Use of PCR to study epidemiology of Serratia marcescens isolates in nosocomial infection

Serratia infections: from military experiments to current practice

Serratia species, in particular Serratia marcescens, are significant human pathogens. S. marcescens has a long and interesting taxonomic, medical experimentation, military experimentation, and human clinical infection history. The organisms in this genus, particularly S. marcescens, were long thought to be nonpathogenic. Because S. marcescens was thought to be a nonpathogen and is usually red pigmented, the U.S. military conducted experiments that attempted to ascertain the spread of this organism released over large areas. In the process, members of both the public and the military were exposed to S. marcescens, and this was uncovered by the press in the 1970s, leading to U.S. congressional hearings. S. marcescens was found to be a certain human pathogen by the mid-1960s. S. marcescens and S. liquefaciens have been isolated as causative agents of numerous outbreaks and opportunistic infections, and the association of these organisms with point sources such as medical devices and various solutions given to hospitalized patients is striking. Serratia species appear to be common environmental organisms, and this helps to explain the large number of nosocomial infections due to these bacteria. Since many nosocomial infections are caused by multiply antibiotic-resistant strains of S. marcescens, this increases the danger to hospitalized patients, and hospital personnel should be vigilant in preventing nosocomial outbreaks due to this organism. S. marcescens, and probably other species in the genus, carries several antibiotic resistance determinants and is also capable of acquiring resistance genes. S. marcescens and S. liquefaciens are usually identified well in the clinical laboratory, but the other species are rare enough that laboratory technologists may not recognize them. 16S rRNA gene sequencing may enable better identification of some of the less common Serratia species.

Institutional spread of clonally related Serratia marcescens isolates with a novel AmpC cephalosporinase (S4): a 4-year experience in Taiwan

Resistance of Serratia marcescens, a nosocomial pathogen of Enterobacteriaceae, to the extended-spectrum beta-lactams is usually mediated by an overproduced AmpC cephalosporinase. We aimed to characterize the molecular epidemiology and AmpC of S. marcescens isolates recovered from 1 medical center in southern Taiwan. AmpC-encoding genes for SRT families were investigated by polymerase chain reaction and DNA sequencing. From August 1999 through July 2003, 69 nonrepetitive bloodstream isolates were enrolled. Excluding 11 isolates, which also produced an extended-spectrum beta-lactamase, 58 isolates carried an AmpC-encoding gene, including a novel S4 gene with 98% identity to SRT-1 gene (n = 50), SRT-2 gene (n = 3), SST-1 gene (n = 1), and others (n = 4). Isolates with S4 exhibited a phenotype of resistance to cefotaxime (CTX) but not ceftazidime. Genotype analysis by pulsed-field gel electrophoresis revealed that 45 (90%) of the isolates carrying S4 gene belonged to 2 major epidemic clones, including types A (n = 28) and B (n = 17). In conclusion, the AmpC-like S4 beta-lactamase may confer CTX resistance of the S. marcescens population. Strains carrying the S4 gene with prolonged dissemination were closely related.

Molecular characterization of Serratia marcescens strains by RFLP and sequencing of PCR-amplified 16S rDNA and 16S-23S rDNA intergenic spacer

AIMS

To establish the specific DNA patterns in 16S rDNA and 16S-23S rDNA intergenic spacer (IGS) regions from different kinds of Serratia marcescens strains using polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequences analysis.

METHODS AND RESULTS

Two pairs of primers based on the 16S rDNA and 16S-23S rDNA IGS were applied to amplify the rrn operons of two kinds of S. marcescens strains. About 1500 bp for 16S rDNA and four fragments of different sizes for 16S-23S rDNA IGS were obtained. PCR-amplified fragments were analysed by RFLP and sequence analysis. Two distinct restriction patterns revealing three to five bands between two kinds of strains were detected with each specific enzyme. According to the sequence analysis, two kinds of strains showed approximately 97% sequence homology of 16S rDNA. However, there was much difference in the sequences of IGS between the two kinds of strains. Intercistronic tRNA of strains H3010 and A3 demonstrated an order of tRNA of 5'-16S-tRNA(Ala)-tRNA(Ile)-23S-3', but strain B17 harboured the tRNA of 5'-16S-tRNA(Glu)-tRNA(Ile)-23S-3'.

CONCLUSIONS

The method was specific, sensitive and accurate, providing a new technique for differentiating different strains from the same species.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper provided the first molecular characterization of 16S rDNA and 16S-23S rDNA IGS from S. marcescens strains.

Histopathology and genotyping in infectious spondylitis of HIV- and HIV+ patients

Approximately 2 million South Africans are HIV/TB coinfected, and many develop skeletal disease. The resurgence of spinal tuberculosis, including atypical forms, is due largely to HIV-associated immune suppression. We investigated the impact of HIV coinfection on the histological features of the disease and the occurrence of atypical opportunistic organisms in infectious spondylitis in an HIV/TB endemic region. We analyzed blood and tissue biopsies from 60 patients with tuberculous spondylitis. Investigations included full blood counts, CD4/CD8 counts, HIV-1 serology and RNA quantification (tissue and plasma), acid-fast bacilli localization and routine TB culture, histopathologic evaluation of biopsies, and bacterial genotyping using the 16S rDNA gene. Twenty-two patients (37%) were HIV positive with a mean age of 29 years (range, 2-65 years). Forty-one (68%) tissue specimens were culture negative for Mycobacterium tuberculosis (Mtb), although nontuberculous mycobacteria (NTM) were identified in three HIV-negative patients. Histopathologic features were characteristic of TB infection in 91.4% of all specimens tested and 100% of the HIV-infected group. Genotyping of 10 culture-positive isolates identified Mtb (3/10), NTMs (2/10), and environmental bacilli (3/10). Our observations suggest HIV-induced immune suppression impacts the histological and clinical features of infectious spondylitis but has no impact on the incidence of NTMs in this setting.

Characterization of Serratia marcescens isolates from subgingival biofilm, extraoral infections and environment by prodigiosin production, serotyping, and genotyping

INTRODUCTION

Serratia marcescens is widely distributed in nature, and has emerged in the last years as an important nosocomial pathogen. The organism may also be found in subgingival biofilm in periodontitis patients. This study aimed to verify the subgingival prevalence of S. marcescens in different periodontal conditions and to evaluate whether the oral cavity would harbor strains similar to those causing infectious diseases.

METHODS

The subgingival occurrence of S. marcescens was determined in 334 subjects. The phenotypic and genotypic diversity of 23 isolates from subgingival biofilm, 22 from extra-oral infections and 10 environmental strains, was compared by prodigiosin production, O and H serotyping and genotyping using polymorphic GC-rich repetitive sequences-polymerase chain reaction.

RESULTS

S. marcescens was found more frequently in severe periodontitis patients (4.1%) than in gingivitis (3.2%) and healthy subjects (2.5%), but these differences were not statistically significant. Analysis of serotype distribution, prodigiosin production, and genotyping revealed that environmental strains were markedly different from most human isolates, either oral or extraoral.

CONCLUSION

These data suggest that S. marcescens isolates from subgingival biofilm are not just contaminants from the environment, but that the oral cavity may act as a reservoir of strains able to promote human infections. However, further studies are needed to elucidate the role of this bacterium in the pathogenesis of periodontal diseases.

Identification of Serratia marcescens populations of nosocomial origin by RAPD-PCR

BACKGROUND

Serratia marcescens has been increasingly identified as a cause of infection in the immunocompromised host and in high-mortality-rate nosocomial outbreaks. It is thus important to use identification methods that allow study of the dynamics and evolution of nosocomial S. marcescens strains. The aim of this study was to identify S. marcescens strains isolated from nosocomial outbreaks in two pediatric hospitals by random amplification polymorphic DNA polymerase chain reaction (RAPD-PCR).

METHODS

RAPD-PCR was used to study five S. marcescens populations isolated from four different nosocomial outbreaks that occurred in two pediatric hospitals. This method was compared with the widely used biotyping system described by Grimont and Grimont.

RESULTS

The combination of biotypification and RAPD-PCR allowed accurate identification of S. marcescens strains isolated in nosocomial outbreaks at pediatric hospitals; by RAPD-PCR, we were able to analyze clonal variations in S. marcescens populations. We established bacterial dissemination patterns in hospital environments according to hospital administration of medical services and compared changes in bacterial DNA amplification patterns in each hospital related with clonal variations by selective pressures.

CONCLUSIONS

RAPD-PCR is a useful method to identify S. marcescens strains associated with nosocomial outbreaks.

Genotyping of Serratia marcescens Strains Associated with Cucurbit Yellow Vine Disease by Repetitive Elements-Based Polymerase Chain Reaction and DNA-DNA Hybridization

ABSTRACT The bacterium that causes cucurbit yellow vine disease (CYVD) has been placed in the species Serratia marcescens based on 16S rDNA and groE sequence analysis. However, phenotypic comparison of the organism with S. marcescens strains isolated from a variety of ecological niches showed significant heterogeneity. In this study, we compared the genomic DNA of S. marcescens strains from different niches as well as type strains of other Serratia spp. through repetitive elements-based polymerase chain reaction (rep-PCR) and DNA-DNA hybridization. With the former, CYVD strains showed identical banding patterns despite the fact that they were from different cucurbit hosts, geographic locations, and years of isolation. In the phylogenetic trees generated from rep-PCR banding patterns, CYVD strains clearly were differentiated from other strains but formed a loosely related group with S. marcescens strains from other niches. The homogeneity of CYVD strains was supported further by the DNA relatedness study, in that labeled DNA from the cantaloupe isolate, C01-A, showed an average relative binding ratio (RBR) of 99%, and 0.33% divergence to other CYVD strains. Used as a representative strain of CYVD, the labeled C01-A had a RBR of 76%, and a 4.5% divergence to the S. marcescens type strain. These data confirm the previous placement of CYVD strains in S. marcescens. Our investigations, including rep-PCR, DNA-DNA hybridization, and previous phenotyping experiments, have demonstrated that CYVD-associated strains of S. marcescens cluster together in a group significantly different from other strains of the species.

One predominant type of genetically closely related Shigella sonnei prevalent in four sequential outbreaks in school children

Seventy-six Shigella sonnei isolates from four sequential outbreaks in school children were analyzed to determine their relatedness. Outbreak strains exhibited two major antibiograms, 9 plasmid profiles, 10 enterobacterial repetitive intergenic consensus sequence (ERIC)-PCR patterns, and 17 pulsed-field gel electrophoresis (PFGE) patterns. Of typing methods, ERIC-PCR types generally coincided with the PFGE types within these outbreak strains. However, ERIC-PCR analysis could not discriminate an epidemiologically unrelated strain from some outbreak strains. Further computer-assisted analysis for similarity of the PFGE patterns revealed that the main culprits of these four sequential outbreaks were strains of pulsotype C (88.2% of total outbreak isolates). The results indicate that PFGE can provide more explicit relatedness of outbreak strains than the other typing methods examined. In conclusion, based on PFGE analysis, one predominant pulsotype of multiple genetically related strains of S. sonnei was prevalent in these four sequential outbreaks.

Use of pulsed-field gel electrophoresis to investigate an outbreak of Serratia marcescens infection in a neonatal intensive care unit

Serratia marcescens is a well-recognized hospital-acquired pathogen, which has been associated with a number of specific outbreaks, particularly in critically ill neonates. We used pulsed-field gel electrophoresis (PEGE) typing to analyse an outbreak in a neonatal intensive care unit (NICU). We included samples from nine patients, three handwashes and ten environmental isolates from an outbreak (February to August 1999) in addition to four patient isolates from different wards of our hospital during the same time period. The clinical presentations of the outbreak included bacteraemia (four cases), pneumonia (three cases), umbilical wound infection (one case) and conjunctivitis (one case). Nine outbreak isolates exhibited an identical PFGE fingerprint, while the epidemiologically unrelated strains demonstrated distinct patterns. Epidemiological investigation failed to reveal a common source of the outbreak, although the epidemic S. marcescens strain was isolated from hand-washes and doors of incubators. We concluded that cross-transmission via transient contamination of hands was the major route for this outbreak. Strict handwashing practices, the cohorting and isolation of colonized and infected patients, and the regular dis-infection of incubators are crucial steps for preventing the transmission of S. marcescens in an NICU. This PFGE method is highly discriminatory for the thorough epidemiological investigation of an outbreak of S. marcescens.

Comparison of results generated by serotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence PCR used to characterize penicillin-resistant pneumococci from the United States

One hundred forty-seven isolates of Streptococcus pneumoniae with high-level penicillin resistance collected during a national surveillance program in the United States were characterized by serotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence (BOX element) PCR. The results generated by each method were compared by frequency of association to examine whether relationships existed between the various typing methods and statistically to determine association with the geographic source of the isolate or the age of the patient from whom the isolate was obtained. When the data were examined by pairwise analysis of individual strain classifications produced by each typing method, no statistically significant relationships between strain type, geographic location, or patient age were identified, suggesting that distinct clones of penicillin-resistant S. pneumoniae have been widely distributed throughout the United States. However, we did observed shared expression of two or three typing markers at a high frequency (>50%) among clusters of strains, indicating a certain level of concordance between the various typing methods used to classify penicillin-resistant S. pneumoniae.

Genotyping of clinical Serratia marcescens isolates: a comparison of PCR-based methods

The polymerase chain reaction (PCR)-based procedures of randomly amplified polymorphic DNA (RAPD) and repetitive element (RE)-based PCR were used to amplify total DNA prepared from each of 62 clinical Serratia marcescens isolates. Three different random primers, designated 1060, 1254 and 1283, were used individually in RAPD-PCR. Primers representing enterobacterial repetitive intergenic consensus (ERIC) sequences, extragenic palindromic (REP) elements, and polymorphic GC-rich repetitive sequences (PGRS) constituted the repetitive element-PCR. We were able to generate 40, 40 and 58 genotypic groupings using the 1060, 1254 and 1283 RAPD primers, respectively. Using the ERIC, REP and PGRS primers, 19, 54 and 60 unique genotypic profiles were yielded, respectively. The PGRS primers, which were developed to amplify GC-rich repetitive sequences in the genome of Mycobacteria, were the most discriminatory. These data indicate that both of these PCR-based approaches are a valid means of discriminating strain differences among isolates of S. marcescens and the amount of differentiation depends on the primer used. These techniques should prove useful for routine surveillance or in examining outbreaks of S. marcescens in clinical settings.

Outbreak investigation of nosocomial enterobacter cloacae bacteraemia in a neonatal intensive care unit

Over a period of 7 months, 23 patients hospitalized in a neonatal intensive care unit (NICU) developed nosocomial Enterobacter cloacae bacteraemia. Contaminated saline for preparing heparin solution was initially identified as the common source of E. cloacae bacteraemia. Although environmental sanitation was enforced, the outbreak continued. E. cloacae has always been isolated from various cultures of the environmental specimens, from the hands of personnel and from the faeces of patients. All of the 23 bacteraemic isolates and 8 stool isolates from infected infants, as well as the 17 isolates from environmental specimens were found to be of the same genotype using the polymerase chain reaction-based DNA fingerprinting method. After various infection control methods were instituted, the outbreak eventually came under control. For epidemiological investigation, 23 neonates without E. cloacae bacteraemia were matched for case-control study. Nineteen (83%) of the case-patients were premature. The significant risk factors leading to E. cloacae bacteraemia in the NICU included small gestation age, low birthweight, exposure to personnel with contaminated hands and the presence of E. cloacae in the stool carriage (p=0.003, 0.007, 0.018 and 0.040, respectively). The gastrointestinal tracts of the patients and environmental surfaces appeared to be the principal sites of bacterial reservoir. In conclusion, the outbreak of E. cloacae bacteraemia was caused by a particular strain and possibly via multiple modes of transmission, including a bottle of contaminated saline as an initial common source, endogenous spread from the gastrointestinal tract and successive cross-infections between patients, hands of personnel and the environment. Effective infection control requires a multidisciplinary approach and reinforcement of infection control procedures, including aseptic technique, hand washing, proper isolation and disinfection of environmental surfaces.

RAPD-fingerprinting of Serratia marcescens after formaldehyde inactivation of DNase activity

Serratia marcescens strains commonly cause hospital outbreaks. A random amplified polymorphic DNA (RAPD) assay was applied to the epidemiology of Ser. marcescens using formaldehyde fixation and boiling of bacterial cells for DNA extraction. The method preserved bacterial DNA and gave optimal results of RAPD-fingerprinting, facilitating the investigation of hospital infections caused by Ser. marcescens.

Application of infrequent-restriction-site PCR to clinical isolates of Acinetobacter baumannii and Serratia marcescens

We applied infrequent-restriction-site PCR (IRS-PCR) to the investigation of an outbreak caused by 23 isolates of Acinetobacter baumannii in an intensive care unit from November 1996 to May 1997 and a pseudoepidemic caused by 16 isolates of Serratia marcescens in a delivery room from May to September 1996. In the epidemiologic investigation of the outbreak caused by A. baumannii, environmental sampling and screening of all health care workers revealed the same species from the Y piece of a mechanical ventilator and the hands of two health care personnel. IRS-PCR showed that all outbreak-related strains were genotypically identical and that three strains from surveillance cultures were also identical to the outbreak-related strains. In a pseudoepidemic caused by S. marcescens, IRS-PCR identified two different genotypes, and among them one genotype was predominant (15 of 16 [93.8%] isolates). Extensive surveillance failed to find any source of S. marcescens. Validation of the result of IRS-PCR by comparison with that of field inversion gel electrophoresis (FIGE) showed that they were completely concordant. These results suggest that IRS-PCR is comparable to FIGE for molecular epidemiologic studies. In addition, IRS-PCR was less laborious and less time-consuming than FIGE. To our knowledge, this is the first report of the application of IRS-PCR to A. baumannii and S. marcescens.

Risk factors for acquisition of Serratia marcescens in a surgical intensive care unit

Between January 1996 and May 1997, a four-fold increased rate of isolation of Serratia marcescens was observed amongst patients admitted to the surgical Intensive Care Unit (SICU) of the Leiden University Medical Center compared to the preceding years. Random amplification of polymorphic DNA showed the involvement of genotypically distinct strains, implicating multiple different sources. After improvement of hygienic measures the frequency of isolation of S. marcescens returned to baseline. A case-control study was performed to assess patient-related risk factors for acquisition of S. marcescens. Nineteen cases and 38 controls were included. Hospital- and SICU-stay were significantly longer in case patients than in controls. By univariate analysis, statistically significant differences were found in body weight, the duration of mechanical ventilatory support, the cumulative use of antimicrobial agents, the use of aminoglycosides, parenteral nutrition and tube feeding. The sum of the number of days per invasive device (deep intravenous lines, arterial lines, wound drains and urinary catheters) was higher in cases than in controls (P = 0.08). Categorically, a cumulative number of device-days > 25 was a statistically significant risk factor for acquisition of S. marcescens. Multivariable logistic regression analysis showed that body weight, parenteral feeding and mechanical ventilation were independent predictors of acquisition of S. marcescens. As transmission of S. marcescens appears to be by the hands of personnel, the identified risk factors may act by necessitating an increased frequency and intensity of direct contacts.

Long-lasting contamination of a vitrectomy apparatus with Serratia marcescens

OBJECTIVE

To investigate the contamination of a vitrectomy apparatus with Serratia marcescens.

DESIGN

Descriptive microbiological and molecular environmental study.

SETTING

An 1,800-bed university hospital.

RESULTS

S. marcescens was found inside the vitrectomy apparatus at the pressure transducer. Molecular typing by randomly amplified polymorphic DNA-automated laser fluorescence analysis and pulsed-field gel electrophoresis identified a single pattern for all strains isolated from the apparatus. Surprisingly, the contaminating strain was identical to two strains of S. marcescens isolated nearly 2 years earlier from two patients who were involved in a small outbreak of acute postoperative endophthalmitis following cataract surgery at another hospital. The emergency vitrectomies in these patients were performed at our hospital with the same apparatus that was found to be contaminated 2 years later.

CONCLUSION

Performing a systematic environmental search for the assumed bacterial reservoir within the system of the vitrectomy apparatus finally made it possible to find and eliminate the nidus for the gram-negative rod. Molecular typing demonstrated that all isolates belonged to a single genotype, and revealed unexpectedly a link to two vitrectomies performed 2 years earlier. The data support the hypothesis that the source of the contamination was one of these patients, and thus contamination of the apparatus was present for almost 2 years.

Typing of nosocomial strains of Serratia marcescens: comparison of pulsed-field gel electrophoresis of macrorestriction fragments with biotyping, esterase typing and ribotyping

Fifty nosocomial isolates of Serratia marcescens, collected in six Belgian hospitals between 1986 and 1990, were characterized by using pulsed-field gel electrophoresis (PFGE) with XbaI. The results were compared with those previously obtained by three other methods: biotyping, esterase electrophoresis typing and ribotyping with EcoRI and HindIII. Macrorestriction analysis (42 PFGE groups) and esterase typing (42 zymotypes) proved to be the most discriminating, followed by ribotyping (28 ribotypes) and biotyping (10 biochemical profiles). Biotyping would serve as a screen to identify isolates, due to its accessibility. Esterase typing provided a reliable tool to make subdivisions within biotypes because of congruence between biochemical groups and esterase patterns. Additional discrimination was still achieved by ribotyping and PFGE. It is concluded that the combined results of these four markers were useful for distinguishing all epidemic and sporadic isolates.

Heterogeneous Serratia marcescens genotypes from a nosocomial pediatric outbreak

OBJECTIVE

Define the applicability of a rapid molecular typing scheme to study the epidemiology of a Serratia marcescens outbreak.

DESIGN

With the assistance of a simple bacterial lysis technique, isolates of S marcescens from a putative outbreak were genotyped with the polymerase chain reaction technology for which primers were chosen on the basis of previously defined enterobacterial repetitive intergenic consensus sequences.

SETTING

Pediatric ICU.

PATIENTS

Intensively monitored patients who were found to yield S marcescens from any body site during the epidemic period.

RESULTS

Over an 8-month period, 12 ICU patients were either infected or colonized with S marcescens. All of these patients were transiently supported by artificial ventilation. During the epidemiologic investigation, a dilution error in a high-level glutaraldehyde disinfectant, which was being used for some ventilator components, was observed. Rectification of the error was associated with an abrupt termination of the outbreak. Enterobacterial repetitive intergenic consensus polymerase chain reaction was easily applicable to this setting and it defined 4 distinct genotypes among the 12 isolates.

CONCLUSION

The typing method is easily implemented and offers great promise as an epidemiologic tool. The associated investigation served to emphasize that an outbreak may occur with more than one epidemic strain and that strain heterogeneity itself does not exclude an outbreak.

Use of pulsed-field gel electrophoresis to investigate an outbreak of Serratia marcescens

Pulsed-field gel electrophoresis (PFGE) typing was applied to the epidemiological investigation of 20 Serratia marcescens isolates collected from urine specimens of 17 patients and three urinals over a 2-month period. Twenty-five epidemiologically unrelated strains were also tested to determine the discriminatory power of PFGE. The PFGE fingerprints of each isolate were consistent in three different tests. The 20 outbreak isolates had an identical PFGE fingerprint pattern, while the epidemiologically unrelated strains demonstrated unique PFGE fingerprint patterns. The source of the outbreak was inadequately disinfected urinals. We conclude that PFGE served as a highly discriminatory and reproducible method for the epidemiological investigation of the outbreak of S. marcescens infection addressed by this study.

Use of pulsed-field gel electrophoresis typing to study an outbreak of infection due to Serratia marcescens in a neonatal intensive care unit

Serratia marcescens is a well-known cause of nosocomial infections and outbreaks, particularly in critically ill neonates and immunocompromised patients. Numerous methods have been proposed for typing. We used pulsed-field gel electrophoresis (PFGE) typing to analyze an outbreak in a neonatal intensive care unit (NICU). We included 23 patient isolates from an outbreak (March to July 1995), and 10 patient isolates from different wards during the same time period. PFGE of whole-cell DNA digested by SpeI was used as a marker of strain identity. The most common presentation of the infection was sepsis in 18 of 23 (78%) neonates. Only four different biotypes were identified; biotype A8d accounted for 84% of the strains. PFGE typing revealed two clones responsible for two different clonal strain dissemination outbreaks from March to July, with 24 patient isolates being pattern A and 4 patient isolates being pattern E. PFGE typing suggests cross transmission between patients in the NICU and other wards. The isolates from 5 other patients showed distinct PFGE patterns. Extensive investigation and cultures failed to identify any environmental or staff reservoir of S. marcescens. This is one of the first reports applying PFGE to the study of S. marcescens, and this method was a useful marker of strain identity. PFGE typing distinguished strains which appeared to be the same by biotyping.

Comparative DNA analysis of Bordetella pertussis clinical isolates by pulsed-field gel electrophoresis, randomly amplified polymorphism DNA, and ERIC polymerase chain reaction

We used DNA fingerprinting by pulsed-field gel electrophoresis (PFGE), randomly amplified polymorphic DNA (RAPD) and PCR amplification of enterobacterial repetitive intergenic consensus sequences (ERIC-PCR) to compare 15 clinical isolates of Bordetella pertussis recovered between August 1993 and September 1995 from 13 infants and two adults, living in the same geographic area. PFGE produced 10 patterns and made it possible to differentiate all the isolates and to indicate an intrafamilial transmission. RAPD and ERIC-PCR generated banding patterns with small differences and had a poor discriminatory power. During the last 2 years, at Armand-Troussau pediatric hospital, 10 distinct clones of clinical B. pertussis isolates, with a predominant clone including seven strains, could be determined by the PFGE method.

Serratia marcescens nosocomial outbreak due to contamination of hexetidine solution

During a 10-week period, 16 patients in a neurosurgery intensive care unit were involved in an outbreak of Serratia marcescens. The epidemic strain was found in several flasks of 1:4 diluted hexetidine solution, an antiseptic used for patient mouth washing. Testing of the bactericidal activity of the diluted antiseptic revealed that all the epidemic strains were able to grow in the diluted antiseptic solution. Strains isolated from clinical samples and from the antiseptic solution were compared by random amplification of polymorphic DNA. Epidemiologic typing data implicated the diluted antiseptic solution as the single source of this S. marcescens outbreak.

Typing of nosocomial strains of Serratia marcescens: comparison of restriction enzyme cleaved genomic DNA fragment (PFGE) analysis with bacteriocin typing, biochemical profiles and serotyping

Eighty-eight selected clinical isolates of Serratia marcescens, representing 27 putative outbreaks of nosocomial cross-infection encountered during 1980-1995, were tested comparatively by bacteriocin typing, carbon source assimilation tests, serotyping (O and H antigens), and restriction pattern (RFLP) analysis of restriction cleaved (SpeI, XbaI) genomic DNA fragments after pulsed-field gel electrophoresis (PFGE). Serotyping served as the "gold standard" of the phenotypic methods. One pseudo-outbreak (bacteriocin typing incriminated type 26) was uncovered through serotyping as well as the biochemical profile and confirmed by PFGE analysis of genomic DNA. Bacteriocin typing and determination of biochemical profiles disclosed several instances of phenotypic variation; serotyping revealed two episodes of shifts from motility (H12) to nonmotility. Resolution of restricted genomic DNA fragments with the PFGE procedure permitted detection of 27 PFGE patterns (A-M, N-1-N-3, O-1, O-2, P-1-P-3, Q-1-Q-3, R-1-R-3, S-1, and T). Based on the analysis of PFGE patterns against the background of epidemiological data, the number of nosocomically significant strains of S. marcescens could be reduced to 16 (PFGE patterns A-M, N-2, O-1, P-2, and T). It was concluded that PFGE analysis of restricted genomic DNA of S. marcescens was superior to the three phenotypic methods.

Phenotypic variation of clinical Serratia marcescens isolates repeatedly recovered from individual patients

A total of 129 selected isolates of Serratia marcescens which had been recovered from 50 patients during the 1980-1995 period and which revealed phenotypic variation in terms of bacteriocin (phage tail) susceptibility, carbon source assimilation, or serotype, were reexamined with these three phenotypic methods. Seven isolates (5.4%) were bacteriocin nontypable; all 129 isolates utilized carbon sources and could be serotyped. Fourty-eight isolates from 20 patients yielded unambiguous results with these 3 phenotypic methods and were excluded from further analysis. Among the remaining 81 isolates from 30 patients, isolates from 2 patients revealed phenotypic variation in bacteriocin susceptibility only, whereas isolates from 6 patients showed variant bacteriocin types and variant biochemical profiles, but were of identical serotype. Isolates from 20 patients revealed variant biochemical profiles only. Three patients had become superinfected with strains of S. marcescens of different phenotype and genotype. In 4 patients, previously motile (H12) isolates had become nonmotile (H-). PFGE analysis of XbaI and SpeI-restricted genomic DNA of the 81 isolates of the 30 patients demonstrated the isolates of 22 patients to be genotypically identical. The isolates from 3 patients were closely related by genotype, and those from an additional patient proved to be possibly related. PFGE analysis demonstrated one patient to have become infected by two genotypically different strains of S. marcescens of identical serotype, which, however, differed in bacteriocin type and biochemical profile. It was concluded that PFGE analysis of restricted genomic S. marcescens DNA was superior to the three phenotypic methods examined comparatively. Serotyping was more reliable than bacteriocin typing, and the latter technique yielded fewer phenotypic variants than determination of biochemical profiles among consecutively recovered isolates from patients with long-lasting S. marcescens infection.

Epidemiological typing of Flavimonas oryzihabitans by PCR and pulsed-field gel electrophoresis

Flavimonas oryzihabitans has emerged as a potential nosocomial pathogen in recent years. The typing method for characterization of this species has never been reported before. Pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-based PCR were used to generate DNA fingerprints for 14F. oryzihabitans isolates obtained from eight episodes of nosocomial infections during a 2-year period. Both techniques successfully classified these clinical isolates into eight distinct genotypes, thus indicating that all of these episodes of infections were independent. In contrast, repeated isolates from the same patient were assigned to identical genotypes. The reproducibility of both techniques was good. Therefore, we conclude that both PFGE and ERIC-PCR have comparable reproducible and discriminatory powers for the typing of F. oryzihabitans and may be useful for clarifying the epidemiology of this species; however, ERIC-PCR has the advantages of both speed and simplicity.

Comparison of different PCR approaches for characterization of Burkholderia (Pseudomonas) cepacia isolates

In this study, we evaluated three PCR methods for epidemiological typing of Burkholderia (Pseudomonas) cepacia--PCR-ribotyping, arbitrarily primed PCR (AP-PCR) and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR)--and compared them with pulsed-field gel electrophoresis. The analysis was performed with 31 isolates of B. cepacia, comprising 23 epidemiologically unrelated isolates and 8 isolates collected from the same patient during two episodes of bacteremia. Pulsed-field gel electrophoresis, ERIC-PCR, and AP-PCR identified 23 distinct types among the 23 unrelated isolates, while PCR-ribotyping only identified 12 strain types, even after AluI digestion of the amplification products. Among the eight isolates collected from the same patient, all typing techniques revealed two clones of strains. The day-to-day reproducibilities of PCR-ribotyping and ERIC-PCR were good, while greater day-to-day variations were noted in the fingerprints obtained by AP-PCR. We conclude that all three PCR techniques are useful for rapid epidemiological typing of B. cepacia, but ERIC-PCR seems to be more reproducible and discriminative.

DNA fingerprinting of Pseudomonas aeruginosa serotype O11 by enterobacterial repetitive intergenic consensus-polymerase chain reaction and pulsed-field gel electrophoresis

We report the use of pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-based polymerase chain reaction (PCR) to characterize clinical isolates of Pseudomonas aeruginosa serotype O11 collected from an incident of hospital-acquired infection. Both typing techniques differentiated 20 different strain types among seven epidemiologically related isolates and 22 epidemiologically unrelated isolates. There was complete concordance between these two techniques. Our results indicate that the ERIC-based PCR technique represents a rapid and simple means for typing P. aeruginosa serotype O11 with a level of discrimination equivalent to that of PFGE.

Epidemiological survey of an outbreak of multiresistant Serratia marcescens by PCR-fingerprinting

During an outbreak of Serratia marcescens from May to November 1993 43 strains obtained from 27 ICU patients infected or colonized with multiresistant S. marcescens were genotypically characterized with random amplified polymerase chain reaction (RAPD-PCR)-fingerprinting. In addition, 43 epidemiologically unrelated control isolates were selected. PCR-fingerprinting identified ten different genotypes of S. marcescens among the outbreak related strains. One predominant genotype was demonstrated in 21/43 isolates of 11/27 patients. A cluster of this genotype was found in seven/eight patients on the cardiosurgical ICU. The epidemiologically unrelated strains all showed different genotypes as compared to the predominant type. This survey proved RAPD-PCR to be a highly discriminatory and reproducible method for epidemiological studies of S. marcescens strains in nosocomial outbreaks.

Analysis of clonal relationships among isolates of Shigella sonnei by different molecular typing methods

Shigella sonnei is a major cause of diarrheal disease in developed as well as in developing countries. Epidemiologic studies of this organism have been limited by the lack of a simple and effective method for comparing strains. In this study, we have compared different molecular typing methods, i.e., plasmid profile analysis, restriction endonuclease analysis of plasmids, rRNA gene restriction analysis (ribotyping), pulsed-field gel electrophoresis (PFGE), and enterobacterial repetitive intergenic consensus (ERIC) sequence-based PCR (ERIC-PCR) for typing 20 clinical isolates of S. sonnei collected from six incidents of infection. PFGE and ERIC-PCR fingerprintings had the highest discriminatory power for discrimination of epidemiologically related isolates from epidemiologically unrelated strains of S. sonnei, and both gave seven distinct strain types among these isolates and the type strain of the species. Plasmid study and ribotyping produced only six and typing techniques demonstrated two distinct patterns, respectively, among these strains. All of these molecular an identical fingerprint for eight temporally related sporadic isolates. It is possible that these temporally related isolates belonged to a single bacterial clone and circulated obscurely through the community. Our results indicate that the ERIC-PCR technique represents a rapid and simple means for typing S. sonnei with a level of discrimination equivalent to that of PFGE but greater than those of plasmid profile analysis, restriction endonuclease analysis of plasmids, and ribotyping.