok (27 isolates) and Singapore (16 isolates) were studied.

RESULTS

The RFLP patterns generated were reproducible and highly discriminatory between strains. Analysis of RFLPs produced by HincII restriction of rRNA genes established 9 patterns amongst the 43 isolates examined. Strains present within a common serovar could be further subdivided by RFLP typing. Identical RFLP patterns were found in some strains that belonged to various serovars.

CONCLUSION

RFLP typing based on heterogeneities of rRNA gene restriction patterns could be advantageously used to complement monoclonal antibody based serotyping for further subdivision of serovars. Higher sensitivity of this combined approach would enable better differentiation of strains in epidemiological studies.